Friedlander, Tamar, et al. “Intrinsic Limits to Gene Regulation by Global Crosstalk.”10.1038/ncomms12307__Nature Communications, vol. 7, 12307, Nature Publishing Group, 2016, doi:10.1038/ncomms12307.

Parise, Francesca, et al. “Bayesian Inference for Stochastic Individual-Based Models of Ecological Systems: A Pest Control Simulation Study.”10.3389/fenvs.2015.00042__Frontiers in Environmental Science, vol. 3, 42, Frontiers, 2015, doi:10.3389/fenvs.2015.00042.

Ruess, Jakob. “Minimal Moment Equations for Stochastic Models of Biochemical Reaction Networks with Partially Finite State Space.”10.1063/1.4937937__Journal of Chemical Physics, vol. 143, no. 24, 244103, American Institute of Physics, 2015, doi:10.1063/1.4937937.

Ruess, Jakob, et al. “Iterative Experiment Design Guides the Characterization of a Light-Inducible Gene Expression Circuit.”10.1073/pnas.1423947112__PNAS, vol. 112, no. 26, National Academy of Sciences, 2015, pp. 8148–53, doi:10.1073/pnas.1423947112.

Gilson, Matthieu, et al. “Editorial: Emergent Neural Computation from the Interaction of Different Forms of Plasticity.”10.3389/fncom.2015.00145__Frontiers in Computational Neuroscience, vol. 9, no. 11, 145, Frontiers Research Foundation, 2015, doi:10.3389/fncom.2015.00145.

Der, Ralf, and Georg S. Martius. “Novel Plasticity Rule Can Explain the Development of Sensorimotor Intelligence.”10.1073/pnas.1508400112__PNAS, vol. 112, no. 45, National Academy of Sciences, 2015, pp. 24–32, doi:10.1073/pnas.1508400112.

Bogomolov, Sergiy, et al. Adaptive Moment Closure for Parameter Inference of Biochemical Reaction Networks. Vol. 9308, Springer, 2015, pp. 77–89, doi:10.1007/978-3-319-23401-4_8.

Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.”10.1371/journal.pcbi.1004304__PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.

Tkadik, Gasper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.”10.1073/pnas.1514188112__PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.

Ruess, Jakob, and John Lygeros. “Moment-Based Methods for Parameter Inference and Experiment Design for Stochastic Biochemical Reaction Networks.”10.1145/2688906__ACM Transactions on Modeling and Computer Simulation, vol. 25, no. 2, 8, ACM, 2015, doi:10.1145/2688906.

Tkadik, Gasper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.”10.1534/genetics.114.171850__Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.

Sokolowski, Thomas R., and Gasper Tkadik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.”10.1103/PhysRevE.91.062710__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 91, no. 6, 062710, American Institute of Physics, 2015, doi:10.1103/PhysRevE.91.062710.

Friedlander, Tamar, et al. Supporting Information Text. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s001.

Friedlander, Tamar, et al. “Evolution of Bow-Tie Architectures in Biology.”10.1371/journal.pcbi.1004055__PLoS Computational Biology, vol. 11, no. 3, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.

Friedlander, Tamar, et al. Evolutionary Simulation Code. Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004055.s002.

Tugrul, Murat, et al. Other Fitness Models for Comparison &; for Interacting TFBSs. Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.s001.

Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.”10.1371/journal.pgen.1005639__PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.

Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.”10.1103/PhysRevLett.115.248101__Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.

Martius, Georg S., and Eckehard Olbrich. “Quantifying Emergent Behavior of Autonomous Robots.”10.3390/e17107266__Entropy, vol. 17, no. 10, MDPI, 2015, pp. 7266–97, doi:10.3390/e17107266.

Savin, Cristina, and Sophie Denève. Spatio-Temporal Representations of Uncertainty in Spiking Neural Networks. Vol. 3, no. January, Neural Information Processing Systems, 2014, pp. 2024–32.

Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.”10.7554/eLife.03722__ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.

Kollár, Richard, et al. “Mathematical Model of Alternative Mechanism of Telomere Length Maintenance.”10.1103/PhysRevE.89.032701__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 3, 032701, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.032701.

Ezard, Thomas, et al. “The Fitness Costs of Adaptation via Phenotypic Plasticity and Maternal Effects.”10.1111/1365-2435.12207__Functional Ecology, vol. 28, no. 3, Wiley-Blackwell, 2014, pp. 693–701, doi:10.1111/1365-2435.12207.

Humplik, Jan, et al. “Evolutionary Dynamics of Infectious Diseases in Finite Populations.”10.1016/j.jtbi.2014.06.039__Journal of Theoretical Biology, vol. 360, Elsevier, 2014, pp. 149–62, doi:10.1016/j.jtbi.2014.06.039.

Savin, Cristina, and Jochen Triesch. “Emergence of Task-Dependent Representations in Working Memory Circuits.”10.3389/fncom.2014.00057__Frontiers in Computational Neuroscience, vol. 8, no. MAY, 57, Frontiers Research Foundation, 2014, doi:10.3389/fncom.2014.00057.

Bodova, Katarina, et al. “Characterizing Spiking in Noisy Type II Neurons.”10.1016/j.jtbi.2014.09.041__10.1016/j.jtbi.2014.09.041__Journal of Theoretical Biology, vol. 365, Academic Press, 2014, pp. 40–54, doi:10.1016/j.jtbi.2014.09.041.

Botella Soler, Vicente, and Paul Glendinning. “Hierarchy and Polysynchrony in an Adaptive Network .”10.1103/PhysRevE.89.062809__Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 89, no. 6, 062809, American Institute of Physics, 2014, doi:10.1103/PhysRevE.89.062809.

Rieckh, Georg, and Gasper Tkadik. “Noise and Information Transmission in Promoters with Multiple Internal States.”10.1016/j.bpj.2014.01.014__Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.

Tkadik, Gasper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.”10.1371/journal.pone.0085841__PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.

Prizak, Roshan, et al. “Fitness Consequences of Maternal and Grandmaternal Effects.”10.1002/ece3.1150__Ecology and Evolution, vol. 4, no. 15, Wiley-Blackwell, 2014, pp. 3139–45, doi:10.1002/ece3.1150.

Simmons, Kristina, et al. Data from: Transformation of Stimulus Correlations by the Retina. Dryad, 2014, doi:10.5061/dryad.246qg.

Tkadik, Gasper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.”10.1371/journal.pcbi.1003408__PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.

Valderrama, Mario, et al. “Neuronal Oscillations Scale up and Scale down the Brain Dynamics .”10.1002/9783527671632.ch08__Multiscale Analysis and Nonlinear Dynamics: From Genes to the Brain, edited by Misha Meyer and Z. Pesenson, Wiley-VCH, 2013, doi:10.1002/9783527671632.ch08.

Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.”10.1162/NECO_a_00463__Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.

Tkadik, Gasper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.”10.1088/1742-5468/2013/03/P03011__Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.

Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.”10.1088/1742-5468/2013/03/P03015__Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, 015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.

Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.”10.1371/journal.pcbi.1002922__PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.

Botella Soler, Vicente, et al. “Lyapunov Exponent and Topological Entropy Plateaus in Piecewise Linear Maps.”10.1088/1751-8113/46/12/125101__Journal of Physics A: Mathematical and Theoretical, vol. 46, no. 12, 125101, IOP Publishing Ltd., 2013, doi:10.1088/1751-8113/46/12/125101.

Tkadik, Gasper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.”10.1103/PhysRevLett.110.058104__Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.

Dubuis, Julien, et al. “Positional Information, in Bits.”10.1073/pnas.1315642110__PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.

Wakamoto, Yurichi, et al. “Dynamic Persistence of Antibiotic-Stressed Mycobacteria.”10.1126/science.1229858__Science, vol. 339, no. 6115, American Association for the Advancement of Science, 2013, pp. 91–95, doi:10.1126/science.1229858.

Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.”10.1371/journal.pcbi.1003344__PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.

Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.”10.1103/PhysRevLett.110.018701__Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.

Tkadik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.”10.1103/PhysRevE.85.041903__10.1103/PhysRevE.85.041903__Physical Review E Statistical Nonlinear and Soft Matter Physics , vol. 85, no. 4, 041903, American Institute of Physics, 2012, doi:10.1103/PhysRevE.85.041903.

Rieckh, Georg, et al. “A 2.5D-Fourier-BEM Model for Vibrations in a Tunnel Running through Layered Anisotropic Soil.”10.1016/j.enganabound.2011.12.014__10.1016/j.enganabound.2011.12.014__Engineering Analysis with Boundary Elements, vol. 36, no. 6, Elsevier, 2012, pp. 960–67, doi:10.1016/j.enganabound.2011.12.014.

Tkadik, Gasper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.”10.1088/0953-8984/23/15/153102__Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.

Tkadik, Gasper, et al. “Natural Images from the Birthplace of the Human Eye.”10.1371/journal.pone.0020409__PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.