--- _id: '1188' abstract: - lang: eng text: "We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations." acknowledgement: D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night. article_number: '123502' author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Davide full_name: Masoero, Davide last_name: Masoero citation: ama: 'De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f' apa: 'De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. IOPscience. https://doi.org/10.1088/1742-5468/aa4e8f' chicago: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.' ieee: 'D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOPscience, 2016.' ista: 'De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.' mla: 'De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOPscience, 2016, doi:10.1088/1742-5468/aa4e8f.' short: 'D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).' date_created: 2018-12-11T11:50:37Z date_published: 2016-12-30T00:00:00Z date_updated: 2021-01-12T06:48:57Z day: '30' department: - _id: GaTk doi: 10.1088/1742-5468/aa4e8f ec_funded: 1 intvolume: ' 2016' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1606.09048 month: '12' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: ' Journal of Statistical Mechanics: Theory and Experiment' publication_status: published publisher: IOPscience publist_id: '6165' quality_controlled: '1' scopus_import: 1 status: public title: Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016 year: '2016' ... --- _id: '1203' abstract: - lang: eng text: Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae. acknowledgement: We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support. author: - first_name: Fang full_name: Hu, Fang last_name: Hu - first_name: Lavanya full_name: Rishishwar, Lavanya last_name: Rishishwar - first_name: Ambily full_name: Sivadas, Ambily last_name: Sivadas - first_name: Gabriel full_name: Mitchell, Gabriel id: 315BCD80-F248-11E8-B48F-1D18A9856A87 last_name: Mitchell - first_name: Jordan full_name: King, Jordan last_name: King - first_name: Timothy full_name: Murphy, Timothy last_name: Murphy - first_name: Janet full_name: Gilsdorf, Janet last_name: Gilsdorf - first_name: Leonard full_name: Mayer, Leonard last_name: Mayer - first_name: Xin full_name: Wang, Xin last_name: Wang citation: ama: Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16 apa: Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16 chicago: Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16. ieee: F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016. ista: Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017. mla: Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16. short: F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017. date_created: 2018-12-11T11:50:41Z date_published: 2016-12-01T00:00:00Z date_updated: 2021-01-12T06:49:04Z day: '01' department: - _id: GaTk doi: 10.1128/JCM.01511-16 intvolume: ' 54' issue: '12' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/ month: '12' oa: 1 oa_version: Submitted Version page: 3010 - 3017 publication: Journal of Clinical Microbiology publication_status: published publisher: American Society for Microbiology publist_id: '6146' quality_controlled: '1' scopus_import: 1 status: public title: Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 54 year: '2016' ... --- _id: '1214' abstract: - lang: eng text: 'With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object''s internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.' acknowledgement: RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi. article_number: '7759138' author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Raphael full_name: Hostettler, Raphael last_name: Hostettler - first_name: Alois full_name: Knoll, Alois last_name: Knoll - first_name: Ralf full_name: Der, Ralf last_name: Der citation: ama: 'Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:10.1109/IROS.2016.7759138' apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138' chicago: 'Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138.' ieee: 'G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.' ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.' mla: 'Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE, 2016, doi:10.1109/IROS.2016.7759138.' short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016. conference: end_date: 2016-09-14 location: Daejeon, Korea name: 'IEEE RSJ International Conference on Intelligent Robots and Systems IROS ' start_date: 2016-09-09 date_created: 2018-12-11T11:50:45Z date_published: 2016-11-28T00:00:00Z date_updated: 2021-01-12T06:49:08Z day: '28' department: - _id: ChLa - _id: GaTk doi: 10.1109/IROS.2016.7759138 language: - iso: eng month: '11' oa_version: None publication_status: published publisher: IEEE publist_id: '6121' quality_controlled: '1' scopus_import: 1 status: public title: 'Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm' type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016-November year: '2016' ... --- _id: '1220' abstract: - lang: eng text: Theoretical and numerical aspects of aerodynamic efficiency of propulsion systems coupled to the boundary layer of a fuselage are studied. We discuss the effects of local flow fields, which are affected both by conservative flow acceleration as well as total pressure losses, on the efficiency of boundary layer immersed propulsion devices. We introduce the concept of a boundary layer retardation turbine that helps reduce skin friction over the fuselage. We numerically investigate efficiency gains offered by boundary layer and wake interacting devices. We discuss the results in terms of a total energy consumption framework and show that efficiency gains of any device depend on all the other elements of the propulsion system. author: - first_name: Gregor full_name: Mikić, Gregor last_name: Mikić - first_name: Alex full_name: Stoll, Alex last_name: Stoll - first_name: Joe full_name: Bevirt, Joe last_name: Bevirt - first_name: Rok full_name: Grah, Rok id: 483E70DE-F248-11E8-B48F-1D18A9856A87 last_name: Grah orcid: 0000-0003-2539-3560 - first_name: Mark full_name: Moore, Mark last_name: Moore citation: ama: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. In: AIAA; 2016:1-19. doi:10.2514/6.2016-3764' apa: 'Mikić, G., Stoll, A., Bevirt, J., Grah, R., & Moore, M. (2016). Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency (pp. 1–19). Presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA: AIAA. https://doi.org/10.2514/6.2016-3764' chicago: Mikić, Gregor, Alex Stoll, Joe Bevirt, Rok Grah, and Mark Moore. “Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency,” 1–19. AIAA, 2016. https://doi.org/10.2514/6.2016-3764. ieee: 'G. Mikić, A. Stoll, J. Bevirt, R. Grah, and M. Moore, “Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency,” presented at the AIAA: Aviation Technology, Integration, and Operations Conference, Washington, D.C., USA, 2016, pp. 1–19.' ista: 'Mikić G, Stoll A, Bevirt J, Grah R, Moore M. 2016. Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency. AIAA: Aviation Technology, Integration, and Operations Conference, 1–19.' mla: Mikić, Gregor, et al. Fuselage Boundary Layer Ingestion Propulsion Applied to a Thin Haul Commuter Aircraft for Optimal Efficiency. AIAA, 2016, pp. 1–19, doi:10.2514/6.2016-3764. short: G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 2016, pp. 1–19. conference: end_date: 2016-06-17 location: Washington, D.C., USA name: 'AIAA: Aviation Technology, Integration, and Operations Conference' start_date: 2016-06-13 date_created: 2018-12-11T11:50:47Z date_published: 2016-06-01T00:00:00Z date_updated: 2023-02-21T10:17:50Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.2514/6.2016-3764 language: - iso: eng main_file_link: - open_access: '1' url: https://ntrs.nasa.gov/search.jsp?R=20160010167&hterms=Fuselage+boundary+layer+ingestion+propulsion+applied+thin+haul+commuter+aircraft+optimal+efficiency&qs=N%3D0%26Ntk%3DAll%26Ntt%3DFuselage%2520boundary%2520layer%2520ingestion%2520propulsion%2520applied%2520to%2520a%2520thin%2520haul%2520commuter%2520aircraft%2520for%2520optimal%2520efficiency%26Ntx%3Dmode%2520matchallpartial%26Nm%3D123%7CCollection%7CNASA%2520STI%7C%7C17%7CCollection%7CNACA month: '06' oa: 1 oa_version: Preprint page: 1 - 19 publication_status: published publisher: AIAA publist_id: '6114' quality_controlled: '1' scopus_import: 1 status: public title: Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 year: '2016' ... --- _id: '1242' abstract: - lang: eng text: A crucial step in the regulation of gene expression is binding of transcription factor (TF) proteins to regulatory sites along the DNA. But transcription factors act at nanomolar concentrations, and noise due to random arrival of these molecules at their binding sites can severely limit the precision of regulation. Recent work on the optimization of information flow through regulatory networks indicates that the lower end of the dynamic range of concentrations is simply inaccessible, overwhelmed by the impact of this noise. Motivated by the behavior of homeodomain proteins, such as the maternal morphogen Bicoid in the fruit fly embryo, we suggest a scheme in which transcription factors also act as indirect translational regulators, binding to the mRNA of other regulatory proteins. Intuitively, each mRNA molecule acts as an independent sensor of the input concentration, and averaging over these multiple sensors reduces the noise. We analyze information flow through this scheme and identify conditions under which it outperforms direct transcriptional regulation. Our results suggest that the dual role of homeodomain proteins is not just a historical accident, but a solution to a crucial physics problem in the regulation of gene expression. acknowledgement: "We thank T. Gregor, A. Prochaintz, and others for\r\nhelpful discussions. This work was supported in part by\r\nGrants No. PHY-1305525 and No. CCF-0939370 from the\r\nUS National Science Foundation and by the W.M. Keck\r\nFoundation. A.M.W. acknowledges the support by European\r\nResearch Council (ERC) Grant No. MCCIG PCIG10–GA-\r\n2011–303561. G.T. and T.R.S. were supported by Austrian\r\nScience Fund (FWF) Grant No. P28844S." article_number: '022404' author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Aleksandra full_name: Walczak, Aleksandra last_name: Walczak - first_name: William full_name: Bialek, William last_name: Bialek - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Sokolowski TR, Walczak A, Bialek W, Tkačik G. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2016;93(2). doi:10.1103/PhysRevE.93.022404 apa: Sokolowski, T. R., Walczak, A., Bialek, W., & Tkačik, G. (2016). Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.93.022404 chicago: Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gašper Tkačik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016. https://doi.org/10.1103/PhysRevE.93.022404. ieee: T. R. Sokolowski, A. Walczak, W. Bialek, and G. Tkačik, “Extending the dynamic range of transcription factor action by translational regulation,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2. American Institute of Physics, 2016. ista: Sokolowski TR, Walczak A, Bialek W, Tkačik G. 2016. Extending the dynamic range of transcription factor action by translational regulation. Physical Review E Statistical Nonlinear and Soft Matter Physics. 93(2), 022404. mla: Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404. short: T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (2016). date_created: 2018-12-11T11:50:54Z date_published: 2016-02-04T00:00:00Z date_updated: 2021-01-12T06:49:20Z day: '04' department: - _id: GaTk doi: 10.1103/PhysRevE.93.022404 intvolume: ' 93' issue: '2' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1507.02562 month: '02' oa: 1 oa_version: Preprint project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '6088' quality_controlled: '1' scopus_import: 1 status: public title: Extending the dynamic range of transcription factor action by translational regulation type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 93 year: '2016' ... --- _id: '1244' abstract: - lang: eng text: Cell polarity refers to a functional spatial organization of proteins that is crucial for the control of essential cellular processes such as growth and division. To establish polarity, cells rely on elaborate regulation networks that control the distribution of proteins at the cell membrane. In fission yeast cells, a microtubule-dependent network has been identified that polarizes the distribution of signaling proteins that restricts growth to cell ends and targets the cytokinetic machinery to the middle of the cell. Although many molecular components have been shown to play a role in this network, it remains unknown which molecular functionalities are minimally required to establish a polarized protein distribution in this system. Here we show that a membrane-binding protein fragment, which distributes homogeneously in wild-type fission yeast cells, can be made to concentrate at cell ends by attaching it to a cytoplasmic microtubule end-binding protein. This concentration results in a polarized pattern of chimera proteins with a spatial extension that is very reminiscent of natural polarity patterns in fission yeast. However, chimera levels fluctuate in response to microtubule dynamics, and disruption of microtubules leads to disappearance of the pattern. Numerical simulations confirm that the combined functionality of membrane anchoring and microtubule tip affinity is in principle sufficient to create polarized patterns. Our chimera protein may thus represent a simple molecular functionality that is able to polarize the membrane, onto which additional layers of molecular complexity may be built to provide the temporal robustness that is typical of natural polarity patterns. acknowledgement: "We thank Sophie Martin, Ken Sawin, Stephen Huisman,\r\nand Damian Brunner for strains; Julianne\r\nTeapal, Marcel Janson, Sergio Rincon,\r\nand Phong Tran for technical assistance; Andrew Mugler and Bela Mulder for\r\ndiscussions; and Sander Tans, Phong Tran,\r\nand Anne Paoletti for critical reading\r\nof the manuscript. This work is part of the research program of the\r\n“\r\nStichting\r\nvoor Fundamenteel Onderzoek de Materie,\r\n”\r\nwhich is financially supported by\r\nthe\r\n“\r\nNederlandse organisatie voor Wete\r\nnschappelijk Onderzoek (NWO).\r\n”" author: - first_name: Pierre full_name: Recouvreux, Pierre last_name: Recouvreux - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Aristea full_name: Grammoustianou, Aristea last_name: Grammoustianou - first_name: Pieter full_name: Tenwolde, Pieter last_name: Tenwolde - first_name: Marileen full_name: Dogterom, Marileen last_name: Dogterom citation: ama: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 2016;113(7):1811-1816. doi:10.1073/pnas.1419248113 apa: Recouvreux, P., Sokolowski, T. R., Grammoustianou, A., Tenwolde, P., & Dogterom, M. (2016). Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1419248113 chicago: Recouvreux, Pierre, Thomas R Sokolowski, Aristea Grammoustianou, Pieter Tenwolde, and Marileen Dogterom. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS. National Academy of Sciences, 2016. https://doi.org/10.1073/pnas.1419248113. ieee: P. Recouvreux, T. R. Sokolowski, A. Grammoustianou, P. Tenwolde, and M. Dogterom, “Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells,” PNAS, vol. 113, no. 7. National Academy of Sciences, pp. 1811–1816, 2016. ista: Recouvreux P, Sokolowski TR, Grammoustianou A, Tenwolde P, Dogterom M. 2016. Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells. PNAS. 113(7), 1811–1816. mla: Recouvreux, Pierre, et al. “Chimera Proteins with Affinity for Membranes and Microtubule Tips Polarize in the Membrane of Fission Yeast Cells.” PNAS, vol. 113, no. 7, National Academy of Sciences, 2016, pp. 1811–16, doi:10.1073/pnas.1419248113. short: P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816. date_created: 2018-12-11T11:50:55Z date_published: 2016-02-16T00:00:00Z date_updated: 2021-01-12T06:49:21Z day: '16' department: - _id: GaTk doi: 10.1073/pnas.1419248113 intvolume: ' 113' issue: '7' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/ month: '02' oa: 1 oa_version: Submitted Version page: 1811 - 1816 publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '6085' quality_controlled: '1' scopus_import: 1 status: public title: Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 113 year: '2016' ... --- _id: '1248' abstract: - lang: eng text: Life depends as much on the flow of information as on the flow of energy. Here we review the many efforts to make this intuition precise. Starting with the building blocks of information theory, we explore examples where it has been possible to measure, directly, the flow of information in biological networks, or more generally where information-theoretic ideas have been used to guide the analysis of experiments. Systems of interest range from single molecules (the sequence diversity in families of proteins) to groups of organisms (the distribution of velocities in flocks of birds), and all scales in between. Many of these analyses are motivated by the idea that biological systems may have evolved to optimize the gathering and representation of information, and we review the experimental evidence for this optimization, again across a wide range of scales. acknowledgement: "Our work was supported in part by the US\r\nNational Science Foundation (PHY–1305525 and CCF–\r\n0939370), by the Austrian Science Foundation (FWF\r\nP25651), by the Human Frontiers Science Program, and\r\nby the Simons and Swartz Foundations." author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Bialek W. Information processing in living systems. Annual Review of Condensed Matter Physics. 2016;7:89-117. doi:10.1146/annurev-conmatphys-031214-014803 apa: Tkačik, G., & Bialek, W. (2016). Information processing in living systems. Annual Review of Condensed Matter Physics. Annual Reviews. https://doi.org/10.1146/annurev-conmatphys-031214-014803 chicago: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics. Annual Reviews, 2016. https://doi.org/10.1146/annurev-conmatphys-031214-014803. ieee: G. Tkačik and W. Bialek, “Information processing in living systems,” Annual Review of Condensed Matter Physics, vol. 7. Annual Reviews, pp. 89–117, 2016. ista: Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117. mla: Tkačik, Gašper, and William Bialek. “Information Processing in Living Systems.” Annual Review of Condensed Matter Physics, vol. 7, Annual Reviews, 2016, pp. 89–117, doi:10.1146/annurev-conmatphys-031214-014803. short: G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117. date_created: 2018-12-11T11:50:56Z date_published: 2016-03-10T00:00:00Z date_updated: 2021-01-12T06:49:23Z day: '10' department: - _id: GaTk doi: 10.1146/annurev-conmatphys-031214-014803 intvolume: ' 7' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1412.8752 month: '03' oa: 1 oa_version: Preprint page: 89 - 117 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: Annual Review of Condensed Matter Physics publication_status: published publisher: Annual Reviews publist_id: '6080' quality_controlled: '1' scopus_import: 1 status: public title: Information processing in living systems type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1260' abstract: - lang: eng text: In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way. article_number: '1650067' article_processing_charge: No article_type: original author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 2016;27(6). doi:10.1142/S0129183116500674 apa: De Martino, D. (2016). The dual of the space of interactions in neural network models. International Journal of Modern Physics C. World Scientific Publishing. https://doi.org/10.1142/S0129183116500674 chicago: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C. World Scientific Publishing, 2016. https://doi.org/10.1142/S0129183116500674. ieee: D. De Martino, “The dual of the space of interactions in neural network models,” International Journal of Modern Physics C, vol. 27, no. 6. World Scientific Publishing, 2016. ista: De Martino D. 2016. The dual of the space of interactions in neural network models. International Journal of Modern Physics C. 27(6), 1650067. mla: De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.” International Journal of Modern Physics C, vol. 27, no. 6, 1650067, World Scientific Publishing, 2016, doi:10.1142/S0129183116500674. short: D. De Martino, International Journal of Modern Physics C 27 (2016). date_created: 2018-12-11T11:51:00Z date_published: 2016-06-01T00:00:00Z date_updated: 2021-01-12T06:49:28Z day: '01' department: - _id: GaTk doi: 10.1142/S0129183116500674 external_id: arxiv: - '1505.02963' intvolume: ' 27' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1505.02963 month: '06' oa: 1 oa_version: Preprint publication: International Journal of Modern Physics C publication_status: published publisher: World Scientific Publishing publist_id: '6065' quality_controlled: '1' scopus_import: 1 status: public title: The dual of the space of interactions in neural network models type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 27 year: '2016' ... --- _id: '1266' abstract: - lang: eng text: 'Cortical networks exhibit ‘global oscillations’, in which neural spike times are entrained to an underlying oscillatory rhythm, but where individual neurons fire irregularly, on only a fraction of cycles. While the network dynamics underlying global oscillations have been well characterised, their function is debated. Here, we show that such global oscillations are a direct consequence of optimal efficient coding in spiking networks with synaptic delays and noise. To avoid firing unnecessary spikes, neurons need to share information about the network state. Ideally, membrane potentials should be strongly correlated and reflect a ‘prediction error’ while the spikes themselves are uncorrelated and occur rarely. We show that the most efficient representation is when: (i) spike times are entrained to a global Gamma rhythm (implying a consistent representation of the error); but (ii) few neurons fire on each cycle (implying high efficiency), while (iii) excitation and inhibition are tightly balanced. This suggests that cortical networks exhibiting such dynamics are tuned to achieve a maximally efficient population code.' acknowledgement: Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’. article_number: e13824 author: - first_name: Matthew J full_name: Chalk, Matthew J id: 2BAAC544-F248-11E8-B48F-1D18A9856A87 last_name: Chalk orcid: 0000-0001-7782-4436 - first_name: Boris full_name: Gutkin, Boris last_name: Gutkin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: Chalk MJ, Gutkin B, Denève S. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 2016;5(2016JULY). doi:10.7554/eLife.13824 apa: Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824 chicago: Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824. ieee: M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016. ista: Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824. mla: Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824. short: M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016). date_created: 2018-12-11T11:51:02Z date_published: 2016-07-01T00:00:00Z date_updated: 2021-01-12T06:49:30Z day: '01' ddc: - '571' department: - _id: GaTk doi: 10.7554/eLife.13824 file: - access_level: open_access checksum: dc52d967dc76174477bb258d84be2899 content_type: application/pdf creator: system date_created: 2018-12-12T10:11:20Z date_updated: 2020-07-14T12:44:42Z file_id: '4874' file_name: IST-2016-700-v1+1_e13824-download.pdf file_size: 2819055 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 5' issue: 2016JULY language: - iso: eng month: '07' oa: 1 oa_version: Published Version publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '6056' pubrep_id: '700' quality_controlled: '1' scopus_import: 1 status: public title: Neural oscillations as a signature of efficient coding in the presence of synaptic delays tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 5 year: '2016' ... --- _id: '1290' abstract: - lang: eng text: We developed a competition-based screening strategy to identify compounds that invert the selective advantage of antibiotic resistance. Using our assay, we screened over 19,000 compounds for the ability to select against the TetA tetracycline-resistance efflux pump in Escherichia coli and identified two hits, β-thujaplicin and disulfiram. Treating a tetracycline-resistant population with β-thujaplicin selects for loss of the resistance gene, enabling an effective second-phase treatment with doxycycline. acknowledgement: "This work was supported in part by National Institute of Allergy and Infectious Diseases grant U54 AI057159, US National Institutes of Health grants R01 GM081617 (to R.K.) and GM086258 (to J.C.), European Research Council FP7 ERC grant 281891 (to R.K.) and a National Science Foundation Graduate Fellowship (to L.K.S.).\r\n" author: - first_name: Laura full_name: Stone, Laura last_name: Stone - first_name: Michael full_name: Baym, Michael last_name: Baym - first_name: Tami full_name: Lieberman, Tami last_name: Lieberman - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Jon full_name: Clardy, Jon last_name: Clardy - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 2016;12(11):902-904. doi:10.1038/nchembio.2176 apa: Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176 chicago: Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176. ieee: L. Stone, M. Baym, T. Lieberman, R. P. Chait, J. Clardy, and R. Kishony, “Compounds that select against the tetracycline-resistance efflux pump,” Nature Chemical Biology, vol. 12, no. 11. Nature Publishing Group, pp. 902–904, 2016. ista: Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904. mla: Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176. short: L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904. date_created: 2018-12-11T11:51:10Z date_published: 2016-11-01T00:00:00Z date_updated: 2021-01-12T06:49:39Z day: '01' department: - _id: CaGu - _id: GaTk doi: 10.1038/nchembio.2176 intvolume: ' 12' issue: '11' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/ month: '11' oa: 1 oa_version: Preprint page: 902 - 904 publication: Nature Chemical Biology publication_status: published publisher: Nature Publishing Group publist_id: '6026' quality_controlled: '1' scopus_import: 1 status: public title: Compounds that select against the tetracycline-resistance efflux pump type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2016' ... --- _id: '1320' abstract: - lang: eng text: 'In recent years, several biomolecular systems have been shown to be scale-invariant (SI), i.e. to show the same output dynamics when exposed to geometrically scaled input signals (u → pu, p > 0) after pre-adaptation to accordingly scaled constant inputs. In this article, we show that SI systems-as well as systems invariant with respect to other input transformations-can realize nonlinear differential operators: when excited by inputs obeying functional forms characteristic for a given class of invariant systems, the systems'' outputs converge to constant values directly quantifying the speed of the input.' acknowledgement: The research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement n° [291734]. Work supported in part by grants AFOSR FA9550-14-1-0060 and NIH 1R01GM100473. article_number: '7526722' author: - first_name: Moritz full_name: Lang, Moritz id: 29E0800A-F248-11E8-B48F-1D18A9856A87 last_name: Lang - first_name: Eduardo full_name: Sontag, Eduardo last_name: Sontag citation: ama: 'Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722' apa: 'Lang, M., & Sontag, E. (2016). Scale-invariant systems realize nonlinear differential operators (Vol. 2016–July). Presented at the ACC: American Control Conference, Boston, MA, USA: IEEE. https://doi.org/10.1109/ACC.2016.7526722' chicago: Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,” Vol. 2016–July. IEEE, 2016. https://doi.org/10.1109/ACC.2016.7526722. ieee: 'M. Lang and E. Sontag, “Scale-invariant systems realize nonlinear differential operators,” presented at the ACC: American Control Conference, Boston, MA, USA, 2016, vol. 2016–July.' ista: 'Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.' mla: Lang, Moritz, and Eduardo Sontag. Scale-Invariant Systems Realize Nonlinear Differential Operators. Vol. 2016–July, 7526722, IEEE, 2016, doi:10.1109/ACC.2016.7526722. short: M. Lang, E. Sontag, in:, IEEE, 2016. conference: end_date: 2016-07-08 location: Boston, MA, USA name: 'ACC: American Control Conference' start_date: 2016-07-06 date_created: 2018-12-11T11:51:21Z date_published: 2016-07-28T00:00:00Z date_updated: 2021-01-12T06:49:51Z day: '28' ddc: - '003' - '621' department: - _id: CaGu - _id: GaTk doi: 10.1109/ACC.2016.7526722 ec_funded: 1 file: - access_level: local checksum: 7219432b43defc62a0d45f48d4ce6a19 content_type: application/pdf creator: system date_created: 2018-12-12T10:16:17Z date_updated: 2020-07-14T12:44:43Z file_id: '5203' file_name: IST-2017-810-v1+1_root.pdf file_size: 539166 relation: main_file file_date_updated: 2020-07-14T12:44:43Z has_accepted_license: '1' language: - iso: eng month: '07' oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: IEEE publist_id: '5950' pubrep_id: '810' quality_controlled: '1' scopus_import: 1 status: public title: Scale-invariant systems realize nonlinear differential operators type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 2016-July year: '2016' ... --- _id: '1332' abstract: - lang: eng text: Antibiotic-sensitive and -resistant bacteria coexist in natural environments with low, if detectable, antibiotic concentrations. Except possibly around localized antibiotic sources, where resistance can provide a strong advantage, bacterial fitness is dominated by stresses unaffected by resistance to the antibiotic. How do such mixed and heterogeneous conditions influence the selective advantage or disadvantage of antibiotic resistance? Here we find that sub-inhibitory levels of tetracyclines potentiate selection for or against tetracycline resistance around localized sources of almost any toxin or stress. Furthermore, certain stresses generate alternating rings of selection for and against resistance around a localized source of the antibiotic. In these conditions, localized antibiotic sources, even at high strengths, can actually produce a net selection against resistance to the antibiotic. Our results show that interactions between the effects of an antibiotic and other stresses in inhomogeneous environments can generate pervasive, complex patterns of selection both for and against antibiotic resistance. acknowledgement: This work was partially supported by US National Institutes of Health grant R01-GM081617, Israeli Centers of Research Excellence I-CORE Program ISF Grant No. 152/11, and the European Research Council FP7 ERC Grant 281891. article_number: '10333' author: - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Adam full_name: Palmer, Adam last_name: Palmer - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Chait RP, Palmer A, Yelin I, Kishony R. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 2016;7. doi:10.1038/ncomms10333 apa: Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333 chicago: Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333. ieee: R. P. Chait, A. Palmer, I. Yelin, and R. Kishony, “Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Chait RP, Palmer A, Yelin I, Kishony R. 2016. Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. 7, 10333. mla: Chait, Remy P., et al. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications, vol. 7, 10333, Nature Publishing Group, 2016, doi:10.1038/ncomms10333. short: R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:25Z date_published: 2016-01-20T00:00:00Z date_updated: 2021-01-12T06:49:57Z day: '20' ddc: - '570' - '579' department: - _id: CaGu - _id: GaTk doi: 10.1038/ncomms10333 file: - access_level: open_access checksum: ef147bcbb8bd37e9079cf3ce06f5815d content_type: application/pdf creator: system date_created: 2018-12-12T10:13:52Z date_updated: 2020-07-14T12:44:44Z file_id: '5039' file_name: IST-2016-662-v1+1_ncomms10333.pdf file_size: 1844107 relation: main_file file_date_updated: 2020-07-14T12:44:44Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '01' oa: 1 oa_version: Published Version publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5936' pubrep_id: '662' quality_controlled: '1' scopus_import: 1 status: public title: Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '1342' abstract: - lang: eng text: A key aspect of bacterial survival is the ability to evolve while migrating across spatially varying environmental challenges. Laboratory experiments, however, often study evolution in well-mixed systems. Here, we introduce an experimental device, the microbial evolution and growth arena (MEGA)-plate, in which bacteria spread and evolved on a large antibiotic landscape (120 × 60 centimeters) that allowed visual observation of mutation and selection in a migrating bacterial front.While resistance increased consistently, multiple coexisting lineages diversified both phenotypically and genotypically. Analyzing mutants at and behind the propagating front,we found that evolution is not always led by the most resistant mutants; highly resistant mutants may be trapped behindmore sensitive lineages.TheMEGA-plate provides a versatile platformfor studying microbial adaption and directly visualizing evolutionary dynamics. author: - first_name: Michael full_name: Baym, Michael last_name: Baym - first_name: Tami full_name: Lieberman, Tami last_name: Lieberman - first_name: Eric full_name: Kelsic, Eric last_name: Kelsic - first_name: Remy P full_name: Chait, Remy P id: 3464AE84-F248-11E8-B48F-1D18A9856A87 last_name: Chait orcid: 0000-0003-0876-3187 - first_name: Rotem full_name: Gross, Rotem last_name: Gross - first_name: Idan full_name: Yelin, Idan last_name: Yelin - first_name: Roy full_name: Kishony, Roy last_name: Kishony citation: ama: Baym M, Lieberman T, Kelsic E, et al. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 2016;353(6304):1147-1151. doi:10.1126/science.aag0822 apa: Baym, M., Lieberman, T., Kelsic, E., Chait, R. P., Gross, R., Yelin, I., & Kishony, R. (2016). Spatiotemporal microbial evolution on antibiotic landscapes. Science. American Association for the Advancement of Science. https://doi.org/10.1126/science.aag0822 chicago: Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science. American Association for the Advancement of Science, 2016. https://doi.org/10.1126/science.aag0822. ieee: M. Baym et al., “Spatiotemporal microbial evolution on antibiotic landscapes,” Science, vol. 353, no. 6304. American Association for the Advancement of Science, pp. 1147–1151, 2016. ista: Baym M, Lieberman T, Kelsic E, Chait RP, Gross R, Yelin I, Kishony R. 2016. Spatiotemporal microbial evolution on antibiotic landscapes. Science. 353(6304), 1147–1151. mla: Baym, Michael, et al. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.” Science, vol. 353, no. 6304, American Association for the Advancement of Science, 2016, pp. 1147–51, doi:10.1126/science.aag0822. short: M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151. date_created: 2018-12-11T11:51:29Z date_published: 2016-09-09T00:00:00Z date_updated: 2021-01-12T06:50:01Z day: '09' department: - _id: CaGu - _id: GaTk doi: 10.1126/science.aag0822 intvolume: ' 353' issue: '6304' language: - iso: eng main_file_link: - open_access: '1' url: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/ month: '09' oa: 1 oa_version: Preprint page: 1147 - 1151 publication: Science publication_status: published publisher: American Association for the Advancement of Science publist_id: '5911' quality_controlled: '1' scopus_import: 1 status: public title: Spatiotemporal microbial evolution on antibiotic landscapes type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 353 year: '2016' ... --- _id: '1394' abstract: - lang: eng text: "The solution space of genome-scale models of cellular metabolism provides a map between physically\r\nviable flux configurations and cellular metabolic phenotypes described, at the most basic level, by the\r\ncorresponding growth rates. By sampling the solution space of E. coliʼs metabolic network, we show\r\nthat empirical growth rate distributions recently obtained in experiments at single-cell resolution can\r\nbe explained in terms of a trade-off between the higher fitness of fast-growing phenotypes and the\r\nhigher entropy of slow-growing ones. Based on this, we propose a minimal model for the evolution of\r\na large bacterial population that captures this trade-off. The scaling relationships observed in\r\nexperiments encode, in such frameworks, for the same distance from the maximum achievable growth\r\nrate, the same degree of growth rate maximization, and/or the same rate of phenotypic change. Being\r\ngrounded on genome-scale metabolic network reconstructions, these results allow for multiple\r\nimplications and extensions in spite of the underlying conceptual simplicity." acknowledgement: "The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038." article_number: '036005' author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 - first_name: Fabrizio full_name: Capuani, Fabrizio last_name: Capuani - first_name: Andrea full_name: De Martino, Andrea last_name: De Martino citation: ama: 'De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005' apa: 'De Martino, D., Capuani, F., & De Martino, A. (2016). Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/3/036005' chicago: 'De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/3/036005.' ieee: 'D. De Martino, F. Capuani, and A. De Martino, “Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli,” Physical Biology, vol. 13, no. 3. IOP Publishing Ltd., 2016.' ista: 'De Martino D, Capuani F, De Martino A. 2016. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 13(3), 036005.' mla: 'De Martino, Daniele, et al. “Growth against Entropy in Bacterial Metabolism: The Phenotypic Trade-off behind Empirical Growth Rate Distributions in E. Coli.” Physical Biology, vol. 13, no. 3, 036005, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/3/036005.' short: D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016). date_created: 2018-12-11T11:51:46Z date_published: 2016-05-27T00:00:00Z date_updated: 2021-01-12T06:50:23Z day: '27' department: - _id: GaTk doi: 10.1088/1478-3975/13/3/036005 ec_funded: 1 intvolume: ' 13' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: https://arxiv.org/abs/1601.03243 month: '05' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Biology publication_status: published publisher: IOP Publishing Ltd. publist_id: '5815' quality_controlled: '1' scopus_import: 1 status: public title: 'Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli' type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2016' ... --- _id: '1420' abstract: - lang: eng text: 'Selection, mutation, and random drift affect the dynamics of allele frequencies and consequently of quantitative traits. While the macroscopic dynamics of quantitative traits can be measured, the underlying allele frequencies are typically unobserved. Can we understand how the macroscopic observables evolve without following these microscopic processes? This problem has been studied previously by analogy with statistical mechanics: the allele frequency distribution at each time point is approximated by the stationary form, which maximizes entropy. We explore the limitations of this method when mutation is small (4Nμ < 1) so that populations are typically close to fixation, and we extend the theory in this regime to account for changes in mutation strength. We consider a single diallelic locus either under directional selection or with overdominance and then generalize to multiple unlinked biallelic loci with unequal effects. We find that the maximum-entropy approximation is remarkably accurate, even when mutation and selection change rapidly. ' article_processing_charge: No author: - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 citation: ama: Bodova K, Tkačik G, Barton NH. A general approximation for the dynamics of quantitative traits. Genetics. 2016;202(4):1523-1548. doi:10.1534/genetics.115.184127 apa: Bodova, K., Tkačik, G., & Barton, N. H. (2016). A general approximation for the dynamics of quantitative traits. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.115.184127 chicago: Bodova, Katarina, Gašper Tkačik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics. Genetics Society of America, 2016. https://doi.org/10.1534/genetics.115.184127. ieee: K. Bodova, G. Tkačik, and N. H. Barton, “A general approximation for the dynamics of quantitative traits,” Genetics, vol. 202, no. 4. Genetics Society of America, pp. 1523–1548, 2016. ista: Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548. mla: Bodova, Katarina, et al. “A General Approximation for the Dynamics of Quantitative Traits.” Genetics, vol. 202, no. 4, Genetics Society of America, 2016, pp. 1523–48, doi:10.1534/genetics.115.184127. short: K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548. date_created: 2018-12-11T11:51:55Z date_published: 2016-04-06T00:00:00Z date_updated: 2022-08-01T10:49:55Z day: '06' department: - _id: GaTk - _id: NiBa doi: 10.1534/genetics.115.184127 ec_funded: 1 external_id: arxiv: - '1510.08344' intvolume: ' 202' issue: '4' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1510.08344 month: '04' oa: 1 oa_version: Preprint page: 1523 - 1548 project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 255008E4-B435-11E9-9278-68D0E5697425 grant_number: RGP0065/2012 name: Information processing and computation in fish groups publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5787' quality_controlled: '1' scopus_import: '1' status: public title: A general approximation for the dynamics of quantitative traits type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 202 year: '2016' ... --- _id: '1485' abstract: - lang: eng text: In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism. article_number: '016003' author: - first_name: Daniele full_name: De Martino, Daniele id: 3FF5848A-F248-11E8-B48F-1D18A9856A87 last_name: De Martino orcid: 0000-0002-5214-4706 citation: ama: De Martino D. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 2016;13(1). doi:10.1088/1478-3975/13/1/016003 apa: De Martino, D. (2016). Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. IOP Publishing Ltd. https://doi.org/10.1088/1478-3975/13/1/016003 chicago: De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing Ltd., 2016. https://doi.org/10.1088/1478-3975/13/1/016003. ieee: D. De Martino, “Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis,” Physical Biology, vol. 13, no. 1. IOP Publishing Ltd., 2016. ista: De Martino D. 2016. Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis. Physical Biology. 13(1), 016003. mla: De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology, vol. 13, no. 1, 016003, IOP Publishing Ltd., 2016, doi:10.1088/1478-3975/13/1/016003. short: D. De Martino, Physical Biology 13 (2016). date_created: 2018-12-11T11:52:18Z date_published: 2016-01-29T00:00:00Z date_updated: 2021-01-12T06:51:04Z day: '29' department: - _id: GaTk doi: 10.1088/1478-3975/13/1/016003 ec_funded: 1 intvolume: ' 13' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1505.04613 month: '01' oa: 1 oa_version: Preprint project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Physical Biology publication_status: published publisher: IOP Publishing Ltd. publist_id: '5702' quality_controlled: '1' scopus_import: 1 status: public title: Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 13 year: '2016' ... --- _id: '1148' abstract: - lang: eng text: Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. © 2016 Elsevier Ireland Ltd acknowledgement: This work is based on the CMSB 2015 paper “Adaptive moment closure for parameter inference of biochemical reaction networks” (Bogomolov et al., 2015). The work was partly supported by the German Research Foundation (DFG) as part of the Transregional Collaborative Research Center “Automatic Verification and Analysis of Complex Systems” (SFB/TR 14 AVACS1), by the European Research Council (ERC) under grant 267989 (QUAREM) and by the Austrian Science Fund (FWF) under grants S11402-N23 (RiSE) and Z211-N23 (Wittgenstein Award). J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. author: - first_name: Christian full_name: Schilling, Christian last_name: Schilling - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 2016;149:15-25. doi:10.1016/j.biosystems.2016.07.005 apa: Schilling, C., Bogomolov, S., Henzinger, T. A., Podelski, A., & Ruess, J. (2016). Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. Elsevier. https://doi.org/10.1016/j.biosystems.2016.07.005 chicago: Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems. Elsevier, 2016. https://doi.org/10.1016/j.biosystems.2016.07.005. ieee: C. Schilling, S. Bogomolov, T. A. Henzinger, A. Podelski, and J. Ruess, “Adaptive moment closure for parameter inference of biochemical reaction networks,” Biosystems, vol. 149. Elsevier, pp. 15–25, 2016. ista: Schilling C, Bogomolov S, Henzinger TA, Podelski A, Ruess J. 2016. Adaptive moment closure for parameter inference of biochemical reaction networks. Biosystems. 149, 15–25. mla: Schilling, Christian, et al. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Biosystems, vol. 149, Elsevier, 2016, pp. 15–25, doi:10.1016/j.biosystems.2016.07.005. short: C. Schilling, S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, Biosystems 149 (2016) 15–25. date_created: 2018-12-11T11:50:24Z date_published: 2016-11-01T00:00:00Z date_updated: 2023-02-23T10:08:46Z day: '01' department: - _id: ToHe - _id: GaTk doi: 10.1016/j.biosystems.2016.07.005 ec_funded: 1 intvolume: ' 149' language: - iso: eng month: '11' oa_version: None page: 15 - 25 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Biosystems publication_status: published publisher: Elsevier publist_id: '6210' quality_controlled: '1' related_material: record: - id: '1658' relation: earlier_version status: public scopus_import: 1 status: public title: Adaptive moment closure for parameter inference of biochemical reaction networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 149 year: '2016' ... --- _id: '8094' abstract: - lang: eng text: 'With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object''s internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with.' article_processing_charge: No author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Rafael full_name: Hostettler, Rafael last_name: Hostettler - first_name: Alois full_name: Knoll, Alois last_name: Knoll - first_name: Ralf full_name: Der, Ralf last_name: Der citation: ama: 'Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: Proceedings of the Artificial Life Conference 2016. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029' apa: 'Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In Proceedings of the Artificial Life Conference 2016 (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029' chicago: Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029. ieee: G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in Proceedings of the Artificial Life Conference 2016, Cancun, Mexico, 2016, vol. 28, pp. 142–143. ista: 'Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. Proceedings of the Artificial Life Conference 2016. ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.' mla: Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” Proceedings of the Artificial Life Conference 2016, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029. short: G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, Proceedings of the Artificial Life Conference 2016, MIT Press, 2016, pp. 142–143. conference: end_date: 2016-07-08 location: Cancun, Mexico name: 'ALIFE 2016: 15th International Conference on the Synthesis and Simulation of Living Systems' start_date: 2016-07-04 date_created: 2020-07-05T22:00:47Z date_published: 2016-09-01T00:00:00Z date_updated: 2021-01-12T08:16:53Z day: '01' ddc: - '610' department: - _id: ChLa - _id: GaTk doi: 10.7551/978-0-262-33936-0-ch029 ec_funded: 1 file: - access_level: open_access checksum: cff63e7a4b8ac466ba51a9c84153a940 content_type: application/pdf creator: cziletti date_created: 2020-07-06T12:59:09Z date_updated: 2020-07-14T12:48:09Z file_id: '8096' file_name: 2016_ProcALIFE_Martius.pdf file_size: 678670 relation: main_file file_date_updated: 2020-07-14T12:48:09Z has_accepted_license: '1' intvolume: ' 28' language: - iso: eng month: '09' oa: 1 oa_version: Published Version page: 142-143 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Proceedings of the Artificial Life Conference 2016 publication_identifier: isbn: - '9780262339360' publication_status: published publisher: MIT Press quality_controlled: '1' scopus_import: 1 status: public title: Self-organized control of an tendon driven arm by differential extrinsic plasticity tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: conference user_id: D865714E-FA4E-11E9-B85B-F5C5E5697425 volume: 28 year: '2016' ... --- _id: '1197' abstract: - lang: eng text: Across the nervous system, certain population spiking patterns are observed far more frequently than others. A hypothesis about this structure is that these collective activity patterns function as population codewords–collective modes–carrying information distinct from that of any single cell. We investigate this phenomenon in recordings of ∼150 retinal ganglion cells, the retina’s output. We develop a novel statistical model that decomposes the population response into modes; it predicts the distribution of spiking activity in the ganglion cell population with high accuracy. We found that the modes represent localized features of the visual stimulus that are distinct from the features represented by single neurons. Modes form clusters of activity states that are readily discriminated from one another. When we repeated the same visual stimulus, we found that the same mode was robustly elicited. These results suggest that retinal ganglion cells’ collective signaling is endowed with a form of error-correcting code–a principle that may hold in brain areas beyond retina. acknowledgement: JSP was supported by a C.V. Starr Fellowship from the Starr Foundation (http://www.starrfoundation.org/). GT was supported by Austrian Research Foundation (https://www.fwf.ac.at/en/) grant FWF P25651. MJB received support from National Eye Institute (https://nei.nih.gov/) grant EY 14196 and from the National Science Foundation grant 1504977. The authors thank Cristina Savin and Vicent Botella-Soler for helpful comments on the manuscript. article_number: e1005855 author: - first_name: Jason full_name: Prentice, Jason last_name: Prentice - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Mark full_name: Ioffe, Mark last_name: Ioffe - first_name: Adrianna full_name: Loback, Adrianna last_name: Loback - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. Error-robust modes of the retinal population code. PLoS Computational Biology. 2016;12(11). doi:10.1371/journal.pcbi.1005148 apa: Prentice, J., Marre, O., Ioffe, M., Loback, A., Tkačik, G., & Berry, M. (2016). Error-robust modes of the retinal population code. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1005148 chicago: Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gašper Tkačik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology. Public Library of Science, 2016. https://doi.org/10.1371/journal.pcbi.1005148. ieee: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, and M. Berry, “Error-robust modes of the retinal population code,” PLoS Computational Biology, vol. 12, no. 11. Public Library of Science, 2016. ista: Prentice J, Marre O, Ioffe M, Loback A, Tkačik G, Berry M. 2016. Error-robust modes of the retinal population code. PLoS Computational Biology. 12(11), e1005855. mla: Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148. short: J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (2016). date_created: 2018-12-11T11:50:40Z date_published: 2016-11-17T00:00:00Z date_updated: 2023-02-23T14:05:40Z day: '17' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1005148 file: - access_level: open_access checksum: 47b08cbd4dbf32b25ba161f5f4b262cc content_type: application/pdf creator: kschuh date_created: 2019-01-25T10:35:00Z date_updated: 2020-07-14T12:44:38Z file_id: '5884' file_name: 2016_PLOS_Prentice.pdf file_size: 4492021 relation: main_file file_date_updated: 2020-07-14T12:44:38Z has_accepted_license: '1' intvolume: ' 12' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '6153' quality_controlled: '1' related_material: record: - id: '9709' relation: research_data status: public scopus_import: 1 status: public title: Error-robust modes of the retinal population code tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 12 year: '2016' ... --- _id: '948' abstract: - lang: eng text: Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations. acknowledgement: DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS) alternative_title: - Advances in Neural Information Processing Systems author: - first_name: Travis full_name: Monk, Travis last_name: Monk - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Jörg full_name: Lücke, Jörg last_name: Lücke citation: ama: 'Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems; 2016:4285-4293.' apa: 'Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems.' chicago: Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016. ieee: 'T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.' ista: 'Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.' mla: Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics. Vol. 29, Neural Information Processing Systems, 2016, pp. 4285–93. short: T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems, 2016, pp. 4285–4293. conference: end_date: 2016-12-10 location: Barcelona, Spaine name: 'NIPS: Neural Information Processing Systems' start_date: 2016-12-05 date_created: 2018-12-11T11:49:21Z date_published: 2016-01-01T00:00:00Z date_updated: 2021-01-12T08:22:08Z day: '01' department: - _id: GaTk ec_funded: 1 intvolume: ' 29' language: - iso: eng main_file_link: - url: https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics month: '01' oa_version: None page: 4285 - 4293 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Neural Information Processing Systems publist_id: '6469' quality_controlled: '1' scopus_import: 1 status: public title: Neurons equipped with intrinsic plasticity learn stimulus intensity statistics type: conference user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 29 year: '2016' ... --- _id: '1270' abstract: - lang: eng text: A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework. acknowledgement: The authors would like to thank Thomas Sokolowski and Filipe Tostevin for helpful discussions. PH and UG were funded by the German Excellence Initiative via the program "Nanosystems Initiative Munich" (https://www.nano-initiative-munich.de) and the German Research Foundation via the SFB 1032 "Nanoagents for Spatiotemporal Control of Molecular and Cellular Reactions" (http://www.sfb1032.physik.uni-muenchen.de). GT was funded by the Austrian Science Fund (FWF P 28844) (http://www.fwf.ac.at). article_number: e0163628 author: - first_name: Patrick full_name: Hillenbrand, Patrick last_name: Hillenbrand - first_name: Ulrich full_name: Gerland, Ulrich last_name: Gerland - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: 'Hillenbrand P, Gerland U, Tkačik G. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 2016;11(9). doi:10.1371/journal.pone.0163628' apa: 'Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628' chicago: 'Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One. Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.' ieee: 'P. Hillenbrand, U. Gerland, and G. Tkačik, “Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information,” PLoS One, vol. 11, no. 9. Public Library of Science, 2016.' ista: 'Hillenbrand P, Gerland U, Tkačik G. 2016. Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information. PLoS One. 11(9), e0163628.' mla: 'Hillenbrand, Patrick, et al. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.” PLoS One, vol. 11, no. 9, e0163628, Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.' short: P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016). date_created: 2018-12-11T11:51:03Z date_published: 2016-09-27T00:00:00Z date_updated: 2023-02-23T14:11:37Z day: '27' ddc: - '571' department: - _id: GaTk doi: 10.1371/journal.pone.0163628 file: - access_level: open_access checksum: 3d0d55d373096a033bd9cf79288c8586 content_type: application/pdf creator: system date_created: 2018-12-12T10:10:47Z date_updated: 2020-07-14T12:44:42Z file_id: '4837' file_name: IST-2016-696-v1+1_journal.pone.0163628.PDF file_size: 4950415 relation: main_file file_date_updated: 2020-07-14T12:44:42Z has_accepted_license: '1' intvolume: ' 11' issue: '9' language: - iso: eng month: '09' oa: 1 oa_version: Published Version project: - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: PLoS One publication_status: published publisher: Public Library of Science publist_id: '6050' pubrep_id: '696' quality_controlled: '1' related_material: record: - id: '9869' relation: research_data status: public - id: '9870' relation: research_data status: public - id: '9871' relation: research_data status: public scopus_import: 1 status: public title: 'Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2016' ... --- _id: '9870' abstract: - lang: eng text: The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined. article_processing_charge: No author: - first_name: Patrick full_name: Hillenbrand, Patrick last_name: Hillenbrand - first_name: Ulrich full_name: Gerland, Ulrich last_name: Gerland - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002 apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002 chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002. ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016. ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002. mla: Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002. short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016). date_created: 2021-08-10T09:23:45Z date_published: 2016-09-27T00:00:00Z date_updated: 2023-02-21T16:56:40Z day: '27' department: - _id: GaTk doi: 10.1371/journal.pone.0163628.s002 month: '09' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1270' relation: used_in_publication status: public status: public title: Computation of positional information in an Ising model type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9869' abstract: - lang: eng text: A lower bound on the error of a positional estimator with limited positional information is derived. article_processing_charge: No author: - first_name: Patrick full_name: Hillenbrand, Patrick last_name: Hillenbrand - first_name: Ulrich full_name: Gerland, Ulrich last_name: Gerland - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001 apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001 chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001. ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016. ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001. mla: Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001. short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016). date_created: 2021-08-10T08:53:48Z date_published: 2016-09-27T00:00:00Z date_updated: 2023-02-21T16:56:40Z day: '27' department: - _id: GaTk doi: 10.1371/journal.pone.0163628.s001 month: '09' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1270' relation: used_in_publication status: public status: public title: Error bound on an estimator of position type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '9871' abstract: - lang: eng text: The positional information in a discrete morphogen field with Gaussian noise is computed. article_processing_charge: No author: - first_name: Patrick full_name: Hillenbrand, Patrick last_name: Hillenbrand - first_name: Ulrich full_name: Gerland, Ulrich last_name: Gerland - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003 apa: Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003 chicago: Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003. ieee: P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016. ista: Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003. mla: Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003. short: P. Hillenbrand, U. Gerland, G. Tkačik, (2016). date_created: 2021-08-10T09:27:35Z date_updated: 2023-02-21T16:56:40Z day: '27' department: - _id: GaTk doi: 10.1371/journal.pone.0163628.s003 month: '09' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1270' relation: used_in_publication status: public status: public title: Computation of positional information in a discrete morphogen field type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2016' ... --- _id: '1128' abstract: - lang: eng text: "The process of gene expression is central to the modern understanding of how cellular systems\r\nfunction. In this process, a special kind of regulatory proteins, called transcription factors,\r\nare important to determine how much protein is produced from a given gene. As biological\r\ninformation is transmitted from transcription factor concentration to mRNA levels to amounts of\r\nprotein, various sources of noise arise and pose limits to the fidelity of intracellular signaling.\r\nThis thesis concerns itself with several aspects of stochastic gene expression: (i) the mathematical\r\ndescription of complex promoters responsible for the stochastic production of biomolecules,\r\n(ii) fundamental limits to information processing the cell faces due to the interference from multiple\r\nfluctuating signals, (iii) how the presence of gene expression noise influences the evolution\r\nof regulatory sequences, (iv) and tools for the experimental study of origins and consequences\r\nof cell-cell heterogeneity, including an application to bacterial stress response systems." alternative_title: - ISTA Thesis article_processing_charge: No author: - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh citation: ama: Rieckh G. Studying the complexities of transcriptional regulation. 2016. apa: Rieckh, G. (2016). Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria. chicago: Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016. ieee: G. Rieckh, “Studying the complexities of transcriptional regulation,” Institute of Science and Technology Austria, 2016. ista: Rieckh G. 2016. Studying the complexities of transcriptional regulation. Institute of Science and Technology Austria. mla: Rieckh, Georg. Studying the Complexities of Transcriptional Regulation. Institute of Science and Technology Austria, 2016. short: G. Rieckh, Studying the Complexities of Transcriptional Regulation, Institute of Science and Technology Austria, 2016. date_created: 2018-12-11T11:50:18Z date_published: 2016-08-01T00:00:00Z date_updated: 2023-09-07T11:44:34Z day: '01' ddc: - '570' degree_awarded: PhD department: - _id: GaTk file: - access_level: closed checksum: ec453918c3bf8e6f460fd1156ef7b493 content_type: application/pdf creator: dernst date_created: 2019-08-13T11:46:25Z date_updated: 2019-08-13T11:46:25Z file_id: '6815' file_name: Thesis_Georg_Rieckh_w_signature_page.pdf file_size: 2614660 relation: main_file - access_level: open_access checksum: 51ae398166370d18fd22478b6365c4da content_type: application/pdf creator: dernst date_created: 2020-09-21T11:30:40Z date_updated: 2020-09-21T11:30:40Z file_id: '8542' file_name: Thesis_Georg_Rieckh.pdf file_size: 6096178 relation: main_file success: 1 file_date_updated: 2020-09-21T11:30:40Z has_accepted_license: '1' language: - iso: eng month: '08' oa: 1 oa_version: Published Version page: '114' publication_identifier: issn: - 2663-337X publication_status: published publisher: Institute of Science and Technology Austria publist_id: '6232' status: public supervisor: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 title: Studying the complexities of transcriptional regulation type: dissertation user_id: c635000d-4b10-11ee-a964-aac5a93f6ac1 year: '2016' ... --- _id: '1358' abstract: - lang: eng text: 'Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements.' article_number: '12307' author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Calin C full_name: Guet, Calin C id: 47F8433E-F248-11E8-B48F-1D18A9856A87 last_name: Guet orcid: 0000-0001-6220-2052 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307 apa: Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307 chicago: Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307. ieee: T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016. ista: Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307. mla: Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307. short: T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016). date_created: 2018-12-11T11:51:34Z date_published: 2016-08-04T00:00:00Z date_updated: 2023-09-07T12:53:49Z day: '04' ddc: - '576' department: - _id: GaTk - _id: NiBa - _id: CaGu doi: 10.1038/ncomms12307 ec_funded: 1 file: - access_level: open_access checksum: fe3f3a1526d180b29fe691ab11435b78 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:01Z date_updated: 2020-07-14T12:44:46Z file_id: '4919' file_name: IST-2016-627-v1+1_ncomms12307.pdf file_size: 861805 relation: main_file - access_level: open_access checksum: 164864a1a675f3ad80e9917c27aba07f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:02Z date_updated: 2020-07-14T12:44:46Z file_id: '4920' file_name: IST-2016-627-v1+2_ncomms12307-s1.pdf file_size: 1084703 relation: main_file file_date_updated: 2020-07-14T12:44:46Z has_accepted_license: '1' intvolume: ' 7' language: - iso: eng month: '08' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation - _id: 254E9036-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P28844-B27 name: Biophysics of information processing in gene regulation publication: Nature Communications publication_status: published publisher: Nature Publishing Group publist_id: '5887' pubrep_id: '627' quality_controlled: '1' related_material: record: - id: '6071' relation: dissertation_contains status: public scopus_import: 1 status: public title: Intrinsic limits to gene regulation by global crosstalk tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 7 year: '2016' ... --- _id: '10794' abstract: - lang: eng text: Mathematical models are of fundamental importance in the understanding of complex population dynamics. For instance, they can be used to predict the population evolution starting from different initial conditions or to test how a system responds to external perturbations. For this analysis to be meaningful in real applications, however, it is of paramount importance to choose an appropriate model structure and to infer the model parameters from measured data. While many parameter inference methods are available for models based on deterministic ordinary differential equations, the same does not hold for more detailed individual-based models. Here we consider, in particular, stochastic models in which the time evolution of the species abundances is described by a continuous-time Markov chain. These models are governed by a master equation that is typically difficult to solve. Consequently, traditional inference methods that rely on iterative evaluation of parameter likelihoods are computationally intractable. The aim of this paper is to present recent advances in parameter inference for continuous-time Markov chain models, based on a moment closure approximation of the parameter likelihood, and to investigate how these results can help in understanding, and ultimately controlling, complex systems in ecology. Specifically, we illustrate through an agricultural pest case study how parameters of a stochastic individual-based model can be identified from measured data and how the resulting model can be used to solve an optimal control problem in a stochastic setting. In particular, we show how the matter of determining the optimal combination of two different pest control methods can be formulated as a chance constrained optimization problem where the control action is modeled as a state reset, leading to a hybrid system formulation. acknowledgement: "The authors would like to acknowledge contributions from Baptiste Mottet who performed preliminary analysis regarding parameter inference for the considered case study in a student project (Mottet, 2014/2015).\r\nThe research leading to these results has received funding from the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007-2013) under REA grant agreement No. [291734] and from SystemsX under the project SignalX." article_number: '42' article_processing_charge: No article_type: original author: - first_name: Francesca full_name: Parise, Francesca last_name: Parise - first_name: John full_name: Lygeros, John last_name: Lygeros - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: 'Parise F, Lygeros J, Ruess J. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 2015;3. doi:10.3389/fenvs.2015.00042' apa: 'Parise, F., Lygeros, J., & Ruess, J. (2015). Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. Frontiers. https://doi.org/10.3389/fenvs.2015.00042' chicago: 'Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science. Frontiers, 2015. https://doi.org/10.3389/fenvs.2015.00042.' ieee: 'F. Parise, J. Lygeros, and J. Ruess, “Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study,” Frontiers in Environmental Science, vol. 3. Frontiers, 2015.' ista: 'Parise F, Lygeros J, Ruess J. 2015. Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study. Frontiers in Environmental Science. 3, 42.' mla: 'Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.” Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.' short: F. Parise, J. Lygeros, J. Ruess, Frontiers in Environmental Science 3 (2015). date_created: 2022-02-25T11:42:25Z date_published: 2015-06-10T00:00:00Z date_updated: 2022-02-25T11:59:23Z day: '10' ddc: - '000' - '570' department: - _id: ToHe - _id: GaTk doi: 10.3389/fenvs.2015.00042 ec_funded: 1 file: - access_level: open_access checksum: 26c222487564e1be02a11d688d6f769d content_type: application/pdf creator: dernst date_created: 2022-02-25T11:55:26Z date_updated: 2022-02-25T11:55:26Z file_id: '10795' file_name: 2015_FrontiersEnvironmScience_Parise.pdf file_size: 1371201 relation: main_file success: 1 file_date_updated: 2022-02-25T11:55:26Z has_accepted_license: '1' intvolume: ' 3' keyword: - General Environmental Science language: - iso: eng month: '06' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Frontiers in Environmental Science publication_identifier: issn: - 2296-665X publication_status: published publisher: Frontiers quality_controlled: '1' scopus_import: '1' status: public title: 'Bayesian inference for stochastic individual-based models of ecological systems: a pest control simulation study' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2015' ... --- _id: '1539' abstract: - lang: eng text: 'Many stochastic models of biochemical reaction networks contain some chemical species for which the number of molecules that are present in the system can only be finite (for instance due to conservation laws), but also other species that can be present in arbitrarily large amounts. The prime example of such networks are models of gene expression, which typically contain a small and finite number of possible states for the promoter but an infinite number of possible states for the amount of mRNA and protein. One of the main approaches to analyze such models is through the use of equations for the time evolution of moments of the chemical species. Recently, a new approach based on conditional moments of the species with infinite state space given all the different possible states of the finite species has been proposed. It was argued that this approach allows one to capture more details about the full underlying probability distribution with a smaller number of equations. Here, I show that the result that less moments provide more information can only stem from an unnecessarily complicated description of the system in the classical formulation. The foundation of this argument will be the derivation of moment equations that describe the complete probability distribution over the finite state space but only low-order moments over the infinite state space. I will show that the number of equations that is needed is always less than what was previously claimed and always less than the number of conditional moment equations up to the same order. To support these arguments, a symbolic algorithm is provided that can be used to derive minimal systems of unconditional moment equations for models with partially finite state space. ' article_number: '244103' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 citation: ama: Ruess J. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 2015;143(24). doi:10.1063/1.4937937 apa: Ruess, J. (2015). Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. American Institute of Physics. https://doi.org/10.1063/1.4937937 chicago: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics. American Institute of Physics, 2015. https://doi.org/10.1063/1.4937937. ieee: J. Ruess, “Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space,” Journal of Chemical Physics, vol. 143, no. 24. American Institute of Physics, 2015. ista: Ruess J. 2015. Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space. Journal of Chemical Physics. 143(24), 244103. mla: Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.” Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937. short: J. Ruess, Journal of Chemical Physics 143 (2015). date_created: 2018-12-11T11:52:36Z date_published: 2015-12-22T00:00:00Z date_updated: 2021-01-12T06:51:28Z day: '22' ddc: - '000' department: - _id: ToHe - _id: GaTk doi: 10.1063/1.4937937 ec_funded: 1 file: - access_level: open_access checksum: 838657118ae286463a2b7737319f35ce content_type: application/pdf creator: system date_created: 2018-12-12T10:07:43Z date_updated: 2020-07-14T12:45:01Z file_id: '4641' file_name: IST-2016-593-v1+1_Minimal_moment_equations.pdf file_size: 605355 relation: main_file file_date_updated: 2020-07-14T12:45:01Z has_accepted_license: '1' intvolume: ' 143' issue: '24' language: - iso: eng month: '12' oa: 1 oa_version: Published Version project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Journal of Chemical Physics publication_status: published publisher: American Institute of Physics publist_id: '5632' pubrep_id: '593' quality_controlled: '1' scopus_import: 1 status: public title: Minimal moment equations for stochastic models of biochemical reaction networks with partially finite state space type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 143 year: '2015' ... --- _id: '1538' abstract: - lang: eng text: Systems biology rests on the idea that biological complexity can be better unraveled through the interplay of modeling and experimentation. However, the success of this approach depends critically on the informativeness of the chosen experiments, which is usually unknown a priori. Here, we propose a systematic scheme based on iterations of optimal experiment design, flow cytometry experiments, and Bayesian parameter inference to guide the discovery process in the case of stochastic biochemical reaction networks. To illustrate the benefit of our methodology, we apply it to the characterization of an engineered light-inducible gene expression circuit in yeast and compare the performance of the resulting model with models identified from nonoptimal experiments. In particular, we compare the parameter posterior distributions and the precision to which the outcome of future experiments can be predicted. Moreover, we illustrate how the identified stochastic model can be used to determine light induction patterns that make either the average amount of protein or the variability in a population of cells follow a desired profile. Our results show that optimal experiment design allows one to derive models that are accurate enough to precisely predict and regulate the protein expression in heterogeneous cell populations over extended periods of time. acknowledgement: 'J.R., F.P., and J.L. acknowledge support from the European Commission under the Network of Excellence HYCON2 (highly-complex and networked control systems) and SystemsX.ch under the SignalX Project. J.R. acknowledges support from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme FP7/2007-2013 under REA (Research Executive Agency) Grant 291734. M.K. acknowledges support from Human Frontier Science Program Grant RP0061/2011 (www.hfsp.org). ' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Francesca full_name: Parise, Francesca last_name: Parise - first_name: Andreas full_name: Milias Argeitis, Andreas last_name: Milias Argeitis - first_name: Mustafa full_name: Khammash, Mustafa last_name: Khammash - first_name: John full_name: Lygeros, John last_name: Lygeros citation: ama: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 2015;112(26):8148-8153. doi:10.1073/pnas.1423947112 apa: Ruess, J., Parise, F., Milias Argeitis, A., Khammash, M., & Lygeros, J. (2015). Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1423947112 chicago: Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1423947112. ieee: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, and J. Lygeros, “Iterative experiment design guides the characterization of a light-inducible gene expression circuit,” PNAS, vol. 112, no. 26. National Academy of Sciences, pp. 8148–8153, 2015. ista: Ruess J, Parise F, Milias Argeitis A, Khammash M, Lygeros J. 2015. Iterative experiment design guides the characterization of a light-inducible gene expression circuit. PNAS. 112(26), 8148–8153. mla: Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.” PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112. short: J. Ruess, F. Parise, A. Milias Argeitis, M. Khammash, J. Lygeros, PNAS 112 (2015) 8148–8153. date_created: 2018-12-11T11:52:36Z date_published: 2015-06-30T00:00:00Z date_updated: 2021-01-12T06:51:27Z day: '30' department: - _id: ToHe - _id: GaTk doi: 10.1073/pnas.1423947112 ec_funded: 1 external_id: pmid: - '26085136' intvolume: ' 112' issue: '26' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4491780/ month: '06' oa: 1 oa_version: Submitted Version page: 8148 - 8153 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5633' quality_controlled: '1' scopus_import: 1 status: public title: Iterative experiment design guides the characterization of a light-inducible gene expression circuit type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1564' article_number: '145' author: - first_name: Matthieu full_name: Gilson, Matthieu last_name: Gilson - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Friedemann full_name: Zenke, Friedemann last_name: Zenke citation: ama: 'Gilson M, Savin C, Zenke F. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 2015;9(11). doi:10.3389/fncom.2015.00145' apa: 'Gilson, M., Savin, C., & Zenke, F. (2015). Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2015.00145' chicago: 'Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015. https://doi.org/10.3389/fncom.2015.00145.' ieee: 'M. Gilson, C. Savin, and F. Zenke, “Editorial: Emergent neural computation from the interaction of different forms of plasticity,” Frontiers in Computational Neuroscience, vol. 9, no. 11. Frontiers Research Foundation, 2015.' ista: 'Gilson M, Savin C, Zenke F. 2015. Editorial: Emergent neural computation from the interaction of different forms of plasticity. Frontiers in Computational Neuroscience. 9(11), 145.' mla: 'Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.” Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.' short: M. Gilson, C. Savin, F. Zenke, Frontiers in Computational Neuroscience 9 (2015). date_created: 2018-12-11T11:52:45Z date_published: 2015-11-30T00:00:00Z date_updated: 2021-01-12T06:51:37Z day: '30' ddc: - '570' department: - _id: GaTk doi: 10.3389/fncom.2015.00145 ec_funded: 1 file: - access_level: open_access checksum: cea73b6d3ef1579f32da10b82f4de4fd content_type: application/pdf creator: system date_created: 2018-12-12T10:12:09Z date_updated: 2020-07-14T12:45:02Z file_id: '4927' file_name: IST-2016-479-v1+1_fncom-09-00145.pdf file_size: 187038 relation: main_file file_date_updated: 2020-07-14T12:45:02Z has_accepted_license: '1' intvolume: ' 9' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5607' pubrep_id: '479' quality_controlled: '1' scopus_import: 1 status: public title: 'Editorial: Emergent neural computation from the interaction of different forms of plasticity' tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9 year: '2015' ... --- _id: '1570' abstract: - lang: eng text: Grounding autonomous behavior in the nervous system is a fundamental challenge for neuroscience. In particular, self-organized behavioral development provides more questions than answers. Are there special functional units for curiosity, motivation, and creativity? This paper argues that these features can be grounded in synaptic plasticity itself, without requiring any higher-level constructs. We propose differential extrinsic plasticity (DEP) as a new synaptic rule for self-learning systems and apply it to a number of complex robotic systems as a test case. Without specifying any purpose or goal, seemingly purposeful and adaptive rhythmic behavior is developed, displaying a certain level of sensorimotor intelligence. These surprising results require no systemspecific modifications of the DEP rule. They rather arise from the underlying mechanism of spontaneous symmetry breaking,which is due to the tight brain body environment coupling. The new synaptic rule is biologically plausible and would be an interesting target for neurobiological investigation. We also argue that this neuronal mechanism may have been a catalyst in natural evolution. author: - first_name: Ralf full_name: Der, Ralf last_name: Der - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius citation: ama: Der R, Martius GS. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 2015;112(45):E6224-E6232. doi:10.1073/pnas.1508400112 apa: Der, R., & Martius, G. S. (2015). Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1508400112 chicago: Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1508400112. ieee: R. Der and G. S. Martius, “Novel plasticity rule can explain the development of sensorimotor intelligence,” PNAS, vol. 112, no. 45. National Academy of Sciences, pp. E6224–E6232, 2015. ista: Der R, Martius GS. 2015. Novel plasticity rule can explain the development of sensorimotor intelligence. PNAS. 112(45), E6224–E6232. mla: Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.” PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. E6224–32, doi:10.1073/pnas.1508400112. short: R. Der, G.S. Martius, PNAS 112 (2015) E6224–E6232. date_created: 2018-12-11T11:52:47Z date_published: 2015-11-10T00:00:00Z date_updated: 2021-01-12T06:51:40Z day: '10' department: - _id: ChLa - _id: GaTk doi: 10.1073/pnas.1508400112 ec_funded: 1 external_id: pmid: - '26504200' intvolume: ' 112' issue: '45' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4653169/ month: '11' oa: 1 oa_version: Submitted Version page: E6224 - E6232 pmid: 1 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5601' quality_controlled: '1' scopus_import: 1 status: public title: Novel plasticity rule can explain the development of sensorimotor intelligence type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1658' abstract: - lang: eng text: Continuous-time Markov chain (CTMC) models have become a central tool for understanding the dynamics of complex reaction networks and the importance of stochasticity in the underlying biochemical processes. When such models are employed to answer questions in applications, in order to ensure that the model provides a sufficiently accurate representation of the real system, it is of vital importance that the model parameters are inferred from real measured data. This, however, is often a formidable task and all of the existing methods fail in one case or the other, usually because the underlying CTMC model is high-dimensional and computationally difficult to analyze. The parameter inference methods that tend to scale best in the dimension of the CTMC are based on so-called moment closure approximations. However, there exists a large number of different moment closure approximations and it is typically hard to say a priori which of the approximations is the most suitable for the inference procedure. Here, we propose a moment-based parameter inference method that automatically chooses the most appropriate moment closure method. Accordingly, contrary to existing methods, the user is not required to be experienced in moment closure techniques. In addition to that, our method adaptively changes the approximation during the parameter inference to ensure that always the best approximation is used, even in cases where different approximations are best in different regions of the parameter space. alternative_title: - LNCS author: - first_name: Sergiy full_name: Bogomolov, Sergiy id: 369D9A44-F248-11E8-B48F-1D18A9856A87 last_name: Bogomolov orcid: 0000-0002-0686-0365 - first_name: Thomas A full_name: Henzinger, Thomas A id: 40876CD8-F248-11E8-B48F-1D18A9856A87 last_name: Henzinger orcid: 0000−0002−2985−7724 - first_name: Andreas full_name: Podelski, Andreas last_name: Podelski - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: Christian full_name: Schilling, Christian last_name: Schilling citation: ama: Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. Adaptive moment closure for parameter inference of biochemical reaction networks. 2015;9308:77-89. doi:10.1007/978-3-319-23401-4_8 apa: 'Bogomolov, S., Henzinger, T. A., Podelski, A., Ruess, J., & Schilling, C. (2015). Adaptive moment closure for parameter inference of biochemical reaction networks. Presented at the CMSB: Computational Methods in Systems Biology, Nantes, France: Springer. https://doi.org/10.1007/978-3-319-23401-4_8' chicago: Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.” Lecture Notes in Computer Science. Springer, 2015. https://doi.org/10.1007/978-3-319-23401-4_8. ieee: S. Bogomolov, T. A. Henzinger, A. Podelski, J. Ruess, and C. Schilling, “Adaptive moment closure for parameter inference of biochemical reaction networks,” vol. 9308. Springer, pp. 77–89, 2015. ista: Bogomolov S, Henzinger TA, Podelski A, Ruess J, Schilling C. 2015. Adaptive moment closure for parameter inference of biochemical reaction networks. 9308, 77–89. mla: Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8. short: S. Bogomolov, T.A. Henzinger, A. Podelski, J. Ruess, C. Schilling, 9308 (2015) 77–89. conference: end_date: 2015-09-18 location: Nantes, France name: 'CMSB: Computational Methods in Systems Biology' start_date: 2015-09-16 date_created: 2018-12-11T11:53:18Z date_published: 2015-09-01T00:00:00Z date_updated: 2023-02-21T16:17:24Z day: '01' department: - _id: ToHe - _id: GaTk doi: 10.1007/978-3-319-23401-4_8 ec_funded: 1 intvolume: ' 9308' language: - iso: eng month: '09' oa_version: None page: 77 - 89 project: - _id: 25EE3708-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '267989' name: Quantitative Reactive Modeling - _id: 25F42A32-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: Z211 name: The Wittgenstein Prize - _id: 25832EC2-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: S 11407_N23 name: Rigorous Systems Engineering - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication_status: published publisher: Springer publist_id: '5492' quality_controlled: '1' related_material: record: - id: '1148' relation: later_version status: public scopus_import: 1 series_title: Lecture Notes in Computer Science status: public title: Adaptive moment closure for parameter inference of biochemical reaction networks type: conference user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 9308 year: '2015' ... --- _id: '1697' abstract: - lang: eng text: Motion tracking is a challenge the visual system has to solve by reading out the retinal population. It is still unclear how the information from different neurons can be combined together to estimate the position of an object. Here we recorded a large population of ganglion cells in a dense patch of salamander and guinea pig retinas while displaying a bar moving diffusively. We show that the bar’s position can be reconstructed from retinal activity with a precision in the hyperacuity regime using a linear decoder acting on 100+ cells. We then took advantage of this unprecedented precision to explore the spatial structure of the retina’s population code. The classical view would have suggested that the firing rates of the cells form a moving hill of activity tracking the bar’s position. Instead, we found that most ganglion cells in the salamander fired sparsely and idiosyncratically, so that their neural image did not track the bar. Furthermore, ganglion cell activity spanned an area much larger than predicted by their receptive fields, with cells coding for motion far in their surround. As a result, population redundancy was high, and we could find multiple, disjoint subsets of neurons that encoded the trajectory with high precision. This organization allows for diverse collections of ganglion cells to represent high-accuracy motion information in a form easily read out by downstream neural circuits. acknowledgement: 'This work was supported by grants EY 014196 and EY 017934 to MJB, ANR OPTIMA, the French State program Investissements d’Avenir managed by the Agence Nationale de la Recherche [LIFESENSES: ANR-10-LABX-65], and by a EC grant from the Human Brain Project (CLAP) to OM, the Austrian Research Foundation FWF P25651 to VBS and GT. VBS is partially supported by contracts MEC, Spain (Grant No. AYA2010- 22111-C03-02, Grant No. AYA2013-48623-C2-2 and FEDER Funds).' article_number: e1004304 author: - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Vicente full_name: Botella Soler, Vicente id: 421234E8-F248-11E8-B48F-1D18A9856A87 last_name: Botella Soler orcid: 0000-0002-8790-1914 - first_name: Kristina full_name: Simmons, Kristina last_name: Simmons - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Michael full_name: Berry, Michael last_name: Berry citation: ama: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 2015;11(7). doi:10.1371/journal.pcbi.1004304 apa: Marre, O., Botella Soler, V., Simmons, K., Mora, T., Tkačik, G., & Berry, M. (2015). High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004304 chicago: Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gašper Tkačik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004304. ieee: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, and M. Berry, “High accuracy decoding of dynamical motion from a large retinal population,” PLoS Computational Biology, vol. 11, no. 7. Public Library of Science, 2015. ista: Marre O, Botella Soler V, Simmons K, Mora T, Tkačik G, Berry M. 2015. High accuracy decoding of dynamical motion from a large retinal population. PLoS Computational Biology. 11(7), e1004304. mla: Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304. short: O. Marre, V. Botella Soler, K. Simmons, T. Mora, G. Tkačik, M. Berry, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:53:31Z date_published: 2015-07-01T00:00:00Z date_updated: 2021-01-12T06:52:35Z day: '01' ddc: - '570' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004304 file: - access_level: open_access checksum: 472b979f3f1cffb37b3e503f085115ca content_type: application/pdf creator: system date_created: 2018-12-12T10:16:25Z date_updated: 2020-07-14T12:45:12Z file_id: '5212' file_name: IST-2016-455-v1+1_journal.pcbi.1004304.pdf file_size: 4673930 relation: main_file file_date_updated: 2020-07-14T12:45:12Z has_accepted_license: '1' intvolume: ' 11' issue: '7' language: - iso: eng month: '07' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5447' pubrep_id: '455' quality_controlled: '1' scopus_import: 1 status: public title: High accuracy decoding of dynamical motion from a large retinal population tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1701' abstract: - lang: eng text: 'The activity of a neural network is defined by patterns of spiking and silence from the individual neurons. Because spikes are (relatively) sparse, patterns of activity with increasing numbers of spikes are less probable, but, with more spikes, the number of possible patterns increases. This tradeoff between probability and numerosity is mathematically equivalent to the relationship between entropy and energy in statistical physics. We construct this relationship for populations of up to N = 160 neurons in a small patch of the vertebrate retina, using a combination of direct and model-based analyses of experiments on the response of this network to naturalistic movies. We see signs of a thermodynamic limit, where the entropy per neuron approaches a smooth function of the energy per neuron as N increases. The form of this function corresponds to the distribution of activity being poised near an unusual kind of critical point. We suggest further tests of criticality, and give a brief discussion of its functional significance. ' acknowledgement: "Research was supported in part by National Science Foundation Grants PHY-1305525, PHY-1451171, and CCF-0939370, by National Institutes of Health Grant R01 EY14196, and by Austrian Science Foundation Grant FWF P25651. Additional support was provided by the\r\nFannie and John Hertz Foundation, by the Swartz Foundation, by the W. M. Keck Foundation, and by the Simons Foundation." author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Thierry full_name: Mora, Thierry last_name: Mora - first_name: Olivier full_name: Marre, Olivier last_name: Marre - first_name: Dario full_name: Amodei, Dario last_name: Amodei - first_name: Stephanie full_name: Palmer, Stephanie last_name: Palmer - first_name: Michael full_name: Berry Ii, Michael last_name: Berry Ii - first_name: William full_name: Bialek, William last_name: Bialek citation: ama: Tkačik G, Mora T, Marre O, et al. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 2015;112(37):11508-11513. doi:10.1073/pnas.1514188112 apa: Tkačik, G., Mora, T., Marre, O., Amodei, D., Palmer, S., Berry Ii, M., & Bialek, W. (2015). Thermodynamics and signatures of criticality in a network of neurons. PNAS. National Academy of Sciences. https://doi.org/10.1073/pnas.1514188112 chicago: Tkačik, Gašper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS. National Academy of Sciences, 2015. https://doi.org/10.1073/pnas.1514188112. ieee: G. Tkačik et al., “Thermodynamics and signatures of criticality in a network of neurons,” PNAS, vol. 112, no. 37. National Academy of Sciences, pp. 11508–11513, 2015. ista: Tkačik G, Mora T, Marre O, Amodei D, Palmer S, Berry Ii M, Bialek W. 2015. Thermodynamics and signatures of criticality in a network of neurons. PNAS. 112(37), 11508–11513. mla: Tkačik, Gašper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112. short: G. Tkačik, T. Mora, O. Marre, D. Amodei, S. Palmer, M. Berry Ii, W. Bialek, PNAS 112 (2015) 11508–11513. date_created: 2018-12-11T11:53:33Z date_published: 2015-09-15T00:00:00Z date_updated: 2021-01-12T06:52:37Z day: '15' department: - _id: GaTk doi: 10.1073/pnas.1514188112 external_id: pmid: - '26330611' intvolume: ' 112' issue: '37' language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4577210/ month: '09' oa: 1 oa_version: Submitted Version page: 11508 - 11513 pmid: 1 project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: PNAS publication_status: published publisher: National Academy of Sciences publist_id: '5440' quality_controlled: '1' scopus_import: 1 status: public title: Thermodynamics and signatures of criticality in a network of neurons type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 112 year: '2015' ... --- _id: '1861' abstract: - lang: eng text: Continuous-time Markov chains are commonly used in practice for modeling biochemical reaction networks in which the inherent randomness of themolecular interactions cannot be ignored. This has motivated recent research effort into methods for parameter inference and experiment design for such models. The major difficulty is that such methods usually require one to iteratively solve the chemical master equation that governs the time evolution of the probability distribution of the system. This, however, is rarely possible, and even approximation techniques remain limited to relatively small and simple systems. An alternative explored in this article is to base methods on only some low-order moments of the entire probability distribution. We summarize the theory behind such moment-based methods for parameter inference and experiment design and provide new case studies where we investigate their performance. acknowledgement: "HYCON2; EC; European Commission\r\n" article_number: '8' author: - first_name: Jakob full_name: Ruess, Jakob id: 4A245D00-F248-11E8-B48F-1D18A9856A87 last_name: Ruess orcid: 0000-0003-1615-3282 - first_name: John full_name: Lygeros, John last_name: Lygeros citation: ama: Ruess J, Lygeros J. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 2015;25(2). doi:10.1145/2688906 apa: Ruess, J., & Lygeros, J. (2015). Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. ACM. https://doi.org/10.1145/2688906 chicago: Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation. ACM, 2015. https://doi.org/10.1145/2688906. ieee: J. Ruess and J. Lygeros, “Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks,” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2. ACM, 2015. ista: Ruess J, Lygeros J. 2015. Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks. ACM Transactions on Modeling and Computer Simulation. 25(2), 8. mla: Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.” ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906. short: J. Ruess, J. Lygeros, ACM Transactions on Modeling and Computer Simulation 25 (2015). date_created: 2018-12-11T11:54:25Z date_published: 2015-02-01T00:00:00Z date_updated: 2021-01-12T06:53:41Z day: '01' department: - _id: ToHe - _id: GaTk doi: 10.1145/2688906 intvolume: ' 25' issue: '2' language: - iso: eng month: '02' oa_version: None publication: ACM Transactions on Modeling and Computer Simulation publication_status: published publisher: ACM publist_id: '5238' quality_controlled: '1' scopus_import: 1 status: public title: Moment-based methods for parameter inference and experiment design for stochastic biochemical reaction networks type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 25 year: '2015' ... --- _id: '1885' abstract: - lang: eng text: 'The concept of positional information is central to our understanding of how cells determine their location in a multicellular structure and thereby their developmental fates. Nevertheless, positional information has neither been defined mathematically nor quantified in a principled way. Here we provide an information-theoretic definition in the context of developmental gene expression patterns and examine the features of expression patterns that affect positional information quantitatively. We connect positional information with the concept of positional error and develop tools to directly measure information and error from experimental data. We illustrate our framework for the case of gap gene expression patterns in the early Drosophila embryo and show how information that is distributed among only four genes is sufficient to determine developmental fates with nearly single-cell resolution. Our approach can be generalized to a variety of different model systems; procedures and examples are discussed in detail. ' author: - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 - first_name: Julien full_name: Dubuis, Julien last_name: Dubuis - first_name: Mariela full_name: Petkova, Mariela last_name: Petkova - first_name: Thomas full_name: Gregor, Thomas last_name: Gregor citation: ama: 'Tkačik G, Dubuis J, Petkova M, Gregor T. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 2015;199(1):39-59. doi:10.1534/genetics.114.171850' apa: 'Tkačik, G., Dubuis, J., Petkova, M., & Gregor, T. (2015). Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. Genetics Society of America. https://doi.org/10.1534/genetics.114.171850' chicago: 'Tkačik, Gašper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics. Genetics Society of America, 2015. https://doi.org/10.1534/genetics.114.171850.' ieee: 'G. Tkačik, J. Dubuis, M. Petkova, and T. Gregor, “Positional information, positional error, and readout precision in morphogenesis: A mathematical framework,” Genetics, vol. 199, no. 1. Genetics Society of America, pp. 39–59, 2015.' ista: 'Tkačik G, Dubuis J, Petkova M, Gregor T. 2015. Positional information, positional error, and readout precision in morphogenesis: A mathematical framework. Genetics. 199(1), 39–59.' mla: 'Tkačik, Gašper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.' short: G. Tkačik, J. Dubuis, M. Petkova, T. Gregor, Genetics 199 (2015) 39–59. date_created: 2018-12-11T11:54:32Z date_published: 2015-01-01T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '01' department: - _id: GaTk doi: 10.1534/genetics.114.171850 intvolume: ' 199' issue: '1' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1404.5599 month: '01' oa: 1 oa_version: Preprint page: 39 - 59 publication: Genetics publication_status: published publisher: Genetics Society of America publist_id: '5210' quality_controlled: '1' scopus_import: 1 status: public title: 'Positional information, positional error, and readout precision in morphogenesis: A mathematical framework' type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 199 year: '2015' ... --- _id: '1940' abstract: - lang: eng text: We typically think of cells as responding to external signals independently by regulating their gene expression levels, yet they often locally exchange information and coordinate. Can such spatial coupling be of benefit for conveying signals subject to gene regulatory noise? Here we extend our information-theoretic framework for gene regulation to spatially extended systems. As an example, we consider a lattice of nuclei responding to a concentration field of a transcriptional regulator (the "input") by expressing a single diffusible target gene. When input concentrations are low, diffusive coupling markedly improves information transmission; optimal gene activation functions also systematically change. A qualitatively new regulatory strategy emerges where individual cells respond to the input in a nearly step-like fashion that is subsequently averaged out by strong diffusion. While motivated by early patterning events in the Drosophila embryo, our framework is generically applicable to spatially coupled stochastic gene expression models. article_number: '062710' author: - first_name: Thomas R full_name: Sokolowski, Thomas R id: 3E999752-F248-11E8-B48F-1D18A9856A87 last_name: Sokolowski orcid: 0000-0002-1287-3779 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Sokolowski TR, Tkačik G. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2015;91(6). doi:10.1103/PhysRevE.91.062710 apa: Sokolowski, T. R., & Tkačik, G. (2015). Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.91.062710 chicago: Sokolowski, Thomas R, and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015. https://doi.org/10.1103/PhysRevE.91.062710. ieee: T. R. Sokolowski and G. Tkačik, “Optimizing information flow in small genetic networks. IV. Spatial coupling,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6. American Institute of Physics, 2015. ista: Sokolowski TR, Tkačik G. 2015. Optimizing information flow in small genetic networks. IV. Spatial coupling. Physical Review E Statistical Nonlinear and Soft Matter Physics. 91(6), 062710. mla: Sokolowski, Thomas R., and Gašper Tkačik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710. short: T.R. Sokolowski, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 91 (2015). date_created: 2018-12-11T11:54:49Z date_published: 2015-06-15T00:00:00Z date_updated: 2021-01-12T06:54:13Z day: '15' department: - _id: GaTk doi: 10.1103/PhysRevE.91.062710 intvolume: ' 91' issue: '6' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1501.04015 month: '06' oa: 1 oa_version: Preprint publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5145' quality_controlled: '1' scopus_import: 1 status: public title: Optimizing information flow in small genetic networks. IV. Spatial coupling type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 91 year: '2015' ... --- _id: '9718' article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham E. full_name: Mayo, Avraham E. last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Supporting information text. 2015. doi:10.1371/journal.pcbi.1004055.s001 apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Supporting information text. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s001 chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s001. ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Supporting information text.” Public Library of Science, 2015. ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Supporting information text, Public Library of Science, 10.1371/journal.pcbi.1004055.s001. mla: Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001. short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015). date_created: 2021-07-26T08:35:23Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T10:16:13Z day: '23' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055.s001 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1827' relation: used_in_publication status: public status: public title: Supporting information text type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1827' abstract: - lang: eng text: Bow-tie or hourglass structure is a common architectural feature found in many biological systems. A bow-tie in a multi-layered structure occurs when intermediate layers have much fewer components than the input and output layers. Examples include metabolism where a handful of building blocks mediate between multiple input nutrients and multiple output biomass components, and signaling networks where information from numerous receptor types passes through a small set of signaling pathways to regulate multiple output genes. Little is known, however, about how bow-tie architectures evolve. Here, we address the evolution of bow-tie architectures using simulations of multi-layered systems evolving to fulfill a given input-output goal. We find that bow-ties spontaneously evolve when the information in the evolutionary goal can be compressed. Mathematically speaking, bow-ties evolve when the rank of the input-output matrix describing the evolutionary goal is deficient. The maximal compression possible (the rank of the goal) determines the size of the narrowest part of the network—that is the bow-tie. A further requirement is that a process is active to reduce the number of links in the network, such as product-rule mutations, otherwise a non-bow-tie solution is found in the evolutionary simulations. This offers a mechanism to understand a common architectural principle of biological systems, and a way to quantitate the effective rank of the goals under which they evolved. article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham full_name: Mayo, Avraham last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo A, Tlusty T, Alon U. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 2015;11(3). doi:10.1371/journal.pcbi.1004055 apa: Friedlander, T., Mayo, A., Tlusty, T., & Alon, U. (2015). Evolution of bow-tie architectures in biology. PLoS Computational Biology. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055 chicago: Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology. Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055. ieee: T. Friedlander, A. Mayo, T. Tlusty, and U. Alon, “Evolution of bow-tie architectures in biology,” PLoS Computational Biology, vol. 11, no. 3. Public Library of Science, 2015. ista: Friedlander T, Mayo A, Tlusty T, Alon U. 2015. Evolution of bow-tie architectures in biology. PLoS Computational Biology. 11(3). mla: Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.” PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055. short: T. Friedlander, A. Mayo, T. Tlusty, U. Alon, PLoS Computational Biology 11 (2015). date_created: 2018-12-11T11:54:14Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T14:07:51Z day: '23' ddc: - '576' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055 ec_funded: 1 file: - access_level: open_access checksum: b8aa66f450ff8de393014b87ec7d2efb content_type: application/pdf creator: system date_created: 2018-12-12T10:15:39Z date_updated: 2020-07-14T12:45:17Z file_id: '5161' file_name: IST-2016-452-v1+1_journal.pcbi.1004055.pdf file_size: 1811647 relation: main_file file_date_updated: 2020-07-14T12:45:17Z has_accepted_license: '1' intvolume: ' 11' issue: '3' language: - iso: eng month: '03' oa: 1 oa_version: Published Version project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: PLoS Computational Biology publication_status: published publisher: Public Library of Science publist_id: '5278' pubrep_id: '452' quality_controlled: '1' related_material: record: - id: '9718' relation: research_data status: public - id: '9773' relation: research_data status: public scopus_import: 1 status: public title: Evolution of bow-tie architectures in biology tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 3E5EF7F0-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '9773' article_processing_charge: No author: - first_name: Tamar full_name: Friedlander, Tamar id: 36A5845C-F248-11E8-B48F-1D18A9856A87 last_name: Friedlander - first_name: Avraham E. full_name: Mayo, Avraham E. last_name: Mayo - first_name: Tsvi full_name: Tlusty, Tsvi last_name: Tlusty - first_name: Uri full_name: Alon, Uri last_name: Alon citation: ama: Friedlander T, Mayo AE, Tlusty T, Alon U. Evolutionary simulation code. 2015. doi:10.1371/journal.pcbi.1004055.s002 apa: Friedlander, T., Mayo, A. E., Tlusty, T., & Alon, U. (2015). Evolutionary simulation code. Public Library of Science. https://doi.org/10.1371/journal.pcbi.1004055.s002 chicago: Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pcbi.1004055.s002. ieee: T. Friedlander, A. E. Mayo, T. Tlusty, and U. Alon, “Evolutionary simulation code.” Public Library of Science, 2015. ista: Friedlander T, Mayo AE, Tlusty T, Alon U. 2015. Evolutionary simulation code, Public Library of Science, 10.1371/journal.pcbi.1004055.s002. mla: Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002. short: T. Friedlander, A.E. Mayo, T. Tlusty, U. Alon, (2015). date_created: 2021-08-05T12:58:07Z date_published: 2015-03-23T00:00:00Z date_updated: 2023-02-23T10:16:13Z day: '23' department: - _id: GaTk doi: 10.1371/journal.pcbi.1004055.s002 month: '03' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1827' relation: used_in_publication status: public status: public title: Evolutionary simulation code type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '9712' article_processing_charge: No author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gašper full_name: Tkačik, Gašper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkačik orcid: 0000-0002-6699-1455 citation: ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Other fitness models for comparison & for interacting TFBSs. 2015. doi:10.1371/journal.pgen.1005639.s001 apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Other fitness models for comparison & for interacting TFBSs. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639.s001 chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Other Fitness Models for Comparison & for Interacting TFBSs.” Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639.s001. ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Other fitness models for comparison & for interacting TFBSs.” Public Library of Science, 2015. ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Other fitness models for comparison & for interacting TFBSs, Public Library of Science, 10.1371/journal.pgen.1005639.s001. mla: Tugrul, Murat, et al. Other Fitness Models for Comparison & for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001. short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, (2015). date_created: 2021-07-23T12:00:37Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-02-23T10:09:08Z day: '06' department: - _id: NiBa - _id: CaGu - _id: GaTk doi: 10.1371/journal.pgen.1005639.s001 month: '11' oa_version: Published Version publisher: Public Library of Science related_material: record: - id: '1666' relation: used_in_publication status: public status: public title: Other fitness models for comparison & for interacting TFBSs type: research_data_reference user_id: 6785fbc1-c503-11eb-8a32-93094b40e1cf year: '2015' ... --- _id: '1666' abstract: - lang: eng text: Evolution of gene regulation is crucial for our understanding of the phenotypic differences between species, populations and individuals. Sequence-specific binding of transcription factors to the regulatory regions on the DNA is a key regulatory mechanism that determines gene expression and hence heritable phenotypic variation. We use a biophysical model for directional selection on gene expression to estimate the rates of gain and loss of transcription factor binding sites (TFBS) in finite populations under both point and insertion/deletion mutations. Our results show that these rates are typically slow for a single TFBS in an isolated DNA region, unless the selection is extremely strong. These rates decrease drastically with increasing TFBS length or increasingly specific protein-DNA interactions, making the evolution of sites longer than ∼ 10 bp unlikely on typical eukaryotic speciation timescales. Similarly, evolution converges to the stationary distribution of binding sequences very slowly, making the equilibrium assumption questionable. The availability of longer regulatory sequences in which multiple binding sites can evolve simultaneously, the presence of “pre-sites” or partially decayed old sites in the initial sequence, and biophysical cooperativity between transcription factors, can all facilitate gain of TFBS and reconcile theoretical calculations with timescales inferred from comparative genomics. author: - first_name: Murat full_name: Tugrul, Murat id: 37C323C6-F248-11E8-B48F-1D18A9856A87 last_name: Tugrul orcid: 0000-0002-8523-0758 - first_name: Tiago full_name: Paixao, Tiago id: 2C5658E6-F248-11E8-B48F-1D18A9856A87 last_name: Paixao orcid: 0000-0003-2361-3953 - first_name: Nicholas H full_name: Barton, Nicholas H id: 4880FE40-F248-11E8-B48F-1D18A9856A87 last_name: Barton orcid: 0000-0002-8548-5240 - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Tugrul M, Paixao T, Barton NH, Tkačik G. Dynamics of transcription factor binding site evolution. PLoS Genetics. 2015;11(11). doi:10.1371/journal.pgen.1005639 apa: Tugrul, M., Paixao, T., Barton, N. H., & Tkačik, G. (2015). Dynamics of transcription factor binding site evolution. PLoS Genetics. Public Library of Science. https://doi.org/10.1371/journal.pgen.1005639 chicago: Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gašper Tkačik. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics. Public Library of Science, 2015. https://doi.org/10.1371/journal.pgen.1005639. ieee: M. Tugrul, T. Paixao, N. H. Barton, and G. Tkačik, “Dynamics of transcription factor binding site evolution,” PLoS Genetics, vol. 11, no. 11. Public Library of Science, 2015. ista: Tugrul M, Paixao T, Barton NH, Tkačik G. 2015. Dynamics of transcription factor binding site evolution. PLoS Genetics. 11(11). mla: Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639. short: M. Tugrul, T. Paixao, N.H. Barton, G. Tkačik, PLoS Genetics 11 (2015). date_created: 2018-12-11T11:53:21Z date_published: 2015-11-06T00:00:00Z date_updated: 2023-09-07T11:53:49Z day: '06' ddc: - '576' department: - _id: NiBa - _id: CaGu - _id: GaTk doi: 10.1371/journal.pgen.1005639 ec_funded: 1 file: - access_level: open_access checksum: a4e72fca5ccf40ddacf4d08c8e46b554 content_type: application/pdf creator: system date_created: 2018-12-12T10:07:58Z date_updated: 2020-07-14T12:45:10Z file_id: '4657' file_name: IST-2016-463-v1+1_journal.pgen.1005639.pdf file_size: 2580778 relation: main_file file_date_updated: 2020-07-14T12:45:10Z has_accepted_license: '1' intvolume: ' 11' issue: '11' language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: PLoS Genetics publication_status: published publisher: Public Library of Science publist_id: '5483' pubrep_id: '463' quality_controlled: '1' related_material: record: - id: '9712' relation: research_data status: public - id: '1131' relation: dissertation_contains status: public scopus_import: 1 status: public title: Dynamics of transcription factor binding site evolution tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 11 year: '2015' ... --- _id: '1576' abstract: - lang: eng text: 'Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect regulatory crosstalk: the possibility that noncognate TFs could initiate transcription, with potentially disastrous effects for the cell. Here, we estimate the importance of crosstalk, suggest that its avoidance strongly constrains equilibrium models of TF binding, and propose an alternative nonequilibrium scheme that implements kinetic proofreading to suppress erroneous initiation. This proposal is consistent with the observed covalent modifications of the transcriptional apparatus and predicts increased noise in gene expression as a trade-off for improved specificity. Using information theory, we quantify this trade-off to find when optimal proofreading architectures are favored over their equilibrium counterparts. Such architectures exhibit significant super-Poisson noise at low expression in steady state.' article_number: '248101' author: - first_name: Sarah A full_name: Cepeda Humerez, Sarah A id: 3DEE19A4-F248-11E8-B48F-1D18A9856A87 last_name: Cepeda Humerez - first_name: Georg full_name: Rieckh, Georg id: 34DA8BD6-F248-11E8-B48F-1D18A9856A87 last_name: Rieckh - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Cepeda Humerez SA, Rieckh G, Tkačik G. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 2015;115(24). doi:10.1103/PhysRevLett.115.248101 apa: Cepeda Humerez, S. A., Rieckh, G., & Tkačik, G. (2015). Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. American Physical Society. https://doi.org/10.1103/PhysRevLett.115.248101 chicago: Cepeda Humerez, Sarah A, Georg Rieckh, and Gašper Tkačik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters. American Physical Society, 2015. https://doi.org/10.1103/PhysRevLett.115.248101. ieee: S. A. Cepeda Humerez, G. Rieckh, and G. Tkačik, “Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation,” Physical Review Letters, vol. 115, no. 24. American Physical Society, 2015. ista: Cepeda Humerez SA, Rieckh G, Tkačik G. 2015. Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation. Physical Review Letters. 115(24), 248101. mla: Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101. short: S.A. Cepeda Humerez, G. Rieckh, G. Tkačik, Physical Review Letters 115 (2015). date_created: 2018-12-11T11:52:49Z date_published: 2015-12-08T00:00:00Z date_updated: 2023-09-07T12:55:21Z day: '08' department: - _id: GaTk doi: 10.1103/PhysRevLett.115.248101 ec_funded: 1 intvolume: ' 115' issue: '24' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1504.05716 month: '12' oa: 1 oa_version: Preprint project: - _id: 25B07788-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '250152' name: Limits to selection in biology and in evolutionary computation publication: Physical Review Letters publication_status: published publisher: American Physical Society publist_id: '5595' quality_controlled: '1' related_material: record: - id: '6473' relation: part_of_dissertation status: public scopus_import: 1 status: public title: Stochastic proofreading mechanism alleviates crosstalk in transcriptional regulation type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 115 year: '2015' ... --- _id: '1655' abstract: - lang: eng text: Quantifying behaviors of robots which were generated autonomously from task-independent objective functions is an important prerequisite for objective comparisons of algorithms and movements of animals. The temporal sequence of such a behavior can be considered as a time series and hence complexity measures developed for time series are natural candidates for its quantification. The predictive information and the excess entropy are such complexity measures. They measure the amount of information the past contains about the future and thus quantify the nonrandom structure in the temporal sequence. However, when using these measures for systems with continuous states one has to deal with the fact that their values will depend on the resolution with which the systems states are observed. For deterministic systems both measures will diverge with increasing resolution. We therefore propose a new decomposition of the excess entropy in resolution dependent and resolution independent parts and discuss how they depend on the dimensionality of the dynamics, correlations and the noise level. For the practical estimation we propose to use estimates based on the correlation integral instead of the direct estimation of the mutual information based on next neighbor statistics because the latter allows less control of the scale dependencies. Using our algorithm we are able to show how autonomous learning generates behavior of increasing complexity with increasing learning duration. acknowledgement: This work was supported by the DFG priority program 1527 (Autonomous Learning) and by the European Community’s Seventh Framework Programme (FP7/2007-2013) under grant agreement no. 318723 (MatheMACS) and from the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme (FP7/2007-2013) under REA grant agreement no. 291734. article_processing_charge: No author: - first_name: Georg S full_name: Martius, Georg S id: 3A276B68-F248-11E8-B48F-1D18A9856A87 last_name: Martius - first_name: Eckehard full_name: Olbrich, Eckehard last_name: Olbrich citation: ama: Martius GS, Olbrich E. Quantifying emergent behavior of autonomous robots. Entropy. 2015;17(10):7266-7297. doi:10.3390/e17107266 apa: Martius, G. S., & Olbrich, E. (2015). Quantifying emergent behavior of autonomous robots. Entropy. MDPI. https://doi.org/10.3390/e17107266 chicago: Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy. MDPI, 2015. https://doi.org/10.3390/e17107266. ieee: G. S. Martius and E. Olbrich, “Quantifying emergent behavior of autonomous robots,” Entropy, vol. 17, no. 10. MDPI, pp. 7266–7297, 2015. ista: Martius GS, Olbrich E. 2015. Quantifying emergent behavior of autonomous robots. Entropy. 17(10), 7266–7297. mla: Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.” Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266. short: G.S. Martius, E. Olbrich, Entropy 17 (2015) 7266–7297. date_created: 2018-12-11T11:53:17Z date_published: 2015-10-23T00:00:00Z date_updated: 2023-10-17T11:42:00Z day: '23' ddc: - '000' department: - _id: ChLa - _id: GaTk doi: 10.3390/e17107266 ec_funded: 1 file: - access_level: open_access checksum: 945d99631a96e0315acb26dc8541dcf9 content_type: application/pdf creator: system date_created: 2018-12-12T10:12:25Z date_updated: 2020-07-14T12:45:08Z file_id: '4943' file_name: IST-2016-464-v1+1_entropy-17-07266.pdf file_size: 6455007 relation: main_file file_date_updated: 2020-07-14T12:45:08Z has_accepted_license: '1' intvolume: ' 17' issue: '10' language: - iso: eng month: '10' oa: 1 oa_version: Published Version page: 7266 - 7297 project: - _id: 25681D80-B435-11E9-9278-68D0E5697425 call_identifier: FP7 grant_number: '291734' name: International IST Postdoc Fellowship Programme publication: Entropy publication_status: published publisher: MDPI publist_id: '5495' pubrep_id: '464' quality_controlled: '1' scopus_import: '1' status: public title: Quantifying emergent behavior of autonomous robots tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 17 year: '2015' ... --- _id: '1708' abstract: - lang: eng text: It has been long argued that, because of inherent ambiguity and noise, the brain needs to represent uncertainty in the form of probability distributions. The neural encoding of such distributions remains however highly controversial. Here we present a novel circuit model for representing multidimensional real-valued distributions using a spike based spatio-temporal code. Our model combines the computational advantages of the currently competing models for probabilistic codes and exhibits realistic neural responses along a variety of classic measures. Furthermore, the model highlights the challenges associated with interpreting neural activity in relation to behavioral uncertainty and points to alternative population-level approaches for the experimental validation of distributed representations. author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Sophie full_name: Denève, Sophie last_name: Denève citation: ama: 'Savin C, Denève S. Spatio-temporal representations of uncertainty in spiking neural networks. In: Vol 3. Neural Information Processing Systems; 2014:2024-2032.' apa: 'Savin, C., & Denève, S. (2014). Spatio-temporal representations of uncertainty in spiking neural networks (Vol. 3, pp. 2024–2032). Presented at the NIPS: Neural Information Processing Systems, Montreal, Canada: Neural Information Processing Systems.' chicago: Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014. ieee: 'C. Savin and S. Denève, “Spatio-temporal representations of uncertainty in spiking neural networks,” presented at the NIPS: Neural Information Processing Systems, Montreal, Canada, 2014, vol. 3, no. January, pp. 2024–2032.' ista: 'Savin C, Denève S. 2014. Spatio-temporal representations of uncertainty in spiking neural networks. NIPS: Neural Information Processing Systems vol. 3, 2024–2032.' mla: Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32. short: C. Savin, S. Denève, in:, Neural Information Processing Systems, 2014, pp. 2024–2032. conference: end_date: 2014-12-13 location: Montreal, Canada name: 'NIPS: Neural Information Processing Systems' start_date: 2014-12-08 date_created: 2018-12-11T11:53:35Z date_published: 2014-01-01T00:00:00Z date_updated: 2021-01-12T06:52:40Z day: '01' department: - _id: GaTk intvolume: ' 3' issue: January language: - iso: eng main_file_link: - url: http://papers.nips.cc/paper/5343-spatio-temporal-representations-of-uncertainty-in-spiking-neural-networks.pdf month: '01' oa_version: None page: 2024 - 2032 publication_status: published publisher: Neural Information Processing Systems publist_id: '5427' quality_controlled: '1' scopus_import: 1 status: public title: Spatio-temporal representations of uncertainty in spiking neural networks type: conference user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 3 year: '2014' ... --- _id: '1886' abstract: - lang: eng text: 'Information processing in the sensory periphery is shaped by natural stimulus statistics. In the periphery, a transmission bottleneck constrains performance; thus efficient coding implies that natural signal components with a predictably wider range should be compressed. In a different regime—when sampling limitations constrain performance—efficient coding implies that more resources should be allocated to informative features that are more variable. We propose that this regime is relevant for sensory cortex when it extracts complex features from limited numbers of sensory samples. To test this prediction, we use central visual processing as a model: we show that visual sensitivity for local multi-point spatial correlations, described by dozens of independently-measured parameters, can be quantitatively predicted from the structure of natural images. This suggests that efficient coding applies centrally, where it extends to higher-order sensory features and operates in a regime in which sensitivity increases with feature variability.' article_number: e03722 author: - first_name: Ann full_name: Hermundstad, Ann last_name: Hermundstad - first_name: John full_name: Briguglio, John last_name: Briguglio - first_name: Mary full_name: Conte, Mary last_name: Conte - first_name: Jonathan full_name: Victor, Jonathan last_name: Victor - first_name: Vijay full_name: Balasubramanian, Vijay last_name: Balasubramanian - first_name: Gasper full_name: Tkacik, Gasper id: 3D494DCA-F248-11E8-B48F-1D18A9856A87 last_name: Tkacik orcid: 0000-0002-6699-1455 citation: ama: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. Variance predicts salience in central sensory processing. eLife. 2014;(November). doi:10.7554/eLife.03722 apa: Hermundstad, A., Briguglio, J., Conte, M., Victor, J., Balasubramanian, V., & Tkačik, G. (2014). Variance predicts salience in central sensory processing. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.03722 chicago: Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gašper Tkačik. “Variance Predicts Salience in Central Sensory Processing.” ELife. eLife Sciences Publications, 2014. https://doi.org/10.7554/eLife.03722. ieee: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, and G. Tkačik, “Variance predicts salience in central sensory processing,” eLife, no. November. eLife Sciences Publications, 2014. ista: Hermundstad A, Briguglio J, Conte M, Victor J, Balasubramanian V, Tkačik G. 2014. Variance predicts salience in central sensory processing. eLife. (November), e03722. mla: Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722. short: A. Hermundstad, J. Briguglio, M. Conte, J. Victor, V. Balasubramanian, G. Tkačik, ELife (2014). date_created: 2018-12-11T11:54:32Z date_published: 2014-11-14T00:00:00Z date_updated: 2021-01-12T06:53:50Z day: '14' ddc: - '570' department: - _id: GaTk doi: 10.7554/eLife.03722 file: - access_level: open_access checksum: 766ac8999ac6e3364f10065a06024b8f content_type: application/pdf creator: system date_created: 2018-12-12T10:12:04Z date_updated: 2020-07-14T12:45:20Z file_id: '4922' file_name: IST-2016-420-v1+1_e03722.full.pdf file_size: 5117086 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' issue: November language: - iso: eng month: '11' oa: 1 oa_version: Published Version project: - _id: 254D1A94-B435-11E9-9278-68D0E5697425 call_identifier: FWF grant_number: P 25651-N26 name: Sensitivity to higher-order statistics in natural scenes publication: eLife publication_status: published publisher: eLife Sciences Publications publist_id: '5209' pubrep_id: '420' quality_controlled: '1' scopus_import: 1 status: public title: Variance predicts salience in central sensory processing tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 year: '2014' ... --- _id: '1896' abstract: - lang: eng text: 'Biopolymer length regulation is a complex process that involves a large number of biological, chemical, and physical subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length regulation of telomeres - nucleoprotein structures at the ends of linear chromosomes consisting of tandemly repeated DNA sequences and a specialized set of proteins. Maintenance of telomeres is often facilitated by the enzyme telomerase but, particularly in telomerase-free systems, the maintenance of chromosomal termini depends on alternative lengthening of telomeres (ALT) mechanisms mediated by recombination. Various linear and circular DNA structures were identified to participate in ALT, however, dynamics of the whole process is still poorly understood. We propose a chemical kinetics model of ALT with kinetic rates systematically derived from the biophysics of DNA diffusion and looping. The reaction system is reduced to a coagulation-fragmentation system by quasi-steady-state approximation. The detailed treatment of kinetic rates yields explicit formulas for expected size distributions of telomeres that demonstrate the key role played by the J factor, a quantitative measure of bending of polymers. The results are in agreement with experimental data and point out interesting phenomena: an appearance of very long telomeric circles if the total telomere density exceeds a critical value (excess mass) and a nonlinear response of the telomere size distributions to the amount of telomeric DNA in the system. The results can be of general importance for understanding dynamics of telomeres in telomerase-independent systems as this mode of telomere maintenance is similar to the situation in tumor cells lacking telomerase activity. Furthermore, due to its universality, the model may also serve as a prototype of an interaction between linear and circular DNA structures in various settings.' acknowledgement: The work was supported by the VEGA Grant No. 1/0459/13 (R.K. and K.B.). article_number: '032701' article_processing_charge: No author: - first_name: Richard full_name: Kollár, Richard last_name: Kollár - first_name: Katarína full_name: Bod'ová, Katarína id: 2BA24EA0-F248-11E8-B48F-1D18A9856A87 last_name: Bod'ová orcid: 0000-0002-7214-0171 - first_name: Jozef full_name: Nosek, Jozef last_name: Nosek - first_name: Ľubomír full_name: Tomáška, Ľubomír last_name: Tomáška citation: ama: Kollár R, Bodova K, Nosek J, Tomáška Ľ. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 2014;89(3). doi:10.1103/PhysRevE.89.032701 apa: Kollár, R., Bodova, K., Nosek, J., & Tomáška, Ľ. (2014). Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics. https://doi.org/10.1103/PhysRevE.89.032701 chicago: Kollár, Richard, Katarina Bodova, Jozef Nosek, and Ľubomír Tomáška. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014. https://doi.org/10.1103/PhysRevE.89.032701. ieee: R. Kollár, K. Bodova, J. Nosek, and Ľ. Tomáška, “Mathematical model of alternative mechanism of telomere length maintenance,” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3. American Institute of Physics, 2014. ista: Kollár R, Bodova K, Nosek J, Tomáška Ľ. 2014. Mathematical model of alternative mechanism of telomere length maintenance. Physical Review E Statistical Nonlinear and Soft Matter Physics. 89(3), 032701. mla: Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701. short: R. Kollár, K. Bodova, J. Nosek, Ľ. Tomáška, Physical Review E Statistical Nonlinear and Soft Matter Physics 89 (2014). date_created: 2018-12-11T11:54:35Z date_published: 2014-03-04T00:00:00Z date_updated: 2022-08-01T10:50:10Z day: '04' department: - _id: NiBa - _id: GaTk doi: 10.1103/PhysRevE.89.032701 intvolume: ' 89' issue: '3' language: - iso: eng main_file_link: - open_access: '1' url: http://arxiv.org/abs/1402.0430 month: '03' oa: 1 oa_version: Submitted Version publication: Physical Review E Statistical Nonlinear and Soft Matter Physics publication_status: published publisher: American Institute of Physics publist_id: '5198' scopus_import: '1' status: public title: Mathematical model of alternative mechanism of telomere length maintenance type: journal_article user_id: 2DF688A6-F248-11E8-B48F-1D18A9856A87 volume: 89 year: '2014' ... --- _id: '1909' abstract: - lang: eng text: 'Summary: Phenotypes are often environmentally dependent, which requires organisms to track environmental change. The challenge for organisms is to construct phenotypes using the most accurate environmental cue. Here, we use a quantitative genetic model of adaptation by additive genetic variance, within- and transgenerational plasticity via linear reaction norms and indirect genetic effects respectively. We show how the relative influence on the eventual phenotype of these components depends on the predictability of environmental change (fast or slow, sinusoidal or stochastic) and the developmental lag τ between when the environment is perceived and when selection acts. We then decompose expected mean fitness into three components (variance load, adaptation and fluctuation load) to study the fitness costs of within- and transgenerational plasticity. A strongly negative maternal effect coefficient m minimizes the variance load, but a strongly positive m minimises the fluctuation load. The adaptation term is maximized closer to zero, with positive or negative m preferred under different environmental scenarios. Phenotypic plasticity is higher when τ is shorter and when the environment changes frequently between seasonal extremes. Expected mean population fitness is highest away from highest observed levels of phenotypic plasticity. Within- and transgenerational plasticity act in concert to deliver well-adapted phenotypes, which emphasizes the need to study both simultaneously when investigating phenotypic evolution.' acknowledgement: 'Engineering and Physical Sciences Research Council. Grant Number: EP/H031928/1' author: - first_name: Thomas full_name: Ezard, Thomas last_name: Ezard - first_name: Roshan full_name: Prizak, Roshan id: 4456104E-F248-11E8-B48F-1D18A9856A87 last_name: Prizak - first_name: Rebecca full_name: Hoyle, Rebecca last_name: Hoyle citation: ama: Ezard T, Prizak R, Hoyle R. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 2014;28(3):693-701. doi:10.1111/1365-2435.12207 apa: Ezard, T., Prizak, R., & Hoyle, R. (2014). The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. Wiley-Blackwell. https://doi.org/10.1111/1365-2435.12207 chicago: Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology. Wiley-Blackwell, 2014. https://doi.org/10.1111/1365-2435.12207. ieee: T. Ezard, R. Prizak, and R. Hoyle, “The fitness costs of adaptation via phenotypic plasticity and maternal effects,” Functional Ecology, vol. 28, no. 3. Wiley-Blackwell, pp. 693–701, 2014. ista: Ezard T, Prizak R, Hoyle R. 2014. The fitness costs of adaptation via phenotypic plasticity and maternal effects. Functional Ecology. 28(3), 693–701. mla: Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.” Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207. short: T. Ezard, R. Prizak, R. Hoyle, Functional Ecology 28 (2014) 693–701. date_created: 2018-12-11T11:54:40Z date_published: 2014-06-01T00:00:00Z date_updated: 2021-01-12T06:54:00Z day: '01' ddc: - '570' department: - _id: NiBa - _id: GaTk doi: 10.1111/1365-2435.12207 file: - access_level: open_access checksum: 3cbe8623174709a8ceec2103246f8fe0 content_type: application/pdf creator: system date_created: 2018-12-12T10:15:45Z date_updated: 2020-07-14T12:45:20Z file_id: '5167' file_name: IST-2016-419-v1+1_Ezard_et_al-2014-Functional_Ecology.pdf file_size: 536154 relation: main_file file_date_updated: 2020-07-14T12:45:20Z has_accepted_license: '1' intvolume: ' 28' issue: '3' language: - iso: eng month: '06' oa: 1 oa_version: Published Version page: 693 - 701 publication: Functional Ecology publication_status: published publisher: Wiley-Blackwell publist_id: '5186' pubrep_id: '419' scopus_import: 1 status: public title: The fitness costs of adaptation via phenotypic plasticity and maternal effects tmp: image: /images/cc_by.png legal_code_url: https://creativecommons.org/licenses/by/4.0/legalcode name: Creative Commons Attribution 4.0 International Public License (CC-BY 4.0) short: CC BY (4.0) type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 28 year: '2014' ... --- _id: '1928' abstract: - lang: eng text: In infectious disease epidemiology the basic reproductive ratio, R0, is defined as the average number of new infections caused by a single infected individual in a fully susceptible population. Many models describing competition for hosts between non-interacting pathogen strains in an infinite population lead to the conclusion that selection favors invasion of new strains if and only if they have higher R0 values than the resident. Here we demonstrate that this picture fails in finite populations. Using a simple stochastic SIS model, we show that in general there is no analogous optimization principle. We find that successive invasions may in some cases lead to strains that infect a smaller fraction of the host population, and that mutually invasible pathogen strains exist. In the limit of weak selection we demonstrate that an optimization principle does exist, although it differs from R0 maximization. For strains with very large R0, we derive an expression for this local fitness function and use it to establish a lower bound for the error caused by neglecting stochastic effects. Furthermore, we apply this weak selection limit to investigate the selection dynamics in the presence of a trade-off between the virulence and the transmission rate of a pathogen. acknowledgement: J.H. received support from the Zdenek Bakala Foundation and the Mobility Fund of Charles University in Prague. author: - first_name: Jan full_name: Humplik, Jan id: 2E9627A8-F248-11E8-B48F-1D18A9856A87 last_name: Humplik - first_name: Alison full_name: Hill, Alison last_name: Hill - first_name: Martin full_name: Nowak, Martin last_name: Nowak citation: ama: Humplik J, Hill A, Nowak M. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 2014;360:149-162. doi:10.1016/j.jtbi.2014.06.039 apa: Humplik, J., Hill, A., & Nowak, M. (2014). Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. Elsevier. https://doi.org/10.1016/j.jtbi.2014.06.039 chicago: Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology. Elsevier, 2014. https://doi.org/10.1016/j.jtbi.2014.06.039. ieee: J. Humplik, A. Hill, and M. Nowak, “Evolutionary dynamics of infectious diseases in finite populations,” Journal of Theoretical Biology, vol. 360. Elsevier, pp. 149–162, 2014. ista: Humplik J, Hill A, Nowak M. 2014. Evolutionary dynamics of infectious diseases in finite populations. Journal of Theoretical Biology. 360, 149–162. mla: Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.” Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039. short: J. Humplik, A. Hill, M. Nowak, Journal of Theoretical Biology 360 (2014) 149–162. date_created: 2018-12-11T11:54:46Z date_published: 2014-11-07T00:00:00Z date_updated: 2021-01-12T06:54:08Z day: '07' department: - _id: GaTk doi: 10.1016/j.jtbi.2014.06.039 intvolume: ' 360' language: - iso: eng month: '11' oa_version: None page: 149 - 162 publication: Journal of Theoretical Biology publication_status: published publisher: Elsevier publist_id: '5166' scopus_import: 1 status: public title: Evolutionary dynamics of infectious diseases in finite populations type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 360 year: '2014' ... --- _id: '1931' abstract: - lang: eng text: A wealth of experimental evidence suggests that working memory circuits preferentially represent information that is behaviorally relevant. Still, we are missing a mechanistic account of how these representations come about. Here we provide a simple explanation for a range of experimental findings, in light of prefrontal circuits adapting to task constraints by reward-dependent learning. In particular, we model a neural network shaped by reward-modulated spike-timing dependent plasticity (r-STDP) and homeostatic plasticity (intrinsic excitability and synaptic scaling). We show that the experimentally-observed neural representations naturally emerge in an initially unstructured circuit as it learns to solve several working memory tasks. These results point to a critical, and previously unappreciated, role for reward-dependent learning in shaping prefrontal cortex activity. acknowledgement: Supported in part by EC MEXT project PLICON and the LOEWE-Program “Neuronal Coordination Research Focus Frankfurt” (NeFF). Jochen Triesch was supported by the Quandt foundation. article_number: '57' author: - first_name: Cristina full_name: Savin, Cristina id: 3933349E-F248-11E8-B48F-1D18A9856A87 last_name: Savin - first_name: Jochen full_name: Triesch, Jochen last_name: Triesch citation: ama: Savin C, Triesch J. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 2014;8(MAY). doi:10.3389/fncom.2014.00057 apa: Savin, C., & Triesch, J. (2014). Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. Frontiers Research Foundation. https://doi.org/10.3389/fncom.2014.00057 chicago: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014. https://doi.org/10.3389/fncom.2014.00057. ieee: C. Savin and J. Triesch, “Emergence of task-dependent representations in working memory circuits,” Frontiers in Computational Neuroscience, vol. 8, no. MAY. Frontiers Research Foundation, 2014. ista: Savin C, Triesch J. 2014. Emergence of task-dependent representations in working memory circuits. Frontiers in Computational Neuroscience. 8(MAY), 57. mla: Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.” Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057. short: C. Savin, J. Triesch, Frontiers in Computational Neuroscience 8 (2014). date_created: 2018-12-11T11:54:46Z date_published: 2014-05-28T00:00:00Z date_updated: 2021-01-12T06:54:09Z day: '28' department: - _id: GaTk doi: 10.3389/fncom.2014.00057 intvolume: ' 8' issue: MAY language: - iso: eng main_file_link: - open_access: '1' url: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4035833/ month: '05' oa: 1 oa_version: Submitted Version publication: Frontiers in Computational Neuroscience publication_status: published publisher: Frontiers Research Foundation publist_id: '5163' quality_controlled: '1' scopus_import: 1 status: public title: Emergence of task-dependent representations in working memory circuits type: journal_article user_id: 4435EBFC-F248-11E8-B48F-1D18A9856A87 volume: 8 year: '2014' ...