[{"article_processing_charge":"No","day":"01","scopus_import":"1","date_published":"2021-02-01T00:00:00Z","article_type":"original","citation":{"mla":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development, vol. 148, no. 2, dev176065, The Company of Biologists, 2021, doi:10.1242/dev.176065.","short":"G. Tkačik, T. Gregor, Development 148 (2021).","chicago":"Tkačik, Gašper, and Thomas Gregor. “The Many Bits of Positional Information.” Development. The Company of Biologists, 2021. https://doi.org/10.1242/dev.176065.","ama":"Tkačik G, Gregor T. The many bits of positional information. Development. 2021;148(2). doi:10.1242/dev.176065","ista":"Tkačik G, Gregor T. 2021. The many bits of positional information. Development. 148(2), dev176065.","apa":"Tkačik, G., & Gregor, T. (2021). The many bits of positional information. Development. The Company of Biologists. https://doi.org/10.1242/dev.176065","ieee":"G. Tkačik and T. Gregor, “The many bits of positional information,” Development, vol. 148, no. 2. The Company of Biologists, 2021."},"publication":"Development","issue":"2","abstract":[{"text":"Half a century after Lewis Wolpert's seminal conceptual advance on how cellular fates distribute in space, we provide a brief historical perspective on how the concept of positional information emerged and influenced the field of developmental biology and beyond. We focus on a modern interpretation of this concept in terms of information theory, largely centered on its application to cell specification in the early Drosophila embryo. We argue that a true physical variable (position) is encoded in local concentrations of patterning molecules, that this mapping is stochastic, and that the processes by which positions and corresponding cell fates are determined based on these concentrations need to take such stochasticity into account. With this approach, we shift the focus from biological mechanisms, molecules, genes and pathways to quantitative systems-level questions: where does positional information reside, how it is transformed and accessed during development, and what fundamental limits it is subject to?","lang":"eng"}],"type":"journal_article","oa_version":"Published Version","intvolume":" 148","title":"The many bits of positional information","status":"public","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9226","publication_identifier":{"eissn":["1477-9129"]},"month":"02","language":[{"iso":"eng"}],"doi":"10.1242/dev.176065","project":[{"grant_number":"P28844-B27","_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","name":"Biophysics of information processing in gene regulation"}],"quality_controlled":"1","isi":1,"oa":1,"main_file_link":[{"url":"https://doi.org/10.1242/dev.176065","open_access":"1"}],"external_id":{"isi":["000613906000007"],"pmid":["33526425"]},"article_number":"dev176065","volume":148,"date_updated":"2023-08-07T13:57:30Z","date_created":"2021-03-07T23:01:25Z","author":[{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Gregor, Thomas","first_name":"Thomas","last_name":"Gregor"}],"department":[{"_id":"GaTk"}],"publisher":"The Company of Biologists","publication_status":"published","pmid":1,"acknowledgement":"This work was supported in part by the National Science Foundation, through the Center for the Physics of Biological Function (PHY-1734030), by the National Institutes of Health (R01GM097275) and by the Fonds zur Förderung der wissenschaftlichen Forschung (FWF P28844). Deposited in PMC for release after 12 months.","year":"2021"},{"abstract":[{"text":"The ability to adapt to changes in stimulus statistics is a hallmark of sensory systems. Here, we developed a theoretical framework that can account for the dynamics of adaptation from an information processing perspective. We use this framework to optimize and analyze adaptive sensory codes, and we show that codes optimized for stationary environments can suffer from prolonged periods of poor performance when the environment changes. To mitigate the adversarial effects of these environmental changes, sensory systems must navigate tradeoffs between the ability to accurately encode incoming stimuli and the ability to rapidly detect and adapt to changes in the distribution of these stimuli. We derive families of codes that balance these objectives, and we demonstrate their close match to experimentally observed neural dynamics during mean and variance adaptation. Our results provide a unifying perspective on adaptation across a range of sensory systems, environments, and sensory tasks.","lang":"eng"}],"type":"journal_article","oa_version":"Preprint","intvolume":" 24","status":"public","title":"Efficient and adaptive sensory codes","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","_id":"9439","article_processing_charge":"No","day":"20","scopus_import":"1","date_published":"2021-05-20T00:00:00Z","page":"998-1009","article_type":"original","citation":{"chicago":"Mlynarski, Wiktor F, and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience. Springer Nature, 2021. https://doi.org/10.1038/s41593-021-00846-0.","short":"W.F. Mlynarski, A.M. Hermundstad, Nature Neuroscience 24 (2021) 998–1009.","mla":"Mlynarski, Wiktor F., and Ann M. Hermundstad. “Efficient and Adaptive Sensory Codes.” Nature Neuroscience, vol. 24, Springer Nature, 2021, pp. 998–1009, doi:10.1038/s41593-021-00846-0.","ieee":"W. F. Mlynarski and A. M. Hermundstad, “Efficient and adaptive sensory codes,” Nature Neuroscience, vol. 24. Springer Nature, pp. 998–1009, 2021.","apa":"Mlynarski, W. F., & Hermundstad, A. M. (2021). Efficient and adaptive sensory codes. Nature Neuroscience. Springer Nature. https://doi.org/10.1038/s41593-021-00846-0","ista":"Mlynarski WF, Hermundstad AM. 2021. Efficient and adaptive sensory codes. Nature Neuroscience. 24, 998–1009.","ama":"Mlynarski WF, Hermundstad AM. Efficient and adaptive sensory codes. Nature Neuroscience. 2021;24:998-1009. doi:10.1038/s41593-021-00846-0"},"publication":"Nature Neuroscience","ec_funded":1,"volume":24,"date_created":"2021-05-30T22:01:24Z","date_updated":"2023-08-08T13:51:14Z","author":[{"id":"358A453A-F248-11E8-B48F-1D18A9856A87","last_name":"Mlynarski","first_name":"Wiktor F","full_name":"Mlynarski, Wiktor F"},{"full_name":"Hermundstad, Ann M.","first_name":"Ann M.","last_name":"Hermundstad"}],"department":[{"_id":"GaTk"}],"publisher":"Springer Nature","publication_status":"published","acknowledgement":"We thank D. Kastner and T. Münch for generously providing figures from their work. We also thank V. Jayaraman, M. Noorman, T. Ma, and K. Krishnamurthy for useful discussions and feedback on the manuscript. W.F.M. was funded by the European Union’s Horizon 2020 Research and Innovation Programme under Marie Skłodowska-Curie Grant Agreement No. 754411. A.M.H. was supported by the Howard Hughes Medical Institute.","year":"2021","publication_identifier":{"issn":["1097-6256"],"eissn":["1546-1726"]},"month":"05","language":[{"iso":"eng"}],"doi":"10.1038/s41593-021-00846-0","project":[{"_id":"260C2330-B435-11E9-9278-68D0E5697425","grant_number":"754411","name":"ISTplus - Postdoctoral Fellowships","call_identifier":"H2020"}],"quality_controlled":"1","isi":1,"oa":1,"external_id":{"isi":["000652577300003"]},"main_file_link":[{"open_access":"1","url":"https://doi.org/10.1101/669200 "}]},{"month":"08","publication_identifier":{"eissn":["19448252"],"issn":["19448244"]},"language":[{"iso":"eng"}],"doi":"10.1021/acsami.1c09850","isi":1,"quality_controlled":"1","project":[{"name":"Cellular navigation along spatial gradients","call_identifier":"H2020","_id":"25FE9508-B435-11E9-9278-68D0E5697425","grant_number":"724373"}],"tmp":{"name":"Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 International (CC BY-NC-ND 4.0)","legal_code_url":"https://creativecommons.org/licenses/by-nc-nd/4.0/legalcode","short":"CC BY-NC-ND (4.0)","image":"/images/cc_by_nc_nd.png"},"external_id":{"isi":["000683741400026"],"pmid":["34283577"]},"oa":1,"license":"https://creativecommons.org/licenses/by-nc-nd/4.0/","file_date_updated":"2021-08-09T09:44:03Z","ec_funded":1,"date_updated":"2023-08-10T14:22:48Z","date_created":"2021-08-08T22:01:28Z","volume":13,"author":[{"first_name":"Themistoklis","last_name":"Zisis","full_name":"Zisis, Themistoklis"},{"id":"346C1EC6-F248-11E8-B48F-1D18A9856A87","last_name":"Schwarz","first_name":"Jan","full_name":"Schwarz, Jan"},{"last_name":"Balles","first_name":"Miriam","full_name":"Balles, Miriam"},{"first_name":"Maibritt","last_name":"Kretschmer","full_name":"Kretschmer, Maibritt"},{"id":"34E27F1C-F248-11E8-B48F-1D18A9856A87","last_name":"Nemethova","first_name":"Maria","full_name":"Nemethova, Maria"},{"full_name":"Chait, Remy P","last_name":"Chait","first_name":"Remy P","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Hauschild, Robert","last_name":"Hauschild","first_name":"Robert","orcid":"0000-0001-9843-3522","id":"4E01D6B4-F248-11E8-B48F-1D18A9856A87"},{"first_name":"Janina","last_name":"Lange","full_name":"Lange, Janina"},{"first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052","full_name":"Guet, Calin C"},{"orcid":"0000-0002-4561-241X","id":"41E9FBEA-F248-11E8-B48F-1D18A9856A87","last_name":"Sixt","first_name":"Michael K","full_name":"Sixt, Michael K"},{"first_name":"Stefan","last_name":"Zahler","full_name":"Zahler, Stefan"}],"publication_status":"published","publisher":"American Chemical Society","department":[{"_id":"MiSi"},{"_id":"GaTk"},{"_id":"Bio"},{"_id":"CaGu"}],"acknowledgement":"We would like to thank Charlott Leu for the production of our chromium wafers, Louise Ritter for her contribution of the IF stainings in Figure 4, Shokoufeh Teymouri for her help with the Bioinert coated slides, and finally Prof. Dr. Joachim Rädler for his valuable scientific guidance.","year":"2021","pmid":1,"day":"04","article_processing_charge":"Yes (in subscription journal)","has_accepted_license":"1","scopus_import":"1","date_published":"2021-08-04T00:00:00Z","article_type":"original","page":"35545–35560","publication":"ACS Applied Materials and Interfaces","citation":{"mla":"Zisis, Themistoklis, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces, vol. 13, no. 30, American Chemical Society, 2021, pp. 35545–35560, doi:10.1021/acsami.1c09850.","short":"T. Zisis, J. Schwarz, M. Balles, M. Kretschmer, M. Nemethova, R.P. Chait, R. Hauschild, J. Lange, C.C. Guet, M.K. Sixt, S. Zahler, ACS Applied Materials and Interfaces 13 (2021) 35545–35560.","chicago":"Zisis, Themistoklis, Jan Schwarz, Miriam Balles, Maibritt Kretschmer, Maria Nemethova, Remy P Chait, Robert Hauschild, et al. “Sequential and Switchable Patterning for Studying Cellular Processes under Spatiotemporal Control.” ACS Applied Materials and Interfaces. American Chemical Society, 2021. https://doi.org/10.1021/acsami.1c09850.","ama":"Zisis T, Schwarz J, Balles M, et al. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 2021;13(30):35545–35560. doi:10.1021/acsami.1c09850","ista":"Zisis T, Schwarz J, Balles M, Kretschmer M, Nemethova M, Chait RP, Hauschild R, Lange J, Guet CC, Sixt MK, Zahler S. 2021. Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. 13(30), 35545–35560.","apa":"Zisis, T., Schwarz, J., Balles, M., Kretschmer, M., Nemethova, M., Chait, R. P., … Zahler, S. (2021). Sequential and switchable patterning for studying cellular processes under spatiotemporal control. ACS Applied Materials and Interfaces. American Chemical Society. https://doi.org/10.1021/acsami.1c09850","ieee":"T. Zisis et al., “Sequential and switchable patterning for studying cellular processes under spatiotemporal control,” ACS Applied Materials and Interfaces, vol. 13, no. 30. American Chemical Society, pp. 35545–35560, 2021."},"abstract":[{"text":"Attachment of adhesive molecules on cell culture surfaces to restrict cell adhesion to defined areas and shapes has been vital for the progress of in vitro research. In currently existing patterning methods, a combination of pattern properties such as stability, precision, specificity, high-throughput outcome, and spatiotemporal control is highly desirable but challenging to achieve. Here, we introduce a versatile and high-throughput covalent photoimmobilization technique, comprising a light-dose-dependent patterning step and a subsequent functionalization of the pattern via click chemistry. This two-step process is feasible on arbitrary surfaces and allows for generation of sustainable patterns and gradients. The method is validated in different biological systems by patterning adhesive ligands on cell-repellent surfaces, thereby constraining the growth and migration of cells to the designated areas. We then implement a sequential photopatterning approach by adding a second switchable patterning step, allowing for spatiotemporal control over two distinct surface patterns. As a proof of concept, we reconstruct the dynamics of the tip/stalk cell switch during angiogenesis. Our results show that the spatiotemporal control provided by our “sequential photopatterning” system is essential for mimicking dynamic biological processes and that our innovative approach has great potential for further applications in cell science.","lang":"eng"}],"issue":"30","type":"journal_article","file":[{"creator":"asandaue","content_type":"application/pdf","file_size":7123293,"access_level":"open_access","file_name":"2021_ACSAppliedMaterialsAndInterfaces_Zisis.pdf","success":1,"checksum":"b043a91d9f9200e467b970b692687ed3","date_created":"2021-08-09T09:44:03Z","date_updated":"2021-08-09T09:44:03Z","file_id":"9833","relation":"main_file"}],"oa_version":"Published Version","title":"Sequential and switchable patterning for studying cellular processes under spatiotemporal control","ddc":["620","570"],"status":"public","intvolume":" 13","_id":"9822","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8"},{"month":"06","publication_identifier":{"issn":["1053-587X"],"eissn":["1941-0476"]},"external_id":{"isi":["000682123900002"],"arxiv":["2102.04832"]},"oa":1,"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/2102.04832"}],"isi":1,"quality_controlled":"1","doi":"10.1109/TSP.2021.3087899","language":[{"iso":"eng"}],"year":"2021","acknowledgement":"The author thanks his colleagues K. Huszár and G. Tkačik for valuable discussions and comments on the manuscript.","publication_status":"published","publisher":"Institute of Electrical and Electronics Engineers","department":[{"_id":"GaTk"}],"author":[{"last_name":"Gabrielaitis","first_name":"Mantas","orcid":"0000-0002-7758-2016","id":"4D5B0CBC-F248-11E8-B48F-1D18A9856A87","full_name":"Gabrielaitis, Mantas"}],"date_created":"2021-08-08T22:01:31Z","date_updated":"2023-08-10T14:19:33Z","volume":69,"scopus_import":"1","day":"09","article_processing_charge":"No","publication":"IEEE Transactions on Signal Processing","citation":{"ista":"Gabrielaitis M. 2021. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 69, 4039–4054.","apa":"Gabrielaitis, M. (2021). Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers. https://doi.org/10.1109/TSP.2021.3087899","ieee":"M. Gabrielaitis, “Fast and accurate amplitude demodulation of wideband signals,” IEEE Transactions on Signal Processing, vol. 69. Institute of Electrical and Electronics Engineers, pp. 4039–4054, 2021.","ama":"Gabrielaitis M. Fast and accurate amplitude demodulation of wideband signals. IEEE Transactions on Signal Processing. 2021;69:4039-4054. doi:10.1109/TSP.2021.3087899","chicago":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing. Institute of Electrical and Electronics Engineers, 2021. https://doi.org/10.1109/TSP.2021.3087899.","mla":"Gabrielaitis, Mantas. “Fast and Accurate Amplitude Demodulation of Wideband Signals.” IEEE Transactions on Signal Processing, vol. 69, Institute of Electrical and Electronics Engineers, 2021, pp. 4039–54, doi:10.1109/TSP.2021.3087899.","short":"M. Gabrielaitis, IEEE Transactions on Signal Processing 69 (2021) 4039–4054."},"article_type":"original","page":"4039 - 4054","date_published":"2021-06-09T00:00:00Z","type":"journal_article","abstract":[{"lang":"eng","text":"Amplitude demodulation is a classical operation used in signal processing. For a long time, its effective applications in practice have been limited to narrowband signals. In this work, we generalize amplitude demodulation to wideband signals. We pose demodulation as a recovery problem of an oversampled corrupted signal and introduce special iterative schemes belonging to the family of alternating projection algorithms to solve it. Sensibly chosen structural assumptions on the demodulation outputs allow us to reveal the high inferential accuracy of the method over a rich set of relevant signals. This new approach surpasses current state-of-the-art demodulation techniques apt to wideband signals in computational efficiency by up to many orders of magnitude with no sacrifice in quality. Such performance opens the door for applications of the amplitude demodulation procedure in new contexts. In particular, the new method makes online and large-scale offline data processing feasible, including the calculation of modulator-carrier pairs in higher dimensions and poor sampling conditions, independent of the signal bandwidth. We illustrate the utility and specifics of applications of the new method in practice by using natural speech and synthetic signals."}],"_id":"9828","user_id":"4359f0d1-fa6c-11eb-b949-802e58b17ae8","status":"public","title":"Fast and accurate amplitude demodulation of wideband signals","intvolume":" 69","oa_version":"Preprint"},{"isi":1,"quality_controlled":"1","tmp":{"name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","short":"CC BY (4.0)","image":"/images/cc_by.png"},"external_id":{"pmid":["33857170"],"isi":["000641474900072"]},"oa":1,"language":[{"iso":"eng"}],"doi":"10.1371/journal.pone.0248940","publication_identifier":{"eissn":["19326203"]},"month":"04","publisher":"Public Library of Science","department":[{"_id":"GaTk"}],"publication_status":"published","pmid":1,"acknowledgement":"The authors would like to thank Ulisse Ferrari for useful discussions and feedback.","year":"2021","volume":16,"date_created":"2021-05-02T22:01:28Z","date_updated":"2023-10-18T08:17:42Z","author":[{"full_name":"Chalk, Matthew J","last_name":"Chalk","first_name":"Matthew J","orcid":"0000-0001-7782-4436","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkačik","first_name":"Gašper","full_name":"Tkačik, Gašper"},{"full_name":"Marre, Olivier","last_name":"Marre","first_name":"Olivier"}],"article_number":"e0248940","file_date_updated":"2021-05-04T13:22:19Z","article_type":"original","citation":{"mla":"Chalk, Matthew J., et al. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE, vol. 16, no. 4, e0248940, Public Library of Science, 2021, doi:10.1371/journal.pone.0248940.","short":"M.J. Chalk, G. Tkačik, O. Marre, PLoS ONE 16 (2021).","chicago":"Chalk, Matthew J, Gašper Tkačik, and Olivier Marre. “Inferring the Function Performed by a Recurrent Neural Network.” PLoS ONE. Public Library of Science, 2021. https://doi.org/10.1371/journal.pone.0248940.","ama":"Chalk MJ, Tkačik G, Marre O. Inferring the function performed by a recurrent neural network. PLoS ONE. 2021;16(4). doi:10.1371/journal.pone.0248940","ista":"Chalk MJ, Tkačik G, Marre O. 2021. Inferring the function performed by a recurrent neural network. PLoS ONE. 16(4), e0248940.","apa":"Chalk, M. J., Tkačik, G., & Marre, O. (2021). Inferring the function performed by a recurrent neural network. PLoS ONE. Public Library of Science. https://doi.org/10.1371/journal.pone.0248940","ieee":"M. J. Chalk, G. Tkačik, and O. Marre, “Inferring the function performed by a recurrent neural network,” PLoS ONE, vol. 16, no. 4. Public Library of Science, 2021."},"publication":"PLoS ONE","date_published":"2021-04-15T00:00:00Z","scopus_import":"1","article_processing_charge":"No","has_accepted_license":"1","day":"15","intvolume":" 16","ddc":["570"],"title":"Inferring the function performed by a recurrent neural network","status":"public","_id":"9362","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","file":[{"file_name":"2021_pone_Chalk.pdf","access_level":"open_access","file_size":2768282,"content_type":"application/pdf","creator":"kschuh","relation":"main_file","file_id":"9371","date_updated":"2021-05-04T13:22:19Z","date_created":"2021-05-04T13:22:19Z","checksum":"c52da133850307d2031f552d998f00e8","success":1}],"oa_version":"Published Version","type":"journal_article","issue":"4","abstract":[{"text":"A central goal in systems neuroscience is to understand the functions performed by neural circuits. Previous top-down models addressed this question by comparing the behaviour of an ideal model circuit, optimised to perform a given function, with neural recordings. However, this requires guessing in advance what function is being performed, which may not be possible for many neural systems. To address this, we propose an inverse reinforcement learning (RL) framework for inferring the function performed by a neural network from data. We assume that the responses of each neuron in a network are optimised so as to drive the network towards ‘rewarded’ states, that are desirable for performing a given function. We then show how one can use inverse RL to infer the reward function optimised by the network from observing its responses. This inferred reward function can be used to predict how the neural network should adapt its dynamics to perform the same function when the external environment or network structure changes. This could lead to theoretical predictions about how neural network dynamics adapt to deal with cell death and/or varying sensory stimulus statistics.","lang":"eng"}]}]