llya Shmulevich

Summary

Publications

  1. pmc EPEPT: a web service for enhanced P-value estimation in permutation tests
    Theo A Knijnenburg
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 12:411. 2011
  2. pmc Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion
    Eun Ju Lee
    Department of Pathology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas, 77030, USA
    Mol Cancer 4:7. 2005
  3. pmc Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
    Albert C Huang
    University of Washington, Seattle, USA
    BMC Syst Biol 3:20. 2009
  4. ncbi request reprint An inhibition-based stochastic countable-time decision model
    Ilya Shmulevich
    Tampere International Center for Signal Processing, Tampere University of Technology, Finland
    Br J Math Stat Psychol 55:17-25. 2002
  5. pmc Eukaryotic cells are dynamically ordered or critical but not chaotic
    Ilya Shmulevich
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:13439-44. 2005
  6. pmc The role of certain Post classes in Boolean network models of genetic networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 100:10734-9. 2003
  7. ncbi request reprint Binary analysis and optimization-based normalization of gene expression data
    Ilya Shmulevich
    Cancer Genomics Laboratory, Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:555-65. 2002
  8. pmc Data extraction from composite oligonucleotide microarrays
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 85, Houston, TX 77030, USA
    Nucleic Acids Res 31:e36. 2003
  9. ncbi request reprint Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:261-74. 2002
  10. ncbi request reprint Gene perturbation and intervention in probabilistic Boolean networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:1319-31. 2002

Collaborators

Detail Information

Publications59

  1. pmc EPEPT: a web service for enhanced P-value estimation in permutation tests
    Theo A Knijnenburg
    Institute for Systems Biology, Seattle, WA, USA
    BMC Bioinformatics 12:411. 2011
    ..This is computationally expensive and often infeasible. Recently, we proposed an alternative estimator, which requires far fewer permutations compared to the standard empirical approach while still reliably estimating small P-values...
  2. pmc Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion
    Eun Ju Lee
    Department of Pathology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Houston, Texas, 77030, USA
    Mol Cancer 4:7. 2005
    ..The purpose of this study was to assess the role of increased IGFBP2 in ovarian cancer cells...
  3. pmc Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation
    Albert C Huang
    University of Washington, Seattle, USA
    BMC Syst Biol 3:20. 2009
    ..The temporal behavior of the network states progressing toward different cell fate attractors has the potential to elucidate the underlying molecular mechanisms governing differentiation...
  4. ncbi request reprint An inhibition-based stochastic countable-time decision model
    Ilya Shmulevich
    Tampere International Center for Signal Processing, Tampere University of Technology, Finland
    Br J Math Stat Psychol 55:17-25. 2002
    ..This model is compared to an existing inhibition-based continuous-time decision model and the probability distribution functions for work and distraction periods are derived...
  5. pmc Eukaryotic cells are dynamically ordered or critical but not chaotic
    Ilya Shmulevich
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 102:13439-44. 2005
    ....
  6. pmc The role of certain Post classes in Boolean network models of genetic networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Proc Natl Acad Sci U S A 100:10734-9. 2003
    ..Finally, functions from this class have a natural way of ensuring robustness against noise and perturbations, thus representing plausible evolutionarily selected candidates for regulatory rules in genetic networks...
  7. ncbi request reprint Binary analysis and optimization-based normalization of gene expression data
    Ilya Shmulevich
    Cancer Genomics Laboratory, Department of Pathology, University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:555-65. 2002
    ..The choice of this similarity measure frequently has a profound effect on the results of the analysis, yet no standards exist to guide the researcher...
  8. pmc Data extraction from composite oligonucleotide microarrays
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Unit 85, Houston, TX 77030, USA
    Nucleic Acids Res 31:e36. 2003
    ..We propose a novel approach to design so-called composite microarrays, which allow more replicates to be obtained without increasing the number of printed spots...
  9. ncbi request reprint Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:261-74. 2002
    ....
  10. ncbi request reprint Gene perturbation and intervention in probabilistic Boolean networks
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, 1515 Holcombe Blvd, Box 85, Houston, TX 77030, USA
    Bioinformatics 18:1319-31. 2002
    ..We consider the general question of the potential effect of individual genes on the global dynamical network behavior, both from the view of random gene perturbation as well as intervention in order to elicit desired network behavior...
  11. pmc Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites
    Stephen A Ramsey
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Bioinformatics 26:2071-5. 2010
    ....
  12. pmc Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas
    Nathan D Price
    Institute for Systems Biology, Seattle, WA 98103, USA
    Proc Natl Acad Sci U S A 104:3414-9. 2007
    ..We expect that the use of simple marker pairs that exhibit these traits will be of significant clinical use in a variety of contexts...
  13. ncbi request reprint A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy
    Antti Niemistö
    Institute for Systems Biology, Seattle, Washington, USA
    Conf Proc IEEE Eng Med Biol Soc 2007:5559-62. 2007
    ....
  14. ncbi request reprint An integrated study of aberrant gene copy number and gene expression in GIST and LMS
    Da Yang
    Department of Pathology, Sarcoma Medical Oncology The University of Texas M D Anderson Cancer Center, Houston Texas, USA
    Technol Cancer Res Treat 9:171-8. 2010
    ....
  15. pmc A data integration framework for prediction of transcription factor targets
    Matti Nykter
    Institute for Systems Biology, Seattle, Washington, USA
    Ann N Y Acad Sci 1158:205-14. 2009
    ..This analysis shows that with assessment of the quality and biological relevance of the data, reliable predictions can be obtained with this computational framework...
  16. pmc In silico microdissection of microarray data from heterogeneous cell populations
    Harri Lähdesmäki
    Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
    BMC Bioinformatics 6:54. 2005
    ..Similarly, irrelevant gene combinations can be discovered in the case of gene expression based classification...
  17. pmc Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals
    Vladimir Litvak
    Institute for Systems Biology, Seattle, Washington, USA
    Nat Immunol 10:437-43. 2009
    ..Our results suggest a mechanism that enables the innate immune system to detect the duration of infection and to respond appropriately...
  18. ncbi request reprint Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays
    Rongcai Jiang
    Department of Pathology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Proteomics 6:2964-71. 2006
    ..The marked association of phosphorylation of AKT at Thr308, but not Ser473, with glioblastoma suggests a specific event of PI3K pathway activation in glioma progression...
  19. ncbi request reprint Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression
    Gregory N Fuller
    Department of Pathology, University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Oncol Rep 14:651-6. 2005
    ....
  20. ncbi request reprint Robust estimation of protein expression ratios with lysate microarray technology
    Cristian Mircean
    Department of Pathology, University of Texas M D Anderson Cancer Center, Houston, USA
    Bioinformatics 21:1935-42. 2005
    ..This study aims to develop suitable algorithms that yield accurate representations of the relative expression levels in different samples from multiple data points...
  21. doi request reprint NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells
    Limei Hu
    Department of Pathology, The University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    Lab Invest 89:531-48. 2009
    ..NGAL may therefore be a new target for therapeutic intervention in colorectal carcinoma...
  22. pmc Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images
    Jyrki Selinummi
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS ONE 4:e7497. 2009
    ..This technique, however, has a number of drawbacks such as the limited number of available fluorescent channels in microscopes, overlapping excitation and emission spectra of the stains, and phototoxicity...
  23. pmc SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments
    David B Burdick
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 11:377. 2010
    ..However, the existing software systems for managing and processing these data have not provided the flexible infrastructure that research requires...
  24. pmc Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics
    Stephen A Ramsey
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS Comput Biol 4:e1000021. 2008
    ..The network incorporates known regulators and gives insight into the transcriptional control of macrophage activation. Our analysis identified a novel regulator (TGIF1) that may have a role in macrophage activation...
  25. pmc Genome-wide analysis of effectors of peroxisome biogenesis
    Ramsey A Saleem
    Institute for Systems Biology, Seattle, Washington, USA
    PLoS ONE 5:e11953. 2010
    ..By integration with extant data sets, we present a total of 211 genes linked to peroxisome biogenesis and highlight the complex networks through which information flows during peroxisome biogenesis and function...
  26. pmc Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data
    Miika Ahdesmäki
    Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
    BMC Bioinformatics 8:233. 2007
    ..In many circumstances we are interested in finding targets that are expressed periodically. To tackle the problems of uneven sampling and unknown type of noise in periodicity detection, we propose to use robust regression...
  27. ncbi request reprint Critical networks exhibit maximal information diversity in structure-dynamics relationships
    Matti Nykter
    Institute of Signal Processing, Tampere University of Technology, Tampere, Finland
    Phys Rev Lett 100:058702. 2008
    ..Here we use an information theoretic approach to study structure-dynamics relationships within a unified framework and show that these relationships are most diverse in the critical regime...
  28. pmc Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues
    Alexander V Ratushny
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS Comput Biol 7:e1002091. 2011
    ....
  29. ncbi request reprint Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies
    Matti Nykter
    Department of Pathology, The University of Texas M D Anderson Cancer Center, Houston, Texas, USA
    Technol Cancer Res Treat 5:177-82. 2006
    ..Further, unsupervised analysis often proves to be a critical quality control step in identifying structural problems that may exist. Finally, MDS analysis further supports that GIST is a distinct type of sarcoma...
  30. pmc A regression model approach to enable cell morphology correction in high-throughput flow cytometry
    Theo A Knijnenburg
    Institute for Systems Biology, 401 Terry Avenue North, 1441 North 34th Street, Seattle, WA 98109 5234, USA
    Mol Syst Biol 7:531. 2011
    ..We identify a group of epigenetic regulators and nucleoporins that, by maintaining an 'unresponsive population,' may provide the population with the advantage of diversified bet hedging...
  31. pmc Adaptable data management for systems biology investigations
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 10:79. 2009
    ..To support these requirements data management systems are needed that can be rapidly built and readily adapted for new usage...
  32. ncbi request reprint Pathway analysis of informative genes from microarray data reveals that metabolism and signal transduction genes distinguish different subtypes of lymphomas
    Cristian Mircean
    Institute of Signal Processing, Tampere University of Technology, FIN 33101 Tampere, Finland
    Int J Oncol 24:497-504. 2004
    ....
  33. pmc Gene expression dynamics in the macrophage exhibit criticality
    Matti Nykter
    Institute of Signal Processing, Tampere University of Technology, 33101 Tampere, Finland
    Proc Natl Acad Sci U S A 105:1897-900. 2008
    ....
  34. pmc Deterministic and stochastic models of genetic regulatory networks
    Ilya Shmulevich
    Institute for Systems Biology, Seattle, Washington, USA
    Methods Enzymol 467:335-56. 2009
    ..For each combination of these categories, a model is presented and discussed in the context of the yeast cell cycle, illustrating how different types of questions can be addressed by different model classes...
  35. pmc Simcluster: clustering enumeration gene expression data on the simplex space
    Ricardo Z N Vencio
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    BMC Bioinformatics 8:246. 2007
    ..Therefore, pattern recognition methods commonly used for microarray data analysis may be non-informative for the data generated by transcript enumeration techniques since they ignore certain fundamental properties of this space...
  36. ncbi request reprint Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis
    Harri Lähdesmäki
    Cancer Genomics Laboratory, Department of Pathology, The University of Texas M D Anderson Cancer Center, Houston, TX 77030, USA
    Int J Oncol 24:1589-96. 2004
    ..The results also suggest that the altered cell adhesion and migration potentials that are required for tumors to metastasize already exist in the primary tumors as a whole...
  37. pmc ProbCD: enrichment analysis accounting for categorization uncertainty
    Ricardo Z N Vencio
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103 8904, USA
    BMC Bioinformatics 8:383. 2007
    ....
  38. ncbi request reprint Extraction of the number of peroxisomes in yeast cells by automated image analysis
    Antti Niemistö
    Institute of Signal Processing, Tampere University of Technology, Finland
    Conf Proc IEEE Eng Med Biol Soc 1:2353-6. 2006
    ..The peroxisomes are detected by thresholding the fluorescent image. The method is tested with several images of a budding yeast Saccharomyces cerevisiae population, and the results are compared with manually obtained results...
  39. ncbi request reprint Entropy of complex relevant components of Boolean networks
    Peter Krawitz
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Phys Rev E Stat Nonlin Soft Matter Phys 76:036115. 2007
    ..We also demonstrate that basin entropy can be estimated from time-series data and is therefore also applicable to nondeterministic networks models...
  40. pmc Probabilistic analysis of gene expression measurements from heterogeneous tissues
    Timo Erkkilä
    Department of Signal Processing, Tampere University of Technology, Finland
    Bioinformatics 26:2571-7. 2010
    ....
  41. doi request reprint Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer
    Da Yang
    Department of Pathology, University of Texas MD Anderson Cancer Center, Houston, TX 77030, USA
    JAMA 306:1557-65. 2011
    ..Attempts to determine the clinical significance of BRCA1/2 mutations in ovarian cancer have produced conflicting results...
  42. pmc Fewer permutations, more accurate P-values
    Theo A Knijnenburg
    Institute for Systems Biology, Seattle, WA, USA
    Bioinformatics 25:i161-8. 2009
    ..Thereby, it imposes upon itself the need for a very large number of permutations when small P-values are to be accurately estimated. This is computationally expensive and often infeasible...
  43. ncbi request reprint Tumor specific gene expression profiles in human leiomyosarcoma: an evaluation of intratumor heterogeneity
    Ilya Shmulevich
    Department of Pathology, The University of Texas M D Anderson Cancer Center, 1515 Holcombe Boulevard, Houston, TX 77030, USA
    Cancer 94:2069-75. 2002
    ..The authors also identified genes that are expressed differentially in tumor and normal tissue...
  44. pmc Biochemical and statistical network models for systems biology
    Nathan D Price
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    Curr Opin Biotechnol 18:365-70. 2007
    ..In particular, we discuss a number of modeling approaches in the context of the assumptions that they entail, the types of data required for their inference, and the range of their applicability...
  45. ncbi request reprint Analysis of angiogenesis using in vitro experiments and stochastic growth models
    Antti Niemistö
    Institute of Signal Processing, Tampere University of Technology, P O Box 553, 33101 Tampere, Finland
    Phys Rev E Stat Nonlin Soft Matter Phys 72:062902. 2005
    ..It is found that invasion percolation is better than diffusion limited aggregation at matching experimental data. We also present evidence that the distribution of the lengths of real tubule complexes follows a power law...
  46. pmc The Innate Immune Database (IIDB)
    Martin Korb
    Institute for Systems Biology, 1441 North 34thStreet, Seattle, Washington 98103 8904, USA
    BMC Immunol 9:7. 2008
    ..It provides a broad resource to the research community, and a stepping stone towards the delineation of the network of transcriptional regulatory interactions underlying the integrated response of macrophages to pathogens...
  47. pmc Systems biology driven software design for the research enterprise
    John Boyle
    Institute for Systems Biology, 1441 N 34th Street, Seattle, WA 98103, USA
    BMC Bioinformatics 9:295. 2008
    ..As scientists work in isolated groups, integration with other groups is rarely a consideration when building the required software tools...
  48. pmc Probabilistic inference of transcription factor binding from multiple data sources
    Harri Lähdesmäki
    Institute for Systems Biology, Seattle, Washington, United States of America
    PLoS ONE 3:e1820. 2008
    ..Test data set, a web tool, source codes and supplementary data are available at: http://www.probtf.org...
  49. ncbi request reprint Basin entropy in Boolean network ensembles
    Peter Krawitz
    Institute for Systems Biology, Seattle, Washington 98103, USA
    Phys Rev Lett 98:158701. 2007
    ....
  50. pmc Activities and sensitivities in boolean network models
    Ilya Shmulevich
    Cancer Genomics Laboratory, University of Texas M D Anderson Cancer Center, Houston, Texas 77030, USA
    Phys Rev Lett 93:048701. 2004
    ..Finally, we demonstrate the important role of the average sensitivity in determining the dynamical behavior of a Boolean network...
  51. pmc Taming data
    Alan Aderem
    Institute for Systems Biology, 1441 North 34th Street, Seattle, WA 98103, USA
    Cell Host Microbe 4:312-3. 2008
    ..innatedb.ca), a publicly available, manually curated database of experimentally verified molecular interactions and pathways involved in innate immunity, is a powerful new resource that facilitates such integrative systems-level analyses...
  52. ncbi request reprint Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas
    Tohru Kobayashi
    The Second Department of Internal Medicine, Mie University School of Medicine, Tsu, 514 8507, Japan
    Cancer Res 63:60-6. 2003
    ..Those results suggest that CD5(+) and CD5(-) DLBCLs have different gene expression signatures in both tumor cells and their vascular systems...
  53. ncbi request reprint Differential gene and protein expression in primary breast malignancies and their lymph node metastases as revealed by combined cDNA microarray and tissue microarray analysis
    Xishan Hao
    Tianjin Medical University Cancer Hospital, Tianjin, China
    Cancer 100:1110-22. 2004
    ..Metastatic disease is a major adverse prognostic factor in breast carcinoma. Lymph node metastases often represent the first step in the metastatic process...
  54. pmc Critical dynamics in genetic regulatory networks: examples from four kingdoms
    Enrique Balleza
    Instituto de Ciencias Fisicas, Universidad Nacional Autonoma de Mexico, Cuernavaca, Morelos, Mexico
    PLoS ONE 3:e2456. 2008
    ..The generality of this result suggests that criticality at the genetic level might constitute a fundamental evolutionary mechanism that generates the great diversity of dynamically robust living forms that we observe around us...
  55. ncbi request reprint Identification of combination gene sets for glioma classification
    Seungchan Kim
    Department of Electrical Engineering, Texas A and M University, College Station, Texas 77840, USA
    Mol Cancer Ther 1:1229-36. 2002
    ..Two-gene and three-gene combinations thus provide robust classifiers possessing the potential to translate expression microarray results into diagnostic histopathological assays for clinical utilization...
  56. ncbi request reprint Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha)
    Jun Morikawa
    The Second Department of Internal Medicine, Mie University School of Medicine, 2 174 Edobashi, Tsu 514 8507, Japan
    Int J Oncol 23:617-25. 2003
    ....
  57. ncbi request reprint Growing genetic regulatory networks from seed genes
    Ronaldo F Hashimoto
    Department of Electrical Engineering, Texas A and M University, College Station, TX, USA 77843, USA
    Bioinformatics 20:1241-7. 2004
    ..Computationally and mathematically, it is more feasible to model and simulate a network with a small number of genes. In addition, it is more likely that a small set of genes maintains a specific core regulatory mechanism...
  58. ncbi request reprint Robust quantification of in vitro angiogenesis through image analysis
    Antti Niemistö
    IEEE Trans Med Imaging 24:549-53. 2005
    ..We have implemented a software package that utilizes the methods. The software as well as a set of test images are available at http://www.cs.tut.fi/sgn/csb/angioquant/...
  59. pmc Model selection in genomics
    Ilya Shmulevich
    Environ Health Perspect 111:A328-9. 2003