Misun, Patrick, Axel Birchler, Moritz Lang, Andreas Hierlemann, and Olivier Frey. “Fabrication and Operation of Microfluidic Hanging Drop Networks.”https://doi.org/10.1007/978-1-4939-7792-5_15__Methods in Molecular Biology. Springer, 2018.https://doi.org/10.1007/978-1-4939-7792-5_15 .

Granados, Alejandro, Julian Pietsch, Sarah A Cepeda Humerez, Isebail Farquhar, Gasper Tkadik, and Peter Swain. “Distributed and Dynamic Intracellular Organization of Extracellular Information.”https://doi.org/10.1073/pnas.1716659115__PNAS. National Academy of Sciences, 2018.https://doi.org/10.1073/pnas.1716659115 .

Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Evolutionary Pathways for the Generation of New Self-Incompatibility Haplotypes in a Non-Self Recognition System.”https://doi.org/10.1534/genetics.118.300748__Genetics. Genetics Society of America, 2018.https://doi.org/10.1534/genetics.118.300748 .

Bodova, Katarina, Tadeas Priklopil, David Field, Nicholas H Barton, and Melinda Pickup. “Supplemental Material for Bodova et Al., 2018.”https://doi.org/10.25386/genetics.6148304.v1__Genetics Society of America, 2018.https://doi.org/10.25386/genetics.6148304.v1 .

Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gasper Tkadik. “Probabilistic Models of Individual and Collective Animal Behavior.”https://doi.org/10.1371/journal.pone.0193049__PLoS One. Public Library of Science, 2018.https://doi.org/10.1371/journal.pone.0193049 .

Pleska, Maros, Moritz Lang, Dominik Refardt, Bruce Levin, and Calin C Guet. “Phage-Host Population Dynamics Promotes Prophage Acquisition in Bacteria with Innate Immunity.”https://doi.org/10.1038/s41559-017-0424-z__Nature Ecology and Evolution. Springer Nature, 2018.https://doi.org/10.1038/s41559-017-0424-z .

Bod’Ová, Katarína, Gabriel Mitchell, Roy Harpaz, Elad Schneidman, and Gasper Tkadik. “Implementation of the Inference Method in Matlab.”https://doi.org/10.1371/journal.pone.0193049.s001__Public Library of Science, 2018.https://doi.org/10.1371/journal.pone.0193049.s001 .

Ferrari, Ulisse, Stephane Deny, Matthew J Chalk, Gasper Tkadik, Olivier Marre, and Thierry Mora. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.”https://doi.org/10.1103/PhysRevE.98.042410__Physical Review E. American Physical Society, 2018.https://doi.org/10.1103/PhysRevE.98.042410 .

Chalk, Matthew J, Olivier Marre, and Gasper Tkadik. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.”https://doi.org/10.1073/pnas.1711114115__PNAS. National Academy of Sciences, 2018.https://doi.org/10.1073/pnas.1711114115 .

Bodova, Katarina, Jan Haskovec, and Peter Markowich. “Well Posedness and Maximum Entropy Approximation for the Dynamics of Quantitative Traits.”https://doi.org/10.1016/j.physd.2017.10.015__Physica D: Nonlinear Phenomena. Elsevier, 2018.https://doi.org/10.1016/j.physd.2017.10.015 .

Palmer, Adam, Remy P Chait, and Roy Kishony. “Nonoptimal Gene Expression Creates Latent Potential for Antibiotic Resistance.”https://doi.org/10.1093/molbev/msy163__Molecular Biology and Evolution. Oxford University Press, 2018.https://doi.org/10.1093/molbev/msy163 .

Botella Soler, Vicente, Stephane Deny, Georg S Martius, Olivier Marre, and Gasper Tkadik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”https://doi.org/10.1371/journal.pcbi.1006057__PLoS Computational Biology. Public Library of Science, 2018.https://doi.org/10.1371/journal.pcbi.1006057 .

Deny, Stephane, Olivier Marre, Vicente Botella-Soler, Georg S Martius, and Gasper Tkadik. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.”https://doi.org/10.15479/AT:ISTA:98__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:98 .

De Martino, Daniele, Andersson Anna Mc, Tobias Bergmiller, Calin C Guet, and Gasper Tkadik. “Statistical Mechanics for Metabolic Networks during Steady State Growth.”https://doi.org/10.1038/s41467-018-05417-9__Nature Communications. Springer Nature, 2018.https://doi.org/10.1038/s41467-018-05417-9 .

De Martino, Daniele, and Gasper Tkadik. “Supporting Materials ‘STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.’”https://doi.org/10.15479/AT:ISTA:62__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:62 .

Igler, Claudia, Mato Lagator, Gasper Tkadik, Jonathan P Bollback, and Calin C Guet. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”https://doi.org/10.1038/s41559-018-0651-y__Nature Ecology and Evolution. Nature Publishing Group, 2018.https://doi.org/10.1038/s41559-018-0651-y .

Igler, Claudia, Mato Lagator, Gasper Tkadik, Jonathan P Bollback, and Calin C Guet. “Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.”https://doi.org/10.15479/AT:ISTA:108__Institute of Science and Technology Austria, 2018.https://doi.org/10.15479/AT:ISTA:108 .

Chait, Remy P, Jakob Ruess, Tobias Bergmiller, Gasper Tkadik, and Calin C Guet. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.”https://doi.org/10.1038/s41467-017-01683-1__Nature Communications. Nature Publishing Group, 2017.https://doi.org/10.1038/s41467-017-01683-1 .

Der, Ralf, and Georg S Martius. “Dynamical Self Consistency Leads to Behavioral Development and Emergent Social Interactions in Robots.”https://doi.org/10.1109/DEVLRN.2016.7846789__IEEE, 2017.https://doi.org/10.1109/DEVLRN.2016.7846789 .

Der, Ralf, and Georg S Martius. “Self Organized Behavior Generation for Musculoskeletal Robots.”https://doi.org/10.3389/fnbot.2017.00008__Frontiers in Neurorobotics. Frontiers Research Foundation, 2017.https://doi.org/10.3389/fnbot.2017.00008 .

Humplik, Jan, and Gasper Tkadik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.”https://doi.org/10.1371/journal.pcbi.1005763__PLoS Computational Biology. Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005763 .

Harpaz, Roy, Gasper Tkadik, and Elad Schneidman. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.”https://doi.org/10.1073/pnas.1703817114__PNAS. National Academy of Sciences, 2017.https://doi.org/10.1073/pnas.1703817114 .

Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gasper Tkadik, and Michael Berry. “Data from: Error-Robust Modes of the Retinal Population Code.”https://doi.org/10.5061/dryad.1f1rc__Dryad, 2017.https://doi.org/10.5061/dryad.1f1rc .

Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Sensory Noise Predicts Divisive Reshaping of Receptive Fields.”https://doi.org/10.1371/journal.pcbi.1005582__PLoS Computational Biology. Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005582 .

Chalk, Matthew J, Paul Masset, Boris Gutkin, and Sophie Denève. “Supplementary Appendix.”https://doi.org/10.1371/journal.pcbi.1005582.s001__Public Library of Science, 2017.https://doi.org/10.1371/journal.pcbi.1005582.s001 .

Mitosch, Karin, Georg Rieckh, and Mark Tobias Bollenbach. “Noisy Response to Antibiotic Stress Predicts Subsequent Single Cell Survival in an Acidic Environment.”https://doi.org/10.1016/j.cels.2017.03.001__Cell Systems. Cell Press, 2017.https://doi.org/10.1016/j.cels.2017.03.001 .

Martin Del Campo Sanchez, Abraham, Sarah A Cepeda Humerez, and Caroline Uhler. “Exact Goodness-of-Fit Testing for the Ising Model.”https://doi.org/10.1111/sjos.12251__Scandinavian Journal of Statistics. Wiley-Blackwell, 2017.https://doi.org/10.1111/sjos.12251 .

Deny, Stephane, Ulisse Ferrari, Emilie Mace, Pierre Yger, Romain Caplette, Serge Picaud, Gasper Tkadik, and Olivier Marre. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.”https://doi.org/10.1038/s41467-017-02159-y__Nature Communications. Nature Publishing Group, 2017.https://doi.org/10.1038/s41467-017-02159-y .

Levina (Martius), Anna, and Viola Priesemann. “Subsampling Scaling.”https://doi.org/10.1038/ncomms15140__Nature Communications. Nature Publishing Group, 2017.https://doi.org/10.1038/ncomms15140 .

Friedlander, Tamar, Roshan Prizak, Nicholas H Barton, and Gasper Tkadik. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.”https://doi.org/10.1038/s41467-017-00238-8__Nature Communications. Nature Publishing Group, 2017.https://doi.org/10.1038/s41467-017-00238-8 .

De Martino, Daniele. “Scales and Multimodal Flux Distributions in Stationary Metabolic Network Models via Thermodynamics.”https://doi.org/10.1103/PhysRevE.95.062419__https://doi.org/10.1103/PhysRevE.95.062419__Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017.https://doi.org/10.1103/PhysRevE.95.062419 .

De Martino, Daniele, Fabrizio Capuani, and Andrea De Martino. “Quantifying the Entropic Cost of Cellular Growth Control.”https://doi.org/10.1103/PhysRevE.96.010401__https://doi.org/10.1103/PhysRevE.96.010401__Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2017.https://doi.org/10.1103/PhysRevE.96.010401 .

Zagórski, Marcin P, Yoji Tabata, Nathalie Brandenberg, Matthias Lutolf, Gasper Tkadik, Tobias Bollenbach, James Briscoe, and Anna Kicheva. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.”https://doi.org/10.1126/science.aam5887__Science. American Association for the Advancement of Science, 2017.https://doi.org/10.1126/science.aam5887 .

Colabrese, Simona, Daniele De Martino, Luca Leuzzi, and Enzo Marinari. “Phase Transitions in Integer Linear Problems.”https://doi.org/10.1088/1742-5468/aa85c3__https://doi.org/10.1088/1742-5468/aa85c3__Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2017.https://doi.org/10.1088/1742-5468/aa85c3 .

Savin, Cristina, and Gasper Tkadik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.”https://doi.org/10.1016/j.conb.2017.08.001__Current Opinion in Neurobiology. Elsevier, 2017.https://doi.org/10.1016/j.conb.2017.08.001 .

De Martino, Daniele. “Maximum Entropy Modeling of Metabolic Networks by Constraining Growth-Rate Moments Predicts Coexistence of Phenotypes.”https://doi.org/10.1103/PhysRevE.96.060401__Physical Review E. American Physical Society, 2017.https://doi.org/10.1103/PhysRevE.96.060401 .

Lang, Moritz, and Eduardo Sontag. “Zeros of Nonlinear Systems with Input Invariances.”https://doi.org/10.1016/j.automatica.2017.03.030__Automatica. International Federation of Automatic Control, 2017.https://doi.org/10.1016/j.automatica.2017.03.030 .

Marre, Olivier, Gasper Tkadik, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells.”https://doi.org/10.15479/AT:ISTA:61__Institute of Science and Technology Austria, 2017.https://doi.org/10.15479/AT:ISTA:61 .

Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkadik, and Calin C Guet. “Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity.”https://doi.org/10.15479/AT:ISTA:53__Institute of Science and Technology Austria, 2017.https://doi.org/10.15479/AT:ISTA:53 .

Bergmiller, Tobias, Anna M Andersson, Kathrin Tomasek, Enrique Balleza, Daniel Kiviet, Robert Hauschild, Gasper Tkadik, and Calin C Guet. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.”https://doi.org/10.1126/science.aaf4762__Science. American Association for the Advancement of Science, 2017.https://doi.org/10.1126/science.aaf4762 .

Barone, Vanessa, Moritz Lang, Gabriel Krens, Saurabh Pradhan, Shayan Shamipour, Keisuke Sako, Mateusz K Sikora, Calin C Guet, and Carl-Philipp J Heisenberg. “An Effective Feedback Loop between Cell-Cell Contact Duration and Morphogen Signaling Determines Cell Fate.”https://doi.org/10.1016/j.devcel.2017.09.014__Developmental Cell. Cell Press, 2017.https://doi.org/10.1016/j.devcel.2017.09.014 .

Chalk, Matthew J, Olivier Marre, and Gasper Tkadik. “Relevant Sparse Codes with Variational Information Bottleneck,” 29:1965–73. Neural Information Processing Systems, 2016.

Savin, Cristina, and Gasper Tkadik. “Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods,” 29:3610–18. Neural Information Processing Systems, 2016.

Lang, Moritz, and Jörg Stelling. “Modular Parameter Identification of Biomolecular Networks.”https://doi.org/10.1137/15M103306X__SIAM Journal on Scientific Computing. Society for Industrial and Applied Mathematics , 2016.https://doi.org/10.1137/15M103306X .

Tkadik, Gasper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on &;quot;Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function&;quot; by O. C. Martin et Al.”https://doi.org/10.1016/j.plrev.2016.06.005__Physics of Life Reviews. Elsevier, 2016.https://doi.org/10.1016/j.plrev.2016.06.005 .

De Martino, Daniele, and Davide Masoero. “Asymptotic Analysis of Noisy Fitness Maximization, Applied to Metabolism &;amp; Growth.”https://doi.org/10.1088/1742-5468/aa4e8f__https://doi.org/10.1088/1742-5468/aa4e8f__Journal of Statistical Mechanics: Theory and Experiment. IOPscience, 2016.https://doi.org/10.1088/1742-5468/aa4e8f .

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.”https://doi.org/10.1128/JCM.01511-16__Journal of Clinical Microbiology. American Society for Microbiology, 2016.https://doi.org/10.1128/JCM.01511-16 .

Martius, Georg S, Raphael Hostettler, Alois Knoll, and Ralf Der. “Compliant Control for Soft Robots: Emergent Behavior of a Tendon Driven Anthropomorphic Arm,”https://doi.org/10.1109/IROS.2016.7759138__Vol. 2016–November. IEEE, 2016.https://doi.org/10.1109/IROS.2016.7759138 .

Miki, 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,”https://doi.org/10.2514/6.2016-3764__1–19. AIAA, 2016.https://doi.org/10.2514/6.2016-3764 .

Sokolowski, Thomas R, Aleksandra Walczak, William Bialek, and Gasper Tkadik. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.”https://doi.org/10.1103/PhysRevE.93.022404__Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2016.https://doi.org/10.1103/PhysRevE.93.022404 .

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.”https://doi.org/10.1073/pnas.1419248113__PNAS. National Academy of Sciences, 2016.https://doi.org/10.1073/pnas.1419248113 .

Tkadik, Gasper, and William Bialek. “Information Processing in Living Systems.”https://doi.org/10.1146/annurev-conmatphys-031214-014803__Annual Review of Condensed Matter Physics. Annual Reviews, 2016.https://doi.org/10.1146/annurev-conmatphys-031214-014803 .

De Martino, Daniele. “The Dual of the Space of Interactions in Neural Network Models.”https://doi.org/10.1142/S0129183116500674__International Journal of Modern Physics C. World Scientific Publishing, 2016.https://doi.org/10.1142/S0129183116500674 .

Chalk, Matthew J, Boris Gutkin, and Sophie Denève. “Neural Oscillations as a Signature of Efficient Coding in the Presence of Synaptic Delays.”https://doi.org/10.7554/eLife.13824__ELife. eLife Sciences Publications, 2016.https://doi.org/10.7554/eLife.13824 .

Stone, Laura, Michael Baym, Tami Lieberman, Remy P Chait, Jon Clardy, and Roy Kishony. “Compounds That Select against the Tetracycline-Resistance Efflux Pump.”https://doi.org/10.1038/nchembio.2176__Nature Chemical Biology. Nature Publishing Group, 2016.https://doi.org/10.1038/nchembio.2176 .

Lang, Moritz, and Eduardo Sontag. “Scale-Invariant Systems Realize Nonlinear Differential Operators,”https://doi.org/10.1109/ACC.2016.7526722__Vol. 2016–July. IEEE, 2016.https://doi.org/10.1109/ACC.2016.7526722 .

Chait, Remy P, Adam Palmer, Idan Yelin, and Roy Kishony. “Pervasive Selection for and against Antibiotic Resistance in Inhomogeneous Multistress Environments.”https://doi.org/10.1038/ncomms10333__Nature Communications. Nature Publishing Group, 2016.https://doi.org/10.1038/ncomms10333 .

Baym, Michael, Tami Lieberman, Eric Kelsic, Remy P Chait, Rotem Gross, Idan Yelin, and Roy Kishony. “Spatiotemporal Microbial Evolution on Antibiotic Landscapes.”https://doi.org/10.1126/science.aag0822__Science. American Association for the Advancement of Science, 2016.https://doi.org/10.1126/science.aag0822 .

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.”https://doi.org/10.1088/1478-3975/13/3/036005__Physical Biology. IOP Publishing Ltd., 2016.https://doi.org/10.1088/1478-3975/13/3/036005 .

Bodova, Katarina, Gasper Tkadik, and Nicholas H Barton. “A General Approximation for the Dynamics of Quantitative Traits.”https://doi.org/10.1534/genetics.115.184127__Genetics. Genetics Society of America, 2016.https://doi.org/10.1534/genetics.115.184127 .

De Martino, Daniele. “Genome-Scale Estimate of the Metabolic Turnover of E. Coli from the Energy Balance Analysis.”https://doi.org/10.1088/1478-3975/13/1/016003__Physical Biology. IOP Publishing Ltd., 2016.https://doi.org/10.1088/1478-3975/13/1/016003 .

Schilling, Christian, Sergiy Bogomolov, Thomas A Henzinger, Andreas Podelski, and Jakob Ruess. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.”https://doi.org/10.1016/j.biosystems.2016.07.005__Biosystems. Elsevier, 2016.https://doi.org/10.1016/j.biosystems.2016.07.005 .

Martius, Georg S, Rafael Hostettler, Alois Knoll, and Ralf Der. “Self-Organized Control of an Tendon Driven Arm by Differential Extrinsic Plasticity.”https://doi.org/10.7551/978-0-262-33936-0-ch029__In Proceedings of the Artificial Life Conference 2016, 28:142–43. MIT Press, 2016.https://doi.org/10.7551/978-0-262-33936-0-ch029 .

Prentice, Jason, Olivier Marre, Mark Ioffe, Adrianna Loback, Gasper Tkadik, and Michael Berry. “Error-Robust Modes of the Retinal Population Code.”https://doi.org/10.1371/journal.pcbi.1005148__PLoS Computational Biology. Public Library of Science, 2016.https://doi.org/10.1371/journal.pcbi.1005148 .

Monk, Travis, Cristina Savin, and Jörg Lücke. “Neurons Equipped with Intrinsic Plasticity Learn Stimulus Intensity Statistics,” 29:4285–93. Neural Information Processing Systems, 2016.

Hillenbrand, Patrick, Ulrich Gerland, and Gasper Tkadik. “Beyond the French Flag Model: Exploiting Spatial and Gene Regulatory Interactions for Positional Information.”https://doi.org/10.1371/journal.pone.0163628__PLoS One. Public Library of Science, 2016.https://doi.org/10.1371/journal.pone.0163628 .

Hillenbrand, Patrick, Ulrich Gerland, and Gasper Tkadik. “Computation of Positional Information in an Ising Model.”https://doi.org/10.1371/journal.pone.0163628.s002__Public Library of Science, 2016.https://doi.org/10.1371/journal.pone.0163628.s002 .

Hillenbrand, Patrick, Ulrich Gerland, and Gasper Tkadik. “Error Bound on an Estimator of Position.”https://doi.org/10.1371/journal.pone.0163628.s001__Public Library of Science, 2016.https://doi.org/10.1371/journal.pone.0163628.s001 .

Hillenbrand, Patrick, Ulrich Gerland, and Gasper Tkadik. “Computation of Positional Information in a Discrete Morphogen Field.”https://doi.org/10.1371/journal.pone.0163628.s003__Public Library of Science, 2016.https://doi.org/10.1371/journal.pone.0163628.s003 .

Rieckh, Georg. “Studying the Complexities of Transcriptional Regulation.” Institute of Science and Technology Austria, 2016.

Friedlander, Tamar, Roshan Prizak, Calin C Guet, Nicholas H Barton, and Gasper Tkadik. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”https://doi.org/10.1038/ncomms12307__Nature Communications. Nature Publishing Group, 2016.https://doi.org/10.1038/ncomms12307 .

Parise, Francesca, John Lygeros, and Jakob Ruess. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.”https://doi.org/10.3389/fenvs.2015.00042__Frontiers in Environmental Science. Frontiers, 2015.https://doi.org/10.3389/fenvs.2015.00042 .

Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.”https://doi.org/10.1063/1.4937937__Journal of Chemical Physics. American Institute of Physics, 2015.https://doi.org/10.1063/1.4937937 .

Ruess, Jakob, Francesca Parise, Andreas Milias Argeitis, Mustafa Khammash, and John Lygeros. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.”https://doi.org/10.1073/pnas.1423947112__PNAS. National Academy of Sciences, 2015.https://doi.org/10.1073/pnas.1423947112 .

Gilson, Matthieu, Cristina Savin, and Friedemann Zenke. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.”https://doi.org/10.3389/fncom.2015.00145__Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2015.https://doi.org/10.3389/fncom.2015.00145 .

Der, Ralf, and Georg S Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.”https://doi.org/10.1073/pnas.1508400112__PNAS. National Academy of Sciences, 2015.https://doi.org/10.1073/pnas.1508400112 .

Bogomolov, Sergiy, Thomas A Henzinger, Andreas Podelski, Jakob Ruess, and Christian Schilling. “Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks.”https://doi.org/10.1007/978-3-319-23401-4_8__Lecture Notes in Computer Science. Springer, 2015.https://doi.org/10.1007/978-3-319-23401-4_8 .

Marre, Olivier, Vicente Botella Soler, Kristina Simmons, Thierry Mora, Gasper Tkadik, and Michael Berry. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.”https://doi.org/10.1371/journal.pcbi.1004304__PLoS Computational Biology. Public Library of Science, 2015.https://doi.org/10.1371/journal.pcbi.1004304 .

Tkadik, Gasper, Thierry Mora, Olivier Marre, Dario Amodei, Stephanie Palmer, Michael Berry Ii, and William Bialek. “Thermodynamics and Signatures of Criticality in a Network of Neurons.”https://doi.org/10.1073/pnas.1514188112__PNAS. National Academy of Sciences, 2015.https://doi.org/10.1073/pnas.1514188112 .

Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.”https://doi.org/10.1145/2688906__ACM Transactions on Modeling and Computer Simulation. ACM, 2015.https://doi.org/10.1145/2688906 .

Tkadik, Gasper, Julien Dubuis, Mariela Petkova, and Thomas Gregor. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.”https://doi.org/10.1534/genetics.114.171850__Genetics. Genetics Society of America, 2015.https://doi.org/10.1534/genetics.114.171850 .

Sokolowski, Thomas R, and Gasper Tkadik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.”https://doi.org/10.1103/PhysRevE.91.062710__Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2015.https://doi.org/10.1103/PhysRevE.91.062710 .

Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Supporting Information Text.”https://doi.org/10.1371/journal.pcbi.1004055.s001__Public Library of Science, 2015.https://doi.org/10.1371/journal.pcbi.1004055.s001 .

Friedlander, Tamar, Avraham Mayo, Tsvi Tlusty, and Uri Alon. “Evolution of Bow-Tie Architectures in Biology.”https://doi.org/10.1371/journal.pcbi.1004055__PLoS Computational Biology. Public Library of Science, 2015.https://doi.org/10.1371/journal.pcbi.1004055 .

Friedlander, Tamar, Avraham E. Mayo, Tsvi Tlusty, and Uri Alon. “Evolutionary Simulation Code.”https://doi.org/10.1371/journal.pcbi.1004055.s002__Public Library of Science, 2015.https://doi.org/10.1371/journal.pcbi.1004055.s002 .

Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkadik. “Other Fitness Models for Comparison &; for Interacting TFBSs.”https://doi.org/10.1371/journal.pgen.1005639.s001__Public Library of Science, 2015.https://doi.org/10.1371/journal.pgen.1005639.s001 .

Tugrul, Murat, Tiago Paixao, Nicholas H Barton, and Gasper Tkadik. “Dynamics of Transcription Factor Binding Site Evolution.”https://doi.org/10.1371/journal.pgen.1005639__PLoS Genetics. Public Library of Science, 2015.https://doi.org/10.1371/journal.pgen.1005639 .

Cepeda Humerez, Sarah A, Georg Rieckh, and Gasper Tkadik. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.”https://doi.org/10.1103/PhysRevLett.115.248101__Physical Review Letters. American Physical Society, 2015.https://doi.org/10.1103/PhysRevLett.115.248101 .

Martius, Georg S, and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.”https://doi.org/10.3390/e17107266__Entropy. MDPI, 2015.https://doi.org/10.3390/e17107266 .

Savin, Cristina, and Sophie Denève. “Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks,” 3:2024–32. Neural Information Processing Systems, 2014.

Hermundstad, Ann, John Briguglio, Mary Conte, Jonathan Victor, Vijay Balasubramanian, and Gasper Tkadik. “Variance Predicts Salience in Central Sensory Processing.”https://doi.org/10.7554/eLife.03722__ELife. eLife Sciences Publications, 2014.https://doi.org/10.7554/eLife.03722 .

Kollár, Richard, Katarina Bodova, Jozef Nosek, and dubomír Tomáska. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.”https://doi.org/10.1103/PhysRevE.89.032701__Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014.https://doi.org/10.1103/PhysRevE.89.032701 .

Ezard, Thomas, Roshan Prizak, and Rebecca Hoyle. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.”https://doi.org/10.1111/1365-2435.12207__Functional Ecology. Wiley-Blackwell, 2014.https://doi.org/10.1111/1365-2435.12207 .

Humplik, Jan, Alison Hill, and Martin Nowak. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.”https://doi.org/10.1016/j.jtbi.2014.06.039__Journal of Theoretical Biology. Elsevier, 2014.https://doi.org/10.1016/j.jtbi.2014.06.039 .

Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.”https://doi.org/10.3389/fncom.2014.00057__Frontiers in Computational Neuroscience. Frontiers Research Foundation, 2014.https://doi.org/10.3389/fncom.2014.00057 .

Bodova, Katarina, David Paydarfar, and Daniel Forger. “Characterizing Spiking in Noisy Type II Neurons.”https://doi.org/10.1016/j.jtbi.2014.09.041__https://doi.org/10.1016/j.jtbi.2014.09.041__Journal of Theoretical Biology. Academic Press, 2014.https://doi.org/10.1016/j.jtbi.2014.09.041 .

Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .”https://doi.org/10.1103/PhysRevE.89.062809__Physical Review E Statistical Nonlinear and Soft Matter Physics. American Institute of Physics, 2014.https://doi.org/10.1103/PhysRevE.89.062809 .

Rieckh, Georg, and Gasper Tkadik. “Noise and Information Transmission in Promoters with Multiple Internal States.”https://doi.org/10.1016/j.bpj.2014.01.014__Biophysical Journal. Biophysical Society, 2014.https://doi.org/10.1016/j.bpj.2014.01.014 .

Tkadik, Gasper, Anandamohan Ghosh, Elad Schneidman, and Ronen Segev. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.”https://doi.org/10.1371/journal.pone.0085841__PLoS One. Public Library of Science, 2014.https://doi.org/10.1371/journal.pone.0085841 .

Prizak, Roshan, Thomas Ezard, and Rebecca Hoyle. “Fitness Consequences of Maternal and Grandmaternal Effects.”https://doi.org/10.1002/ece3.1150__Ecology and Evolution. Wiley-Blackwell, 2014.https://doi.org/10.1002/ece3.1150 .