[{"volume":113,"date_created":"2018-12-11T11:50:55Z","year":"2016","day":"16","oa":1,"month":"02","author":[{"first_name":"Pierre","last_name":"Recouvreux","full_name":"Recouvreux, Pierre"},{"full_name":"Sokolowski, Thomas R","first_name":"Thomas R","last_name":"Sokolowski","orcid":"0000-0002-1287-3779","id":"3E999752-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Grammoustianou, Aristea","last_name":"Grammoustianou","first_name":"Aristea"},{"full_name":"Tenwolde, Pieter","first_name":"Pieter","last_name":"Tenwolde"},{"full_name":"Dogterom, Marileen","first_name":"Marileen","last_name":"Dogterom"}],"quality_controlled":"1","citation":{"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.","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","short":"P. Recouvreux, T.R. Sokolowski, A. Grammoustianou, P. Tenwolde, M. Dogterom, PNAS 113 (2016) 1811–1816.","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.","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.","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."},"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"}],"publication":"PNAS","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4763754/","open_access":"1"}],"date_published":"2016-02-16T00:00:00Z","external_id":{"isi":["000370220000046"]},"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”","publist_id":"6085","isi":1,"publisher":"National Academy of Sciences","title":"Chimera proteins with affinity for membranes and microtubule tips polarize in the membrane of fission yeast cells","department":[{"_id":"GaTk"}],"oa_version":"Submitted Version","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","page":"1811 - 1816","publication_status":"published","issue":"7","status":"public","date_updated":"2025-09-22T09:15:17Z","intvolume":" 113","scopus_import":"1","doi":"10.1073/pnas.1419248113","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"1244"},{"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.","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.","short":"G. Tkačik, W. Bialek, Annual Review of Condensed Matter Physics 7 (2016) 89–117.","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","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","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.","ista":"Tkačik G, Bialek W. 2016. Information processing in living systems. Annual Review of Condensed Matter Physics. 7, 89–117."},"abstract":[{"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.","lang":"eng"}],"publication":"Annual Review of Condensed Matter Physics","main_file_link":[{"url":"https://arxiv.org/abs/1412.8752","open_access":"1"}],"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.","date_published":"2016-03-10T00:00:00Z","external_id":{"arxiv":["1412.8752"],"isi":["000372188500005"]},"publist_id":"6080","publisher":"Annual Reviews","isi":1,"volume":7,"date_created":"2018-12-11T11:50:56Z","year":"2016","day":"10","oa":1,"month":"03","author":[{"full_name":"Tkacik, Gasper","first_name":"Gasper","last_name":"Tkacik","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Bialek, William","first_name":"William","last_name":"Bialek"}],"quality_controlled":"1","publication_status":"published","status":"public","date_updated":"2025-09-22T09:12:56Z","intvolume":" 7","doi":"10.1146/annurev-conmatphys-031214-014803","scopus_import":"1","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"1248","title":"Information processing in living systems","department":[{"_id":"GaTk"}],"oa_version":"Preprint","type":"journal_article","project":[{"grant_number":"P 25651-N26","name":"Sensitivity to higher-order statistics in natural scenes","call_identifier":"FWF","_id":"254D1A94-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"page":"89 - 117"},{"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.","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.","short":"D. De Martino, International Journal of Modern Physics C 27 (2016).","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","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.","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."},"corr_author":"1","abstract":[{"lang":"eng","text":"In this work, the Gardner problem of inferring interactions and fields for an Ising neural network from given patterns under a local stability hypothesis is addressed under a dual perspective. By means of duality arguments, an integer linear system is defined whose solution space is the dual of the Gardner space and whose solutions represent mutually unstable patterns. We propose and discuss Monte Carlo methods in order to find and remove unstable patterns and uniformly sample the space of interactions thereafter. We illustrate the problem on a set of real data and perform ensemble calculation that shows how the emergence of phase dominated by unstable patterns can be triggered in a nonlinear discontinuous way."}],"publication":"International Journal of Modern Physics C","main_file_link":[{"url":"https://arxiv.org/abs/1505.02963","open_access":"1"}],"external_id":{"arxiv":["1505.02963"],"isi":["000377674800010"]},"date_published":"2016-06-01T00:00:00Z","publist_id":"6065","isi":1,"publisher":"World Scientific Publishing","volume":27,"date_created":"2018-12-11T11:51:00Z","year":"2016","article_number":"1650067","day":"01","oa":1,"month":"06","author":[{"last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"}],"quality_controlled":"1","issue":"6","publication_status":"published","status":"public","date_updated":"2025-09-22T09:01:25Z","intvolume":" 27","scopus_import":"1","doi":"10.1142/S0129183116500674","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"1260","title":"The dual of the space of interactions in neural network models","department":[{"_id":"GaTk"}],"oa_version":"Preprint","type":"journal_article","article_type":"original","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1},{"ddc":["571"],"file":[{"content_type":"application/pdf","date_created":"2018-12-12T10:11:20Z","access_level":"open_access","date_updated":"2020-07-14T12:44:42Z","file_name":"IST-2016-700-v1+1_e13824-download.pdf","checksum":"dc52d967dc76174477bb258d84be2899","file_size":2819055,"relation":"main_file","file_id":"4874","creator":"system"}],"_id":"1266","article_processing_charge":"No","language":[{"iso":"eng"}],"date_updated":"2025-09-22T08:49:58Z","status":"public","issue":"2016JULY","publication_status":"published","doi":"10.7554/eLife.13824","scopus_import":"1","intvolume":" 5","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","pubrep_id":"700","department":[{"_id":"GaTk"}],"title":"Neural oscillations as a signature of efficient coding in the presence of synaptic delays","type":"journal_article","oa_version":"Published Version","publist_id":"6056","file_date_updated":"2020-07-14T12:44:42Z","external_id":{"isi":["000380855400001"]},"date_published":"2016-07-01T00:00:00Z","acknowledgement":"Boris Gutkin acknowledges funding by the Russian Academic Excellence Project '5-100’.","isi":1,"publisher":"eLife Sciences Publications","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","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."}],"corr_author":"1","citation":{"apa":"Chalk, M. J., Gutkin, B., & Denève, S. (2016). Neural oscillations as a signature of efficient coding in the presence of synaptic delays. ELife. eLife Sciences Publications. https://doi.org/10.7554/eLife.13824","chicago":"Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife. eLife Sciences Publications, 2016. https://doi.org/10.7554/eLife.13824.","short":"M.J. Chalk, B. Gutkin, S. Denève, ELife 5 (2016).","ieee":"M. J. Chalk, B. Gutkin, and S. Denève, “Neural oscillations as a signature of efficient coding in the presence of synaptic delays,” eLife, vol. 5, no. 2016JULY. eLife Sciences Publications, 2016.","ista":"Chalk MJ, Gutkin B, Denève S. 2016. Neural oscillations as a signature of efficient coding in the presence of synaptic delays. eLife. 5(2016JULY), e13824.","mla":"Chalk, Matthew J., et al. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.” ELife, vol. 5, no. 2016JULY, e13824, eLife Sciences Publications, 2016, doi:10.7554/eLife.13824.","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"},"publication":"eLife","oa":1,"quality_controlled":"1","author":[{"last_name":"Chalk","first_name":"Matthew J","id":"2BAAC544-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-7782-4436","full_name":"Chalk, Matthew J"},{"full_name":"Gutkin, Boris","last_name":"Gutkin","first_name":"Boris"},{"last_name":"Denève","first_name":"Sophie","full_name":"Denève, Sophie"}],"month":"07","volume":5,"article_number":"e13824","day":"01","year":"2016","date_created":"2018-12-11T11:51:02Z"},{"month":"09","related_material":{"record":[{"id":"9869","status":"public","relation":"research_data"},{"relation":"research_data","status":"public","id":"9870"},{"relation":"research_data","id":"9871","status":"public"}]},"author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"first_name":"Ulrich","last_name":"Gerland","full_name":"Gerland, Ulrich"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","last_name":"Tkacik","first_name":"Gasper","full_name":"Tkacik, Gasper"}],"quality_controlled":"1","oa":1,"date_created":"2018-12-11T11:51:03Z","year":"2016","article_number":"e0163628","day":"27","volume":11,"has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"Public Library of Science","isi":1,"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).","date_published":"2016-09-27T00:00:00Z","external_id":{"isi":["000384169900025"]},"file_date_updated":"2020-07-14T12:44:42Z","publist_id":"6050","publication":"PLoS One","citation":{"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.","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","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.","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.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, PLoS One 11 (2016).","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","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."},"corr_author":"1","abstract":[{"lang":"eng","text":"A crucial step in the early development of multicellular organisms involves the establishment of spatial patterns of gene expression which later direct proliferating cells to take on different cell fates. These patterns enable the cells to infer their global position within a tissue or an organism by reading out local gene expression levels. The patterning system is thus said to encode positional information, a concept that was formalized recently in the framework of information theory. Here we introduce a toy model of patterning in one spatial dimension, which can be seen as an extension of Wolpert's paradigmatic "French Flag" model, to patterning by several interacting, spatially coupled genes subject to intrinsic and extrinsic noise. Our model, a variant of an Ising spin system, allows us to systematically explore expression patterns that optimally encode positional information. We find that optimal patterning systems use positional cues, as in the French Flag model, together with gene-gene interactions to generate combinatorial codes for position which we call "Counter" patterns. Counter patterns can also be stabilized against noise and variations in system size or morphogen dosage by longer-range spatial interactions of the type invoked in the Turing model. The simple setup proposed here qualitatively captures many of the experimentally observed properties of biological patterning systems and allows them to be studied in a single, theoretically consistent framework."}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","project":[{"call_identifier":"FWF","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","_id":"254E9036-B435-11E9-9278-68D0E5697425"}],"oa_version":"Published Version","type":"journal_article","title":"Beyond the French flag model: Exploiting spatial and gene regulatory interactions for positional information","department":[{"_id":"GaTk"}],"pubrep_id":"696","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"1270","file":[{"creator":"system","file_id":"4837","relation":"main_file","file_size":4950415,"date_updated":"2020-07-14T12:44:42Z","access_level":"open_access","checksum":"3d0d55d373096a033bd9cf79288c8586","file_name":"IST-2016-696-v1+1_journal.pone.0163628.PDF","date_created":"2018-12-12T10:10:47Z","content_type":"application/pdf"}],"ddc":["571"],"intvolume":" 11","scopus_import":"1","doi":"10.1371/journal.pone.0163628","issue":"9","publication_status":"published","status":"public","date_updated":"2025-09-22T08:46:15Z"},{"day":"01","year":"2016","date_created":"2018-12-11T11:51:10Z","volume":12,"quality_controlled":"1","author":[{"first_name":"Laura","last_name":"Stone","full_name":"Stone, Laura"},{"full_name":"Baym, Michael","last_name":"Baym","first_name":"Michael"},{"full_name":"Lieberman, Tami","last_name":"Lieberman","first_name":"Tami"},{"full_name":"Chait, Remy P","first_name":"Remy P","last_name":"Chait","orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Clardy, Jon","first_name":"Jon","last_name":"Clardy"},{"full_name":"Kishony, Roy","first_name":"Roy","last_name":"Kishony"}],"month":"11","oa":1,"main_file_link":[{"open_access":"1","url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5069154/"}],"publication":"Nature Chemical Biology","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"}],"citation":{"apa":"Stone, L., Baym, M., Lieberman, T., Chait, R. P., Clardy, J., & Kishony, R. (2016). Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. Nature Publishing Group. https://doi.org/10.1038/nchembio.2176","chicago":"Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology. Nature Publishing Group, 2016. https://doi.org/10.1038/nchembio.2176.","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.","ista":"Stone L, Baym M, Lieberman T, Chait RP, Clardy J, Kishony R. 2016. Compounds that select against the tetracycline-resistance efflux pump. Nature Chemical Biology. 12(11), 902–904.","mla":"Stone, Laura, et al. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.” Nature Chemical Biology, vol. 12, no. 11, Nature Publishing Group, 2016, pp. 902–04, doi:10.1038/nchembio.2176.","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"},"publisher":"Nature Publishing Group","isi":1,"publist_id":"6026","external_id":{"isi":["000386798800008"]},"date_published":"2016-11-01T00:00:00Z","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","type":"journal_article","oa_version":"Preprint","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Compounds that select against the tetracycline-resistance efflux pump","page":"902 - 904","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","doi":"10.1038/nchembio.2176","scopus_import":"1","intvolume":" 12","date_updated":"2025-09-22T08:30:48Z","status":"public","issue":"11","publication_status":"published","_id":"1290","article_processing_charge":"No","language":[{"iso":"eng"}]},{"language":[{"iso":"eng"}],"article_processing_charge":"No","OA_type":"green","ddc":["003","621"],"_id":"1320","file":[{"date_created":"2018-12-12T10:16:17Z","content_type":"application/pdf","checksum":"7219432b43defc62a0d45f48d4ce6a19","file_name":"IST-2017-810-v1+1_root.pdf","date_updated":"2025-06-25T11:46:36Z","access_level":"open_access","file_size":539166,"relation":"main_file","creator":"system","file_id":"5203"}],"status":"public","publication_status":"published","conference":{"end_date":"2016-07-08","name":"ACC: American Control Conference","start_date":"2016-07-06","location":"Boston, MA, USA"},"date_updated":"2025-06-25T11:46:37Z","scopus_import":"1","doi":"10.1109/ACC.2016.7526722","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","title":"Scale-invariant systems realize nonlinear differential operators","pubrep_id":"810","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"type":"conference","oa_version":"Submitted Version","file_date_updated":"2025-06-25T11:46:36Z","date_published":"2016-07-28T00:00:00Z","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.","OA_place":"repository","publist_id":"5950","has_accepted_license":"1","publisher":"IEEE","citation":{"ama":"Lang M, Sontag E. Scale-invariant systems realize nonlinear differential operators. In: Vol 2016-July. IEEE; 2016. doi:10.1109/ACC.2016.7526722","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.","ista":"Lang M, Sontag E. 2016. Scale-invariant systems realize nonlinear differential operators. ACC: American Control Conference vol. 2016–July, 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.","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.","short":"M. Lang, E. Sontag, in:, IEEE, 2016.","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"},"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."}],"oa":1,"month":"07","quality_controlled":"1","author":[{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz"},{"full_name":"Sontag, Eduardo","last_name":"Sontag","first_name":"Eduardo"}],"volume":"2016-July","date_created":"2018-12-11T11:51:21Z","day":"28","article_number":"7526722","year":"2016"},{"title":"Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"pubrep_id":"662","oa_version":"Published Version","type":"journal_article","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","publication_status":"published","status":"public","date_updated":"2025-09-22T08:22:19Z","intvolume":" 7","scopus_import":"1","doi":"10.1038/ncomms10333","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"1332","file":[{"date_created":"2018-12-12T10:13:52Z","content_type":"application/pdf","checksum":"ef147bcbb8bd37e9079cf3ce06f5815d","file_name":"IST-2016-662-v1+1_ncomms10333.pdf","date_updated":"2020-07-14T12:44:44Z","access_level":"open_access","file_size":1844107,"relation":"main_file","creator":"system","file_id":"5039"}],"ddc":["570","579"],"volume":7,"date_created":"2018-12-11T11:51:25Z","year":"2016","article_number":"10333","day":"20","oa":1,"month":"01","author":[{"orcid":"0000-0003-0876-3187","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","first_name":"Remy P","last_name":"Chait","full_name":"Chait, Remy P"},{"first_name":"Adam","last_name":"Palmer","full_name":"Palmer, Adam"},{"first_name":"Idan","last_name":"Yelin","full_name":"Yelin, Idan"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"quality_controlled":"1","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.","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","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.","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.","apa":"Chait, R. P., Palmer, A., Yelin, I., & Kishony, R. (2016). Pervasive selection for and against antibiotic resistance in inhomogeneous multistress environments. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms10333","chicago":"Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms10333.","short":"R.P. Chait, A. Palmer, I. Yelin, R. Kishony, Nature Communications 7 (2016)."},"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."}],"publication":"Nature Communications","external_id":{"isi":["000369021700002"]},"date_published":"2016-01-20T00:00:00Z","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.","file_date_updated":"2020-07-14T12:44:44Z","publist_id":"5936","has_accepted_license":"1","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"Nature Publishing Group","isi":1},{"isi":1,"publisher":"American Association for the Advancement of Science","publist_id":"5911","date_published":"2016-09-09T00:00:00Z","external_id":{"isi":["000382626800052"]},"publication":"Science","main_file_link":[{"url":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5534434/","open_access":"1"}],"abstract":[{"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.","lang":"eng"}],"citation":{"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.","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.","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.","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","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."},"author":[{"full_name":"Baym, Michael","first_name":"Michael","last_name":"Baym"},{"full_name":"Lieberman, Tami","last_name":"Lieberman","first_name":"Tami"},{"first_name":"Eric","last_name":"Kelsic","full_name":"Kelsic, Eric"},{"full_name":"Chait, Remy P","id":"3464AE84-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0003-0876-3187","first_name":"Remy P","last_name":"Chait"},{"last_name":"Gross","first_name":"Rotem","full_name":"Gross, Rotem"},{"last_name":"Yelin","first_name":"Idan","full_name":"Yelin, Idan"},{"full_name":"Kishony, Roy","last_name":"Kishony","first_name":"Roy"}],"quality_controlled":"1","month":"09","oa":1,"year":"2016","day":"09","date_created":"2018-12-11T11:51:29Z","volume":353,"_id":"1342","article_processing_charge":"No","language":[{"iso":"eng"}],"doi":"10.1126/science.aag0822","scopus_import":"1","intvolume":" 353","date_updated":"2025-09-22T08:17:11Z","issue":"6304","publication_status":"published","status":"public","page":"1147 - 1151","user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","oa_version":"Preprint","type":"journal_article","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"title":"Spatiotemporal microbial evolution on antibiotic landscapes"},{"quality_controlled":"1","author":[{"first_name":"Tamar","last_name":"Friedlander","id":"36A5845C-F248-11E8-B48F-1D18A9856A87","full_name":"Friedlander, Tamar"},{"full_name":"Prizak, Roshan","first_name":"Roshan","last_name":"Prizak","id":"4456104E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Guet, Calin C","first_name":"Calin C","last_name":"Guet","id":"47F8433E-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0001-6220-2052"},{"full_name":"Barton, Nicholas H","first_name":"Nicholas H","last_name":"Barton","id":"4880FE40-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-8548-5240"},{"id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"}],"related_material":{"record":[{"relation":"dissertation_contains","id":"6071","status":"public"}]},"month":"08","oa":1,"day":"04","article_number":"12307","year":"2016","date_created":"2018-12-11T11:51:34Z","volume":7,"publisher":"Nature Publishing Group","isi":1,"tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"has_accepted_license":"1","publist_id":"5887","file_date_updated":"2020-07-14T12:44:46Z","date_published":"2016-08-04T00:00:00Z","external_id":{"isi":["000380858400001"]},"publication":"Nature Communications","abstract":[{"lang":"eng","text":"Gene regulation relies on the specificity of transcription factor (TF)–DNA interactions. Limited specificity may lead to crosstalk: a regulatory state in which a gene is either incorrectly activated due to noncognate TF–DNA interactions or remains erroneously inactive. As each TF can have numerous interactions with noncognate cis-regulatory elements, crosstalk is inherently a global problem, yet has previously not been studied as such. We construct a theoretical framework to analyse the effects of global crosstalk on gene regulation. We find that crosstalk presents a significant challenge for organisms with low-specificity TFs, such as metazoans. Crosstalk is not easily mitigated by known regulatory schemes acting at equilibrium, including variants of cooperativity and combinatorial regulation. Our results suggest that crosstalk imposes a previously unexplored global constraint on the functioning and evolution of regulatory networks, which is qualitatively distinct from the known constraints that act at the level of individual gene regulatory elements."}],"corr_author":"1","citation":{"ama":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 2016;7. doi:10.1038/ncomms12307","mla":"Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.","ista":"Friedlander T, Prizak R, Guet CC, Barton NH, Tkačik G. 2016. Intrinsic limits to gene regulation by global crosstalk. Nature Communications. 7, 12307.","ieee":"T. Friedlander, R. Prizak, C. C. Guet, N. H. Barton, and G. Tkačik, “Intrinsic limits to gene regulation by global crosstalk,” Nature Communications, vol. 7. Nature Publishing Group, 2016.","chicago":"Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gašper Tkačik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.” Nature Communications. Nature Publishing Group, 2016. https://doi.org/10.1038/ncomms12307.","short":"T. Friedlander, R. Prizak, C.C. Guet, N.H. Barton, G. Tkačik, Nature Communications 7 (2016).","apa":"Friedlander, T., Prizak, R., Guet, C. C., Barton, N. H., & Tkačik, G. (2016). Intrinsic limits to gene regulation by global crosstalk. Nature Communications. Nature Publishing Group. https://doi.org/10.1038/ncomms12307"},"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","ec_funded":1,"project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"},{"_id":"25B07788-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152"},{"_id":"254E9036-B435-11E9-9278-68D0E5697425","grant_number":"P28844-B27","name":"Biophysics of information processing in gene regulation","call_identifier":"FWF"}],"type":"journal_article","oa_version":"Published Version","pubrep_id":"627","department":[{"_id":"GaTk"},{"_id":"NiBa"},{"_id":"CaGu"}],"title":"Intrinsic limits to gene regulation by global crosstalk","ddc":["576"],"file":[{"access_level":"open_access","date_updated":"2020-07-14T12:44:46Z","file_name":"IST-2016-627-v1+1_ncomms12307.pdf","checksum":"fe3f3a1526d180b29fe691ab11435b78","content_type":"application/pdf","date_created":"2018-12-12T10:12:01Z","creator":"system","file_id":"4919","relation":"main_file","file_size":861805},{"creator":"system","file_id":"4920","file_size":1084703,"relation":"main_file","checksum":"164864a1a675f3ad80e9917c27aba07f","file_name":"IST-2016-627-v1+2_ncomms12307-s1.pdf","date_updated":"2020-07-14T12:44:46Z","access_level":"open_access","date_created":"2018-12-12T10:12:02Z","content_type":"application/pdf"}],"_id":"1358","language":[{"iso":"eng"}],"article_processing_charge":"No","scopus_import":"1","doi":"10.1038/ncomms12307","intvolume":" 7","date_updated":"2026-04-08T13:54:24Z","status":"public","publication_status":"published"},{"volume":13,"date_created":"2018-12-11T11:51:46Z","day":"27","article_number":"036005","year":"2016","oa":1,"month":"05","quality_controlled":"1","author":[{"full_name":"De Martino, Daniele","orcid":"0000-0002-5214-4706","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","first_name":"Daniele","last_name":"De Martino"},{"full_name":"Capuani, Fabrizio","last_name":"Capuani","first_name":"Fabrizio"},{"first_name":"Andrea","last_name":"De Martino","full_name":"De Martino, Andrea"}],"citation":{"ama":"De Martino D, Capuani F, De Martino A. Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli. Physical Biology. 2016;13(3). doi:10.1088/1478-3975/13/3/036005","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.","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.","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.","short":"D. De Martino, F. Capuani, A. De Martino, Physical Biology 13 (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"},"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."}],"main_file_link":[{"url":"https://arxiv.org/abs/1601.03243","open_access":"1"}],"publication":"Physical Biology","external_id":{"arxiv":["1601.03243"],"isi":["000380148200014"]},"date_published":"2016-05-27T00:00:00Z","acknowledgement":"The research leading to these results has received funding from the from the Marie\r\nCurie Action ITN NETADIS, grant agreement no. 290038.","publist_id":"5815","publisher":"IOP Publishing","isi":1,"title":"Growth against entropy in bacterial metabolism: the phenotypic trade-off behind empirical growth rate distributions in E. coli","department":[{"_id":"GaTk"}],"type":"journal_article","oa_version":"Preprint","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7"}],"ec_funded":1,"arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","status":"public","publication_status":"published","issue":"3","date_updated":"2025-09-18T14:31:33Z","intvolume":" 13","scopus_import":"1","doi":"10.1088/1478-3975/13/3/036005","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"1394"},{"date_updated":"2025-09-18T14:22:05Z","status":"public","issue":"4","publication_status":"published","doi":"10.1534/genetics.115.184127","scopus_import":"1","intvolume":" 202","_id":"1420","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"},{"_id":"NiBa"}],"title":"A general approximation for the dynamics of quantitative traits","type":"journal_article","oa_version":"Preprint","ec_funded":1,"project":[{"name":"Limits to selection in biology and in evolutionary computation","grant_number":"250152","call_identifier":"FP7","_id":"25B07788-B435-11E9-9278-68D0E5697425"},{"name":"Information processing and computation in fish groups","grant_number":"RGP0065/2012","_id":"255008E4-B435-11E9-9278-68D0E5697425"}],"page":"1523 - 1548","arxiv":1,"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","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"}],"corr_author":"1","citation":{"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.","short":"K. Bodova, G. Tkačik, N.H. Barton, Genetics 202 (2016) 1523–1548.","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","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.","ista":"Bodova K, Tkačik G, Barton NH. 2016. A general approximation for the dynamics of quantitative traits. Genetics. 202(4), 1523–1548."},"main_file_link":[{"url":"http://arxiv.org/abs/1510.08344","open_access":"1"}],"publication":"Genetics","publist_id":"5787","date_published":"2016-04-06T00:00:00Z","external_id":{"arxiv":["1510.08344"],"isi":["000373959100022"]},"isi":1,"publisher":"Genetics Society of America","volume":202,"day":"06","year":"2016","date_created":"2018-12-11T11:51:55Z","oa":1,"quality_controlled":"1","author":[{"last_name":"Bod'ová","first_name":"Katarína","id":"2BA24EA0-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-7214-0171","full_name":"Bod'ová, Katarína"},{"orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","first_name":"Gasper","last_name":"Tkacik","full_name":"Tkacik, Gasper"},{"full_name":"Barton, Nicholas H","last_name":"Barton","first_name":"Nicholas H","orcid":"0000-0002-8548-5240","id":"4880FE40-F248-11E8-B48F-1D18A9856A87"}],"month":"04"},{"date_updated":"2025-09-18T11:34:17Z","issue":"1","publication_status":"published","status":"public","doi":"10.1088/1478-3975/13/1/016003","scopus_import":"1","intvolume":" 13","_id":"1485","article_processing_charge":"No","language":[{"iso":"eng"}],"department":[{"_id":"GaTk"}],"title":"Genome-scale estimate of the metabolic turnover of E. Coli from the energy balance analysis","oa_version":"Preprint","type":"journal_article","ec_funded":1,"project":[{"name":"International IST Postdoc Fellowship Programme","grant_number":"291734","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"user_id":"317138e5-6ab7-11ef-aa6d-ffef3953e345","arxiv":1,"corr_author":"1","abstract":[{"lang":"eng","text":"In this article the notion of metabolic turnover is revisited in the light of recent results of out-of-equilibrium thermodynamics. By means of Monte Carlo methods we perform an exact sampling of the enzymatic fluxes in a genome scale metabolic network of E. Coli in stationary growth conditions from which we infer the metabolites turnover times. However the latter are inferred from net fluxes, and we argue that this approximation is not valid for enzymes working nearby thermodynamic equilibrium. We recalculate turnover times from total fluxes by performing an energy balance analysis of the network and recurring to the fluctuation theorem. We find in many cases values one of order of magnitude lower, implying a faster picture of intermediate metabolism."}],"citation":{"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.","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","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.","short":"D. De Martino, Physical Biology 13 (2016).","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."},"publication":"Physical Biology","main_file_link":[{"open_access":"1","url":"http://arxiv.org/abs/1505.04613"}],"publist_id":"5702","date_published":"2016-01-29T00:00:00Z","external_id":{"arxiv":["1505.04613"],"isi":["000371585200003"]},"isi":1,"publisher":"IOP Publishing","volume":13,"year":"2016","article_number":"016003","day":"29","date_created":"2018-12-11T11:52:18Z","oa":1,"author":[{"last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706","full_name":"De Martino, Daniele"}],"quality_controlled":"1","month":"01"},{"publication_identifier":{"isbn":["9780262339360"]},"date_published":"2016-09-01T00:00:00Z","file_date_updated":"2020-07-14T12:48:09Z","tmp":{"short":"CC BY (4.0)","legal_code_url":"https://creativecommons.org/licenses/by/4.0/legalcode","name":"Creative Commons Attribution 4.0 International Public License (CC-BY 4.0)","image":"/images/cc_by.png"},"publisher":"MIT Press","has_accepted_license":"1","corr_author":"1","abstract":[{"lang":"eng","text":"With the accelerated development of robot technologies, optimal control becomes one of the central themes of research. In traditional approaches, the controller, by its internal functionality, finds appropriate actions on the basis of the history of sensor values, guided by the goals, intentions, objectives, learning schemes, and so forth. The idea is that the controller controls the world---the body plus its environment---as reliably as possible. This paper focuses on new lines of self-organization for developmental robotics. We apply the recently developed differential extrinsic synaptic plasticity to a muscle-tendon driven arm-shoulder system from the Myorobotics toolkit. In the experiments, we observe a vast variety of self-organized behavior patterns: when left alone, the arm realizes pseudo-random sequences of different poses. By applying physical forces, the system can be entrained into definite motion patterns like wiping a table. Most interestingly, after attaching an object, the controller gets in a functional resonance with the object's internal dynamics, starting to shake spontaneously bottles half-filled with water or sensitively driving an attached pendulum into a circular mode. When attached to the crank of a wheel the neural system independently discovers how to rotate it. In this way, the robot discovers affordances of objects its body is interacting with."}],"citation":{"apa":"Martius, G. S., Hostettler, R., Knoll, A., & Der, R. (2016). Self-organized control of an tendon driven arm by differential extrinsic plasticity. In 15th International Conference on the Synthesis and Simulation of Living Systems (Vol. 28, pp. 142–143). Cancun, Mexico: MIT Press. https://doi.org/10.7551/978-0-262-33936-0-ch029","short":"G.S. Martius, R. Hostettler, A. Knoll, R. Der, in:, 15th International Conference on the Synthesis and Simulation of Living Systems, MIT Press, 2016, pp. 142–143.","chicago":"Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” In 15th International Conference on the Synthesis and Simulation of Living Systems, 28:142–43. MIT Press, 2016. https://doi.org/10.7551/978-0-262-33936-0-ch029.","ieee":"G. S. Martius, R. Hostettler, A. Knoll, and R. Der, “Self-organized control of an tendon driven arm by differential extrinsic plasticity,” in 15th International Conference on the Synthesis and Simulation of Living Systems, Cancun, Mexico, 2016, vol. 28, pp. 142–143.","ista":"Martius GS, Hostettler R, Knoll A, Der R. 2016. Self-organized control of an tendon driven arm by differential extrinsic plasticity. 15th International Conference on the Synthesis and Simulation of Living Systems. ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems vol. 28, 142–143.","mla":"Martius, Georg S., et al. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.” 15th International Conference on the Synthesis and Simulation of Living Systems, vol. 28, MIT Press, 2016, pp. 142–43, doi:10.7551/978-0-262-33936-0-ch029.","ama":"Martius GS, Hostettler R, Knoll A, Der R. Self-organized control of an tendon driven arm by differential extrinsic plasticity. In: 15th International Conference on the Synthesis and Simulation of Living Systems. Vol 28. MIT Press; 2016:142-143. doi:10.7551/978-0-262-33936-0-ch029"},"publication":"15th International Conference on the Synthesis and Simulation of Living Systems","oa":1,"author":[{"id":"3A276B68-F248-11E8-B48F-1D18A9856A87","first_name":"Georg S","last_name":"Martius","full_name":"Martius, Georg S"},{"last_name":"Hostettler","first_name":"Rafael","full_name":"Hostettler, Rafael"},{"first_name":"Alois","last_name":"Knoll","full_name":"Knoll, Alois"},{"full_name":"Der, Ralf","first_name":"Ralf","last_name":"Der"}],"quality_controlled":"1","month":"09","volume":28,"year":"2016","day":"01","date_created":"2020-07-05T22:00:47Z","file":[{"creator":"cziletti","file_id":"8096","file_size":678670,"relation":"main_file","date_updated":"2020-07-14T12:48:09Z","access_level":"open_access","checksum":"cff63e7a4b8ac466ba51a9c84153a940","file_name":"2016_ProcALIFE_Martius.pdf","date_created":"2020-07-06T12:59:09Z","content_type":"application/pdf"}],"_id":"8094","ddc":["610"],"language":[{"iso":"eng"}],"article_processing_charge":"No","date_updated":"2025-07-10T11:55:05Z","conference":{"location":"Cancun, Mexico","start_date":"2016-07-04","name":"ALIFE 2016: Conference on the Synthesis and Simulation of Living Systems","end_date":"2016-07-08"},"publication_status":"published","status":"public","scopus_import":"1","doi":"10.7551/978-0-262-33936-0-ch029","intvolume":" 28","ec_funded":1,"project":[{"call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"page":"142-143","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","department":[{"_id":"ChLa"},{"_id":"GaTk"}],"title":"Self-organized control of an tendon driven arm by differential extrinsic plasticity","oa_version":"Published Version","type":"conference"},{"alternative_title":["Advances in Neural Information Processing Systems"],"date_created":"2018-12-11T11:49:21Z","day":"01","year":"2016","volume":29,"month":"01","quality_controlled":"1","author":[{"full_name":"Monk, Travis","last_name":"Monk","first_name":"Travis"},{"full_name":"Savin, Cristina","last_name":"Savin","first_name":"Cristina","id":"3933349E-F248-11E8-B48F-1D18A9856A87"},{"full_name":"Lücke, Jörg","first_name":"Jörg","last_name":"Lücke"}],"oa":1,"main_file_link":[{"url":"https://papers.nips.cc/paper/6582-neurons-equipped-with-intrinsic-plasticity-learn-stimulus-intensity-statistics","open_access":"1"}],"citation":{"short":"T. Monk, C. Savin, J. Lücke, in:, Neural Information Processing Systems Foundation, 2016, pp. 4285–4293.","chicago":"Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems Foundation, 2016.","apa":"Monk, T., Savin, C., & Lücke, J. (2016). Neurons equipped with intrinsic plasticity learn stimulus intensity statistics (Vol. 29, pp. 4285–4293). Presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine: Neural Information Processing Systems Foundation.","ieee":"T. Monk, C. Savin, and J. Lücke, “Neurons equipped with intrinsic plasticity learn stimulus intensity statistics,” presented at the NIPS: Neural Information Processing Systems, Barcelona, Spaine, 2016, vol. 29, pp. 4285–4293.","ista":"Monk T, Savin C, Lücke J. 2016. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. NIPS: Neural Information Processing Systems, Advances in Neural Information Processing Systems, vol. 29, 4285–4293.","ama":"Monk T, Savin C, Lücke J. Neurons equipped with intrinsic plasticity learn stimulus intensity statistics. In: Vol 29. Neural Information Processing Systems Foundation; 2016:4285-4293.","mla":"Monk, Travis, et al. Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics. Vol. 29, Neural Information Processing Systems Foundation, 2016, pp. 4285–93."},"abstract":[{"text":"Experience constantly shapes neural circuits through a variety of plasticity mechanisms. While the functional roles of some plasticity mechanisms are well-understood, it remains unclear how changes in neural excitability contribute to learning. Here, we develop a normative interpretation of intrinsic plasticity (IP) as a key component of unsupervised learning. We introduce a novel generative mixture model that accounts for the class-specific statistics of stimulus intensities, and we derive a neural circuit that learns the input classes and their intensities. We will analytically show that inference and learning for our generative model can be achieved by a neural circuit with intensity-sensitive neurons equipped with a specific form of IP. Numerical experiments verify our analytical derivations and show robust behavior for artificial and natural stimuli. Our results link IP to non-trivial input statistics, in particular the statistics of stimulus intensities for classes to which a neuron is sensitive. More generally, our work paves the way toward new classification algorithms that are robust to intensity variations.","lang":"eng"}],"publisher":"Neural Information Processing Systems Foundation","acknowledgement":"DFG Cluster of Excellence EXC 1077/1 (Hearing4all) and LU 1196/5-1 (JL and TM), People Programme (Marie Curie Actions) FP7/2007-2013 grant agreement no. 291734 (CS)","date_published":"2016-01-01T00:00:00Z","publist_id":"6469","type":"conference","oa_version":"None","title":"Neurons equipped with intrinsic plasticity learn stimulus intensity statistics","department":[{"_id":"GaTk"}],"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","page":"4285 - 4293","project":[{"grant_number":"291734","name":"International IST Postdoc Fellowship Programme","call_identifier":"FP7","_id":"25681D80-B435-11E9-9278-68D0E5697425"}],"ec_funded":1,"intvolume":" 29","scopus_import":"1","status":"public","publication_status":"published","conference":{"start_date":"2016-12-05","location":"Barcelona, Spaine","end_date":"2016-12-10","name":"NIPS: Neural Information Processing Systems"},"date_updated":"2025-06-03T11:18:32Z","language":[{"iso":"eng"}],"article_processing_charge":"No","_id":"948"},{"date_published":"2016-09-27T00:00:00Z","publisher":"Public Library of Science","_id":"9869","article_processing_charge":"No","abstract":[{"lang":"eng","text":"A lower bound on the error of a positional estimator with limited positional information is derived."}],"date_updated":"2025-09-22T08:46:14Z","citation":{"ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Error bound on an estimator of position, Public Library of Science, 10.1371/journal.pone.0163628.s001.","ama":"Hillenbrand P, Gerland U, Tkačik G. Error bound on an estimator of position. 2016. doi:10.1371/journal.pone.0163628.s001","mla":"Hillenbrand, Patrick, et al. Error Bound on an Estimator of Position. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s001.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Error Bound on an Estimator of Position.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s001.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Error bound on an estimator of position. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s001","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Error bound on an estimator of position.” Public Library of Science, 2016."},"status":"public","doi":"10.1371/journal.pone.0163628.s001","author":[{"last_name":"Hillenbrand","first_name":"Patrick","full_name":"Hillenbrand, Patrick"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"full_name":"Tkačik, Gašper","last_name":"Tkačik","first_name":"Gašper","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"related_material":{"record":[{"status":"public","id":"1270","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","department":[{"_id":"GaTk"}],"title":"Error bound on an estimator of position","day":"27","year":"2016","type":"research_data_reference","date_created":"2021-08-10T08:53:48Z","oa_version":"Published Version"},{"department":[{"_id":"GaTk"}],"title":"Computation of positional information in an Ising model","year":"2016","day":"27","oa_version":"Published Version","date_created":"2021-08-10T09:23:45Z","type":"research_data_reference","author":[{"full_name":"Hillenbrand, Patrick","first_name":"Patrick","last_name":"Hillenbrand"},{"full_name":"Gerland, Ulrich","last_name":"Gerland","first_name":"Ulrich"},{"full_name":"Tkačik, Gašper","first_name":"Gašper","last_name":"Tkačik","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-6699-1455"}],"related_material":{"record":[{"id":"1270","status":"public","relation":"used_in_publication"}]},"user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","month":"09","date_updated":"2025-09-22T08:46:14Z","abstract":[{"lang":"eng","text":"The effect of noise in the input field on an Ising model is approximated. Furthermore, methods to compute positional information in an Ising model by transfer matrices and Monte Carlo sampling are outlined."}],"status":"public","citation":{"mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in an Ising Model. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s002.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in an Ising model. 2016. doi:10.1371/journal.pone.0163628.s002","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in an Ising model, Public Library of Science, 10.1371/journal.pone.0163628.s002.","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in an Ising model.” Public Library of Science, 2016.","apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in an Ising model. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s002","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in an Ising Model.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s002.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016)."},"doi":"10.1371/journal.pone.0163628.s002","date_published":"2016-09-27T00:00:00Z","_id":"9870","publisher":"Public Library of Science","article_processing_charge":"No"},{"article_processing_charge":"No","publisher":"Public Library of Science","_id":"9871","doi":"10.1371/journal.pone.0163628.s003","status":"public","citation":{"apa":"Hillenbrand, P., Gerland, U., & Tkačik, G. (2016). Computation of positional information in a discrete morphogen field. Public Library of Science. https://doi.org/10.1371/journal.pone.0163628.s003","chicago":"Hillenbrand, Patrick, Ulrich Gerland, and Gašper Tkačik. “Computation of Positional Information in a Discrete Morphogen Field.” Public Library of Science, 2016. https://doi.org/10.1371/journal.pone.0163628.s003.","short":"P. Hillenbrand, U. Gerland, G. Tkačik, (2016).","ieee":"P. Hillenbrand, U. Gerland, and G. Tkačik, “Computation of positional information in a discrete morphogen field.” Public Library of Science, 2016.","ista":"Hillenbrand P, Gerland U, Tkačik G. 2016. Computation of positional information in a discrete morphogen field, Public Library of Science, 10.1371/journal.pone.0163628.s003.","mla":"Hillenbrand, Patrick, et al. Computation of Positional Information in a Discrete Morphogen Field. Public Library of Science, 2016, doi:10.1371/journal.pone.0163628.s003.","ama":"Hillenbrand P, Gerland U, Tkačik G. Computation of positional information in a discrete morphogen field. 2016. doi:10.1371/journal.pone.0163628.s003"},"abstract":[{"text":"The positional information in a discrete morphogen field with Gaussian noise is computed.","lang":"eng"}],"date_updated":"2025-09-22T08:46:14Z","month":"09","user_id":"6785fbc1-c503-11eb-8a32-93094b40e1cf","related_material":{"record":[{"relation":"used_in_publication","status":"public","id":"1270"}]},"author":[{"full_name":"Hillenbrand, Patrick","last_name":"Hillenbrand","first_name":"Patrick"},{"full_name":"Gerland, Ulrich","first_name":"Ulrich","last_name":"Gerland"},{"last_name":"Tkačik","first_name":"Gašper","orcid":"0000-0002-6699-1455","id":"3D494DCA-F248-11E8-B48F-1D18A9856A87","full_name":"Tkačik, Gašper"}],"type":"research_data_reference","oa_version":"Published Version","date_created":"2021-08-10T09:27:35Z","day":"27","year":"2016","title":"Computation of positional information in a discrete morphogen field","department":[{"_id":"GaTk"}]},{"article_type":"original","oa_version":"Submitted Version","type":"journal_article","department":[{"_id":"CaGu"},{"_id":"GaTk"}],"pubrep_id":"811","title":"Modular parameter identification of biomolecular networks","page":"B988 - B1008","user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","doi":"10.1137/15M103306X","scopus_import":"1","intvolume":" 38","date_updated":"2026-07-06T14:00:20Z","issue":"6","publication_status":"published","status":"public","file":[{"file_size":871964,"relation":"main_file","creator":"system","file_id":"5095","content_type":"application/pdf","date_created":"2018-12-12T10:14:41Z","file_name":"IST-2017-811-v1+1_modular_parameter_identification.pdf","checksum":"781bc3ffd30b2dd65b7727c5a285fc78","access_level":"open_access","date_updated":"2025-06-25T11:26:45Z"}],"_id":"1170","ddc":["003","518","570","621"],"language":[{"iso":"eng"}],"OA_type":"green","article_processing_charge":"No","year":"2016","day":"15","date_created":"2018-12-11T11:50:31Z","volume":38,"author":[{"id":"29E0800A-F248-11E8-B48F-1D18A9856A87","last_name":"Lang","first_name":"Moritz","full_name":"Lang, Moritz"},{"first_name":"Jörg","last_name":"Stelling","full_name":"Stelling, Jörg"}],"quality_controlled":"1","month":"11","oa":1,"publication":"SIAM Journal on Scientific Computing","corr_author":"1","abstract":[{"text":"The increasing complexity of dynamic models in systems and synthetic biology poses computational challenges especially for the identification of model parameters. While modularization of the corresponding optimization problems could help reduce the “curse of dimensionality,” abundant feedback and crosstalk mechanisms prohibit a simple decomposition of most biomolecular networks into subnetworks, or modules. Drawing on ideas from network modularization and multiple-shooting optimization, we present here a modular parameter identification approach that explicitly allows for such interdependencies. Interfaces between our modules are given by the experimentally measured molecular species. This definition allows deriving good (initial) estimates for the inter-module communication directly from the experimental data. Given these estimates, the states and parameter sensitivities of different modules can be integrated independently. To achieve consistency between modules, we iteratively adjust the estimates for inter-module communication while optimizing the parameters. After convergence to an optimal parameter set---but not during earlier iterations---the intermodule communication as well as the individual modules\\' state dynamics agree with the dynamics of the nonmodularized network. Our modular parameter identification approach allows for easy parallelization; it can reduce the computational complexity for larger networks and decrease the probability to converge to suboptimal local minima. We demonstrate the algorithm\\'s performance in parameter estimation for two biomolecular networks, a synthetic genetic oscillator and a mammalian signaling pathway.","lang":"eng"}],"citation":{"apa":"Lang, M., & Stelling, J. (2016). Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics. https://doi.org/10.1137/15M103306X","short":"M. Lang, J. Stelling, SIAM Journal on Scientific Computing 38 (2016) B988–B1008.","chicago":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics, 2016. https://doi.org/10.1137/15M103306X.","ieee":"M. Lang and J. Stelling, “Modular parameter identification of biomolecular networks,” SIAM Journal on Scientific Computing, vol. 38, no. 6. Society for Industrial and Applied Mathematics, pp. B988–B1008, 2016.","ista":"Lang M, Stelling J. 2016. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 38(6), B988–B1008.","mla":"Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.” SIAM Journal on Scientific Computing, vol. 38, no. 6, Society for Industrial and Applied Mathematics, 2016, pp. B988–1008, doi:10.1137/15M103306X.","ama":"Lang M, Stelling J. Modular parameter identification of biomolecular networks. SIAM Journal on Scientific Computing. 2016;38(6):B988-B1008. doi:10.1137/15M103306X"},"publisher":"Society for Industrial and Applied Mathematics","isi":1,"das_tickbox":"1","has_accepted_license":"1","publist_id":"6186","OA_place":"repository","external_id":{"isi":["000391853100010"]},"date_published":"2016-11-15T00:00:00Z","file_date_updated":"2025-06-25T11:26:45Z"},{"external_id":{"isi":["000391973900001"],"arxiv":["1606.09048"]},"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.","date_published":"2016-12-30T00:00:00Z","publist_id":"6165","das_tickbox":"1","publisher":"IOP Publishing","isi":1,"citation":{"ama":"De Martino D, Masoero D. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016;2016(12). doi:10.1088/1742-5468/aa4e8f","mla":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & Growth.” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12, 123502, IOP Publishing, 2016, doi:10.1088/1742-5468/aa4e8f.","ista":"De Martino D, Masoero D. 2016. Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth. Journal of Statistical Mechanics: Theory and Experiment. 2016(12), 123502.","ieee":"D. De Martino and D. Masoero, “Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth,” Journal of Statistical Mechanics: Theory and Experiment, vol. 2016, no. 12. IOP Publishing, 2016.","short":"D. De Martino, D. Masoero, Journal of Statistical Mechanics: Theory and Experiment 2016 (2016).","chicago":"De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism & 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 & growth. Journal of Statistical Mechanics: Theory and Experiment. IOP Publishing. https://doi.org/10.1088/1742-5468/aa4e8f"},"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."}],"publication":"Journal of Statistical Mechanics: Theory and Experiment","main_file_link":[{"open_access":"1","url":"https://arxiv.org/abs/1606.09048"}],"oa":1,"month":"12","author":[{"full_name":"De Martino, Daniele","last_name":"De Martino","first_name":"Daniele","id":"3FF5848A-F248-11E8-B48F-1D18A9856A87","orcid":"0000-0002-5214-4706"},{"last_name":"Masoero","first_name":"Davide","full_name":"Masoero, Davide"}],"quality_controlled":"1","volume":2016,"date_created":"2018-12-11T11:50:37Z","year":"2016","article_number":"123502","day":"30","article_processing_charge":"No","language":[{"iso":"eng"}],"_id":"1188","publication_status":"published","issue":"12","status":"public","date_updated":"2026-07-07T13:11:22Z","intvolume":" 2016","scopus_import":"1","doi":"10.1088/1742-5468/aa4e8f","project":[{"_id":"25681D80-B435-11E9-9278-68D0E5697425","call_identifier":"FP7","grant_number":"291734","name":"International IST Postdoc Fellowship Programme"}],"ec_funded":1,"user_id":"2DF688A6-F248-11E8-B48F-1D18A9856A87","arxiv":1,"title":"Asymptotic analysis of noisy fitness maximization, applied to metabolism & growth","department":[{"_id":"GaTk"}],"oa_version":"Preprint","type":"journal_article"}]