--- _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' ...