Ilya Shmulevich

Publication Activity (10 Years)

Years Active: 1998-2024
Publications (10 Years): 10

Top Topics

Boolean Networks

Clustering Algorithm

Gene Expression

Top Venues

Frontiers Digit. Health

PLoS Comput. Biol.

Publications

Yue Zhang, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, Ilya Shmulevich
A framework towards digital twins for type 2 diabetes. Frontiers Digit. Health 6 (2024)
Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova
Digital twins in medicine. Nat. Comput. Sci. 4 (3) (2024)
Reinhard C. Laubenbacher, Fred Adler, Gary An, Filippo Castiglione, Stephen Eubank, Luis L. Fonseca, James A. Glazier, Tomás Helikar, Marti Jett-Tilton, Denise Kirschner, Paul Macklin, Borna Mehrad, Beth Moore, Virginia Pasour, Ilya Shmulevich, Amber Smith, Isabel Voigt, Thomas E. Yankeelov, Tjalf Ziemssen
Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 6 (2024)
Moriah Echlin, Boris Aguilar, Ilya Shmulevich
Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. Entropy 25 (2) (2023)
Eric A. Stahlberg, Mohamed Abdel-Rahman, Boris Aguilar, Alireza Asadpoure, Robert A. Beckman, Lynn L. Borkon, Jeffrey N. Bryan, Colleen M. Cebulla, Young Hwan Chang, Ansu Chatterjee, Jun Deng, Sepideh Dolatshahi, Olivier Gevaert, Emily J. Greenspan, Wenrui Hao, Tina Hernandez-Boussard, Pamela R. Jackson, Marieke Kuijjer, Adrian Lee, Paul Macklin, Subha Madhavan, Matthew D. McCoy, Navid Mohammad Mirzaei, Talayeh Razzaghi, Heber L. Rocha, Leili Shahriyari, Ilya Shmulevich, Daniel G. Stover, Yi Sun, Tanveer Syeda-Mahmood, Jinhua Wang, Qi Wang, Ioannis K. Zervantonakis
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers Digit. Health 4 (2022)
Moriah Echlin, Boris Aguilar, Max Notarangelo, David L. Gibbs, Ilya Shmulevich
Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters. Entropy 20 (12) (2018)
David L. Gibbs, Ilya Shmulevich
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PLoS Comput. Biol. 13 (6) (2017)
Hsih-te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, Jung-Hsien Chiang
Literature-based discovery of new candidates for drug repurposing. Briefings Bioinform. 18 (3) (2017)
William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard
Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PLoS Comput. Biol. 13 (2) (2017)
William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg
values with an empirical adaptation of Brown's method. Bioinform. 32 (17) (2016)
Septimia Sârbu, Ilya Shmulevich, Olli Yli-Harja, Matti Nykter, Juha Kesseli
Mapping dynamical states to structural classes for Boolean networks using a classification algorithm. EUSIPCO (2015)
Seunghwa Kang, Simon Kahan, Jason E. McDermott, Nicholas S. Flann, Ilya Shmulevich
: accelerating computer simulation of multicellular biological system models. Bioinform. 30 (21) (2014)
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. Bioinform. Syst. Biol. 2012 (2012)
Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison
Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues. PLoS Comput. Biol. 7 (6) (2011)
Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich
EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC Bioinform. 12 (2011)
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 Bioinform. 11 (2010)
Timo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich, Harri Lähdesmäki
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinform. 26 (20) (2010)
David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
Biological information as set-based complexity. IEEE Trans. Inf. Theory 56 (2) (2010)
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)
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)
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 Trans. Inf. Theory 56 (2) (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. Bioinform. 26 (17) (2010)
Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich
-values. Bioinform. 25 (12) (2009)
Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, Edward R. Dougherty
Critical Boolean networks require minimal intervention rate. GENSiPS (2009)
John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich
Adaptable data management for systems biology investigations. BMC Bioinform. 10 (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 Syst. Biol. 3 (2009)
Harri Lähdesmäki, Ilya Shmulevich
Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Mach. Learn. 71 (2-3) (2008)
John Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich
Systems biology driven software design for the research enterprise. BMC Bioinform. 9 (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 Comput. Biol. 4 (3) (2008)
Dan Schonfeld, John Goutsias, Ilya Shmulevich, Ioan Tabus, Ahmed H. Tewfik
Introduction to the Issue on Genomic and Proteomic Signal Processing. IEEE J. Sel. Top. Signal Process. 2 (3) (2008)
David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
Set-based complexity and biological information CoRR (2008)
Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich
Inference of Boolean Networks Using Sensitivity Regularization. EURASIP J. Bioinform. Syst. Biol. 2008 (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 Bioinform. 8 (2007)
Ricardo Z. N. Vêncio, Ilya Shmulevich
ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinform. 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 Bioinform. 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 Process. 86 (4) (2006)
Ioan Tabus, Andrea Hategan, Cristian Mircean, Jorma Rissanen, Ilya Shmulevich, Wei Zhang, Jaakko Astola
Nonlinear modeling of protein expressions in protein arrays. IEEE Trans. Signal Process. 54 (6-2) (2006)
Antti Niemistö, Jyrki Selinummi, Ramsey Saleem, Ilya Shmulevich, John D. Aitchison, Olli Yli-Harja
Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis. EMBC (2006)
Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang
microdissection of microarray data from heterogeneous cell populations. BMC Bioinform. 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. Bioinform. 21 (9) (2005)
Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Medical Imaging 24 (4) (2005)
Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman
Noise in a small genetic circuit that undergoes bifurcation. Complex. 11 (1) (2005)
Marcel Brun, Edward R. Dougherty, Ilya Shmulevich
Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Process. 85 (10) (2005)
Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich
The Role of Redundancy in the Robustness of Random Boolean Networks CoRR (2005)
Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner
Genomic Signal Processing: The Salient Issues. EURASIP J. Adv. Signal Process. 2004 (1) (2004)
Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty
Growing genetic regulatory networks from seed genes. Bioinform. 20 (8) (2004)
Ilya Shmulevich, Harri Lähdesmäki, Karen O. Egiazarian
Spectral methods for testing membership in certain post classes and the class of forcing functions. IEEE Signal Process. Lett. 11 (2) (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. Signal Process. 2004 (8) (2004)
Jaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus
Genomic signal processing. Signal Process. 83 (4) (2003)
Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja
On Learning Gene Regulatory Networks Under the Boolean Network Model. Mach. Learn. 52 (1-2) (2003)
Ciprian Doru Giurcaneanu, Ioan Tabus, Ilya Shmulevich, Wei Zhang
Stability-based cluster analysis applied to microarray data. ISSPA (2) (2003)
Edward R. Dougherty, Ilya Shmulevich
Mappings between probabilistic Boolean networks. Signal Process. 83 (4) (2003)
Ilya Shmulevich, Wei Zhang
Binary analysis and optimization-based normalization of gene expression data. Bioinform. 18 (4) (2002)
Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov
On the robustness of the class of stack filters. IEEE Trans. Signal Process. 50 (7) (2002)
Vladimir Katkovnik, Ilya Shmulevich
Kernel density estimation with adaptive varying window size. Pattern Recognit. Lett. 23 (14) (2002)
Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich
Editorial. EURASIP J. Adv. Signal Process. 2002 (1) (2002)
Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
ayesian automatic relevance determination algorithms for classifying gene expression data. Bioinform. 18 (10) (2002)
Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proc. IEEE 90 (11) (2002)
Ilya Gluhovsky, Vladimir P. Melnik, Ilya Shmulevich
Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications. J. Math. Imaging Vis. 16 (3) (2002)
Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinform. 18 (2) (2002)
Aleksey D. Korshunov, Ilya Shmulevich
On the distribution of the number of monotone Boolean functions relative to the number of lower units. Discret. Math. 257 (2-3) (2002)
Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola
Block-median pyramidal transform: analysis and denoising applications. IEEE Trans. Signal Process. 49 (2) (2001)
Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard W. Harvey, Ilya Shmulevich
Simplified implementation of the recursive median sieve. Signal Process. 81 (7) (2001)
Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
Output distributions of stack filters based on mirrored threshold decomposition. IEEE Trans. Signal Process. 49 (7) (2001)
Ilya Shmulevich, Gonzalo R. Arce
Spectral design of weighted median filters admitting negative weights. IEEE Signal Process. Lett. 8 (12) (2001)
Ilya Shmulevich, Moncef Gabbouj, Jaakko Astola
Complexity of the consistency problem for certain Post classes. IEEE Trans. Syst. Man Cybern. Part B 31 (2) (2001)
Ilya Shmulevich, Aleksey D. Korshunov, Jaakko Astola
Almost all monotone Boolean functions are polynomially learnable using membership queries. Inf. Process. Lett. 79 (5) (2001)
Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich
Breakdown probabilities of recursive stack filters. Signal Process. 81 (1) (2001)
Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
Correction to "output distributionsof stack filters based on mirrored threshold decomposition". IEEE Trans. Signal Process. 49 (9) (2001)
Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich
Editorial. EURASIP J. Adv. Signal Process. 2001 (4) (2001)
Ilya Shmulevich, Olli Yli-Harja, Edward J. Coyle, Dirk-Jan Povel, Kjell Lemström
Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. Comput. Humanit. 35 (1) (2001)
Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich
Reduction factors in finite automata with application to nonlinear filters. EUSIPCO (2000)
Ilya Shmulevich, Bogdan Cramariuc, Moncef Gabbouj
A framework for ordinal-based image correspondence. EUSIPCO (2000)
Bogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela
A New Image Similarity Measure Based on Ordinal Correlation. ICIP (2000)
Ilya Shmulevich, Moncef Gabbouj
Reliable learning using post classes. EUSIPCO (2000)
Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
Statistics of stack filters with mirrored threshold decomposition. ICASSP (2000)
Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
The use of sample selection probabilities for stack filter design. IEEE Signal Process. Lett. 7 (7) (2000)
Vladimir P. Melnik, Karen O. Egiazarian, Ilya Shmulevich, Pauli Kuosmanen
A tree of median pyramidal decompositions with an application to signal denoising. ICASSP (2000)
Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola
Image Denoising Using a Block-Median Pyramid. ICIP (4) (1999)
Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström
Graph-based smoothing of class data with applications in musical key finding. NSIP (1999)
Ilya Shmulevich, Olli Yli-Harja, Karen O. Egiazarian, Jaakko Astola
Output distributions of recursive stack filters. IEEE Signal Process. Lett. 6 (7) (1999)
Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
Optimization of stack filters using sample selection probabilities. NSIP (1999)
Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
Combination of transform based denoising and stack filtering for non-Gaussian noise suppression. NSIP (1999)
Ilya Shmulevich, Edward J. Coyle
On the Structure of Idempotent Monotone Boolean Functions. NMBIA (1998)
Edward J. Coyle, Ilya Shmulevich
A system for machine recognition of music patterns. ICASSP (1998)
Ilya Shmulevich
Generation of idempotent monotone Boolean functions. EUSIPCO (1998)
Ilya Shmulevich, Dirk-Jan Povel
Rhythm complexity measures for music pattern recognition. MMSP (1998)