Ilya Shmulevich

Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich: Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP J. Bioinformatics and Systems Biology 2012: 15 (2012)

Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich: EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC Bioinformatics 12: 411 (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 7(6) (2011)

Ilya Shmulevich, Edward R. Dougherty: Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks. SIAM 2010, isbn 978-0-89871-692-4, pp. I-XIII, 1-267

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 26(17): 2071-2075 (2010)

Timo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich, Harri Lähdesmäki: Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinformatics 26(20): 2571-2577 (2010)

David 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: SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinformatics 11: 377 (2010)

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

David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich: Biological information as set-based complexity. IEEE Transactions on Information Theory 56(2): 667-677 (2010)

Steven Lewis, Sheila Reynolds, Hector Rovira, Mike O'Leary, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle: Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data. CloudCom 2010: 776-779

Hector Rovira, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle: An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity. DILS 2010: 179-191

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich: Fewer permutations, more accurate P-values. Bioinformatics 25(12) (2009)

John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich: Adaptable data management for systems biology investigations. BMC Bioinformatics 10 (2009)

Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, Edward R. Dougherty: Critical Boolean networks require minimal intervention rate. GENSiPS 2009: 1-2

Peter Krawitz, Ilya Shmulevich: Boolean Modeling of Biological Networks. Encyclopedia of Complexity and Systems Science 2009: 599-608

John Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich: Systems biology driven software design for the research enterprise. BMC Bioinformatics 9 (2008)

Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich: Inference of Boolean Networks Using Sensitivity Regularization. EURASIP J. Bioinformatics and Systems Biology 2008 (2008)

Dan Schonfeld, John Goutsias, Ilya Shmulevich, Ioan Tabus, Ahmed H. Tewfik: Introduction to the Issue on Genomic and Proteomic Signal Processing. J. Sel. Topics Signal Processing 2(3): 257-260 (2008)

Harri Lähdesmäki, Ilya Shmulevich: Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Machine Learning 71(2-3): 185-217 (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 4(3) (2008)

David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich: Set-based complexity and biological information. CoRR abs/0801.4024 (2008)

Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja: Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinformatics 8 (2007)

Ricardo Z. N. Vêncio, Ilya Shmulevich: ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinformatics 8 (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 8 (2007)

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

Ioan Tabus, Andrea Hategan, Cristian Mircean, Jorma Rissanen, Ilya Shmulevich, Wei Zhang, Jaakko Astola: Nonlinear modeling of protein expressions in protein arrays. IEEE Transactions on Signal Processing 54(6-2): 2394-2407 (2006)

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 21(9): 1935-1942 (2005)

Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang: In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinformatics 6: 54 (2005)

Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman: Noise in a small genetic circuit that undergoes bifurcation. Complexity 11(1): 45-51 (2005)

Marcel Brun, Edward R. Dougherty, Ilya Shmulevich: Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Processing 85(10): 1993-2013 (2005)

Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich: Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Med. Imaging 24(4): 549-553 (2005)

Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich: The Role of Redundancy in the Robustness of Random Boolean Networks. CoRR abs/nlin/0511018 (2005)

Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty: Growing genetic regulatory networks from seed genes. Bioinformatics 20(8): 1241-1247 (2004)

Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner: Genomic Signal Processing: The Salient Issues. EURASIP J. Adv. Sig. Proc. 2004(1): 146-153 (2004)

Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin, Alexander N. Dolia, Olli Yli-Harja: Correction of Misclassifications Using a Proximity-Based Estimation Method. EURASIP J. Adv. Sig. Proc. 2004(8): 1142-1155 (2004)

Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja: On Learning Gene Regulatory Networks Under the Boolean Network Model. Machine Learning 52(1-2): 147-167 (2003)

Jaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus: Genomic signal processing. Signal Processing 83(4): 691-694 (2003)

Edward R. Dougherty, Ilya Shmulevich: Mappings between probabilistic Boolean networks. Signal Processing 83(4): 799-809 (2003)

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

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

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

Aleksey D. Korshunov, Ilya Shmulevich: On the distribution of the number of monotone Boolean functions relative to the number of lower units. Discrete Mathematics 257(2-3): 463-479 (2002)

Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich: Editorial. EURASIP J. Adv. Sig. Proc. 2002(1): 1-3 (2002)

Ilya Gluhovsky, Vladimir P. Melnik, Ilya Shmulevich: Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications. Journal of Mathematical Imaging and Vision 16(3): 237-249 (2002)

Vladimir Katkovnik, Ilya Shmulevich: Kernel density estimation with adaptive varying window size. Pattern Recognition Letters 23(14): 1641-1648 (2002)

Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov: On the robustness of the class of stack filters. IEEE Transactions on Signal Processing 50(7): 1640-1649 (2002)

Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich: Editorial. EURASIP J. Adv. Sig. Proc. 2001(4): 189-191 (2001)

Ilya Shmulevich, Aleksey D. Korshunov, Jaakko Astola: Almost all monotone Boolean functions are polynomially learnable using membership queries. Inf. Process. Lett. 79(5): 211-213 (2001)

Ilya Shmulevich, Olli Yli-Harja, Edward Coyle, Dirk-Jan Povel, Kjell Lemström: Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. Computers and the Humanities 35(1): 23-35 (2001)

Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich: Breakdown probabilities of recursive stack filters. Signal Processing 81(1): 227-231 (2001)

Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard Harvey, Ilya Shmulevich: Simplified implementation of the recursive median sieve. Signal Processing 81(7): 1565-1570 (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 31(2): 251-253 (2001)

Vladimir P. Melnik, Ilya Shmulevich, Karen Egiazarian, Jaakko Astola: Block-median pyramidal transform: analysis and denoising applications. IEEE Transactions on Signal Processing 49(2): 364-372 (2001)

Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce: Output distributions of stack filters based on mirrored threshold decomposition. IEEE Transactions on Signal Processing 49(7): 1454-1460 (2001)

Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce: Correction to "output distributionsof stack filters based on mirrored threshold decomposition". IEEE Transactions on Signal Processing 49(9): 2162 (2001)

Bogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela: A New Image Similarity Measure Based on Ordinal Correlation. ICIP 2000: 718-721

Vladimir P. Melnik, Ilya Shmulevich, Karen Egiazarian, Jaakko Astola: Image Denoising Using a Block-Median Pyramid. ICIP (4) 1999: 162-166

Ilya Shmulevich, Vladimir P. Melnik, Karen Egiazarian: Combination of transform based denoising and stack filtering for non-Gaussian noise suppression. NSIP 1999: 282-286

Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström: Graph-based smoothing of class data with applications in musical key finding. NSIP 1999: 311-315

Ilya Shmulevich, Vladimir P. Melnik, Karen Egiazarian: Optimization of stack filters using sample selection probabilities. NSIP 1999: 496-500