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 .

Simmons, Kristina, Jason Prentice, Gasper Tkadik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Data from: Transformation of Stimulus Correlations by the Retina.”https://doi.org/10.5061/dryad.246qg__Dryad, 2014.https://doi.org/10.5061/dryad.246qg .

Tkadik, Gasper, Olivier Marre, Dario Amodei, Elad Schneidman, William Bialek, and Michael Berry. “Searching for Collective Behavior in a Large Network of Sensory Neurons.”https://doi.org/10.1371/journal.pcbi.1003408__PLoS Computational Biology. Public Library of Science, 2014.https://doi.org/10.1371/journal.pcbi.1003408 .

Valderrama, Mario, Vicente Botella Soler, and Michel Le Van Quyen. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .”https://doi.org/10.1002/9783527671632.ch08__In Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson. Wiley-VCH, 2013.https://doi.org/10.1002/9783527671632.ch08 .

Rajan, Kanaka, Olivier Marre, and Gasper Tkadik. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.”https://doi.org/10.1162/NECO_a_00463__Neural Computation. MIT Press , 2013.https://doi.org/10.1162/NECO_a_00463 .

Tkadik, Gasper, Olivier Marre, Thierry Mora, Dario Amodei, Michael Berry, and William Bialek. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.”https://doi.org/10.1088/1742-5468/2013/03/P03011__Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013.https://doi.org/10.1088/1742-5468/2013/03/P03011 .

Berry, Michael, Gasper Tkadik, Julien Dubuis, Olivier Marre, and Ravá Da Silveira. “A Simple Method for Estimating the Entropy of Neural Activity.”https://doi.org/10.1088/1742-5468/2013/03/P03015__Journal of Statistical Mechanics Theory and Experiment. IOP Publishing Ltd., 2013.https://doi.org/10.1088/1742-5468/2013/03/P03015 .

Granot Atedgi, Einat, Gasper Tkadik, Ronen Segev, and Elad Schneidman. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.”https://doi.org/10.1371/journal.pcbi.1002922__PLoS Computational Biology. Public Library of Science, 2013.https://doi.org/10.1371/journal.pcbi.1002922 .

Botella Soler, Vicente, José Oteo, Javier Ros, and Paul Glendinning. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.”https://doi.org/10.1088/1751-8113/46/12/125101__Journal of Physics A: Mathematical and Theoretical. IOP Publishing Ltd., 2013.https://doi.org/10.1088/1751-8113/46/12/125101 .

Tkadik, Gasper, Einat Granot Atedgi, Ronen Segev, and Elad Schneidman. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.”https://doi.org/10.1103/PhysRevLett.110.058104__Physical Review Letters. American Physical Society, 2013.https://doi.org/10.1103/PhysRevLett.110.058104 .

Dubuis, Julien, Gasper Tkadik, Eric Wieschaus, Thomas Gregor, and William Bialek. “Positional Information, in Bits.”https://doi.org/10.1073/pnas.1315642110__PNAS. National Academy of Sciences, 2013.https://doi.org/10.1073/pnas.1315642110 .

Wakamoto, Yurichi, Neraaj Dhar, Remy P Chait, Katrin Schneider, François Signorino Gelo, Stanislas Leibler, and John Mckinney. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”https://doi.org/10.1126/science.1229858__Science. American Association for the Advancement of Science, 2013.https://doi.org/10.1126/science.1229858 .

Simmons, Kristina, Jason Prentice, Gasper Tkadik, Jan Homann, Heather Yee, Stephanie Palmer, Philip Nelson, and Vijay Balasubramanian. “Transformation of Stimulus Correlations by the Retina.”https://doi.org/10.1371/journal.pcbi.1003344__PLoS Computational Biology. Public Library of Science, 2013.https://doi.org/10.1371/journal.pcbi.1003344 .

Stephens, Greg, Thierry Mora, Gasper Tkadik, and William Bialek. “Statistical Thermodynamics of Natural Images.”https://doi.org/10.1103/PhysRevLett.110.018701__Physical Review Letters. American Physical Society, 2013.https://doi.org/10.1103/PhysRevLett.110.018701 .

Tkadik, Gasper, Aleksandra Walczak, and William Bialek. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.”https://doi.org/10.1103/PhysRevE.85.041903__https://doi.org/10.1103/PhysRevE.85.041903__Physical Review E Statistical Nonlinear and Soft Matter Physics . American Institute of Physics, 2012.https://doi.org/10.1103/PhysRevE.85.041903 .

Rieckh, Georg, Wolfgang Kreuzer, Holger Waubke, and Peter Balazs. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.”https://doi.org/10.1016/j.enganabound.2011.12.014__https://doi.org/10.1016/j.enganabound.2011.12.014__Engineering Analysis with Boundary Elements. Elsevier, 2012.https://doi.org/10.1016/j.enganabound.2011.12.014 .

Tkadik, Gasper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.”https://doi.org/10.1088/0953-8984/23/15/153102__Journal of Physics: Condensed Matter. IOP Publishing Ltd., 2011.https://doi.org/10.1088/0953-8984/23/15/153102 .

Tkadik, Gasper, Patrick Garrigan, Charles Ratliff, Grega Milcinski, Jennifer Klein, Lucia Seyfarth, Peter Sterling, David Brainard, and Vijay Balasubramanian. “Natural Images from the Birthplace of the Human Eye.”https://doi.org/10.1371/journal.pone.0020409__PLoS One. Public Library of Science, 2011.https://doi.org/10.1371/journal.pone.0020409 .