Ilya Shmulevich

89 papers B 1C 2Misc 3Journal 67Unranked 14

Year	Rank	Type	Title / Venue / Authors
2025	J	`jnl`	Digital twin models for predicting venetoclax and azacitidine-induced neutropenia in patients with acute myeloid leukemia. npj Digit. Medicine Yue Zhang, Jonathan Martinez, Bahar Tercan, Heikki Kuusanmäki, Frank Emmert-Streib, Jerome G. Chandraseelan, Amer Farea, Olli Yli-Harja, Caroline A. Heckman, David L. Gibbs, Vesteinn Thorsson, Ilya Shmulevich, Mika Kontro, Guangrong Qin, Boris Aguilar
2024	J	`jnl`	A framework towards digital twins for type 2 diabetes. Frontiers Digit. Health Yue Zhang, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, Ilya Shmulevich
2024	J	`jnl`	Digital twins in medicine. Nat. Comput. Sci. Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova
2024	J	`jnl`	Toward mechanistic medical digital twins: some use cases in immunology. Frontiers Digit. Health 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
2023	J	`jnl`	Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. Entropy Moriah Echlin, Boris Aguilar, Ilya Shmulevich
2022	J	`jnl`	Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers Digit. Health 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 L. 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 F. Syeda-Mahmood, Jinhua Wang, Qi Wang, Ioannis K. Zervantonakis
2018	J	`jnl`	Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters. Entropy Moriah Echlin, Boris Aguilar, Max Notarangelo, David L. Gibbs, Ilya Shmulevich
2017	J	`jnl`	Literature-based discovery of new candidates for drug repurposing. Briefings Bioinform. Hsih-te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, Jung-Hsien Chiang
2017	J	`jnl`	Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression. PLoS Comput. Biol. William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard
2017	J	`jnl`	Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PLoS Comput. Biol. David L. Gibbs, Ilya Shmulevich
2016	J	`jnl`	Combining dependent Bioinform. William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg
2015	—	`conf`	Mapping dynamical states to structural classes for Boolean networks using a classification algorithm. EUSIPCO Septimia Sârbu, Ilya Shmulevich, Olli Yli-Harja, Matti Nykter, Juha Kesseli
2012	J	`jnl`	Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP J. Bioinform. Syst. Biol. Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich
2011	J	`jnl`	EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC Bioinform. Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich
2011	J	`jnl`	Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues. PLoS Comput. Biol. Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison
2010	—	`conf`	An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity. DILS Hector Rovira, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle
2010	J	`jnl`	Biological information as set-based complexity. IEEE Trans. Inf. Theory David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
2010	J	`jnl`	Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinform. 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
2010	C	`conf`	Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data. CloudCom Steven Lewis, Sheila Reynolds, Hector Rovira, Mike O'Leary, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle
2010	J	`jnl`	Introduction to the special issue on information theory in molecular biology and neuroscience. IEEE Trans. Inf. Theory Olgica Milenkovic, Gil Alterovitz, Gerard Battail, Todd P. Coleman, Joachim Hagenauer, Sean P. Meyn, Nathan D. Price, Marco Ramoni, Ilya Shmulevich, Wojciech Szpankowski
2010	—	`book`	Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks. Ilya Shmulevich, Edward R. Dougherty
2010	J	`jnl`	Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinform. Timo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich, Harri Lähdesmäki
2010	J	`jnl`	SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinform. 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
2009	J	`jnl`	Adaptable data management for systems biology investigations. BMC Bioinform. John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich
2009	—	`ch.`	Boolean Modeling of Biological Networks. Encyclopedia of Complexity and Systems Science Peter M. Krawitz, Ilya Shmulevich
2009	—	`conf`	Critical Boolean networks require minimal intervention rate. GENSiPS Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, Edward R. Dougherty
2009	J	`jnl`	Fewer permutations, more accurate Bioinform. Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich
2009	J	`jnl`	Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation. BMC Syst. Biol. Albert C. Huang, Limei Hu, Stuart A. Kauffman, Wei Zhang, Ilya Shmulevich
2008	J	`jnl`	Inference of Boolean Networks Using Sensitivity Regularization. EURASIP J. Bioinform. Syst. Biol. Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich
2008	J	`jnl`	Introduction to the Issue on Genomic and Proteomic Signal Processing. IEEE J. Sel. Top. Signal Process. Dan Schonfeld, John Goutsias, Ilya Shmulevich, Ioan Tabus, Ahmed H. Tewfik
2008	J	`jnl`	Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Mach. Learn. Harri Lähdesmäki, Ilya Shmulevich
2008	J	`jnl`	Set-based complexity and biological information CoRR David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich
2008	J	`jnl`	Systems biology driven software design for the research enterprise. BMC Bioinform. John Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich
2008	J	`jnl`	Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. PLoS Comput. Biol. 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
2007	J	`jnl`	ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinform. Ricardo Z. N. Vêncio, Ilya Shmulevich
2007	J	`jnl`	Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinform. Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja
2007	J	`jnl`	Simcluster: clustering enumeration gene expression data on the simplex space. BMC Bioinform. Ricardo Z. N. Vêncio, Leonardo Varuzza, Carlos A. de B. Pereira, Helena Paula Brentani, Ilya Shmulevich
2006	—	`conf`	Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis. EMBC Antti Niemistö, Jyrki Selinummi, Ramsey Saleem, Ilya Shmulevich, John D. Aitchison, Olli Yli-Harja
2006	J	`jnl`	Nonlinear modeling of protein expressions in protein arrays. IEEE Trans. Signal Process. Ioan Tabus, Andrea Hategan, Cristian Mircean, Jorma Rissanen, Ilya Shmulevich, Wei Zhang, Jaakko Astola
2006	J	`jnl`	Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja
2005	J	`jnl`	Noise in a small genetic circuit that undergoes bifurcation. Complex. Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman
2005	J	`jnl`	Robust estimation of protein expression ratios with lysate microarray technology. Bioinform. Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang
2005	J	`jnl`	Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Medical Imaging Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich
2005	J	`jnl`	Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Process. Marcel Brun, Edward R. Dougherty, Ilya Shmulevich
2005	J	`jnl`	The Role of Redundancy in the Robustness of Random Boolean Networks CoRR Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich
2004	J	`jnl`	Correction of Misclassifications Using a Proximity-Based Estimation Method. EURASIP J. Adv. Signal Process. Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin, Alexander N. Dolia, Olli Yli-Harja
2004	J	`jnl`	Genomic Signal Processing: The Salient Issues. EURASIP J. Adv. Signal Process. Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner
2004	J	`jnl`	Growing genetic regulatory networks from seed genes. Bioinform. Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty
2004	J	`jnl`	Spectral methods for testing membership in certain post classes and the class of forcing functions. IEEE Signal Process. Lett. Ilya Shmulevich, Harri Lähdesmäki, Karen O. Egiazarian
2003	J	`jnl`	Genomic signal processing. Signal Process. Jaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus
2003	J	`jnl`	Mappings between probabilistic Boolean networks. Signal Process. Edward R. Dougherty, Ilya Shmulevich
2003	J	`jnl`	On Learning Gene Regulatory Networks Under the Boolean Network Model. Mach. Learn. Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja
2003	—	`conf`	Stability-based cluster analysis applied to microarray data. ISSPA (2) Ciprian Doru Giurcaneanu, Ioan Tabus, Ilya Shmulevich, Wei Zhang
2002	J	`jnl`	Binary analysis and optimization-based normalization of gene expression data. Bioinform. Ilya Shmulevich, Wei Zhang
2002	J	`jnl`	Editorial. EURASIP J. Adv. Signal Process. Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich
2002	J	`jnl`	From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proc. IEEE Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
2002	J	`jnl`	Gene perturbation and intervention in probabilistic Boolean networks. Bioinform. Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
2002	J	`jnl`	Kernel density estimation with adaptive varying window size. Pattern Recognit. Lett. Vladimir Katkovnik, Ilya Shmulevich
2002	J	`jnl`	Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications. J. Math. Imaging Vis. Ilya Gluhovsky, Vladimir P. Melnik, Ilya Shmulevich
2002	J	`jnl`	On the distribution of the number of monotone Boolean functions relative to the number of lower units. Discret. Math. Aleksey D. Korshunov, Ilya Shmulevich
2002	J	`jnl`	On the robustness of the class of stack filters. IEEE Trans. Signal Process. Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov
2002	J	`jnl`	Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinform. Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang
2002	J	`jnl`	ayesian automatic relevance determination algorithms for classifying gene expression data. Bioinform. Ilya Shmulevich, Edward R. Dougherty, Wei Zhang
2001	J	`jnl`	Almost all monotone Boolean functions are polynomially learnable using membership queries. Inf. Process. Lett. Ilya Shmulevich, Aleksey D. Korshunov, Jaakko Astola
2001	J	`jnl`	Block-median pyramidal transform: analysis and denoising applications. IEEE Trans. Signal Process. Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola
2001	J	`jnl`	Breakdown probabilities of recursive stack filters. Signal Process. Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich
2001	J	`jnl`	Complexity of the consistency problem for certain Post classes. IEEE Trans. Syst. Man Cybern. Part B Ilya Shmulevich, Moncef Gabbouj, Jaakko Astola
2001	J	`jnl`	Correction to "output distributionsof stack filters based on mirrored threshold decomposition". IEEE Trans. Signal Process. Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
2001	J	`jnl`	Editorial. EURASIP J. Adv. Signal Process. Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich
2001	J	`jnl`	Output distributions of stack filters based on mirrored threshold decomposition. IEEE Trans. Signal Process. Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
2001	J	`jnl`	Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding. Comput. Humanit. Ilya Shmulevich, Olli Yli-Harja, Edward J. Coyle, Dirk-Jan Povel, Kjell Lemström
2001	J	`jnl`	Simplified implementation of the recursive median sieve. Signal Process. Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard W. Harvey, Ilya Shmulevich
2001	J	`jnl`	Spectral design of weighted median filters admitting negative weights. IEEE Signal Process. Lett. Ilya Shmulevich, Gonzalo R. Arce
2000	B	`conf`	A New Image Similarity Measure Based on Ordinal Correlation. ICIP Bogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela
2000	—	`conf`	A framework for ordinal-based image correspondence. EUSIPCO Ilya Shmulevich, Bogdan Cramariuc, Moncef Gabbouj
2000	Misc	`conf`	A tree of median pyramidal decompositions with an application to signal denoising. ICASSP Vladimir P. Melnik, Karen O. Egiazarian, Ilya Shmulevich, Pauli Kuosmanen
2000	—	`conf`	Reduction factors in finite automata with application to nonlinear filters. EUSIPCO Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich
2000	—	`conf`	Reliable learning using post classes. EUSIPCO Ilya Shmulevich, Moncef Gabbouj
2000	Misc	`conf`	Statistics of stack filters with mirrored threshold decomposition. ICASSP Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce
2000	J	`jnl`	The use of sample selection probabilities for stack filter design. IEEE Signal Process. Lett. Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
1999	—	`conf`	Combination of transform based denoising and stack filtering for non-Gaussian noise suppression. NSIP Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
1999	—	`conf`	Graph-based smoothing of class data with applications in musical key finding. NSIP Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström
1999	—	`conf`	Image Denoising Using a Block-Median Pyramid. ICIP (4) Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola
1999	—	`conf`	Optimization of stack filters using sample selection probabilities. NSIP Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian
1999	J	`jnl`	Output distributions of recursive stack filters. IEEE Signal Process. Lett. Ilya Shmulevich, Olli Yli-Harja, Karen O. Egiazarian, Jaakko Astola
1998	Misc	`conf`	A system for machine recognition of music patterns. ICASSP Edward J. Coyle, Ilya Shmulevich
1998	—	`conf`	Generation of idempotent monotone Boolean functions. EUSIPCO Ilya Shmulevich
1998	—	`conf`	On the Structure of Idempotent Monotone Boolean Functions. NMBIA Ilya Shmulevich, Edward J. Coyle
1998	C	`conf`	Rhythm complexity measures for music pattern recognition. MMSP Ilya Shmulevich, Dirk-Jan Povel