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Ilya Shmulevich

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Gene Expression Profiling

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Oligonucleotide Array Sequence Analysis

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Publications

TOP 3
Hamid Mirzaei; Paola Picotti; Max Robinson; Ilya Shmulevich; Ruedi Aebersold; John D Aitchison; Gregory Carter; David J Dilworth; Jimmy K Eng; Timothy Galitski; Bong Kim; Theo A Knijnenburg; Song Li; Jeffrey A Ranish
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.
Da Yang; Yanrui Zhao; Hong Zheng; Russell Broaddus; Kexin Chen; Hanyin Cheng; David Cogdell; Limei Hu; Ping Ji; Jinsong Liu; Gabriel Lopez-Berestein; Matti Nykter; Chad V Pecot; Sheila Reynolds; Cristian Rodriguez-Aguayo; Rajesha Rupaimoole; Ilya Shmulevich; Anil K Sood; Yan Sun; Wei Zhang
Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer.
Lynette M Moore; Matti Annala; David Cogdell; Gregory N Fuller; Virpi Kivinen; Chang-Gong Liu; Xiuping Liu; Yuexin Liu; Raymond Sawaya; Ilya Shmulevich; Olli Yli-Harja; Wei Zhang; Matti Nykter
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.

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All Publications

2013: Hamid Mirzaei; Paola Picotti; Max Robinson; Ilya Shmulevich; Ruedi Aebersold; John D Aitchison; Gregory Carter; David J Dilworth; Jimmy K Eng; Timothy Galitski; Bong Kim; Theo A Knijnenburg; Song Li; Jeffrey A Ranish
Systematic measurement of transcription factor-DNA interactions by targeted mass spectrometry identifies candidate gene regulatory proteins.
Proceedings of the National Academy of Sciences of the United States of America 2013;110(9):3645-50.
2013: Da Yang; Yanrui Zhao; Hong Zheng; Russell Broaddus; Kexin Chen; Hanyin Cheng; David Cogdell; Limei Hu; Ping Ji; Jinsong Liu; Gabriel Lopez-Berestein; Matti Nykter; Chad V Pecot; Sheila Reynolds; Cristian Rodriguez-Aguayo; Rajesha Rupaimoole; Ilya Shmulevich; Anil K Sood; Yan Sun; Wei Zhang
Integrated analyses identify a master microRNA regulatory network for the mesenchymal subtype in serous ovarian cancer.
Cancer cell 2013;23(2):186-99.
2013: Lynette M Moore; Matti Annala; David Cogdell; Gregory N Fuller; Virpi Kivinen; Chang-Gong Liu; Xiuping Liu; Yuexin Liu; Raymond Sawaya; Ilya Shmulevich; Olli Yli-Harja; Wei Zhang; Matti Nykter
Transcriptome and small RNA deep sequencing reveals deregulation of miRNA biogenesis in human glioma.
The Journal of pathology 2013;229(3):449-59.
2013: Avital Sadot; Septimia Sarbu; Hila Amir-Kroll; Juha Kesseli; Matti Nykter; Wei Zhang; Ilya Shmulevich
Information-theoretic analysis of the dynamics of an executable biological model.
PloS one 2013;8(3):e59303.
2013: Antti Larjo; Ilya Shmulevich; Harri Lähdesmäki
Structure learning for Bayesian networks as models of biological networks.
Methods in molecular biology (Clifton, N.J.) 2013;939():35-45.
2012: Edward R Dougherty; Ilya Shmulevich
On the limitations of biological knowledge.
Current genomics 2012;13(7):574-87.
2012: Guoyan Liu; Ilya Shmulevich; Anil K Sood; Yan Sun; Fengxia Xue; Da Yang; Wei Zhang
Differing clinical impact of BRCA1 and BRCA2 mutations in serous ovarian cancer.
Pharmacogenomics 2012;13(13):1523-35.
2012: Ryan Bressler; Andrea Eakin; Theo Knijnenburg; Richard Kreisberg; Jake Lin; Thomas Robinson; Hector Rovira; John Boyle; Ilya Shmulevich
Fastbreak: a tool for analysis and visualization of structural variations in genomic data.
EURASIP journal on bioinformatics & systems biology 2012;2012(1):15.
2012: Brady Bernard; Hector Rovira; Vesteinn Thorsson; Ilya Shmulevich
Increasing coverage of transcription factor position weight matrices through domain-level homology.
PloS one 2012;7(8):e42779.
2012: Yuexin Liu; Ilya Shmulevich; Anil K Sood; Yan Sun; Russell Broaddus; Jinsong Liu; Wei Zhang
Integrated analysis of gene expression and tumor nuclear image profiles associated with chemotherapy response in serous ovarian carcinoma.
PloS one 2012;7(5):e36383.
2011: Da Yang; Kenneth Hess; Sofia Khan; Ilya Shmulevich; Anil K Sood; Yan Sun; Wei Zhang
Association of BRCA1 and BRCA2 mutations with survival, chemotherapy sensitivity, and gene mutator phenotype in patients with ovarian cancer.
JAMA : the journal of the American Medical Association 2011;306(14):1557-65.
2011: Alexander V Ratushny; Ilya Shmulevich; John D Aitchison
Trade-off between responsiveness and noise suppression in biomolecular system responses to environmental cues.
PLoS computational biology 2011;7(6):e1002091.
2011: Theo A Knijnenburg; Garry P Nolan; Oriol Roda; John D Aitchison; Yakun Wan; Ilya Shmulevich
A regression model approach to enable cell morphology correction in high-throughput flow cytometry.
Molecular systems biology 2011;7():531.
2010: Timo Erkkilä; Saara Lehmusvaara; Pekka Ruusuvuori; Tapio Visakorpi; Ilya Shmulevich; Harri Lähdesmäki
Probabilistic analysis of gene expression measurements from heterogeneous tissues.
Bioinformatics (Oxford, England) 2010;26(20):2571-7.
2010: Stephen A Ramsey; Theo A Knijnenburg; Kathleen A Kennedy; Daniel E Zak; Mark Gilchrist; Elizabeth S Gold; Carrie D Johnson; Aaron E Lampano; Vladimir Litvak; Garnet Navarro; Tetyana Stolyar; Alan Aderem; Ilya Shmulevich
Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Bioinformatics (Oxford, England) 2010;26(17):2071-5.
2010: Da Yang; Antti Ylipaa; Jilong Yang; Kelly Hunt; Raphael Pollock; Jonathan Trent; Olli Yli-Harja; Ilya Shmulevich; Matti Nykter; Wei Zhang
An integrated study of aberrant gene copy number and gene expression in GIST and LMS.
Technology in cancer research & treatment 2010;9(2):171-8.
2010: Ramsey A Saleem; Rose Long-O'Donnell; David J Dilworth; Abraham M Armstrong; Arvind P Jamakhandi; Yakun Wan; Theo A Knijnenburg; Antti Niemistö; John Boyle; Richard A Rachubinski; Ilya Shmulevich; John D Aitchison
Genome-wide analysis of effectors of peroxisome biogenesis.
PloS one 2010;5(8):e11953.
2010: David B Burdick; Chris C Cavnor; Jeremy Handcock; Sarah Killcoyne; Jake Lin; Bruz Marzolf; Stephen A Ramsey; Hector Rovira; Ryan Bressler; Ilya Shmulevich; John Boyle
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.
BMC bioinformatics 2010;11():377.
2009: Theo A Knijnenburg; Lodewyk F A Wessels; Marcel J T Reinders; Ilya Shmulevich
Fewer permutations, more accurate P-values.
Bioinformatics (Oxford, England) 2009;25(12):i161-8.
2009: Limei Hu; Walter Hittelman; Tao Lu; Ping Ji; Ralph Arlinghaus; Ilya Shmulevich; Stanley R Hamilton; Wei Zhang
NGAL decreases E-cadherin-mediated cell-cell adhesion and increases cell motility and invasion through Rac1 in colon carcinoma cells.
Laboratory investigation; a journal of technical methods and pathology 2009;89(5):531-48.
2009: Vladimir Litvak; Stephen A Ramsey; Alistair G Rust; Daniel E Zak; Kathleen A Kennedy; Aaron E Lampano; Matti Nykter; Ilya Shmulevich; Alan Aderem
Function of C/EBPdelta in a regulatory circuit that discriminates between transient and persistent TLR4-induced signals.
Nature immunology 2009;10(4):437-43.
2009: R J Taylor; D Falconnet; A Niemistö; S A Ramsey; S Prinz; Ilya Shmulevich; Timothy Galitski; C L Hansen
Dynamic analysis of MAPK signaling using a high-throughput microfluidic single-cell imaging platform.
Proceedings of the National Academy of Sciences of the United States of America 2009;106(10):3758-63.
2009: Matti Nykter; Harri Lähdesmäki; Alistair Rust; Vesteinn Thorsson; Ilya Shmulevich
A data integration framework for prediction of transcription factor targets.
Annals of the New York Academy of Sciences 2009;1158():205-14.
2009: Ilya Shmulevich; John D Aitchison
Deterministic and stochastic models of genetic regulatory networks.
Methods in enzymology 2009;467():335-56.
2009: Jyrki Selinummi; Pekka Ruusuvuori; Irina Podolsky; Adrian Ozinsky; Elizabeth Gold; Olli Yli-Harja; Alan Aderem; Ilya Shmulevich
Bright field microscopy as an alternative to whole cell fluorescence in automated analysis of macrophage images.
PloS one 2009;4(10):e7497.
2009: John Boyle; Hector Rovira; Chris Cavnor; David Burdick; Sarah Killcoyne; Ilya Shmulevich
Adaptable data management for systems biology investigations.
BMC bioinformatics 2009;10():79.
2009: Albert C Huang; Limei Hu; Stuart A Kauffman; Wei Zhang; Ilya Shmulevich
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation.
BMC systems biology 2009;3():20.
2008: Won-Woo Lee; Dapeng Cui; Marta Czesnikiewicz-Guzik; Ricardo Z N Vencio; Ilya Shmulevich; Alan Aderem; Cornelia M Weyand; Jörg J Goronzy
Age-dependent signature of metallothionein expression in primary CD4 T cell responses is due to sustained zinc signaling.
Rejuvenation research 2008;11(6):1001-11.
2008: Alan Aderem; Ilya Shmulevich
Taming data.
Cell host & microbe 2008;4(4):312-3.
2008: Stephen A Ramsey; Sandy L Klemm; Daniel E Zak; Kathleen A Kennedy; Vesteinn Thorsson; Bin Li; Mark Gilchrist; Elizabeth S Gold; Carrie D Johnson; Vladimir Litvak; Garnet Navarro; Jared C Roach; Carrie M Rosenberger; Alistair G Rust; Natalya Yudkovsky; Alan Aderem; Ilya Shmulevich
Uncovering a macrophage transcriptional program by integrating evidence from motif scanning and expression dynamics.
PLoS computational biology 2008;4(3):e1000021.
2008: Matti Nykter; Nathan Price; Maximino Aldana; Stephen A Ramsey; Stuart A Kauffman; Leroy E Hood; Olli Yli-Harja; Ilya Shmulevich
Gene expression dynamics in the macrophage exhibit criticality.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(6):1897-900.
2008: Matti Nykter; Nathan Price; Antti Larjo; Tommi Aho; Stuart A Kauffman; Olli Yli-Harja; Ilya Shmulevich
Critical networks exhibit maximal information diversity in structure-dynamics relationships.
Physical review letters 2008;100(5):058702.
2008: Wenbin Liu; Harri Lähdesmäki; Edward R Dougherty; Ilya Shmulevich
Inference of Boolean networks using sensitivity regularization.
EURASIP journal on bioinformatics & systems biology 2008;():780541.
2008: John Boyle; Christopher Cavnor; Sarah Killcoyne; Ilya Shmulevich
Systems biology driven software design for the research enterprise.
BMC bioinformatics 2008;9():295.
2008: Enrique Balleza; Elena R Alvarez-Buylla; Alvaro Chaos; Stuart Kauffman; Ilya Shmulevich; Maximino Aldana
Critical dynamics in genetic regulatory networks: examples from four kingdoms.
PloS one 2008;3(6):e2456.
2008: Harri Lähdesmäki; Alistair G Rust; Ilya Shmulevich
Probabilistic inference of transcription factor binding from multiple data sources.
PloS one 2008;3(3):e1820.
2008: Martin Korb; Aistair G Rust; Vesteinn Thorsson; Christophe Battail; Bin Li; Daehee Hwang; Kathleen A Kennedy; Jared C Roach; Carrie M Rosenberger; Mark Gilchrist; Daniel Zak; Carrie Johnson; Bruz Marzolf; Alan Aderem; Ilya Shmulevich; Hamid Bolouri
The Innate Immune Database (IIDB).
BMC immunology 2008;9():7.
2007: Peter Krawitz; Ilya Shmulevich
Entropy of complex relevant components of Boolean networks.
Physical review. E, Statistical, nonlinear, and soft matter physics 2007;76(3 Pt 2):036115.
2007: Nathan Price; Ilya Shmulevich
Biochemical and statistical network models for systems biology.
Current opinion in biotechnology 2007;18(4):365-70.
2007: Peter Krawitz; Ilya Shmulevich
Basin entropy in Boolean network ensembles.
Physical review letters 2007;98(15):158701.
2007: Nathan Price; Jonathan Trent; Adel K El-Naggar; David Cogdell; Ellen Taylor; Kelly K Hunt; Raphael E Pollock; Leroy Hood; Ilya Shmulevich; Wei Zhang
Highly accurate two-gene classifier for differentiating gastrointestinal stromal tumors and leiomyosarcomas.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(9):3414-9.
2007: Antti Niemistö; Tomi Korpelainen; Ramsey Saleem; Olli Yli-Harja; John Aitchison; Ilya Shmulevich
A K-means segmentation method for finding 2-D object areas based on 3-D image stacks obtained by confocal microscopy.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2007;2007():5559-62.
2007: Ricardo Z N Vêncio; Ilya Shmulevich
ProbCD: enrichment analysis accounting for categorization uncertainty.
BMC bioinformatics 2007;8():383.
2007: Ricardo Z N Vêncio; Leonardo Varuzza; Carlos A de B Pereira; Helena Brentani; Ilya Shmulevich
Simcluster: clustering enumeration gene expression data on the simplex space.
BMC bioinformatics 2007;8():246.
2006: Rongcai Jiang; Cristian Mircean; Ilya Shmulevich; David Cogdell; Yu Jia; Ioan Tabus; Kenneth Aldape; Raymond Sawaya; Janet M Bruner; Gregory N Fuller; Wei Zhang
Pathway alterations during glioma progression revealed by reverse phase protein lysate arrays.
Proteomics 2006;6(10):2964-71.
2006: Matti Nykter; Kelly K Hunt; Raphael E Pollock; Adel K El-Naggar; Ellen Taylor; Ilya Shmulevich; Olli Yli-Harja; Wei Zhang
Unsupervised analysis uncovers changes in histopathologic diagnosis in supervised genomic studies.
Technology in cancer research & treatment 2006;5(2):177-82.
2006: Antti Niemistö; Jyrki Selinummi; Ramsey Saleem; Ilya Shmulevich; John Aitchison; Olli Yli-Harja
Extraction of the number of peroxisomes in yeast cells by automated image analysis.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2006;1():2353-6.
2005: Antti Niemistö; Valerie Dunmire; Olli Yli-Harja; Wei Zhang; Ilya Shmulevich
Analysis of angiogenesis using in vitro experiments and stochastic growth models.
Physical review. E, Statistical, nonlinear, and soft matter physics 2005;72(6 Pt 1):062902.
2005: Ilya Shmulevich; Stuart A Kauffman; Maximino Aldana
Eukaryotic cells are dynamically ordered or critical but not chaotic.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(38):13439-44.
2005: Gregory N Fuller; Cristian Mircean; Ioan Tabus; Ellen Taylor; Raymond Sawaya; Janet M Bruner; Ilya Shmulevich; Wei Zhang
Molecular voting for glioma classification reflecting heterogeneity in the continuum of cancer progression.
Oncology reports 2005;14(3):651-6.
2005: Cristian Mircean; Ilya Shmulevich; David Cogdell; Woonyoung Choi; Yu Jia; Ioan Tabus; Stanley R Hamilton; Wei Zhang
Robust estimation of protein expression ratios with lysate microarray technology.
Bioinformatics (Oxford, England) 2005;21(9):1935-42.
2005: Antti Niemistö; Valerie Dunmire; Olli Yli-Harja; Wei Zhang; Ilya Shmulevich
Robust quantification of in vitro angiogenesis through image analysis.
IEEE transactions on medical imaging 2005;24(4):549-53.
2005: Eun-Ju Lee; Cristian Mircean; Ilya Shmulevich; Huamin Wang; Jinsong Liu; Antti Niemistö; John J Kavanagh; Je-Ho Lee; Wei Zhang
Insulin-like growth factor binding protein 2 promotes ovarian cancer cell invasion.
Molecular cancer 2005;4(1):7.
2005: Antti Niemisto; Ilya Shmulevich; Olli Yli-Harja; Lucian R Chirieac; Stanley R Hamilton
Automated quantification of lymph node size and number in surgical specimens of stage II colorectal cancer.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2005;6():6313-6.
2004: Ilya Shmulevich; Stuart A Kauffman
Activities and sensitivities in boolean network models.
Physical review letters 2004;93(4):048701.
2004: Harri Lähdesmäki; Xishan Hao; Baocun Sun; Limei Hu; Olli Yli-Harja; Ilya Shmulevich; Wei Zhang
Distinguishing key biological pathways between primary breast cancers and their lymph node metastases by gene function-based clustering analysis.
International journal of oncology 2004;24(6):1589-96.
2004: Ronaldo F Hashimoto; Seungchan Kim; Ilya Shmulevich; Wei Zhang; Michael Bittner; Edward R Dougherty
Growing genetic regulatory networks from seed genes.
Bioinformatics (Oxford, England) 2004;20(8):1241-7.
2004: Xishan Hao; Baocun Sun; Limei Hu; Harri Lähdesmäki; Valerie Dunmire; Yumei Feng; Shi-Wu Zhang; Huamin Wang; Chunlei Wu; Hua Wang; Gregory N Fuller; W Fraser Symmans; Ilya Shmulevich; Wei Zhang
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 2004;100(6):1110-22.
2004: Cristian Mircean; Ioan Tabus; Tohru Kobayashi; Motoko Yamaguchi; Hiroshi Shiku; Ilya Shmulevich; Wei Zhang
Pathway analysis of informative genes from microarray data reveals that metabolism and signal transduction genes distinguish different subtypes of lymphomas.
International journal of oncology 2004;24(3):497-504.
2004: Antti Niemisto; Limei Hu; Olli Yli-Harja; Wei Zhang; Ilya Shmulevich
Quantification of in vitro cell invasion through image analysis.
Conference proceedings : ... Annual International Conference of the IEEE Engineering in Medicine and Biology Society. IEEE Engineering in Medicine and Biology Society. Conference 2004;3():1703-6.
2003: Ilya Shmulevich; Harri Lähdesmäki; Edward R Dougherty; Jaakko Astola; Wei Zhang
The role of certain Post classes in Boolean network models of genetic networks.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(19):10734-9.
2003: Jun Morikawa; Huai Li; Seungchan Kim; Kazuhiro Nishi; Satoshi Ueno; Edward Suh; Edward R Dougherty; Ilya Shmulevich; Hiroshi Shiku; Wei Zhang; Tohru Kobayashi
Identification of signature genes by microarray for acute myeloid leukemia without maturation and acute promyelocytic leukemia with t(15;17)(q22;q12)(PML/RARalpha).
International journal of oncology 2003;23(3):617-25.
2003: Ilya Shmulevich
Model selection in genomics.
Environmental health perspectives 2003;111(6):A328-9.
2003: Ilya Shmulevich; Jaakko Astola; David Cogdell; Stanley R Hamilton; Wei Zhang
Data extraction from composite oligonucleotide microarrays.
Nucleic acids research 2003;31(7):e36.
2003: Ilya Shmulevich; Ilya Gluhovsky; Ronaldo F Hashimoto; Edward R Dougherty; Wei Zhang
Steady-state analysis of genetic regulatory networks modelled by probabilistic boolean networks.
Comparative and functional genomics 2003;4(6):601-8.
2003: Tohru Kobayashi; Motoko Yamaguchi; Seungchan Kim; Jun Morikawa; Shoko Ogawa; Satoshi Ueno; Edward Suh; Edward R Dougherty; Ilya Shmulevich; Hiroshi Shiku; Wei Zhang
Microarray reveals differences in both tumors and vascular specific gene expression in de novo CD5+ and CD5- diffuse large B-cell lymphomas.
Cancer research 2003;63(1):60-6.
2002: Seungchan Kim; Edward R Dougherty; Ilya Shmulevich; Kenneth R Hess; Stanley R Hamilton; Jeffrey M. Trent; Gregory N Fuller; Wei Zhang
Identification of combination gene sets for glioma classification.
Molecular cancer therapeutics 2002;1(13):1229-36.
2002: Ilya Shmulevich; Edward R Dougherty; Wei Zhang
Gene perturbation and intervention in probabilistic Boolean networks.
Bioinformatics (Oxford, England) 2002;18(10):1319-31.
2002: Ilya Shmulevich; A H G S van der Ven
An inhibition-based stochastic countable-time decision model.
The British journal of mathematical and statistical psychology 2002;55(Pt 1):17-25.
2002: Ilya Shmulevich; Wei Zhang
Binary analysis and optimization-based normalization of gene expression data.
Bioinformatics (Oxford, England) 2002;18(4):555-65.
2002: Ilya Shmulevich; Kelly Hunt; Adel El-Naggar; Ellen Taylor; Latha Ramdas; Pilar Labordé; Kenneth R Hess; Raphael Pollock; Wei Zhang
Tumor specific gene expression profiles in human leiomyosarcoma: an evaluation of intratumor heterogeneity.
Cancer 2002;94(7):2069-75.
2002: Ilya Shmulevich; Edward R Dougherty; Seungchan Kim; Wei Zhang
Probabilistic Boolean Networks: a rule-based uncertainty model for gene regulatory networks.
Bioinformatics (Oxford, England) 2002;18(2):261-74.
2001: Ilya Shmulevich; Moncef Gabbouj; Jaakko Astola
Complexity of the consistency problem for certain Post classes.
IEEE transactions on systems, man, and cybernetics. Part B, Cybernetics : a publication of the IEEE Systems, Man, and Cybernetics Society 2001;31(2):251-3.