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Ilya Shmulevich
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2020 – today
- 2024
- [j65]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) - [j64]Yue Zhang
A framework towards digital twins for type 2 diabetes. Frontiers Digit. Health 6 (2024) - [j63]Reinhard C. Laubenbacher
Digital twins in medicine. Nat. Comput. Sci. 4(3): 184-191 (2024) - 2023
- [j62]Moriah Echlin
Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model. Entropy 25(2): 319 (2023) - [d1]John N. Weinstein, Eric A. Collisson, Gordon B. Mills, Kenna R. Mills Shaw, Brad A. Ozenberger, Kyle Ellrott, Ilya Shmulevich, Chris Sander, Joshua M. Stuart:
TCGA Kidney Cancers. UCI Machine Learning Repository, 2023 - 2022
- [j61]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
Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation. Frontiers Digit. Health 4 (2022)
2010 – 2019
- 2018
- [j60]Moriah Echlin
Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters. Entropy 20(12): 954 (2018) - 2017
- [j59]Hsih-te Yang
Literature-based discovery of new candidates for drug repurposing. Briefings Bioinform. 18(3): 488-497 (2017) - [j58]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) - [j57]David L. Gibbs
Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle. PLoS Comput. Biol. 13(6) (2017) - 2016
- [j56]William Poole
Combining dependent P-values with an empirical adaptation of Brown's method. Bioinform. 32(17): 430-436 (2016) - 2015
- [c20]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: 160-164 - 2014
- [j55]Seunghwa Kang, Simon Kahan, Jason E. McDermott
Biocellion: accelerating computer simulation of multicellular biological system models. Bioinform. 30(21): 3101-3108 (2014) - 2012
- [j54]Ryan Bressler, Jake Lin
Fastbreak: a tool for analysis and visualization of structural variations in genomic data. EURASIP J. Bioinform. Syst. Biol. 2012: 15 (2012) - 2011
- [j53]Theo A. Knijnenburg, Jake Lin
EPEPT: A web service for enhanced P-value estimation in permutation tests. BMC Bioinform. 12: 411 (2011) - [j52]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) - 2010
- [b1]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 - [j51]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): 2071-2075 (2010) - [j50]Timo Erkkilä, Saara Lehmusvaara
Probabilistic analysis of gene expression measurements from heterogeneous tissues. Bioinform. 26(20): 2571-2577 (2010) - [j49]David B. Burdick, Christopher C. Cavnor, Jeremy Handcock, Sarah A. Killcoyne
SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments. BMC Bioinform. 11: 377 (2010) - [j48]Olgica Milenkovic, Gil Alterovitz, Gerard Battail, Todd P. Coleman
Introduction to the special issue on information theory in molecular biology and neuroscience. IEEE Trans. Inf. Theory 56(2): 649-652 (2010) - [j47]David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price
Biological information as set-based complexity. IEEE Trans. Inf. Theory 56(2): 667-677 (2010) - [c19]Steven Lewis, Sheila Reynolds, Hector Rovira, Mike O'Leary, Sarah A. Killcoyne
Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data. CloudCom 2010: 776-779 - [c18]Hector Rovira, Sarah A. Killcoyne
An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity. DILS 2010: 179-191
2000 – 2009
- 2009
- [j46]Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich:
Fewer permutations, more accurate P-values. Bioinform. 25(12) (2009) - [j45]John Boyle
Adaptable data management for systems biology investigations. BMC Bioinform. 10 (2009) - [j44]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: 20 (2009) - [c17]Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, Edward R. Dougherty:
Critical Boolean networks require minimal intervention rate. GENSiPS 2009: 1-2 - [r1]Peter M. Krawitz, Ilya Shmulevich:
Boolean Modeling of Biological Networks. Encyclopedia of Complexity and Systems Science 2009: 599-608 - 2008
- [j43]John Boyle
Systems biology driven software design for the research enterprise. BMC Bioinform. 9 (2008) - [j42]Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich:
Inference of Boolean Networks Using Sensitivity Regularization. EURASIP J. Bioinform. Syst. Biol. 2008 (2008) - [j41]Dan Schonfeld, John Goutsias, Ilya Shmulevich, Ioan Tabus
Introduction to the Issue on Genomic and Proteomic Signal Processing. IEEE J. Sel. Top. Signal Process. 2(3): 257-260 (2008) - [j40]Harri Lähdesmäki, Ilya Shmulevich:
Learning the structure of dynamic Bayesian networks from time series and steady state measurements. Mach. Learn. 71(2-3): 185-217 (2008) - [j39]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
Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics. PLoS Comput. Biol. 4(3) (2008) - [i2]David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich:
Set-based complexity and biological information. CoRR abs/0801.4024 (2008) - 2007
- [j38]Miika Ahdesmäki
Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data. BMC Bioinform. 8 (2007) - [j37]Ricardo Z. N. Vêncio
ProbCD: enrichment analysis accounting for categorization uncertainty. BMC Bioinform. 8 (2007) - [j36]Ricardo Z. N. Vêncio
Simcluster: clustering enumeration gene expression data on the simplex space. BMC Bioinform. 8 (2007) - 2006
- [j35]Harri Lähdesmäki, Sampsa Hautaniemi
Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks. Signal Process. 86(4): 814-834 (2006) - [j34]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): 2394-2407 (2006) - [c16]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: 2353-2356 - 2005
- [j33]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): 1935-1942 (2005) - [j32]Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja
In silico microdissection of microarray data from heterogeneous cell populations. BMC Bioinform. 6: 54 (2005) - [j31]Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman:
Noise in a small genetic circuit that undergoes bifurcation. Complex. 11(1): 45-51 (2005) - [j30]Marcel Brun
Steady-state probabilities for attractors in probabilistic Boolean networks. Signal Process. 85(10): 1993-2013 (2005) - [j29]Antti Niemistö, Valerie Dunmire, Olli Yli-Harja
Robust quantification of in vitro angiogenesis through image analysis. IEEE Trans. Medical Imaging 24(4): 549-553 (2005) - [i1]Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich:
The Role of Redundancy in the Robustness of Random Boolean Networks. CoRR abs/nlin/0511018 (2005) - 2004
- [j28]Ronaldo Fumio Hashimoto
Growing genetic regulatory networks from seed genes. Bioinform. 20(8): 1241-1247 (2004) - [j27]Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner:
Genomic Signal Processing: The Salient Issues. EURASIP J. Adv. Signal Process. 2004(1): 146-153 (2004) - [j26]Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin
Correction of Misclassifications Using a Proximity-Based Estimation Method. EURASIP J. Adv. Signal Process. 2004(8): 1142-1155 (2004) - [j25]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): 289-292 (2004) - 2003
- [j24]Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja
On Learning Gene Regulatory Networks Under the Boolean Network Model. Mach. Learn. 52(1-2): 147-167 (2003) - [j23]Jaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus:
Genomic signal processing. Signal Process. 83(4): 691-694 (2003) - [j22]Edward R. Dougherty, Ilya Shmulevich:
Mappings between probabilistic Boolean networks. Signal Process. 83(4): 799-809 (2003) - [c15]Ciprian Doru Giurcaneanu
Stability-based cluster analysis applied to microarray data. ISSPA (2) 2003: 57-60 - 2002
- [j21]Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim
Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks. Bioinform. 18(2): 261-274 (2002) - [j20]Ilya Shmulevich, Wei Zhang:
Binary analysis and optimization-based normalization of gene expression data. Bioinform. 18(4): 555-565 (2002) - [j19]Ilya Shmulevich, Edward R. Dougherty, Wei Zhang:
ayesian automatic relevance determination algorithms for classifying gene expression data. Bioinform. 18(10): 1332-1339 (2002) - [j18]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): 463-479 (2002) - [j17]Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza
Editorial. EURASIP J. Adv. Signal Process. 2002(1): 1-3 (2002) - [j16]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): 237-249 (2002) - [j15]Ilya Shmulevich, Edward R. Dougherty, Wei Zhang:
From Boolean to probabilistic Boolean networks as models of genetic regulatory networks. Proc. IEEE 90(11): 1778-1792 (2002) - [j14]Vladimir Katkovnik
Kernel density estimation with adaptive varying window size. Pattern Recognit. Lett. 23(14): 1641-1648 (2002) - [j13]Ilya Shmulevich, Olli Yli-Harja
On the robustness of the class of stack filters. IEEE Trans. Signal Process. 50(7): 1640-1649 (2002) - 2001
- [j12]Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza
Editorial. EURASIP J. Adv. Signal Process. 2001(4): 189-191 (2001) - [j11]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) - [j10]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): 23-35 (2001) - [j9]Pertti Koivisto, Olli Yli-Harja
Breakdown probabilities of recursive stack filters. Signal Process. 81(1): 227-231 (2001) - [j8]Olli Yli-Harja
Simplified implementation of the recursive median sieve. Signal Process. 81(7): 1565-1570 (2001) - [j7]Ilya Shmulevich, Gonzalo R. Arce:
Spectral design of weighted median filters admitting negative weights. IEEE Signal Process. Lett. 8(12): 313-316 (2001) - [j6]Ilya Shmulevich, Moncef Gabbouj
Complexity of the consistency problem for certain Post classes. IEEE Trans. Syst. Man Cybern. Part B 31(2): 251-253 (2001) - [j5]Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola:
Block-median pyramidal transform: analysis and denoising applications. IEEE Trans. Signal Process. 49(2): 364-372 (2001) - [j4]Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce:
Output distributions of stack filters based on mirrored threshold decomposition. IEEE Trans. Signal Process. 49(7): 1454-1460 (2001) - [j3]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): 2162 (2001) - 2000
- [j2]Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian:
The use of sample selection probabilities for stack filter design. IEEE Signal Process. Lett. 7(7): 189-192 (2000) - [c14]Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich:
Reduction factors in finite automata with application to nonlinear filters. EUSIPCO 2000: 1-4 - [c13]Ilya Shmulevich, Bogdan Cramariuc, Moncef Gabbouj:
A framework for ordinal-based image correspondence. EUSIPCO 2000: 1-4 - [c12]Ilya Shmulevich, Moncef Gabbouj:
Reliable learning using post classes. EUSIPCO 2000: 1-4 - [c11]Vladimir P. Melnik, Karen O. Egiazarian, Ilya Shmulevich, Pauli Kuosmanen:
A tree of median pyramidal decompositions with an application to signal denoising. ICASSP 2000: 117-120 - [c10]Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce:
Statistics of stack filters with mirrored threshold decomposition. ICASSP 2000: 3826-3829 - [c9]Bogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela:
A New Image Similarity Measure Based on Ordinal Correlation. ICIP 2000: 718-721
1990 – 1999
- 1999
- [j1]Ilya Shmulevich, Olli Yli-Harja
Output distributions of recursive stack filters. IEEE Signal Process. Lett. 6(7): 175-178 (1999) - [c8]Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola:
Image Denoising Using a Block-Median Pyramid. ICIP (4) 1999: 162-166 - [c7]Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian:
Combination of transform based denoising and stack filtering for non-Gaussian noise suppression. NSIP 1999: 282-286 - [c6]Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström:
Graph-based smoothing of class data with applications in musical key finding. NSIP 1999: 311-315 - [c5]Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian:
Optimization of stack filters using sample selection probabilities. NSIP 1999: 496-500 - 1998
- [c4]Ilya Shmulevich:
Generation of idempotent monotone Boolean functions. EUSIPCO 1998: 1-3 - [c3]Edward J. Coyle, Ilya Shmulevich:
A system for machine recognition of music patterns. ICASSP 1998: 3597-3600 - [c2]Ilya Shmulevich, Dirk-Jan Povel:
Rhythm complexity measures for music pattern recognition. MMSP 1998: 167-172 - [c1]Ilya Shmulevich, Edward J. Coyle:
On the Structure of Idempotent Monotone Boolean Functions. NMBIA 1998: 339-344
Coauthor Index
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