Publications

From Ilya Nemenman: Theoretical Biophysics @ Emory
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Updated by Ilya Jan 29, 2017.

Up to date citation information for my articles is available from my Google Scholar profile.


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Refereed Articles

  1. C Holmes, M Ghafari, A Anzar, V Saravanan, I Nemenman. Luria-Delbruck, revisited: The classic experiment does not rule out Lamarckian evolution. Submitted, 2017. PDF, Abstract, arXiv.
  2. X Shao, BR Levin, I Nemenman. Single variant bottleneck in the early dynamics of H. influenzae bacteremia in neonatal rats questions the theory of independent action. Submitted, 2016. arXiv.
  3. X Shao, A Mugler, J Kim, HJ Jeong, B Levin, I Nemenman. Growth of bacteria in 3-d colonies. Submitted, 2016. arXiv.
  4. V Singh and I Nemenman. Accurate sensing of multiple ligands with a single receptor. Submitted, 2015. PDF, Abstract, arXiv.
  5. K Srivastava, C Holmes, M Vellema, A Pack, C Elemans, I Nemenman, and S Sober. Motor control by precisely timed spike patterns. PNAS, 2017, 10.1073/pnas.1611734114. PDF, Abstract, arXiv.
  6. K Leung, A Mohammadi, W Ryu, and I Nemenman, Stereotypical escape behavior in Caenorhabditis elegans allows quantification of nociceptive stimuli levels. PLOS Comp Biol 12 (12): e1005262. 2016. PDF, Abstract, arXiv.
  7. V Singh, M Tchernookov, I Nemenman. Effects of receptor correlations on molecular information transmission. Physical Review E 94 (2), 022425, 2016.
  8. T Smith, S Fancher, A Levchenko, I Nemenman, and Andrew Mugler. Role of spatial averaging in multicellular gradient sensing. Submitted, 2016. PDF, Abstract, arXiv.
  9. I Nemenman, ME Wall and CE Strauss. Of fishes and birthdays: Efficient estimation of polymer configurational entropies. Submitted, 2015. PDF, Abstract, arXiv.
  10. L Merchan and I Nemenman. On the sufficiency of pairwise interactions in maximum entropy models of biological networks. J Stat Phys 162 (5), 1294-1308, 2016. PDF, Abstract, arXiv.
  11. A Mugler and A Levchenko and I Nemenman. Limits to the precision of gradient sensing with spatial communication and temporal integration. PNAS, 2016. doi/10.1073/pnas.1509597112 PDF, Abstract, arXiv.
  12. D Ellison, A Mugler, M Brennan, S H Lee, R Huebner, E Shamir, L A Woo, J Kim, P Amar, I Nemenman, A J Ewald, A Levchenko. Cell-cell communication enhances the capacity of cell ensembles to sense shallow gradients during morphogenesis. PNAS, 2016. doi/10.1073/pnas.1516503113 PDF, Abstract, arXiv.
  13. I Nemenman. A mathematical framework for falsifiability. Physics Today 68(10), 11, 2015. PDF, Abstract, arXiv.
  14. B Daniels and I Nemenman. Automated adaptive inference of phenomenological dynamical models. Nature Communications 6, 8133, 2015. PDF, Abstract, arXiv.
  15. B Daniels and I Nemenman. Efficient inference of parsimonious phenomenological models of cellular dynamics using S-systems and alternating regression. PLoS ONE 10: e0119821, 2015. PDF, Abstract, arXiv.
  16. C Tang, D Chehayeb, K Srivastava, I Nemenman, and S Sober. Millisecond-scale motor encoding in a cortical vocal area. PLoS Biol 12, e1002018, 2014. PDF, Abstract, arXiv.
  17. V Singh, M Tchernookov, R Butterfield, and I Nemenman. Director field model of the primary visual cortex for contour detection. PLoS ONE 9, e108991, 2014. PDF, arXiv, Abstract.
  18. D Schwab, I Nemenman, and P Mehta. Zipf’s law and criticality in multivariate data without fine-tuning. Phys Rev Lett 113, 068102, 2014. PDF, arXiv. Abstract.
  19. A Levchenko and I Nemenman. Cellular noise and information transmission. Current Opinion Biotech 28, 156, 2014. PDF, Abstract.
  20. M Tchernookov and I Nemenman, Predictive information in a nonequilibrium critical model. J Stat Phys 153, 442, 2013. PDF, arXiv, Abstract.
  21. X Cheng, L Merchan, M Tchernookov, and I Nemenman. Large number of receptors may reduce cellular response time variation. Physical Biology 10, 035008, 2013. PDF, arXiv, Abstract.
  22. S Stromberg, R Antia, and I Nemenman. Population-expression models of immune response. Physical Biology 10, 035010, 2013. PDF, arXiv, Abstract.
  23. F100prime.gif Recommended J Otwinowski and I Nemenman. Genotype to phenotype mapping and the fitness landscape of the E. coli lac promoter. PLoS ONE 8, e61570, 2013. PDF, arXiv, Abstract.
  24. I Nemenman, Information theory and adaptation. In Quantitative biology: From molecules to Cellular Systems, ME Wall, ed. (Taylor and Francis, 2012). PDF, arXiv, Abstract.
  25. I Nemenman. Gain control in molecular information processing: Lessons from neuroscience. Physical Biology 9, 026003, 2012. PDF, arXiv, Abstract.
  26. I Nemenman. Coincidences and estimation of entropies of random variables with large cardinalities. Entropy 13, 2013-2023, 2011. PDF, arXiv, Abstract.
  27. S Tanase-Nicola and I Nemenman. Fitness in time-dependent environments includes a geometric phase contribution. J Roy Soc Interface doi:10.1098/rsif.2011.0695, 2011. PDF, arXiv, Abstract.
  28. R Cheong, A Rhee, CJ Wang, I Nemenman, and A Levchenko. Information transduction capacity of noisy biochemical signaling networks. Science 334, 354–358, 2011. PDF, Abstract, Supplements.
  29. V Gintautas, M Ham, B Kunsberg, S Barr, S Brumby, C Rasmussen, J George, I Nemenman, L Bettencourt, G Kenyon. Model cortical association fields account for the time course and dependence on target complexity of human contour perception. PLoS Comput Biol 7, e1002162, 2011. PDF, arXiv, Abstract.
  30. J Otwinowski, S Tanase-Nicola, and I Nemenman. Speeding up evolutionary search by small fitness fluctuations. J Stat Phys 144, 367-378, 2011. PDF, arXiv, Abstract.
  31. Y Wei, X Wang, J Liu, I Nemenman, A Singh, H Weiss, and B Levin. The population and evolutionary dynamics of bacteria in physically structured habitats and the adaptive virtues of random motility. Proc Natl Acad Sci (USA) 108, 4047, 2011. PDF, Abstract.
  32. P Bandaru, M Bansal, and I Nemenman. Mass conservation and Inference of metabolic networks from high-throughput mass spectrometry data. J Comp Bio 18, 147, 2011. PDF, arXiv, Abstract.
    • Appeared in RECOMB Systems Biology Satellite, 2010.
  33. N Sinitsyn and I Nemenman, Time-dependent corrections to effective rate and event statistics in Michaelis-Menten kinetics. IET Syst Biol 4, 409, 2010. PDF, arXiv, Abstract.
  34. A Margolin, K Wang, A Califano, and I Nemenman. Multivariate dependence and genetic networks inference. IET Syst Biol 4, 428, 2010. PDF, arXiv, Abstract.
    • Preliminary version appear as: I Nemenman. Information theory, multivariate dependence, and genetic network inference. Technical Report NSF-KITP-04-54, KITP, UCSB, 2004. PDF, arXiv, Abstract.
  35. G Bel, B Munsky, and I Nemenman. The simplicity of completion time distributions for common complex biochemical processes. Physical Biology 7 016003, 2010. PDF, arXiv, Abstract.
  36. B Munsky, I Nemenman, and G Bel. Specificity and Completion Time Distributions of Biochemical Processes. J. Chem. Phys. 131, 235103, 2009. PDF, arXiv, Abstract.
  37. F1000.gif Recommended. K Wang, M Saito, B Bisikirska, M Alvarez, W Lim, P Rajbhandari, Q Shen, I Nemenman, K Basso, A Margolin, U Klein, R Dalla-Favera, and A Califano. Genome-wide identification of post-translational modulators of transcription factor activity in human B cells. Nature Biotech. 27:829, 2009. PDF, Abstract, Supplementary Info.
  38. W de Ronde, B Daniels, A Mugler, N Sinitsyn, and I Nemenman. Statistical properties of multistep enzyme-mediated reactions. IET Syst. Biol. 3:429, 2009. PDF, arXiv, Abstract.
  39. A Mugler, E Ziv, I Nemenman, C Wiggins. Quantifying evolvability in small biological networks. IET Syst. Biol. 3:379, 2009. PDF, arXiv, Abstract.
  40. G Bel and I Nemenman, Ergodic and non-ergodic anomalous diffusion in coupled stochastic processes. New J. Phys. 11 083009, 2009. PDF, arXiv, Abstract.
  41. N Sinitsyn, N Hengartner, and I Nemenman. Adiabatic coarse-graining and simulations of stochastic biochemical networks. Proc. Natl. Acad. Sci. (USA) 106:10546-10551, 2009. PDF, supplement, arXiv, Abstract.
  42. A Mugler, E Ziv, I Nemenman, C Wiggins. Serially-regulated biological networks fully realize a constrained set of functions. IET Systems Biology 2:313, 2008. PDF, arXiv, Abstract.
  43. D Dreisigmeyer, J Stajic, I Nemenman, W Hlavacek, and M Wall. Determinants of bistability in induction of the Escherichia coli lac operon. IET Systems Biology 2:293, 2008. PDF, arXiv, Abstract.
  44. I Nemenman, GD Lewen, W Bialek, RR de Ruyter van Steveninck. Neural Coding of Natural Stimuli: Information at Sub-Millisecond Resolution. PLoS Comput Biol 4(3): e1000025, 2008. PDF, arXiv, Abstract.
    • This paper has been presented at the CNS'07 meeting and is available as: I Nemenman, G Lewen, W Bialek, and R de Ruyter van Steveninck. Neural coding of natural stimuli: information at sub-millisecond resolution. BMC Neurosci. 8 (Suppl 2):S7, 2007. PDF.
  45. NA Sinitsyn and I Nemenman. Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets. Phys. Rev. Lett. 99:220408, 2007. PDF, Abstract.
  46. I Nemenman, GS Escola, WS Hlavacek, PJ Unkefer, CJ Unkefer, ME Wall. Reconstruction of metabolic networks from high-throughput metabolite profiling data: in silico analysis of red blood cell metabolism. Ann. N.Y. Acad. Sci. 1115:102–115, 2007. PDF, arXiv, Abstract.
  47. E Ziv, I Nemenman, and C Wiggins. Optimal signal processing in small stochastic biochemical networks. PLoS ONE 2(10): e1077, 2007. PDF, arXiv, Abstract.
  48. NA Sinitsyn and I Nemenman. Berry phase and pump effect in stochastic chemical kinetics. EPL 77, 58001, 2007. PDF, arXiv, Abstract.
  49. A Margolin, K Wang, WK Lim, M Kustagi, I Nemenman, and A Califano. Reverse engineering cellular networks. Nature Protocols, 1(2):663-672, 2006. PDF, Abstract.
  50. K Wang, I Nemenman, N Banerjee, A Margolin, and A Califano. Genome-wide discovery of modulators of transcriptional interactions in human B lymphocytes. In Lecture Notes in Computer Science, '3909, Proceedings of Research in Computational Molecular Biology: 10th Annual International Conference, RECOMB 2006, pages 348 - 362. Springer, Berlin / Heidelberg, 2006. PDF, arXiv, Abstract
    • Preliminary version: NIPS'05 Computational Biology Workshop.
  51. F1000.gif Must read. A Margolin, I Nemenman, K Basso, U Klein, C Wiggins, G Stolovitzky, Riccardo D Favera, and A Califano. ARACNE: An algorithm for reconstruction of genetic networks in a mammalian cellular context. BMC Bioinformatics, 7 (Suppl. 1):S7, 2006. PDF, arXiv, Abstract.
    • Preliminary version: NIPS'04 Computational Biology Workshop as: A Margolin, I Nemenman, C Wiggins, G Stolovitzky, and A Califano, On the reconstruction of interaction networks with applications to transcriptional regulation. PDF, arXiv.
  52. I Nemenman. Fluctuation-dissipation theorem and models of learning. Neural Comp., 17(9):2006-2033, 2005. PDF, arXiv, Abstract.
  53. I Nemenman, W Bialek, and R de Ruyter van Steveninck. Entropy and information in neural spike trains: Progress on the sampling problem. Phys. Rev. E, 69:056111, 2004. PDF, arXiv, Abstract.
  54. C Wiggins and I Nemenman. Process pathway inference via time series analysis. Experim. Mech., 43(3):361-370, 2003. PDF, arXiv, Abstract.
  55. A Silbergleit, I Nemenman, and I Mandel. On the interaction of point charges in an arbitrary domain. Techn. Phys., 48(2):146-151, 2003. PDF, arXiv, Abstract.
  56. A Silbergleit, I Mandel, and I Nemenman. Potential and field singularity at a surface point charge. J. Math. Phys., 44(10):4460-4466, 2003. PDF, arXiv, Abstract.
  57. I Nemenman, F Shafee, and W Bialek. "Entropy and inference, revisited." In T. G. Dietterich, S. Becker, and Z. Ghahramani, editors, Adv. Neural Inf. Proc. Syst. 14, Cambridge, MA, 2002. MIT Press. PDF, arXiv, Abstract.
  58. I Nemenman and W Bialek. Occam factors and model-independent Bayesian learning of continuous distributions. Phys. Rev. E, 65(2):026137, 2002. PDF, arXiv, Abstract.
    • Preliminary version: I Nemenman and W Bialek, "Learning Continuous Distributions: Simulations With Field Theoretic Priors," in T. Leen, T. Dietterich, and V. Tresp, eds. Adv. Neural Inf. Proc. Syst. 13, pp. 287-293, MIT Press, 2001. PDF.
  59. W Bialek, I Nemenman, and N Tishby. Complexity through nonextensivity. Physica A, 302:89-99, 2001. PDF, arXiv, Abstract.
  60. W Bialek, I Nemenman, and N Tishby. Predictability, complexity, and learning. Neur. Comp., 13:2409-2463, 2001. PDF, arXiv, Abstract.
  61. R Adler, I Nemenman, J Overduin, and D Santiago. On the detectability of quantum spacetime foam with gravitational-wave interferometers. Phys. Lett. B, 477;:424-428, 2000. PDF, arXiv, Abstract.
  62. J Naud, I Nemenman, M Van Raamsdonk, and V Periwal. Minimal subtraction and the Callan-Symanzik equation. Nucl. Phys. B, 540, 1999. PDF, arXiv, Abstract.
  63. I Nemenman and A Silbergleit. Explicit Green's function of a boundary value problem for a sphere and trapped flux analysis in Gravity Probe B experiment. J. Appl. Phys., 86, 1999. PDF, arXiv, Abstract.
  64. A Minkevich and I Nemenman. On the influence of gravitating vacuum on dynamics of homogeneous isotropic models in gauge-theories of gravity. Class. Quant. Grav., 12:1259-1265, 1995. PDF, Abstract.
    • Preliminary version: A Minkevich and I Nemenman. On the influence of gravitating vacuum on dynamics of homogeneous isotropic models in gauge-theories of gravity. Dokl. Akad. Nauk Belar., 39(2):45-51, 1995. In Russian. Abstract.

Editorials

  1. W Hlavacek, S Gnanakaran, B Munsky, M Wall, J Faeder, Y Jiang, I Nemenman, and O Resnekov. The eighth q-bio conference: meeting report and special issue preface. Phys Biol 12 060401, 2015. PDF. Abstract.
  2. I Nemenman, J Faeder, S Gnanakaran, W Hlavacek, B Munsky, M Wall and Y Jiang. The Seventh q-bio Conference: meeting report and preface. Phys Biol 11, 040301, 2014. PDF. Abstract.
  3. I Nemenman, S Gnanakaran, B Munsky, M Wall, Y Jiang, W Hlavacek, and J Faeder. Special section dedicated to The Sixth q-bio Conference: meeting report and preface. Phys Biol 10, 030301, 2013. PDF. Abstract.
  4. I Nemenman, S Gnanakaran, W Hlavacek, Y Jiang, B Munsky, M Wall and J Faeder. The Fifth Annual q-bio Conference on Cellular Information Processing. Phys Biol 9, 050201, 2012. PDF, Abstract.
  5. I Nemenman, J Faeder, W Hlavacek, Y Jiang, M Wall, A Zilman. Selected papers from the Fourth Annual q-bio Conference on Cellular Information Processing. Phys Biol 8, 050301, 2011. PDF, Abstract.
  6. I Nemenman, W Hlavacek, Y Jiang, M Wall, and A Zilman. Editorial: Selected papers from the Third q-bio Conference on Cellular Information Processing. IET Syst Biol 4, 331, 2010. PDF, Abstract.
  7. I Nemenman, W Hlavacek, Y Jiang, and M Wall, Editorial: Selected papers from the Second q-bio Conference on Cellular Information Processing. IET Syst. Biol. 3:297, 2009. PDF, Abstract.
  8. I Nemenman, W Hlavacek, J Edwards, J Faeder, Y Jiang, M Wall. Editorial: Selected papers from the First q-bio Conference on Cellular Information Processing. IET Syst. Biol. 2:203, 2008. PDF, Abstract.
  9. C Teuscher, I Nemenman, F Alexander. Novel computing paradigms: Quo vadis? Physica D 237:v–viii (2008). Abstract, PDF.
  10. J Edwards, J Faeder, W Hlavacek, Y Jiang, I Nemenman, and M Wall. q-bio 2007: a watershed moment in modern biology. Mol. Syst. Biol. 3:148, 2007. PDF, Abstract.

Unpublished Work

  1. K Wang, N Banerjee, A Margolin, I Nemenman, K Basso, R Dalla Favera, and A Califano. Conditional network analysis identifies candidate regulator genes in human B cells. Unpublished manuscript, 2005. PDF, arXiv, Abstract.
  2. A Margolin, N Banerjee, I Nemenman, and A Califano. Reverse engineering of yeast transcriptional network using the ARACNE algorithm. Unpublished manuscript, 2004. PDF, Abstract.
  3. T Holy and I Nemenman. On impossibility of learning in a reparameterization covariant way. Technical Report NSF-KITP-03-123, KITP, UCSB, 2002. PDF, Abstract.
  4. I Nemenman. Information Theory and Learning: A Physical Approach. PhD thesis, Princeton University, Department of Physics, 2000. PDF, arXiv, Abstract.
  5. I Kominis and I Nemenman. BGO dead crystall correction and shower fitting. Technical Report 2157, CERN: L3, 1997. PDF, Abstract.
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