75 Publications

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[75]
2019 | Preprint | IST-REx-ID: 7083   OA
Kavcic, Bor, et al. “Mechanistic Origin of Drug Interactions between Translation-Inhibiting Antibiotics.” BioRxiv, Cold Spring Harbor Laboratory, 2019.
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[74]
2019 | Journal Article | IST-REx-ID: 5945
Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
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[73]
2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
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[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
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[71]
2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
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[70]
2018 | Journal Article | IST-REx-ID: 543   OA
Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.
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[69]
2018 | Research Data | IST-REx-ID: 5587   OA
De Martino, Daniele, and Gasper Tkacik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018, doi:10.15479/AT:ISTA:62.
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[68]
2018 | Journal Article | IST-REx-ID: 67
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
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[67]
2018 | Journal Article | IST-REx-ID: 292
Botella Soler, Vicent, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
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[66]
2018 | Research Data | IST-REx-ID: 5584   OA
Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. IST Austria, 2018, doi:10.15479/AT:ISTA:98.
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[65]
2018 | Journal Article | IST-REx-ID: 406   OA
Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.
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[64]
2018 | Journal Article | IST-REx-ID: 161
De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.
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[63]
2018 | Journal Article | IST-REx-ID: 281
Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
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[62]
2018 | Research Data | IST-REx-ID: 5585
Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. IST Austria, 2018, doi:10.15479/AT:ISTA:108.
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[61]
2017 | Journal Article | IST-REx-ID: 1104   OA
Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.
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[60]
2017 | Research Data | IST-REx-ID: 5562   OA
Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. IST Austria, 2017, doi:10.15479/AT:ISTA:61.
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[59]
2017 | Journal Article | IST-REx-ID: 725   OA
Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
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[58]
2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, Jan, and Gasper Tkacik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
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[57]
2017 | Journal Article | IST-REx-ID: 613   OA
Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
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[56]
2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
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[55]
2017 | Journal Article | IST-REx-ID: 955   OA
Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
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[54]
2017 | Research Data | IST-REx-ID: 5560
Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. IST Austria, 2017, doi:doi:10.15479/AT:ISTA:53.
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[53]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.
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[52]
2017 | Journal Article | IST-REx-ID: 730
Savin, Cristina, and Gasper Tkacik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
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[51]
2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.
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[50]
2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, Gasper, 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.
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[49]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gasper Tkacik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
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.
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[47]
2016 | Journal Article | IST-REx-ID: 1358
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.
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[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
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[45]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik, Gasper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.
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[44]
2016 | Journal Article | IST-REx-ID: 1242   OA
Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404.
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[43]
2016 | Journal Article | IST-REx-ID: 1420   OA
Bod’ová, Katarína, 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.
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[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
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[41]
2015 | Journal Article | IST-REx-ID: 1697   OA
Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
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[40]
2015 | Journal Article | IST-REx-ID: 1940   OA
Sokolowski, Thomas R., and Gasper Tkacik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” 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.
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[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
Tkacik, Gasper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
Tkacik, Gasper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.
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[37]
2015 | Journal Article | IST-REx-ID: 1576
Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
Tkacik, Gasper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.
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[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
Rieckh, Georg, and Gasper Tkacik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
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[34]
2014 | Journal Article | IST-REx-ID: 1886   OA
Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
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[33]
2014 | Journal Article | IST-REx-ID: 2257
Tkacik, Gasper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
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[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.
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[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
Tkacik, Gasper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.
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[30]
2013 | Journal Article | IST-REx-ID: 2850   OA
Tkacik, Gasper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
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[29]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
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[28]
2013 | Journal Article | IST-REx-ID: 2818   OA
Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.
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[27]
2013 | Journal Article | IST-REx-ID: 2863   OA
Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
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[26]
2013 | Journal Article | IST-REx-ID: 2914   OA
Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.
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[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
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[24]
2012 | Journal Article | IST-REx-ID: 3262   OA
Tkacik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” 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.
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.
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[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
Tkacik, Gasper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.
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[21]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
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[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
Tkacik, Gasper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.
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[19]
2010 | Conference Paper | IST-REx-ID: 3430   OA
Tkacik, Gasper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.
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[18]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik, Gasper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107.
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[16]
2010 | Journal Article | IST-REx-ID: 3736
Tkacik, Gasper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107.
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
Tkacik, Gasper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
Tkacik, Gasper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
Tkacik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, American Institute of Physics, 2009, doi:10.1103/PhysRevE.80.031920.
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[12]
2009 | Journal Article | IST-REx-ID: 3745
Tkacik, Gasper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.
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[11]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:10.1073/pnas.0905497106.
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[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik, Gasper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.
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[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
Tkacik, Gasper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
Tkacik, Gasper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
Tkacik, Gasper, et al. “The Role of Input Noise in Transcriptional Regulation.” PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
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[6]
2008 | Journal Article | IST-REx-ID: 3739
Tkacik, Gasper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
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[5]
2007 | Preprint | IST-REx-ID: 3742   OA
Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv, vol. q-QM, ArXiv, 2007.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
Tkacik, Gasper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
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75 Publications

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[75]
2019 | Preprint | IST-REx-ID: 7083   OA
Kavcic, Bor, et al. “Mechanistic Origin of Drug Interactions between Translation-Inhibiting Antibiotics.” BioRxiv, Cold Spring Harbor Laboratory, 2019.
View | Download (ext.)
 
[74]
2019 | Journal Article | IST-REx-ID: 5945
Petkova, Mariela D., et al. “Optimal Decoding of Cellular Identities in a Genetic Network.” Cell, vol. 176, no. 4, Cell Press, 2019, p. 844–855.e15, doi:10.1016/j.cell.2019.01.007.
View | Files available | DOI
 
[73]
2019 | Journal Article | IST-REx-ID: 6784   OA
Ruess, Jakob, et al. “Molecular Noise of Innate Immunity Shapes Bacteria-Phage Ecologies.” PLoS Computational Biology, vol. 15, no. 7, e1007168, Public Library of Science, 2019, doi:10.1371/journal.pcbi.1007168.
View | Files available | DOI
 
[72]
2019 | Journal Article | IST-REx-ID: 6900   OA
Cepeda Humerez, Sarah A., et al. “Estimating Information in Time-Varying Signals.” PLoS Computational Biology, vol. 15, no. 9, Public Library of Science, 2019, p. e1007290, doi:10.1371/journal.pcbi.1007290.
View | Files available | DOI | PubMed | Europe PMC
 
[71]
2018 | Journal Article | IST-REx-ID: 31   OA
Ferrari, Ulisse, et al. “Separating Intrinsic Interactions from Extrinsic Correlations in a Network of Sensory Neurons.” Physical Review E, vol. 98, no. 4, 042410, American Physical Society, 2018, doi:10.1103/PhysRevE.98.042410.
View | DOI | Download (ext.)
 
[70]
2018 | Journal Article | IST-REx-ID: 543   OA
Chalk, Matthew J., et al. “Toward a Unified Theory of Efficient, Predictive, and Sparse Coding.” PNAS, vol. 115, no. 1, National Academy of Sciences, 2018, pp. 186–91, doi:10.1073/pnas.1711114115.
View | DOI | Download (ext.)
 
[69]
2018 | Research Data | IST-REx-ID: 5587   OA
De Martino, Daniele, and Gasper Tkacik. Supporting Materials “STATISTICAL MECHANICS FOR METABOLIC NETWORKS IN STEADY-STATE GROWTH.” IST Austria, 2018, doi:10.15479/AT:ISTA:62.
View | Files available | DOI
 
[68]
2018 | Journal Article | IST-REx-ID: 67
Igler, Claudia, et al. “Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring.” Nature Ecology and Evolution, vol. 2, no. 10, Nature Publishing Group, 2018, pp. 1633–43, doi:10.1038/s41559-018-0651-y.
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[67]
2018 | Journal Article | IST-REx-ID: 292
Botella Soler, Vicent, et al. “Nonlinear Decoding of a Complex Movie from the Mammalian Retina.” PLoS Computational Biology, vol. 14, no. 5, e1006057, Public Library of Science, 2018, doi:10.1371/journal.pcbi.1006057.
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[66]
2018 | Research Data | IST-REx-ID: 5584   OA
Deny, Stephane, et al. Nonlinear Decoding of a Complex Movie from the Mammalian Retina. IST Austria, 2018, doi:10.15479/AT:ISTA:98.
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[65]
2018 | Journal Article | IST-REx-ID: 406   OA
Bod’Ová, Katarína, et al. “Probabilistic Models of Individual and Collective Animal Behavior.” PLoS One, vol. 13, no. 3, Public Library of Science, 2018, doi:10.1371/journal.pone.0193049.
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[64]
2018 | Journal Article | IST-REx-ID: 161
De Martino, Daniele, et al. “Statistical Mechanics for Metabolic Networks during Steady State Growth.” Nature Communications, vol. 9, no. 1, 2988, Springer Nature, 2018, doi:10.1038/s41467-018-05417-9.
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[63]
2018 | Journal Article | IST-REx-ID: 281
Granados, Alejandro, et al. “Distributed and Dynamic Intracellular Organization of Extracellular Information.” PNAS, vol. 115, no. 23, National Academy of Sciences, 2018, pp. 6088–93, doi:10.1073/pnas.1716659115.
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[62]
2018 | Research Data | IST-REx-ID: 5585
Igler, Claudia, et al. Data for the Paper Evolutionary Potential of Transcription Factors for Gene Regulatory Rewiring. IST Austria, 2018, doi:10.15479/AT:ISTA:108.
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[61]
2017 | Journal Article | IST-REx-ID: 1104   OA
Deny, Stephane, et al. “Multiplexed Computations in Retinal Ganglion Cells of a Single Type.” Nature Communications, vol. 8, no. 1, 1964, Nature Publishing Group, 2017, doi:10.1038/s41467-017-02159-y.
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[60]
2017 | Research Data | IST-REx-ID: 5562   OA
Marre, Olivier, et al. Multi-Electrode Array Recording from Salamander Retinal Ganglion Cells. IST Austria, 2017, doi:10.15479/AT:ISTA:61.
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[59]
2017 | Journal Article | IST-REx-ID: 725   OA
Harpaz, Roy, et al. “Discrete Modes of Social Information Processing Predict Individual Behavior of Fish in a Group.” PNAS, vol. 114, no. 38, National Academy of Sciences, 2017, pp. 10149–54, doi:10.1073/pnas.1703817114.
View | DOI | Download (ext.) | PubMed | Europe PMC
 
[58]
2017 | Journal Article | IST-REx-ID: 720   OA
Humplik, Jan, and Gasper Tkacik. “Probabilistic Models for Neural Populations That Naturally Capture Global Coupling and Criticality.” PLoS Computational Biology, vol. 13, no. 9, e1005763, Public Library of Science, 2017, doi:10.1371/journal.pcbi.1005763.
View | Files available | DOI
 
[57]
2017 | Journal Article | IST-REx-ID: 613   OA
Chait, Remy P., et al. “Shaping Bacterial Population Behavior through Computer Interfaced Control of Individual Cells.” Nature Communications, vol. 8, no. 1, 1535, Nature Publishing Group, 2017, doi:10.1038/s41467-017-01683-1.
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[56]
2017 | Journal Article | IST-REx-ID: 943   OA
Zagórski, Marcin P., et al. “Decoding of Position in the Developing Neural Tube from Antiparallel Morphogen Gradients.” Science, vol. 356, no. 6345, American Association for the Advancement of Science, 2017, pp. 1379–83, doi:10.1126/science.aam5887.
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[55]
2017 | Journal Article | IST-REx-ID: 955   OA
Friedlander, Tamar, et al. “Evolution of New Regulatory Functions on Biophysically Realistic Fitness Landscapes.” Nature Communications, vol. 8, no. 1, 216, Nature Publishing Group, 2017, doi:10.1038/s41467-017-00238-8.
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[54]
2017 | Research Data | IST-REx-ID: 5560
Bergmiller, Tobias, et al. Biased Partitioning of the Multi-Drug Efflux Pump AcrAB-TolC Underlies Long-Lived Phenotypic Heterogeneity. IST Austria, 2017, doi:doi:10.15479/AT:ISTA:53.
View | Files available | DOI
 
[53]
2017 | Journal Article | IST-REx-ID: 665
Bergmiller, Tobias, et al. “Biased Partitioning of the Multidrug Efflux Pump AcrAB TolC Underlies Long Lived Phenotypic Heterogeneity.” Science, vol. 356, no. 6335, American Association for the Advancement of Science, 2017, pp. 311–15, doi:10.1126/science.aaf4762.
View | Files available | DOI
 
[52]
2017 | Journal Article | IST-REx-ID: 730
Savin, Cristina, and Gasper Tkacik. “Maximum Entropy Models as a Tool for Building Precise Neural Controls.” Current Opinion in Neurobiology, vol. 46, Elsevier, 2017, pp. 120–26, doi:10.1016/j.conb.2017.08.001.
View | DOI
 
[51]
2016 | Journal Article | IST-REx-ID: 1197   OA
Prentice, Jason, et al. “Error-Robust Modes of the Retinal Population Code.” PLoS Computational Biology, vol. 12, no. 11, e1005855, Public Library of Science, 2016, doi:10.1371/journal.pcbi.1005148.
View | Files available | DOI
 
[50]
2016 | Journal Article | IST-REx-ID: 1248   OA
Tkacik, Gasper, 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.
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[49]
2016 | Conference Paper | IST-REx-ID: 1105
Savin, Cristina, and Gasper Tkacik. Estimating Nonlinear Neural Response Functions Using GP Priors and Kronecker Methods. Vol. 29, Neural Information Processing Systems, 2016, pp. 3610–18.
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[48]
2016 | Journal Article | IST-REx-ID: 1270   OA
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.
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[47]
2016 | Journal Article | IST-REx-ID: 1358
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.
View | Files available | DOI
 
[46]
2016 | Conference Paper | IST-REx-ID: 1082   OA
Chalk, Matthew J., et al. Relevant Sparse Codes with Variational Information Bottleneck. Vol. 29, Neural Information Processing Systems, 2016, pp. 1965–73.
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[45]
2016 | Journal Article | IST-REx-ID: 1171
Tkacik, Gasper. “Understanding Regulatory Networks Requires More than Computing a Multitude of Graph Statistics: Comment on "Drivers of Structural Features in Gene Regulatory Networks: From Biophysical Constraints to Biological Function" by O. C. Martin et Al.” Physics of Life Reviews, vol. 17, Elsevier, 2016, pp. 166–67, doi:10.1016/j.plrev.2016.06.005.
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[44]
2016 | Journal Article | IST-REx-ID: 1242   OA
Sokolowski, Thomas R., et al. “Extending the Dynamic Range of Transcription Factor Action by Translational Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 93, no. 2, 022404, American Institute of Physics, 2016, doi:10.1103/PhysRevE.93.022404.
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[43]
2016 | Journal Article | IST-REx-ID: 1420   OA
Bod’ová, Katarína, 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.
View | DOI | Download (ext.) | arXiv
 
[42]
2015 | Journal Article | IST-REx-ID: 1666   OA
Tugrul, Murat, et al. “Dynamics of Transcription Factor Binding Site Evolution.” PLoS Genetics, vol. 11, no. 11, Public Library of Science, 2015, doi:10.1371/journal.pgen.1005639.
View | Files available | DOI
 
[41]
2015 | Journal Article | IST-REx-ID: 1697   OA
Marre, Olivier, et al. “High Accuracy Decoding of Dynamical Motion from a Large Retinal Population.” PLoS Computational Biology, vol. 11, no. 7, e1004304, Public Library of Science, 2015, doi:10.1371/journal.pcbi.1004304.
View | Files available | DOI
 
[40]
2015 | Journal Article | IST-REx-ID: 1940   OA
Sokolowski, Thomas R., and Gasper Tkacik. “Optimizing Information Flow in Small Genetic Networks. IV. Spatial Coupling.” 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.
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[39]
2015 | Journal Article | IST-REx-ID: 1701   OA
Tkacik, Gasper, et al. “Thermodynamics and Signatures of Criticality in a Network of Neurons.” PNAS, vol. 112, no. 37, National Academy of Sciences, 2015, pp. 11508–13, doi:10.1073/pnas.1514188112.
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[38]
2015 | Journal Article | IST-REx-ID: 1885   OA
Tkacik, Gasper, et al. “Positional Information, Positional Error, and Readout Precision in Morphogenesis: A Mathematical Framework.” Genetics, vol. 199, no. 1, Genetics Society of America, 2015, pp. 39–59, doi:10.1534/genetics.114.171850.
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[37]
2015 | Journal Article | IST-REx-ID: 1576
Cepeda Humerez, Sarah A., et al. “Stochastic Proofreading Mechanism Alleviates Crosstalk in Transcriptional Regulation.” Physical Review Letters, vol. 115, no. 24, 248101, American Physical Society, 2015, doi:10.1103/PhysRevLett.115.248101.
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[36]
2014 | Journal Article | IST-REx-ID: 3263   OA
Tkacik, Gasper, et al. “Adaptation to Changes in Higher-Order Stimulus Statistics in the Salamander Retina.” PLoS One, vol. 9, no. 1, e85841, Public Library of Science, 2014, doi:10.1371/journal.pone.0085841.
View | Files available | DOI
 
[35]
2014 | Journal Article | IST-REx-ID: 2231   OA
Rieckh, Georg, and Gasper Tkacik. “Noise and Information Transmission in Promoters with Multiple Internal States.” Biophysical Journal, vol. 106, no. 5, Biophysical Society, 2014, pp. 1194–204, doi:10.1016/j.bpj.2014.01.014.
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[34]
2014 | Journal Article | IST-REx-ID: 1886   OA
Hermundstad, Ann, et al. “Variance Predicts Salience in Central Sensory Processing.” ELife, no. November, e03722, eLife Sciences Publications, 2014, doi:10.7554/eLife.03722.
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[33]
2014 | Journal Article | IST-REx-ID: 2257
Tkacik, Gasper, et al. “Searching for Collective Behavior in a Large Network of Sensory Neurons.” PLoS Computational Biology, vol. 10, no. 1, e1003408, Public Library of Science, 2014, doi:10.1371/journal.pcbi.1003408.
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[32]
2013 | Journal Article | IST-REx-ID: 2277   OA
Simmons, Kristina, et al. “Transformation of Stimulus Correlations by the Retina.” PLoS Computational Biology, vol. 9, no. 12, e1003344, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1003344.
View | Files available | DOI
 
[31]
2013 | Journal Article | IST-REx-ID: 2913   OA
Tkacik, Gasper, et al. “Retinal Metric: A Stimulus Distance Measure Derived from Population Neural Responses.” Physical Review Letters, vol. 110, no. 5, 058104, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.058104.
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[30]
2013 | Journal Article | IST-REx-ID: 2850   OA
Tkacik, Gasper, et al. “The Simplest Maximum Entropy Model for Collective Behavior in a Neural Network.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03011, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03011.
View | DOI | Download (ext.) | arXiv
 
[29]
2013 | Journal Article | IST-REx-ID: 2851
Berry, Michael, et al. “A Simple Method for Estimating the Entropy of Neural Activity.” Journal of Statistical Mechanics Theory and Experiment, vol. 2013, no. 3, P03015, IOP Publishing Ltd., 2013, doi:10.1088/1742-5468/2013/03/P03015.
View | DOI
 
[28]
2013 | Journal Article | IST-REx-ID: 2818   OA
Rajan, Kanaka, et al. “Learning Quadratic Receptive Fields from Neural Responses to Natural Stimuli.” Neural Computation, vol. 25, no. 7, MIT Press , 2013, pp. 1661–92, doi:10.1162/NECO_a_00463.
View | DOI | Download (ext.) | arXiv
 
[27]
2013 | Journal Article | IST-REx-ID: 2863   OA
Granot Atedgi, Einat, et al. “Stimulus-Dependent Maximum Entropy Models of Neural Population Codes.” PLoS Computational Biology, vol. 9, no. 3, e1002922, Public Library of Science, 2013, doi:10.1371/journal.pcbi.1002922.
View | Files available | DOI
 
[26]
2013 | Journal Article | IST-REx-ID: 2914   OA
Stephens, Greg, et al. “Statistical Thermodynamics of Natural Images.” Physical Review Letters, vol. 110, no. 1, 018701, American Physical Society, 2013, doi:10.1103/PhysRevLett.110.018701.
View | Files available | DOI | Download (ext.) | arXiv
 
[25]
2013 | Journal Article | IST-REx-ID: 3261   OA
Dubuis, Julien, et al. “Positional Information, in Bits.” PNAS, vol. 110, no. 41, National Academy of Sciences, 2013, pp. 16301–08, doi:10.1073/pnas.1315642110.
View | Files available | DOI | PubMed | Europe PMC
 
[24]
2012 | Journal Article | IST-REx-ID: 3262   OA
Tkacik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks. III. A Self-Interacting Gene.” 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.
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[23]
2011 | Journal Article | IST-REx-ID: 3276   OA
Prentice, Jason, et al. “Fast, Scalable, Bayesian Spike Identification for Multi-Electrode Arrays.” PLoS One, vol. 6, no. 7, Public Library of Science, 2011, doi:10.1371/journal.pone.0019884.
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[22]
2011 | Journal Article | IST-REx-ID: 3384   OA
Tkacik, Gasper, et al. “Natural Images from the Birthplace of the Human Eye.” PLoS One, vol. 6, no. 6, e20409, Public Library of Science, 2011, doi:10.1371/journal.pone.0020409.
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[21]
2011 | Journal Article | IST-REx-ID: 3401
Little, Shawn, et al. “The Formation of the Bicoid Morphogen Gradient Requires Protein Movement from Anteriorly Localized Source.” PLoS Biology, vol. 9, no. 3, e1000596, Public Library of Science, 2011, doi:10.1371/journal.pbio.1000596.
View | DOI
 
[20]
2011 | Journal Article | IST-REx-ID: 3374   OA
Tkacik, Gasper, and Aleksandra Walczak. “Information Transmission in Genetic Regulatory Networks a Review.” Journal of Physics: Condensed Matter, vol. 23, no. 15, 153102, IOP Publishing Ltd., 2011, doi:10.1088/0953-8984/23/15/153102.
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[19]
2010 | Conference Paper | IST-REx-ID: 3430   OA
Tkacik, Gasper. Lecture Notes for 2010 Summer School on Quantitative Evolutionary and Comparative Genomics. Elsevier, 2010.
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[18]
2010 | Journal Article | IST-REx-ID: 3738
Walczak, Aleksandra, et al. “Optimizing Information Flow in Small Genetic Networks. II. Feed-Forward Interactions.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 81, no. 4, American Institute of Physics, 2010, doi:10.1103/PhysRevE.81.041905.
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[17]
2010 | Journal Article | IST-REx-ID: 3735
Tkacik, Gasper, et al. “Local Statistics in Natural Scenes Predict the Saliency of Synthetic Textures.” PNAS, vol. 107, no. 42, National Academy of Sciences, 2010, pp. 18149–54, doi:10.1073/pnas.0914916107.
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[16]
2010 | Journal Article | IST-REx-ID: 3736
Tkacik, Gasper, et al. “Optimal Population Coding by Noisy Spiking Neurons.” PNAS, vol. 107, no. 32, National Academy of Sciences, 2010, pp. 14419–24, doi:10.1073/pnas.1004906107.
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[15]
2010 | Preprint | IST-REx-ID: 3743   OA
Tkacik, Gasper. “From Statistical Mechanics to Information Theory: Understanding Biophysical Information-Processing Systems.” ArXiv, vol. q-MN, ArXiv, 2010, pp. 1–52.
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[14]
2009 | Preprint | IST-REx-ID: 3732   OA
Tkacik, Gasper, et al. “Spin Glass Models for a Network of Real Neurons.” ArXiv, vol. q-NC, ArXiv, 2009.
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[13]
2009 | Journal Article | IST-REx-ID: 3737
Tkacik, Gasper, et al. “Optimizing Information Flow in Small Genetic Networks.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 80, no. 3, American Institute of Physics, 2009, doi:10.1103/PhysRevE.80.031920.
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[12]
2009 | Journal Article | IST-REx-ID: 3745
Tkacik, Gasper, and William Bialek. “Diffusion, Dimensionality, and Noise in Transcriptional Regulation.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 79, no. 5, American Institute of Physics, 2009, doi:10.1103/PhysRevE.79.051901.
View | DOI
 
[11]
2009 | Journal Article | IST-REx-ID: 3733
Kryazhimskiy, Sergey, et al. “The Dynamics of Adaptation on Correlated Fitness Landscapes.” PNAS, vol. 106, no. 44, National Academy of Sciences, 2009, pp. 18638–43, doi:10.1073/pnas.0905497106.
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[10]
2009 | Book Chapter | IST-REx-ID: 3747
Tkacik, Gasper, and William Bialek. “Cell Biology: Networks, Regulation, Pathways.” Encyclopedia of Complexity and Systems Science, edited by R. Meyers, Springer, 2009, pp. 719–41, doi:10.1007/978-0-387-30440-3_48.
View | DOI
 
[9]
2008 | Journal Article | IST-REx-ID: 3744   OA
Tkacik, Gasper, and Marcelo Magnasco. “Decoding Spike Timing: The Differential Reverse-Correlation Method.” Biosystems, vol. 93, no. 1–2, Elsevier, 2008, pp. 90–100, doi:10.1016/j.biosystems.2008.04.011.
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[8]
2008 | Journal Article | IST-REx-ID: 3740   OA
Tkacik, Gasper, et al. “Information Flow and Optimization in Transcriptional Regulation.” PNAS, vol. 105, no. 34, National Academy of Sciences, 2008, pp. 12265–70, doi:10.1073/pnas.0806077105.
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[7]
2008 | Journal Article | IST-REx-ID: 3734   OA
Tkacik, Gasper, et al. “The Role of Input Noise in Transcriptional Regulation.” PLoS One, vol. 3, no. 7, Public Library of Science, 2008, doi:10.1371/journal.pone.0002774.
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[6]
2008 | Journal Article | IST-REx-ID: 3739
Tkacik, Gasper, et al. “Information Capacity of Genetic Regulatory Elements.” Physical Review E Statistical Nonlinear and Soft Matter Physics, vol. 78, no. 1, American Institute of Physics, 2008, doi:10.1103/PhysRevE.78.011910.
View | DOI
 
[5]
2007 | Preprint | IST-REx-ID: 3742   OA
Broderick, Tamara, et al. “Faster Solutions of the Inverse Pairwise Ising Problem.” ArXiv, vol. q-QM, ArXiv, 2007.
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[4]
2007 | Journal Article | IST-REx-ID: 3731
Kinney, Justin, et al. “Precise Physical Models of Protein-DNA Interaction from High-Throughput Data.” PNAS, vol. 104, no. 2, National Academy of Sciences, 2007, pp. 501–06, doi:10.1073/pnas.0609908104.
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[3]
2006 | Preprint | IST-REx-ID: 3431   OA
Tkacik, Gasper, et al. “Ising Models for Networks of Real Neurons.” ArXiv, ArXiv, 2006, pp. 1–4.
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[2]
2005 | Journal Article | IST-REx-ID: 3741   OA
Slonim, N., et al. “Information-Based Clustering.” PNAS, vol. 102, no. 51, National Academy of Sciences, 2005, pp. 18297–302, doi:10.1073/pnas.0507432102.
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[1]
2005 | Preprint | IST-REx-ID: 3746   OA
Slonim, Noam, et al. “Estimating Mutual Information and Multi-Information in Large Networks.” ArXiv, ArXiv, 2005, pp. 1–11.
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