Ilya Shmulevich

Ilya Shmulevich received his Ph.D. in Electrical and Computer Engineering from Purdue University, West Lafayette, IN, in 1997. From 1997–1998, he was a postdoctoral researcher at the Nijmegen Institute for Cognition and Information at the University of Nijmegen and National Research Institute for Mathematics and Computer Science at the University of Amsterdam in The Netherlands, where he studied computational models of music perception and recognition. In 1998–2000, he worked as a senior researcher at the Tampere International Center for Signal Processing at the Signal Processing Laboratory in Tampere University of Technology, Tampere, Finland. From 2001-2005, he was an Assistant Professor at the Cancer Genomics Laboratory in the Department of Pathology at The University of Texas M. D. Anderson Cancer Center and an Adjunct Professor in the Department of Statistics in Rice University. Presently, he is an Associate Professor at the Institute for Systems Biology and an Affiliate Professor in the Departments of Bioengineering and Electrical Engineering at the University of Washington. He is an Associate Editor of Environmental Health Perspectives and a Senior Member of the IEEE. His research interests include systems biology, genomics, nonlinear signal and image processing, and computational learning theory.

Biography Updated on 27 June 2007

Personal Home Page

http://www.systemsbiology.org/Scientists_and_Research/Faculty_Groups/Shmulevich_Group

Articles in Scholarly Journals [Incomplete List]

  1. Inference of Boolean Networks Using Sensitivity Regularization
    EURASIP Journal on Bioinformatics and Systems Biology, vol. 2008, Article ID 780541, 12 pages, 2008
  2. Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
    BMC Bioinformatics, vol. 8, no. 1, p. 233, 2007
  3. Propagating organization: an enquiry
    Biology & Philosophy, vol. 23, no. 1, pp. 27–45, 2007
  4. Biochemical and statistical network models for systems biology
    Current Opinion in Biotechnology, vol. 18, no. 4, pp. 365–370, 2007
  5. Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
    Proceedings of the National Academy of Sciences, vol. 104, no. 9, pp. 3414–3419, 2007
  6. Basin Entropy in Boolean Network Ensembles
    Physical Review Letters, vol. 98, no. 15, 2007
  7. Entropy of complex relevant components of Boolean networks
    Physical Review E, vol. 76, no. 3, 2007
  8. Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays
    PROTEOMICS, vol. 6, no. 10, pp. 2964–2971, 2006
  9. Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks
    Signal Processing, vol. 86, no. 4, pp. 814–834, 2006
  10. Nonlinear Modeling of Protein Expressions in Protein Arrays
    IEEE Transactions on Signal Processing, vol. 54, no. 6, pp. 2394–2407, 2006
  11. Guest Editorial Genomic Signal Processing
    IEEE Transactions on Signal Processing, vol. 54, no. 6, pp. 2373–2374, 2006
  12. Robust Quantification of In Vitro Angiogenesis Through Image Analysis
    IEEE Transactions on Medical Imaging, vol. 24, no. 4, pp. 549–553, 2005
  13. Molecular Cancer, vol. 4, no. 1, p. 7, 2005
  14. BMC Bioinformatics, vol. 6, no. 1, p. 54, 2005
  15. Steady-state probabilities for attractors in probabilistic Boolean networks
    Signal Processing, vol. 85, no. 10, pp. 1993–2013, 2005
  16. Noise in a small genetic circuit that undergoes bifurcation
    Complexity, vol. 11, no. 1, pp. 45–51, 2005
  17. Eukaryotic cells are dynamically ordered or critical but not chaotic
    Proceedings of the National Academy of Sciences, vol. 102, no. 38, pp. 13439–13444, 2005
  18. Robust estimation of protein expression ratios with lysate microarray technology
    Bioinformatics, vol. 21, no. 9, pp. 1935–1942, 2005
  19. Analysis of angiogenesis using in vitro experiments and stochastic growth models
    Physical Review E, vol. 72, no. 6, 2005
  20. Growing genetic regulatory networks from seed genes
    Bioinformatics, vol. 20, no. 8, pp. 1241–1247, 2004
  21. Activities and Sensitivities in Boolean Network Models
    Physical Review Letters, vol. 93, no. 4, 2004
  22. Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis
    Cancer, vol. 100, no. 6, pp. 1110–1122, 2004
  23. The number and probability of canalizing functions
    Physica D: Nonlinear Phenomena, vol. 197, no. 3-4, pp. 211–221, 2004
  24. Genomic Signal Processing: The Salient Issues
    EURASIP Journal on Applied Signal Processing, vol. 2004, no. 1, pp. 146–153, 2004
  25. Correction of Misclassifications Using a Proximity-Based Estimation Method
    EURASIP Journal on Applied Signal Processing, vol. 2004, no. 8, pp. 1142–1155, 2004
  26. Spectral Methods for Testing Membership in Certain Post Classes and the Class of Forcing Functions
    IEEE Signal Processing Letters, vol. 11, no. 2, pp. 289–292, 2004
  27. Steady-state analysis of genetic regulatory networks modelled by probabilistic Boolean networks
    Comparative and Functional Genomics, vol. 4, no. 6, pp. 601–608, 2003
  28. Machine Learning, vol. 52, no. 1/2, pp. 147–167, 2003
  29. Genomic signal processing
    Signal Processing, vol. 83, no. 4, pp. 691–694, 2003
  30. Mappings between probabilistic Boolean networks
    Signal Processing, vol. 83, no. 4, pp. 799–809, 2003
  31. The role of certain Post classes in Boolean network models of genetic networks
    Proceedings of the National Academy of Sciences, vol. 100, no. 19, pp. 10734–10739, 2003
  32. Gene perturbation and intervention in probabilistic Boolean networks
    Bioinformatics, vol. 18, no. 10, pp. 1319–1331, 2002
  33. Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks
    Bioinformatics, vol. 18, no. 2, pp. 261–274, 2002
  34. Kernel density estimation with adaptive varying window size
    Pattern Recognition Letters, vol. 23, no. 14, pp. 1641–1648, 2002
  35. Journal of Mathematical Imaging and Vision, vol. 16, no. 3, pp. 237–249, 2002
  36. Tumor specific gene expression profiles in human leiomyosarcoma
    Cancer, vol. 94, no. 7, pp. 2069–2075, 2002
  37. Journal of Biological Systems, vol. 10, no. 4, p. 431, 2002
  38. On the robustness of the class of stack filters
    IEEE Transactions on Signal Processing, vol. 50, no. 7, pp. 1640–1649, 2002
  39. From Boolean to probabilistic Boolean networks as models of genetic regulatory networks
    Proceedings of the IEEE, vol. 90, no. 11, pp. 1778–1792, 2002
  40. Editorial
    EURASIP Journal on Applied Signal Processing, vol. 2002, no. 1, pp. 1–3, 2002
  41. Editorial
    EURASIP Journal on Applied Signal Processing, vol. 2001, no. 4, pp. 189–191, 2001
  42. Almost all monotone Boolean functions are polynomially learnable using membership queries
    Information Processing Letters, vol. 79, no. 5, pp. 211–213, 2001
  43. Breakdown probabilities of recursive stack filters
    Signal Processing, vol. 81, no. 1, pp. 227–231, 2001
  44. Computers and the Humanities, vol. 35, no. 1, pp. 23–35, 2001
  45. Spectral design of weighted median filters admitting negative weights
    IEEE Signal Processing Letters, vol. 8, no. 12, pp. 313–316, 2001
  46. Complexity of the consistency problem for certain Post classes
    IEEE Transactions on Systems, Man and Cybernetics, Part B (Cybernetics), vol. 31, no. 2, pp. 251–253, 2001
  47. Block-median pyramidal transform: analysis and denoising applications
    IEEE Transactions on Signal Processing, vol. 49, no. 2, pp. 364–372, 2001
  48. Output distributions of stack filters based on mirrored threshold decomposition
    IEEE Transactions on Signal Processing, vol. 49, no. 7, pp. 1454–1460, 2001
  49. The use of sample selection probabilities for stack filter design
    IEEE Signal Processing Letters, vol. 7, no. 7, pp. 189–192, 2000
  50. Output distributions of recursive stack filters
    IEEE Signal Processing Letters, vol. 6, no. 7, pp. 175–178, 1999