[{"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino"},{"first_name":"Davide","full_name":"Masoero, Davide","last_name":"Masoero"}],"main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"status":"public","month":"12","issue":"12","_id":"1188","publication_status":"published","quality_controlled":"1","year":"2016","isi":1,"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1088/1742-5468/aa4e8f","publisher":"IOP Publishing","date_published":"2016-12-30T00:00:00Z","department":[{"_id":"GaTk"}],"volume":2016,"language":[{"iso":"eng"}],"day":"30","ec_funded":1,"intvolume":" 2016","publication":" Journal of Statistical Mechanics: Theory and Experiment","external_id":{"arxiv":["1606.09048"],"isi":["000391973900001"]},"type":"journal_article","abstract":[{"lang":"eng","text":"We consider a population dynamics model coupling cell growth to a diffusion in the space of metabolic phenotypes as it can be obtained from realistic constraints-based modelling. \r\nIn the asymptotic regime of slow\r\ndiffusion, that coincides with the relevant experimental range, the resulting\r\nnon-linear Fokker–Planck equation is solved for the steady state in the WKB\r\napproximation that maps it into the ground state of a quantum particle in an\r\nAiry potential plus a centrifugal term. We retrieve scaling laws for growth rate\r\nfluctuations and time response with respect to the distance from the maximum\r\ngrowth rate suggesting that suboptimal populations can have a faster response\r\nto perturbations."}],"date_created":"2018-12-11T11:50:37Z","date_updated":"2025-09-22T09:45:38Z","arxiv":1,"publist_id":"6165","oa":1,"citation":{"ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &amp; Growth.” Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing, 2016. https://doi.org/10.1088/1742-5468/aa4e8f.","apa":"De Martino, D., & Masoero, D. (2016). Asymptotic analysis of noisy fitness maximization, applied to metabolism &amp; growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f"},"article_number":"123502","acknowledgement":"D De Martino is supported by the People Programme (Marie Curie Actions) of the European Union's Seventh Framework Programme (FP7/2007–2013) under REA grant agreement no. [291734]. D Masoero is supported by the FCT scholarship, number SFRH/BPD/75908/2011. D De Martino thanks the Grupo de Física Matemática of the Universidade de Lisboa for the kind hospitality. We also wish to thank Matteo Osella, Vincenzo Vitagliano and Vera Luz Masoero for useful discussions, also late at night.","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1"},{"isi":1,"title":"Error-robust modes of the retinal population code","year":"2016","file":[{"file_size":4492021,"file_id":"5884","date_updated":"2020-07-14T12:44:38Z","date_created":"2019-01-25T10:35:00Z","file_name":"2016_PLOS_Prentice.pdf","content_type":"application/pdf","relation":"main_file","access_level":"open_access","checksum":"47b08cbd4dbf32b25ba161f5f4b262cc","creator":"kschuh"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1371/journal.pcbi.1005148","publisher":"Public Library of Science","project":[{"name":"Sensitivity to higher-order statistics in natural scenes","grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Prentice","full_name":"Prentice, Jason","first_name":"Jason"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"full_name":"Ioffe, Mark","first_name":"Mark","last_name":"Ioffe"},{"last_name":"Loback","first_name":"Adrianna","full_name":"Loback, Adrianna"},{"orcid":"0000-0002-6699-1455","last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper"},{"first_name":"Michael","full_name":"Berry, Michael","last_name":"Berry"}],"month":"11","status":"public","related_material":{"record":[{"relation":"research_data","status":"public","id":"9709"}]},"file_date_updated":"2020-07-14T12:44:38Z","issue":"11","_id":"1197","quality_controlled":"1","publication_status":"published","date_created":"2018-12-11T11:50:40Z","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."}],"type":"journal_article","oa":1,"citation":{"short":"J. Prentice, O. Marre, M. Ioffe, A. Loback, G. Tkačik, M. Berry, PLoS Computational Biology 12 (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.","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","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.","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","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.","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."},"publist_id":"6153","date_updated":"2025-09-22T09:43:12Z","tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"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","article_processing_charge":"No","oa_version":"Published Version","scopus_import":"1","date_published":"2016-11-17T00:00:00Z","department":[{"_id":"GaTk"}],"ddc":["570"],"language":[{"iso":"eng"}],"volume":12,"intvolume":" 12","day":"17","publication":"PLoS Computational Biology","external_id":{"isi":["000391230900008"]},"has_accepted_license":"1"},{"volume":54,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"date_published":"2016-12-01T00:00:00Z","external_id":{"isi":["000389209600026"]},"publication":"Journal of Clinical Microbiology","intvolume":" 54","day":"01","article_processing_charge":"No","acknowledgement":"We are grateful to ABCs for providing strains and the Bacterial Meningitis Laboratory for technical support.","oa":1,"publist_id":"6146","citation":{"ama":"Hu F, Rishishwar L, Sivadas A, et al. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 2016;54(12):3010-3017. doi:10.1128/JCM.01511-16","short":"F. Hu, L. Rishishwar, A. Sivadas, G. Mitchell, J. King, T. Murphy, J. Gilsdorf, L. Mayer, X. Wang, Journal of Clinical Microbiology 54 (2016) 3010–3017.","ista":"Hu F, Rishishwar L, Sivadas A, Mitchell G, King J, Murphy T, Gilsdorf J, Mayer L, Wang X. 2016. Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. 54(12), 3010–3017.","apa":"Hu, F., Rishishwar, L., Sivadas, A., Mitchell, G., King, J., Murphy, T., … Wang, X. (2016). Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination. Journal of Clinical Microbiology. American Society for Microbiology. https://doi.org/10.1128/JCM.01511-16","chicago":"Hu, Fang, Lavanya Rishishwar, Ambily Sivadas, Gabriel Mitchell, Jordan King, Timothy Murphy, Janet Gilsdorf, Leonard Mayer, and Xin Wang. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology. American Society for Microbiology, 2016. https://doi.org/10.1128/JCM.01511-16.","mla":"Hu, Fang, et al. “Comparative Genomic Analysis of Haemophilus Haemolyticus and Nontypeable Haemophilus Influenzae and a New Testing Scheme for Their Discrimination.” Journal of Clinical Microbiology, vol. 54, no. 12, American Society for Microbiology, 2016, pp. 3010–17, doi:10.1128/JCM.01511-16.","ieee":"F. Hu et al., “Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination,” Journal of Clinical Microbiology, vol. 54, no. 12. American Society for Microbiology, pp. 3010–3017, 2016."},"date_updated":"2025-09-22T09:40:28Z","date_created":"2018-12-11T11:50:41Z","abstract":[{"text":"Haemophilus haemolyticus has been recently discovered to have the potential to cause invasive disease. It is closely related to nontypeable Haemophilus influenzae (NT H. influenzae). NT H. influenzae and H. haemolyticus are often misidentified because none of the existing tests targeting the known phenotypes of H. haemolyticus are able to specifically identify H. haemolyticus. Through comparative genomic analysis of H. haemolyticus and NT H. influenzae, we identified genes unique to H. haemolyticus that can be used as targets for the identification of H. haemolyticus. A real-time PCR targeting purT (encoding phosphoribosylglycinamide formyltransferase 2 in the purine synthesis pathway) was developed and evaluated. The lower limit of detection was 40 genomes/PCR; the sensitivity and specificity in detecting H. haemolyticus were 98.9% and 97%, respectively. To improve the discrimination of H. haemolyticus and NT H. influenzae, a testing scheme combining two targets (H. haemolyticus purT and H. influenzae hpd, encoding protein D lipoprotein) was also evaluated and showed 96.7% sensitivity and 98.2% specificity for the identification of H. haemolyticus and 92.8% sensitivity and 100% specificity for the identification of H. influenzae, respectively. The dual-target testing scheme can be used for the diagnosis and surveillance of infection and disease caused by H. haemolyticus and NT H. influenzae.","lang":"eng"}],"type":"journal_article","scopus_import":"1","oa_version":"Submitted Version","month":"12","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5121393/"}],"status":"public","author":[{"full_name":"Hu, Fang","first_name":"Fang","last_name":"Hu"},{"full_name":"Rishishwar, Lavanya","first_name":"Lavanya","last_name":"Rishishwar"},{"last_name":"Sivadas","full_name":"Sivadas, Ambily","first_name":"Ambily"},{"last_name":"Mitchell","first_name":"Gabriel","id":"315BCD80-F248-11E8-B48F-1D18A9856A87","full_name":"Mitchell, Gabriel"},{"full_name":"King, Jordan","first_name":"Jordan","last_name":"King"},{"first_name":"Timothy","full_name":"Murphy, Timothy","last_name":"Murphy"},{"full_name":"Gilsdorf, Janet","first_name":"Janet","last_name":"Gilsdorf"},{"last_name":"Mayer","full_name":"Mayer, Leonard","first_name":"Leonard"},{"full_name":"Wang, Xin","first_name":"Xin","last_name":"Wang"}],"publication_status":"published","quality_controlled":"1","_id":"1203","issue":"12","page":"3010 - 3017","title":"Comparative genomic analysis of Haemophilus haemolyticus and nontypeable Haemophilus influenzae and a new testing scheme for their discrimination","year":"2016","isi":1,"publisher":"American Society for Microbiology","doi":"10.1128/JCM.01511-16","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87","scopus_import":1,"oa_version":"None","doi":"10.1109/IROS.2016.7759138","publisher":"IEEE","date_created":"2018-12-11T11:50:45Z","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. While very successful with classical robots, these methods run into severe difficulties when applied to soft robots, a new field of robotics with large interest for human-robot interaction. We claim that a novel controller paradigm opens new perspective for this field. This paper applies a recently developed neuro controller with differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently develops to rotate it. In this way, the robot discovers affordances of objects its body is interacting with."}],"title":"Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm","year":"2016","type":"conference","publist_id":"6121","citation":{"apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm (Vol. 2016–November). Presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea: IEEE. https://doi.org/10.1109/IROS.2016.7759138","chicago":"Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,” Vol. 2016–November. IEEE, 2016. https://doi.org/10.1109/IROS.2016.7759138.","mla":"Martius, Georg S., et al. Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm. Vol. 2016–November, 7759138, IEEE, 2016, doi:10.1109/IROS.2016.7759138.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm,” presented at the IEEE RSJ International Conference on Intelligent Robots and Systems IROS , Daejeon, Korea, 2016, vol. 2016–November.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. In: Vol 2016-November. IEEE; 2016. doi:10.1109/IROS.2016.7759138","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Compliant control for soft robots: Emergent behavior of a tendon driven anthropomorphic arm. IEEE RSJ International Conference on Intelligent Robots and Systems IROS vol. 2016–November, 7759138.","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, IEEE, 2016."},"date_updated":"2021-01-12T06:49:08Z","article_number":"7759138","acknowledgement":"RD thanks for the hospitality at the Max-Planck-Institute and for helpful discussions with Nihat Ay and Keyan Zahedi.","conference":{"end_date":"2016-09-14","start_date":"2016-09-09","location":"Daejeon, Korea","name":"IEEE RSJ International Conference on Intelligent Robots and Systems IROS "},"day":"28","_id":"1214","quality_controlled":"1","publication_status":"published","author":[{"last_name":"Martius","full_name":"Martius, Georg S","id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S"},{"last_name":"Hostettler","full_name":"Hostettler, Raphael","first_name":"Raphael"},{"first_name":"Alois","full_name":"Knoll, Alois","last_name":"Knoll"},{"first_name":"Ralf","full_name":"Der, Ralf","last_name":"Der"}],"date_published":"2016-11-28T00:00:00Z","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"month":"11","status":"public","language":[{"iso":"eng"}],"volume":"2016-November"},{"month":"06","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"main_file_link":[{"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","open_access":"1"}],"status":"public","language":[{"iso":"eng"}],"author":[{"full_name":"Mikić, Gregor","first_name":"Gregor","last_name":"Mikić"},{"last_name":"Stoll","full_name":"Stoll, Alex","first_name":"Alex"},{"first_name":"Joe","full_name":"Bevirt, Joe","last_name":"Bevirt"},{"last_name":"Grah","full_name":"Grah, Rok","id":"483E70DE-F248-11E8-B48F-1D18A9856A87","first_name":"Rok","orcid":"0000-0003-2539-3560"},{"last_name":"Moore","first_name":"Mark","full_name":"Moore, Mark"}],"date_published":"2016-06-01T00:00:00Z","publication_status":"published","quality_controlled":"1","day":"01","_id":"1220","conference":{"end_date":"2016-06-17","start_date":"2016-06-13","location":"Washington, D.C., USA","name":"AIAA: Aviation Technology, Integration, and Operations Conference"},"page":"1 - 19","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:50:47Z","year":"2016","title":"Fuselage boundary layer ingestion propulsion applied to a thin haul commuter aircraft for optimal efficiency","type":"conference","publist_id":"6114","citation":{"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.","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.","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.","short":"G. Mikić, A. Stoll, J. Bevirt, R. Grah, M. Moore, in:, AIAA, 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.","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"},"oa":1,"date_updated":"2023-02-21T10:17:50Z","scopus_import":1,"oa_version":"Preprint","doi":"10.2514/6.2016-3764","publisher":"AIAA","user_id":"3E5EF7F0-F248-11E8-B48F-1D18A9856A87"},{"date_updated":"2025-09-22T08:17:11Z","oa":1,"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","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.","short":"M. Baym, T. Lieberman, E. Kelsic, R.P. Chait, R. Gross, I. Yelin, R. Kishony, Science 353 (2016) 1147–1151.","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.","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","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.","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."},"publist_id":"5911","type":"journal_article","date_created":"2018-12-11T11:51:29Z","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."}],"article_processing_charge":"No","scopus_import":"1","oa_version":"Preprint","date_published":"2016-09-09T00:00:00Z","volume":353,"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"day":"09","intvolume":" 353","external_id":{"isi":["000382626800052"]},"publication":"Science","title":"Spatiotemporal microbial evolution on antibiotic landscapes","year":"2016","isi":1,"page":"1147 - 1151","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"American Association for the Advancement of Science","doi":"10.1126/science.aag0822","author":[{"last_name":"Baym","first_name":"Michael","full_name":"Baym, Michael"},{"last_name":"Lieberman","first_name":"Tami","full_name":"Lieberman, Tami"},{"first_name":"Eric","full_name":"Kelsic, Eric","last_name":"Kelsic"},{"last_name":"Chait","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","orcid":"0000-0003-0876-3187"},{"last_name":"Gross","full_name":"Gross, Rotem","first_name":"Rotem"},{"full_name":"Yelin, Idan","first_name":"Idan","last_name":"Yelin"},{"last_name":"Kishony","first_name":"Roy","full_name":"Kishony, Roy"}],"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/"}],"status":"public","month":"09","_id":"1342","issue":"6304","quality_controlled":"1","publication_status":"published"},{"date_published":"2016-05-27T00:00:00Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"volume":13,"day":"27","intvolume":" 13","ec_funded":1,"publication":"Physical Biology","external_id":{"isi":["000380148200014"],"arxiv":["1601.03243"]},"type":"journal_article","date_created":"2018-12-11T11:51:46Z","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."}],"date_updated":"2025-09-18T14:31:33Z","oa":1,"citation":{"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.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (2016).","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","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, 2016, doi: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, 2016.","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, 2016. https://doi.org/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. https://doi.org/10.1088/1478-3975/13/3/036005"},"publist_id":"5815","arxiv":1,"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","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1","project":[{"call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"},{"last_name":"Capuani","first_name":"Fabrizio","full_name":"Capuani, Fabrizio"},{"full_name":"De Martino, Andrea","first_name":"Andrea","last_name":"De Martino"}],"main_file_link":[{"url":"https://arxiv.org/abs/1601.03243","open_access":"1"}],"status":"public","month":"05","issue":"3","_id":"1394","publication_status":"published","quality_controlled":"1","title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","isi":1,"year":"2016","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1088/1478-3975/13/3/036005","publisher":"IOP Publishing"},{"author":[{"last_name":"Bod'ová","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","full_name":"Bod'ová, Katarína","first_name":"Katarína","orcid":"0000-0002-7214-0171"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik"},{"orcid":"0000-0002-8548-5240","first_name":"Nicholas H","full_name":"Barton, Nicholas H","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","last_name":"Barton"}],"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425","name":"Information processing and computation in fish groups"}],"main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"status":"public","month":"04","_id":"1420","issue":"4","publication_status":"published","quality_controlled":"1","title":"A general approximation for the dynamics of quantitative traits","isi":1,"year":"2016","corr_author":"1","page":"1523 - 1548","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Genetics Society of America","doi":"10.1534/genetics.115.184127","date_published":"2016-04-06T00:00:00Z","volume":202,"language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"day":"06","ec_funded":1,"intvolume":" 202","external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"publication":"Genetics","date_updated":"2025-09-18T14:22:05Z","citation":{"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.","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.","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.","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","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","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548."},"publist_id":"5787","oa":1,"arxiv":1,"type":"journal_article","abstract":[{"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. ","lang":"eng"}],"date_created":"2018-12-11T11:51:55Z","article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1"},{"scopus_import":"1","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:50:54Z","date_updated":"2025-09-22T09:16:30Z","publist_id":"6088","citation":{"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.","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.","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.","short":"T.R. Sokolowski, A. Walczak, W. Bialek, G. Tkačik, Physical Review E Statistical Nonlinear and Soft Matter Physics 93 (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.","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"},"oa":1,"arxiv":1,"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","article_processing_charge":"No","day":"04","intvolume":" 93","publication":"Physical Review E Statistical Nonlinear and Soft Matter Physics","external_id":{"arxiv":["1507.02562"],"isi":["000369439100005"]},"date_published":"2016-02-04T00:00:00Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"volume":93,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1103/PhysRevE.93.022404","publisher":"American Institute of Physics","title":"Extending the dynamic range of transcription factor action by translational regulation","isi":1,"year":"2016","issue":"2","_id":"1242","quality_controlled":"1","publication_status":"published","project":[{"name":"Biophysics of information processing in gene regulation","grant_number":"P28844-B27","call_identifier":"FWF","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"author":[{"orcid":"0000-0002-1287-3779","last_name":"Sokolowski","full_name":"Sokolowski, Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","first_name":"Thomas R"},{"full_name":"Walczak, Aleksandra","first_name":"Aleksandra","last_name":"Walczak"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"},{"full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455"}],"main_file_link":[{"url":"https://arxiv.org/abs/1507.02562","open_access":"1"}],"status":"public","month":"02"},{"_id":"1244","issue":"7","publication_status":"published","quality_controlled":"1","author":[{"full_name":"Recouvreux, Pierre","first_name":"Pierre","last_name":"Recouvreux"},{"orcid":"0000-0002-1287-3779","last_name":"Sokolowski","first_name":"Thomas R","id":"3E999752-F248-11E8-B48F-1D18A9856A87","full_name":"Sokolowski, Thomas R"},{"full_name":"Grammoustianou, Aristea","first_name":"Aristea","last_name":"Grammoustianou"},{"first_name":"Pieter","full_name":"Tenwolde, Pieter","last_name":"Tenwolde"},{"full_name":"Dogterom, Marileen","first_name":"Marileen","last_name":"Dogterom"}],"month":"02","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"status":"public","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"National Academy of Sciences","doi":"10.1073/pnas.1419248113","isi":1,"title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","year":"2016","page":"1811 - 1816","intvolume":" 113","day":"16","external_id":{"isi":["000370220000046"]},"publication":"PNAS","date_published":"2016-02-16T00:00:00Z","language":[{"iso":"eng"}],"volume":113,"department":[{"_id":"GaTk"}],"oa_version":"Submitted Version","scopus_import":"1","oa":1,"publist_id":"6085","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","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.","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","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.","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.","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.","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"},"date_updated":"2025-09-22T09:15:17Z","date_created":"2018-12-11T11:50:55Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","article_processing_charge":"No","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":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","orcid":"0000-0002-6699-1455"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"}],"project":[{"grant_number":"P 25651-N26","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425","name":"Sensitivity to higher-order statistics in natural scenes"}],"main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"status":"public","month":"03","_id":"1248","quality_controlled":"1","publication_status":"published","year":"2016","title":"Information processing in living systems","isi":1,"page":"89 - 117","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publisher":"Annual Reviews","doi":"10.1146/annurev-conmatphys-031214-014803","date_published":"2016-03-10T00:00:00Z","language":[{"iso":"eng"}],"volume":7,"department":[{"_id":"GaTk"}],"day":"10","intvolume":" 7","external_id":{"isi":["000372188500005"],"arxiv":["1412.8752"]},"publication":"Annual Review of Condensed Matter Physics","date_updated":"2025-09-22T09:12:56Z","citation":{"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.","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.","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.","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","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117.","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","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"},"arxiv":1,"publist_id":"6080","oa":1,"type":"journal_article","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."}],"date_created":"2018-12-11T11:50:56Z","article_processing_charge":"No","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.","oa_version":"Preprint","scopus_import":"1"},{"article_type":"original","issue":"6","_id":"1260","quality_controlled":"1","publication_status":"published","author":[{"orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","full_name":"De Martino, Daniele","first_name":"Daniele","last_name":"De Martino"}],"main_file_link":[{"url":"https://arxiv.org/abs/1505.02963","open_access":"1"}],"status":"public","month":"06","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1142/S0129183116500674","publisher":"World Scientific Publishing","title":"The dual of the space of interactions in neural network models","year":"2016","isi":1,"corr_author":"1","day":"01","intvolume":" 27","publication":"International Journal of Modern Physics C","external_id":{"arxiv":["1505.02963"],"isi":["000377674800010"]},"date_published":"2016-06-01T00:00:00Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"volume":27,"scopus_import":"1","oa_version":"Preprint","type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:51:00Z","date_updated":"2025-09-22T09:01:25Z","citation":{"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.","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.","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.","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","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","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.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016)."},"arxiv":1,"publist_id":"6065","oa":1,"article_number":"1650067","article_processing_charge":"No"},{"ddc":["571"],"language":[{"iso":"eng"}],"volume":5,"department":[{"_id":"GaTk"}],"date_published":"2016-07-01T00:00:00Z","external_id":{"isi":["000380855400001"]},"has_accepted_license":"1","publication":"eLife","intvolume":" 5","day":"01","article_processing_charge":"No","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","article_number":"e13824","publist_id":"6056","oa":1,"citation":{"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.","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.","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.","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","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.","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","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"},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-22T08:49:58Z","date_created":"2018-12-11T11:51:02Z","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."}],"type":"journal_article","scopus_import":"1","oa_version":"Published Version","month":"07","status":"public","author":[{"last_name":"Chalk","first_name":"Matthew J","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436"},{"last_name":"Gutkin","first_name":"Boris","full_name":"Gutkin, Boris"},{"last_name":"Denève","first_name":"Sophie","full_name":"Denève, Sophie"}],"publication_status":"published","quality_controlled":"1","_id":"1266","file_date_updated":"2020-07-14T12:44:42Z","issue":"2016JULY","pubrep_id":"700","file":[{"date_created":"2018-12-12T10:11:20Z","file_name":"IST-2016-700-v1+1_e13824-download.pdf","file_id":"4874","date_updated":"2020-07-14T12:44:42Z","file_size":2819055,"checksum":"dc52d967dc76174477bb258d84be2899","creator":"system","access_level":"open_access","relation":"main_file","content_type":"application/pdf"}],"isi":1,"title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","year":"2016","corr_author":"1","publisher":"eLife Sciences Publications","doi":"10.7554/eLife.13824","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345"},{"intvolume":" 11","day":"27","publication":"PLoS One","external_id":{"isi":["000384169900025"]},"has_accepted_license":"1","date_published":"2016-09-27T00:00:00Z","department":[{"_id":"GaTk"}],"ddc":["571"],"volume":11,"language":[{"iso":"eng"}],"scopus_import":"1","oa_version":"Published Version","date_created":"2018-12-11T11:51:03Z","abstract":[{"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.","lang":"eng"}],"type":"journal_article","oa":1,"publist_id":"6050","citation":{"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.","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.","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","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.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016)."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-22T08:46:15Z","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","article_processing_charge":"No","file_date_updated":"2020-07-14T12:44:42Z","issue":"9","_id":"1270","publication_status":"published","quality_controlled":"1","project":[{"_id":"254E9036-B435-11E9-9278-68D0E5697425","call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation"}],"author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"last_name":"Gerland","full_name":"Gerland, Ulrich","first_name":"Ulrich"},{"last_name":"Tkacik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkacik, Gasper","first_name":"Gasper","orcid":"0000-0002-6699-1455"}],"month":"09","status":"public","related_material":{"record":[{"id":"9869","relation":"research_data","status":"public"},{"status":"public","relation":"research_data","id":"9870"},{"id":"9871","relation":"research_data","status":"public"}]},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1371/journal.pone.0163628","publisher":"Public Library of Science","corr_author":"1","year":"2016","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","isi":1,"pubrep_id":"696","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"3d0d55d373096a033bd9cf79288c8586","creator":"system","file_size":4950415,"file_id":"4837","date_updated":"2020-07-14T12:44:42Z","date_created":"2018-12-12T10:10:47Z","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF"}]},{"article_processing_charge":"No","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","date_updated":"2025-09-22T08:30:48Z","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","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.","short":"L. Stone, M. Baym, T. Lieberman, R.P. Chait, J. Clardy, R. Kishony, Nature Chemical Biology 12 (2016) 902–904.","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.","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.","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.","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"},"oa":1,"publist_id":"6026","type":"journal_article","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:51:10Z","oa_version":"Preprint","scopus_import":"1","volume":12,"language":[{"iso":"eng"}],"department":[{"_id":"CaGu"},{"_id":"GaTk"}],"date_published":"2016-11-01T00:00:00Z","external_id":{"isi":["000386798800008"]},"publication":"Nature Chemical Biology","day":"01","intvolume":" 12","page":"902 - 904","year":"2016","isi":1,"title":"Compounds that select against the tetracycline-resistance efflux pump","publisher":"Nature Publishing Group","doi":"10.1038/nchembio.2176","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"month":"11","author":[{"last_name":"Stone","full_name":"Stone, Laura","first_name":"Laura"},{"full_name":"Baym, Michael","first_name":"Michael","last_name":"Baym"},{"full_name":"Lieberman, Tami","first_name":"Tami","last_name":"Lieberman"},{"orcid":"0000-0003-0876-3187","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait"},{"last_name":"Clardy","full_name":"Clardy, Jon","first_name":"Jon"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"publication_status":"published","quality_controlled":"1","_id":"1290","issue":"11"},{"doi":"10.1109/ACC.2016.7526722","publisher":"IEEE","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","pubrep_id":"810","file":[{"file_size":539166,"file_name":"IST-2017-810-v1+1_root.pdf","date_created":"2018-12-12T10:16:17Z","date_updated":"2025-06-25T11:46:36Z","file_id":"5203","content_type":"application/pdf","relation":"main_file","creator":"system","checksum":"7219432b43defc62a0d45f48d4ce6a19","access_level":"open_access"}],"year":"2016","title":"Scale-invariant systems realize nonlinear differential operators","quality_controlled":"1","publication_status":"published","file_date_updated":"2025-06-25T11:46:36Z","_id":"1320","month":"07","status":"public","OA_place":"repository","project":[{"name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","grant_number":"291734","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"author":[{"last_name":"Lang","first_name":"Moritz","id":"29E0800A-F248-11E8-B48F-1D18A9856A87","full_name":"Lang, Moritz"},{"last_name":"Sontag","first_name":"Eduardo","full_name":"Sontag, Eduardo"}],"oa_version":"Submitted Version","scopus_import":"1","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","conference":{"end_date":"2016-07-08","location":"Boston, MA, USA","start_date":"2016-07-06","name":"ACC: American Control Conference"},"article_processing_charge":"No","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."}],"date_created":"2018-12-11T11:51:21Z","type":"conference","oa":1,"publist_id":"5950","citation":{"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.","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.","ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 7526722.","short":"M. Lang, E. Sontag, in:, IEEE, 2016."},"date_updated":"2025-06-25T11:46:37Z","OA_type":"green","has_accepted_license":"1","ec_funded":1,"day":"28","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["003","621"],"volume":"2016-July","language":[{"iso":"eng"}],"date_published":"2016-07-28T00:00:00Z"},{"publication_status":"published","quality_controlled":"1","file_date_updated":"2020-07-14T12:44:44Z","_id":"1332","month":"01","status":"public","author":[{"orcid":"0000-0003-0876-3187","last_name":"Chait","first_name":"Remy P","full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"last_name":"Palmer","first_name":"Adam","full_name":"Palmer, Adam"},{"last_name":"Yelin","full_name":"Yelin, Idan","first_name":"Idan"},{"last_name":"Kishony","full_name":"Kishony, Roy","first_name":"Roy"}],"doi":"10.1038/ncomms10333","publisher":"Nature Publishing Group","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"662","file":[{"relation":"main_file","content_type":"application/pdf","access_level":"open_access","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","creator":"system","file_size":1844107,"file_id":"5039","date_updated":"2020-07-14T12:44:44Z","date_created":"2018-12-12T10:13:52Z","file_name":"IST-2016-662-v1+1_ncomms10333.pdf"}],"year":"2016","isi":1,"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","publication":"Nature Communications","external_id":{"isi":["000369021700002"]},"has_accepted_license":"1","intvolume":" 7","day":"20","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"ddc":["570","579"],"language":[{"iso":"eng"}],"volume":7,"date_published":"2016-01-20T00:00:00Z","scopus_import":"1","oa_version":"Published Version","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","article_processing_charge":"No","date_created":"2018-12-11T11:51:25Z","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."}],"type":"journal_article","oa":1,"publist_id":"5936","citation":{"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.","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.","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.","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","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","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (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."},"tmp":{"short":"CC BY (4.0)","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode"},"date_updated":"2025-09-22T08:22:19Z"},{"scopus_import":"1","oa_version":"Preprint","abstract":[{"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.","lang":"eng"}],"date_created":"2018-12-11T11:52:18Z","type":"journal_article","citation":{"chicago":"De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.” Physical Biology. IOP Publishing, 2016. https://doi.org/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. 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, 2016.","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, 2016, doi:10.1088/1478-3975/13/1/016003.","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.","short":"D. De Martino, Physical Biology 13 (2016).","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"},"oa":1,"publist_id":"5702","arxiv":1,"date_updated":"2025-09-18T11:34:17Z","article_number":"016003","article_processing_charge":"No","intvolume":" 13","ec_funded":1,"day":"29","publication":"Physical Biology","external_id":{"isi":["000371585200003"],"arxiv":["1505.04613"]},"date_published":"2016-01-29T00:00:00Z","department":[{"_id":"GaTk"}],"volume":13,"language":[{"iso":"eng"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1088/1478-3975/13/1/016003","publisher":"IOP Publishing","year":"2016","corr_author":"1","isi":1,"title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","issue":"1","_id":"1485","quality_controlled":"1","publication_status":"published","project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"author":[{"first_name":"Daniele","full_name":"De Martino, Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","last_name":"De Martino","orcid":"0000-0002-5214-4706"}],"month":"01","main_file_link":[{"url":"http://arxiv.org/abs/1505.04613","open_access":"1"}],"status":"public"},{"author":[{"orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","first_name":"Matthew J","last_name":"Chalk"},{"last_name":"Marre","full_name":"Marre, Olivier","first_name":"Olivier"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"}],"month":"12","status":"public","main_file_link":[{"url":"https://arxiv.org/abs/1605.07332","open_access":"1"}],"related_material":{"link":[{"relation":"other","url":"https://papers.nips.cc/paper/6101-relevant-sparse-codes-with-variational-information-bottleneck"}]},"_id":"1082","quality_controlled":"1","publication_status":"published","title":"Relevant sparse codes with variational information bottleneck","year":"2016","page":"1965-1973","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","publisher":"Neural Information Processing Systems Foundation","date_published":"2016-12-01T00:00:00Z","department":[{"_id":"GaTk"}],"language":[{"iso":"eng"}],"volume":29,"intvolume":" 29","day":"01","alternative_title":["Advances in Neural Information Processing Systems"],"external_id":{"arxiv":["1605.07332"]},"date_created":"2018-12-11T11:50:03Z","abstract":[{"lang":"eng","text":"In many applications, it is desirable to extract only the relevant aspects of data. A principled way to do this is the information bottleneck (IB) method, where one seeks a code that maximises information about a relevance variable, Y, while constraining the information encoded about the original data, X. Unfortunately however, the IB method is computationally demanding when data are high-dimensional and/or non-gaussian. Here we propose an approximate variational scheme for maximising a lower bound on the IB objective, analogous to variational EM. Using this method, we derive an IB algorithm to recover features that are both relevant and sparse. Finally, we demonstrate how kernelised versions of the algorithm can be used to address a broad range of problems with non-linear relation between X and Y."}],"type":"conference","arxiv":1,"oa":1,"publist_id":"6298","citation":{"apa":"Chalk, M. J., Marre, O., & Tkačik, G. (2016). Relevant sparse codes with variational information bottleneck (Vol. 29, pp. 1965–1973). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain: Neural Information Processing Systems Foundation.","chicago":"Chalk, Matthew J, Olivier Marre, and Gašper Tkačik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems Foundation, 2016.","mla":"Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 1965–73.","ieee":"M. J. Chalk, O. Marre, and G. Tkačik, “Relevant sparse codes with variational information bottleneck,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spain, 2016, vol. 29, pp. 1965–1973.","short":"M.J. Chalk, O. Marre, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 1965–1973.","ista":"Chalk MJ, Marre O, Tkačik G. 2016. Relevant sparse codes with variational information bottleneck. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 1965–1973.","ama":"Chalk MJ, Marre O, Tkačik G. Relevant sparse codes with variational information bottleneck. In: Vol 29. Neural Information Processing Systems Foundation; 2016:1965-1973."},"date_updated":"2025-06-03T11:33:51Z","conference":{"location":"Barcelona, Spain","start_date":"2016-12-05","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"article_processing_charge":"No","oa_version":"Preprint","scopus_import":"1"},{"language":[{"iso":"eng"}],"volume":29,"department":[{"_id":"GaTk"}],"date_published":"2016-12-01T00:00:00Z","alternative_title":["Advances in Neural Information Processing Systems"],"day":"01","ec_funded":1,"intvolume":" 29","article_processing_charge":"No","conference":{"name":"NIPS: Neural Information Processing Systems","start_date":"2016-12-05","location":"Barcelona; Spain","end_date":"2016-12-10"},"acknowledgement":"We thank Jozsef Csicsvari for kindly sharing the CA1 data.\r\nThis work was supported by the People Programme (Marie Curie Actions) of the European Union’s Seventh Framework Programme(FP7/2007-2013) under REA grant agreement no. 291734.","date_updated":"2025-06-03T11:36:49Z","publist_id":"6265","citation":{"ista":"Savin C, Tkačik G. 2016. Estimating nonlinear neural response functions using GP priors and Kronecker methods. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 3610–3618.","short":"C. Savin, G. Tkačik, in:, Neural Information Processing Systems Foundation, 2016, pp. 3610–3618.","ama":"Savin C, Tkačik G. Estimating nonlinear neural response functions using GP priors and Kronecker methods. In: Vol 29. Neural Information Processing Systems Foundation; 2016:3610-3618.","chicago":"Savin, Cristina, and Gašper Tkačik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems Foundation, 2016.","apa":"Savin, C., & Tkačik, G. (2016). Estimating nonlinear neural response functions using GP priors and Kronecker methods (Vol. 29, pp. 3610–3618). Presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain: Neural Information Processing Systems Foundation.","mla":"Savin, Cristina, and Gašper Tkačik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 3610–18.","ieee":"C. Savin and G. Tkačik, “Estimating nonlinear neural response functions using GP priors and Kronecker methods,” presented at the NIPS: Neural Information Processing Systems, Barcelona; Spain, 2016, vol. 29, pp. 3610–3618."},"oa":1,"type":"conference","date_created":"2018-12-11T11:50:10Z","abstract":[{"lang":"eng","text":"Jointly characterizing neural responses in terms of several external variables promises novel insights into circuit function, but remains computationally prohibitive in practice. Here we use gaussian process (GP) priors and exploit recent advances in fast GP inference and learning based on Kronecker methods, to efficiently estimate multidimensional nonlinear tuning functions. Our estimator require considerably less data than traditional methods and further provides principled uncertainty estimates. We apply these tools to hippocampal recordings during open field exploration and use them to characterize the joint dependence of CA1 responses on the position of the animal and several other variables, including the animal\\'s speed, direction of motion, and network oscillations.Our results provide an unprecedentedly detailed quantification of the tuning of hippocampal neurons. The model\\'s generality suggests that our approach can be used to estimate neural response properties in other brain regions."}],"oa_version":"None","scopus_import":"1","status":"public","main_file_link":[{"open_access":"1","url":"http://papers.nips.cc/paper/6153-estimating-nonlinear-neural-response-functions-using-gp-priors-and-kronecker-methods"}],"month":"12","author":[{"full_name":"Savin, Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87","first_name":"Cristina","last_name":"Savin"},{"orcid":"0000-0002-6699-1455","first_name":"Gasper","full_name":"Tkacik, Gasper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik"}],"project":[{"grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme"}],"publication_status":"published","quality_controlled":"1","_id":"1105","page":"3610-3618","corr_author":"1","title":"Estimating nonlinear neural response functions using GP priors and Kronecker methods","year":"2016","publisher":"Neural Information Processing Systems Foundation","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87"}]