Publications

From Ilya Nemenman

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In Preparation

  1. A Pesic, D Holz, and I Nemenman. A mystery of pairwise correlations: a limiting behavior of multivariate models. In preparation.
  2. I Nemenman, C Strauss, and M Wall. Estimating free energies of proteins. In preparation. Abstract.
  3. I Nemenman and N Tishby. An axiomatic approach to the theory of information processing in networks, In preparation.
  4. I Nemenman and C Wiggins. On geometric measures of regulatory complexity, In preparation. Abstract.
  5. I Nemenman. Predictive filtering in the phototransduction cascade, In preparation. Abstract.

Articles

  1. A Margolin, K Wang, A Califano, and I Nemenman. Multivariate dependence and genetic networks inference. Submitted.
    • 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.
  2. I Nemenman. Inference of entropies of discrete random variables with unknown cardinalities. Submitted. PDF, arXiv, Abstract.
  3. G Bel, B Munsky, and I Nemenman. Common complex biochemical processes exhibit simple completion time distributions. Physical Biology 7 016003, 2010. PDF, arXiv, Abstract.
  4. B Munsky, G Bel, and I Nemenman. Specificity and Completion Time Distributions of Biochemical Processes. J. Chem. Phys. 131, 235103, 2009. PDF, arXiv, Abstract.
  5. 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.
  6. 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.
  7. A Mugler, E Ziv, I Nemenman, C Wiggins. Quantifying evolvability in small biological networks. IET Syst. Biol. 3:379, 2009. PDF, arXiv, Abstract.
  8. 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.
  9. G Bel and I Nemenman, Ergodic and non-ergodic anomalous diffusion in coupled stochastic processes. New J. Phys. 11 083009, 2009. PDF, arXiv, Abstract.
  10. 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.
  11. 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.
  12. 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.
  13. 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.
  14. C Teuscher, I Nemenman, F Alexander. Novel computing paradigms: Quo vadis? Physica D 237:v–viii (2008). Abstract, PDF.
  15. 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.
  16. 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.
  17. NA Sinitsyn and I Nemenman. Universal geometric theory of mesoscopic stochastic pumps and reversible ratchets. Phys. Rev. Lett. 99:220408, 2007. PDF, Abstract.
  18. 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.
  19. E Ziv, I Nemenman, and C Wiggins. Optimal signal processing in small stochastic biochemical networks. PLoS ONE 2(10): e1077, 2007. PDF, arXiv, Abstract.
  20. NA Sinitsyn and I Nemenman. Berry phase and pump effect in stochastic chemical kinetics. EPL 77, 58001, 2007. PDF, arXiv, Abstract.
  21. 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.
  22. 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.
  23. 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.
  24. I Nemenman. Fluctuation-dissipation theorem and models of learning. Neural Comp., 17(9):2006-2033, 2005. PDF, arXiv, Abstract.
  25. 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.
  26. C Wiggins and I Nemenman. Process pathway inference via time series analysis. Experim. Mech., 43(3):361-370, 2003. PDF, arXiv, Abstract.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. W Bialek, I Nemenman, and N Tishby. Complexity through nonextensivity. Physica A, 302:89-99, 2001. PDF, arXiv, Abstract.
  32. W Bialek, I Nemenman, and N Tishby. Predictability, complexity, and learning. Neur. Comp., 13:2409-2463, 2001. PDF, arXiv, Abstract.
  33. 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.
  34. 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.
  35. 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.
  36. 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.

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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