| Year |
Citation |
Score |
| 2023 |
Roman A, Palanski K, Nemenman I, Ryu WS. A dynamical model of thermal preference reveals independent excitatory and inhibitory learning pathways. Proceedings of the National Academy of Sciences of the United States of America. 120: e2215191120. PMID 36940330 DOI: 10.1073/pnas.2215191120 |
0.503 |
|
| 2023 |
Morrell MC, Nemenman I, Sederberg AJ. Avalanche scaling in large neural populations with distributed coupling to multiple dynamical latent variables. Arxiv. PMID 36713239 |
0.74 |
|
| 2021 |
Morrell MC, Sederberg AJ, Nemenman I. Latent Dynamical Variables Produce Signatures of Spatiotemporal Criticality in Large Biological Systems. Physical Review Letters. 126: 118302. PMID 33798342 DOI: 10.1103/PhysRevLett.126.118302 |
0.753 |
|
| 2020 |
Sederberg A, Nemenman I. Randomly connected networks generate emergent selectivity and predict decoding properties of large populations of neurons. Plos Computational Biology. 16: e1007875. PMID 32379751 DOI: 10.1371/Journal.Pcbi.1007875 |
0.74 |
|
| 2020 |
Singh V, Nemenman I. Universal Properties of Concentration Sensing in Large Ligand-Receptor Networks. Physical Review Letters. 124: 028101. PMID 32004056 DOI: 10.1103/Physrevlett.124.028101 |
0.451 |
|
| 2019 |
Mora T, Nemenman I. Physical Limit to Concentration Sensing in a Changing Environment. Physical Review Letters. 123: 198101. PMID 31765216 DOI: 10.1103/Physrevlett.123.198101 |
0.572 |
|
| 2019 |
Carballo-Pacheco M, Desponds J, Gavrilchenko T, Mayer A, Prizak R, Reddy G, Nemenman I, Mora T. Receptor crosstalk improves concentration sensing of multiple ligands. Physical Review. E. 99: 022423. PMID 30934315 DOI: 10.1103/Physreve.99.022423 |
0.554 |
|
| 2019 |
Daniels BC, Ryu WS, Nemenman I. Automated, predictive, and interpretable inference of escape dynamics. Proceedings of the National Academy of Sciences of the United States of America. PMID 30902894 DOI: 10.1073/pnas.1816531116 |
0.589 |
|
| 2017 |
Shao X, Mugler A, Kim J, Jeong HJ, Levin BR, Nemenman I. Growth of bacteria in 3-d colonies. Plos Computational Biology. 13: e1005679. PMID 28749935 DOI: 10.1371/Journal.Pcbi.1005679 |
0.653 |
|
| 2017 |
Shao X, Levin B, Nemenman I. Single variant bottleneck in the early dynamics of H. influenzae bacteremia in neonatal rats questions the theory of independent action. Physical Biology. 14: 045004. PMID 28617678 DOI: 10.1088/1478-3975/Aa731B |
0.529 |
|
| 2017 |
Singh V, Nemenman I. Simple biochemical networks allow accurate sensing of multiple ligands with a single receptor. Plos Computational Biology. 13: e1005490. PMID 28410433 DOI: 10.1371/Journal.Pcbi.1005490 |
0.467 |
|
| 2016 |
Leung K, Mohammadi A, Ryu WS, Nemenman I. Stereotypical Escape Behavior in Caenorhabditis elegans Allows Quantification of Effective Heat Stimulus Level. Plos Computational Biology. 12: e1005262. PMID 28027302 DOI: 10.1371/Journal.Pcbi.1005262 |
0.648 |
|
| 2016 |
Singh V, Tchernookov M, Nemenman I. Effects of receptor correlations on molecular information transmission. Physical Review. E. 94: 022425. PMID 27627350 DOI: 10.1103/Physreve.94.022425 |
0.764 |
|
| 2016 |
Smith T, Fancher S, Levchenko A, Nemenman I, Mugler A. Role of spatial averaging in multicellular gradient sensing. Physical Biology. 13: 035004. PMID 27203129 DOI: 10.1088/1478-3975/13/3/035004 |
0.561 |
|
| 2016 |
Ellison D, Mugler A, Brennan MD, Lee SH, Huebner RJ, Shamir ER, Woo LA, Kim J, Amar P, Nemenman I, Ewald AJ, Levchenko A. Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. Proceedings of the National Academy of Sciences of the United States of America. PMID 26792522 DOI: 10.1073/Pnas.1516503113 |
0.579 |
|
| 2016 |
Mugler A, Levchenko A, Nemenman I. Limits to the precision of gradient sensing with spatial communication and temporal integration. Proceedings of the National Academy of Sciences of the United States of America. PMID 26792517 DOI: 10.1073/Pnas.1509597112 |
0.561 |
|
| 2016 |
Fancher S, Levchenko A, Nemenman I, Mugler A. Fundamental Limits to the Precision of Multicellular Sensing Biophysical Journal. 110. DOI: 10.1016/J.Bpj.2015.11.1884 |
0.563 |
|
| 2016 |
Merchan L, Nemenman I. On the Sufficiency of Pairwise Interactions in Maximum Entropy Models of Networks Journal of Statistical Physics. 162: 1294-1308. DOI: 10.1007/S10955-016-1456-5 |
0.767 |
|
| 2015 |
Hlavacek WS, Gnanakaran S, Munsky B, Wall ME, Faeder JR, Jiang Y, Nemenman I, Resnekov O. The eighth q-bio conference: meeting report and special issue preface. Physical Biology. 12: 060401. PMID 26716953 DOI: 10.1088/1478-3975/12/6/060401 |
0.592 |
|
| 2015 |
Daniels BC, Nemenman I. Automated adaptive inference of phenomenological dynamical models. Nature Communications. 6: 8133. PMID 26293508 DOI: 10.1038/ncomms9133 |
0.367 |
|
| 2015 |
Daniels BC, Nemenman I. Efficient Inference of Parsimonious Phenomenological Models of Cellular Dynamics Using S-Systems and Alternating Regression Plos One. 10. PMID 25806510 DOI: 10.1371/Journal.Pone.0119821 |
0.323 |
|
| 2014 |
Singh V, Tchernookov M, Butterfield R, Nemenman I. Director field model of the primary visual cortex for contour detection. Plos One. 9: e108991. PMID 25329158 DOI: 10.1371/Journal.Pone.0108991 |
0.753 |
|
| 2014 |
Schwab DJ, Nemenman I, Mehta P. Zipf's law and criticality in multivariate data without fine-tuning. Physical Review Letters. 113: 068102. PMID 25148352 DOI: 10.1103/Physrevlett.113.068102 |
0.345 |
|
| 2014 |
Nemenman I, Faeder JR, Gnanakaran S, Hlavacek WS, Munsky B, Wall ME, Jiang Y. The Seventh q-bio Conference: meeting report and preface. Physical Biology. 11: 040301. PMID 25075709 DOI: 10.1088/1478-3975/11/4/040301 |
0.554 |
|
| 2014 |
Levchenko A, Nemenman I. Cellular noise and information transmission. Current Opinion in Biotechnology. 28: 156-64. PMID 24922112 DOI: 10.1016/J.Copbio.2014.05.002 |
0.33 |
|
| 2013 |
Stromberg SP, Antia R, Nemenman I. Population-expression models of immune response. Physical Biology. 10: 035010. PMID 23735782 DOI: 10.1088/1478-3975/10/3/035010 |
0.317 |
|
| 2013 |
Cheng X, Merchan L, Tchernookov M, Nemenman I. A large number of receptors may reduce cellular response time variation. Physical Biology. 10: 035008. PMID 23735700 DOI: 10.1088/1478-3975/10/3/035008 |
0.731 |
|
| 2013 |
Nemenman I, Gnanakaran S, Munsky B, Wall ME, Jiang Y, Hlavacek WS, Faeder JR. Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Physical Biology. 10: 030301. PMID 23735417 DOI: 10.1088/1478-3975/10/3/030301 |
0.589 |
|
| 2013 |
Otwinowski J, Nemenman I. Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. Plos One. 8: e61570. PMID 23650500 DOI: 10.1371/Journal.Pone.0061570 |
0.596 |
|
| 2013 |
Tchernookov M, Nemenman I. Predictive Information in a Nonequilibrium Critical Model Journal of Statistical Physics. 153: 442-459. DOI: 10.1007/S10955-013-0833-6 |
0.763 |
|
| 2012 |
Nemenman I. Gain control in molecular information processing: Lessons from neuroscience Physical Biology. 9: 26003-26003. PMID 22475952 DOI: 10.1088/1478-3975/9/2/026003 |
0.324 |
|
| 2012 |
Tanase-Nicola S, Nemenman I. Fitness in time-dependent environments includes a geometric phase contribution. Journal of the Royal Society, Interface / the Royal Society. 9: 1354-62. PMID 22112653 DOI: 10.1098/rsif.2011.0695 |
0.314 |
|
| 2012 |
Nemenman I, Gnanakaran S, Hlavacek WS, Jiang Y, Munsky B, Wall ME, Faeder JR. The Fifth Annual q-bio Conference on Cellular Information Processing Physical Biology. 9. DOI: 10.1088/1478-3975/9/5/050201 |
0.588 |
|
| 2012 |
Munsky B, Nemenman I, Bel G. Erratum: “Specificity and completion time distributions of biochemical processes” [J. Chem. Phys. 131, 235103 (2009)] The Journal of Chemical Physics. 136: 209902. DOI: 10.1063/1.4722990 |
0.709 |
|
| 2011 |
Otwinowski J, Tanase-Nicola S, Nemenman I. Speeding up Evolutionary Search by Small Fitness Fluctuations. Journal of Statistical Physics. 144: 367-378. PMID 22822270 DOI: 10.1007/S10955-011-0199-6 |
0.613 |
|
| 2011 |
Gintautas V, Ham MI, Kunsberg B, Barr S, Brumby SP, Rasmussen C, George JS, Nemenman I, Bettencourt LMA, Kenyon GT. Model cortical association fields account for the time course and dependence on target complexity of human contour perception Plos Computational Biology. 7. PMID 21998562 DOI: 10.1371/Journal.Pcbi.1002162 |
0.306 |
|
| 2011 |
Cheong R, Rhee A, Wang CJ, Nemenman I, Levchenko A. Information transduction capacity of noisy biochemical signaling networks. Science (New York, N.Y.). 334: 354-8. PMID 21921160 DOI: 10.1126/Science.1204553 |
0.325 |
|
| 2010 |
Margolin AA, Wang K, Califano A, Nemenman I. Multivariate dependence and genetic networks inference. Iet Systems Biology. 4: 428-40. PMID 21073241 DOI: 10.1049/Iet-Syb.2010.0009 |
0.683 |
|
| 2010 |
Sinitsyn NA, Nemenman I. Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics. Iet Systems Biology. 4: 409-15. PMID 21073239 DOI: 10.1049/iet-syb.2010.0064 |
0.61 |
|
| 2010 |
Bel G, Munsky B, Nemenman I. The simplicity of completion time distributions for common complex biochemical processes. Physical Biology. 7: 016003. PMID 20026876 DOI: 10.1088/1478-3975/7/1/016003 |
0.751 |
|
| 2009 |
de Ronde WH, Daniels BC, Mugler A, Sinitsyn NA, Nemenman I. Mesoscopic statistical properties of multistep enzyme-mediated reactions. Iet Systems Biology. 3: 429. PMID 21028932 DOI: 10.1049/Iet-Syb.2008.0167 |
0.696 |
|
| 2009 |
Mugler A, Ziv E, Nemenman I, Wiggins CH. Quantifying evolvability in small biological networks. Iet Systems Biology. 3: 379-87. PMID 21028928 DOI: 10.1049/Iet-Syb.2008.0165 |
0.579 |
|
| 2009 |
Munsky B, Nemenman I, Bel G. Specificity and completion time distributions of biochemical processes. The Journal of Chemical Physics. 131: 235103. PMID 20025351 DOI: 10.1063/1.3274803 |
0.752 |
|
| 2009 |
Wang K, Saito M, Bisikirska BC, Alvarez MJ, Lim WK, Rajbhandari P, Shen Q, Nemenman I, Basso K, Margolin AA, Klein U, Dalla-Favera R, Califano A. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotechnology. 27: 829-39. PMID 19741643 DOI: 10.1038/Nbt.1563 |
0.66 |
|
| 2009 |
Sinitsyn NA, Hengartner N, Nemenman I. Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proceedings of the National Academy of Sciences of the United States of America. 106: 10546-51. PMID 19525397 DOI: 10.1073/Pnas.0809340106 |
0.622 |
|
| 2009 |
Bel G, Nemenman I. Ergodic and non-ergodic anomalous diffusion in coupled stochastic processes New Journal of Physics. 11: 083009. DOI: 10.1088/1367-2630/11/8/083009 |
0.612 |
|
| 2008 |
Mugler A, Ziv E, Nemenman I, Wiggins CH. Serially regulated biological networks fully realise a constrained set of functions. Iet Systems Biology. 2: 313-22. PMID 19045826 DOI: 10.1049/Iet-Syb:20080097 |
0.566 |
|
| 2008 |
Dreisigmeyer DW, Stajic J, Nemenman I, Hlavacek WS, Wall ME. Determinants of bistability in induction of the Escherichia coli lac operon. Iet Systems Biology. 2: 293-303. PMID 19045824 DOI: 10.1049/Iet-Syb:20080095 |
0.303 |
|
| 2008 |
Nemenman I, Lewen GD, Bialek W, de Ruyter van Steveninck RR. Neural coding of natural stimuli: information at sub-millisecond resolution. Plos Computational Biology. 4: e1000025. PMID 18369423 DOI: 10.1371/journal.pcbi.1000025 |
0.761 |
|
| 2007 |
Sinitsyn NA, Nemenman I. Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets. Physical Review Letters. 99: 220408. PMID 18233271 DOI: 10.1103/Physrevlett.99.220408 |
0.606 |
|
| 2007 |
Edwards JS, Faeder JR, Hlavacek WS, Jiang Y, Nemenman I, Wall ME. Q-bio 2007: a watershed moment in modern biology. Molecular Systems Biology. 3: 148. PMID 18059443 DOI: 10.1038/Msb4100193 |
0.314 |
|
| 2007 |
Ziv E, Nemenman I, Wiggins CH. Optimal signal processing in small stochastic biochemical networks. Plos One. 2: e1077. PMID 17957259 DOI: 10.1371/Journal.Pone.0001077 |
0.352 |
|
| 2007 |
Sinitsyn NA, Nemenman I. The Berry phase and the pump flux in stochastic chemical kinetics Europhysics Letters (Epl). 77: 58001. DOI: 10.1209/0295-5075/77/58001 |
0.603 |
|
| 2006 |
Margolin AA, Wang K, Lim WK, Kustagi M, Nemenman I, Califano A. Reverse engineering cellular networks. Nature Protocols. 1: 662-71. PMID 17406294 DOI: 10.1038/Nprot.2006.106 |
0.675 |
|
| 2006 |
Margolin AA, Nemenman I, Basso K, Wiggins C, Stolovitzky G, Dalla Favera R, Califano A. ARACNE: an algorithm for the reconstruction of gene regulatory networks in a mammalian cellular context. Bmc Bioinformatics. 7: S7. PMID 16723010 DOI: 10.1186/1471-2105-7-S1-S7 |
0.676 |
|
| 2004 |
Nemenman I, Bialek W, de Ruyter van Steveninck R. Entropy and information in neural spike trains: progress on the sampling problem. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 69: 056111. PMID 15244887 DOI: 10.1103/PhysRevE.69.056111 |
0.754 |
|
| 2003 |
Wiggins C, Nemenman I. Process pathway inference via time series analysis Experimental Mechanics. 43: 361-370. DOI: 10.1007/Bf02410536 |
0.307 |
|
| 2002 |
Nemenman I, Bialek W. Occam factors and model independent Bayesian learning of continuous distributions. Physical Review. E, Statistical, Nonlinear, and Soft Matter Physics. 65: 026137. PMID 11863617 DOI: 10.1103/PhysRevE.65.026137 |
0.563 |
|
| 2001 |
Bialek W, Nemenman I, Tishby N. Predictability, complexity, and learning. Neural Computation. 13: 2409-63. PMID 11674845 DOI: 10.1162/089976601753195969 |
0.709 |
|
| 2001 |
Bialek W, Nemenman I, Tishby N. Complexity through nonextensivity Physica a: Statistical Mechanics and Its Applications. 302: 89-99. DOI: 10.1016/S0378-4371(01)00444-7 |
0.695 |
|
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