Ilya Shmulevich - researchr alias

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2010

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experimentsDavid B. Burdick, Christopher C. Cavnor, Jeremy Handcock, Sarah A. Killcoyne, Jake Lin, Bruz Marzolf, Stephen A. Ramsey, Hector Rovira, Ryan Bressler, Ilya Shmulevich, John Boyle. bmcbi, 11:377, 2010. [doi]

Probabilistic analysis of gene expression measurements from heterogeneous tissuesTimo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich, Harri Lähdesmäki. bioinformatics, 26(20):2571-2577, 2010. [doi]

Biological information as set-based complexityDavid J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich. TIT, 56(2):667-677, 2010. [doi]

Howdah - A Flexible Pipeline Framework for Analyzing Genomic DataSteven Lewis, Sheila Reynolds, Hector Rovira, Mike O Leary, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle. cloudcom (empty year): 776-779 [doi]

Introduction to the special issue on information theory in molecular biology and neuroscienceOlgica Milenkovic, Gil Alterovitz, Gerard Battail, Todd P. Coleman, Joachim Hagenauer, Sean P. Meyn, Nathan D. Price, Marco Ramoni, Ilya Shmulevich, Wojciech Szpankowski. TIT, 56(2):649-652, 2010. [doi]

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sitesStephen 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. bioinformatics, 26(17):2071-2075, 2010. [doi]

An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and ComplexityHector Rovira, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle. dils 2010: 179-191 [doi]

Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory NetworksIlya Shmulevich, Edward R. Dougherty. SIAM, 2010. [doi]

2009

Adaptable data management for systems biology investigationsJohn Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich. bmcbi, 10, 2009. [doi]

Fewer permutations, more accurate ::::P::::-valuesTheo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich. bioinformatics, 25(12), 2009. [doi]

2008

Systems biology driven software design for the research enterpriseJohn Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich. bmcbi, 9, 2008. [doi]

Inference of Boolean Networks Using Sensitivity RegularizationWenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich. ejbsb, 2008, 2008. [doi]

Learning the structure of dynamic Bayesian networks from time series and steady state measurementsHarri Lähdesmäki, Ilya Shmulevich. ml, 71(2-3):185-217, 2008. [doi]

2007

2006

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networksHarri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja. sigpro, 86(4):814-834, 2006. [doi]

Nonlinear modeling of protein expressions in protein arraysIoan Tabus, Andrea Hategan, Cristian Mircean, Jorma Rissanen, Ilya Shmulevich, Wei Zhang, Jaakko Astola. tsp, 54(6-2):2394-2407, 2006. [doi]

2005

Steady-state probabilities for attractors in probabilistic Boolean networksMarcel Brun, Edward R. Dougherty, Ilya Shmulevich. sigpro, 85(10):1993-2013, 2005. [doi]

::::In silico ::::microdissection of microarray data from heterogeneous cell populationsHarri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang. bmcbi, 6:54, 2005. [doi]

Robust estimation of protein expression ratios with lysate microarray technologyCristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang. bioinformatics, 21(9):1935-1942, 2005. [doi]

Robust quantification of in vitro angiogenesis through image analysisAntti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich. tmi, 24(4):549-553, 2005. [doi]

Noise in a small genetic circuit that undergoes bifurcationTrent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman. complexity, 11(1):45-51, 2005. [doi]

2004

2003

Genomic signal processingJaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus. sigpro, 83(4):691-694, 2003. [doi]

Mappings between probabilistic Boolean networksEdward R. Dougherty, Ilya Shmulevich. sigpro, 83(4):799-809, 2003. [doi]

On Learning Gene Regulatory Networks Under the Boolean Network ModelHarri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja. ml, 52(1-2):147-167, 2003. [doi]

2002

EditorialKenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich. ejasp, 2002(1):1-3, 2002. [doi]

Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising ApplicationsIlya Gluhovsky, Vladimir P. Melnik, Ilya Shmulevich. jmiv, 16(3):237-249, 2002. [doi]

Kernel density estimation with adaptive varying window sizeVladimir Katkovnik, Ilya Shmulevich. prl, 23(14):1641-1648, 2002. [doi]

On the distribution of the number of monotone Boolean functions relative to the number of lower unitsAleksey D. Korshunov, Ilya Shmulevich. DM, 257(2-3):463-479, 2002. [doi]

Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networksIlya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang. bioinformatics, 18(2):261-274, 2002.

Binary analysis and optimization-based normalization of gene expression dataIlya Shmulevich, Wei Zhang. bioinformatics, 18(4):555-565, 2002.

ayesian automatic relevance determination algorithms for classifying gene expression dataIlya Shmulevich, Edward R. Dougherty, Wei Zhang. bioinformatics, 18(10):1332-1339, 2002.

2001

EditorialKenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich. ejasp, 2001(4):189-191, 2001. [doi]

Breakdown probabilities of recursive stack filtersPertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich. sigpro, 81(1):227-231, 2001. [doi]

Almost all monotone Boolean functions are polynomially learnable using membership queriesIlya Shmulevich, Aleksey D. Korshunov, Jaakko Astola. ipl, 79(5):211-213, 2001. [doi]

Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key FindingIlya Shmulevich, Olli Yli-Harja, Edward Coyle, Dirk-Jan Povel, Kjell Lemström. lre, 35(1):23-35, 2001. [doi]

Complexity of the consistency problem for certain Post classesIlya Shmulevich, Moncef Gabbouj, Jaakko Astola. tsmc, 31(2):251-253, 2001.

Simplified implementation of the recursive median sieveOlli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard Harvey, Ilya Shmulevich. sigpro, 81(7):1565-1570, 2001. [doi]

2000

A New Image Similarity Measure Based on Ordinal CorrelationBogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela. icip 2000:

1999