Difference between revisions of "Publications"

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Up to date citation information for my articles is available from my [http://scholar.google.com/citations?user=enjXdH4AAAAJ&hl=en Google Scholar profile].
 
Up to date citation information for my articles is available from my [http://scholar.google.com/citations?user=enjXdH4AAAAJ&hl=en Google Scholar profile].
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Revision as of 04:10, 30 August 2018

Return to Home or Overview of Professional Activities.

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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