Ilya Shmulevich

According to our database, Ilya Shmulevich authored at least 89 papers between 1998 and 2024.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

2024

Digital twins in medicine.

Reinhard C. Laubenbacher, Borna Mehrad, Ilya Shmulevich, Natalia A. Trayanova

Nat. Comput. Sci., 2024

A framework towards digital twins for type 2 diabetes.

Yue Zhang, Guangrong Qin, Boris Aguilar, Noa Rappaport, James T. Yurkovich, Lance Pflieger, Sui Huang, Leroy Hood, Ilya Shmulevich

Frontiers Digit. Health, 2024

Toward mechanistic medical digital twins: some use cases in immunology.

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

Frontiers Digit. Health, 2024

2023

TCGA Kidney Cancers.

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

Dataset, September, 2023

Characterizing the Impact of Communication on Cellular and Collective Behavior Using a Three-Dimensional Multiscale Cellular Model.

Moriah Echlin, Boris Aguilar, Ilya Shmulevich

Entropy, February, 2023

2022

Exploring approaches for predictive cancer patient digital twins: Opportunities for collaboration and innovation.

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

Frontiers Digit. Health, 2022

2018

Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters.

Moriah Echlin, Boris Aguilar, Max Notarangelo, David L. Gibbs, Ilya Shmulevich

Entropy, 2018

2017

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.

William Poole, Kalle Leinonen, Ilya Shmulevich, Theo A. Knijnenburg, Brady Bernard

PLoS Comput. Biol., 2017

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.

David L. Gibbs, Ilya Shmulevich

PLoS Comput. Biol., 2017

Literature-based discovery of new candidates for drug repurposing.

Hsih-te Yang, Jiun-Huang Ju, Yue-Ting Wong, Ilya Shmulevich, Jung-Hsien Chiang

Briefings Bioinform., 2017

2016

Combining dependent <i>P-</i>values with an empirical adaptation of Brown's method.

William Poole, David L. Gibbs, Ilya Shmulevich, Brady Bernard, Theo A. Knijnenburg

Bioinform., 2016

2015

Mapping dynamical states to structural classes for Boolean networks using a classification algorithm.

Septimia Sârbu, Ilya Shmulevich, Olli Yli-Harja, Matti Nykter, Juha Kesseli

Proceedings of the 23rd European Signal Processing Conference, 2015

2014

<i>Biocellion</i>: accelerating computer simulation of multicellular biological system models.

Seunghwa Kang, Simon Kahan, Jason E. McDermott, Nicholas S. Flann, Ilya Shmulevich

Bioinform., 2014

2012

Fastbreak: a tool for analysis and visualization of structural variations in genomic data.

Ryan Bressler, Jake Lin, Andrea Eakin, Thomas Robinson, Richard Kreisberg, Hector Rovira, Theo A. Knijnenburg, John Boyle, Ilya Shmulevich

EURASIP J. Bioinform. Syst. Biol., 2012

2011

Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues.

Alexander V. Ratushny, Ilya Shmulevich, John D. Aitchison

PLoS Comput. Biol., 2011

EPEPT: A web service for enhanced P-value estimation in permutation tests.

Theo A. Knijnenburg, Jake Lin, Hector Rovira, John Boyle, Ilya Shmulevich

BMC Bioinform., 2011

2010

Introduction to the special issue on information theory in molecular biology and neuroscience.

Olgica Milenkovic, Gil Alterovitz, Gerard Battail, Todd P. Coleman, Joachim Hagenauer, Sean P. Meyn, Nathan D. Price, Marco Ramoni, Ilya Shmulevich, Wojciech Szpankowski

IEEE Trans. Inf. Theory, 2010

Biological information as set-based complexity.

David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich

IEEE Trans. Inf. Theory, 2010

SEQADAPT: an adaptable system for the tracking, storage and analysis of high throughput sequencing experiments.

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

BMC Bioinform., 2010

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.

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

Bioinform., 2010

Probabilistic analysis of gene expression measurements from heterogeneous tissues.

Timo Erkkilä, Saara Lehmusvaara, Pekka Ruusuvuori, Tapio Visakorpi, Ilya Shmulevich, Harri Lähdesmäki

Bioinform., 2010

An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity.

Hector Rovira, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle

Proceedings of the Data Integration in the Life Sciences, 7th International Conference, 2010

Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data.

Steven Lewis, Sheila Reynolds, Hector Rovira, Mike O'Leary, Sarah A. Killcoyne, Ilya Shmulevich, John Boyle

Proceedings of the Cloud Computing, Second International Conference, 2010

Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks.

Ilya Shmulevich, Edward R. Dougherty

SIAM, ISBN: 978-0-89871-692-4, 2010

2009

Boolean Modeling of Biological Networks.

Peter M. Krawitz, Ilya Shmulevich

Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation.

Albert C. Huang, Limei Hu, Stuart A. Kauffman, Wei Zhang, Ilya Shmulevich

BMC Syst. Biol., 2009

Adaptable data management for systems biology investigations.

John Boyle, Hector Rovira, Christopher C. Cavnor, David B. Burdick, Sarah A. Killcoyne, Ilya Shmulevich

BMC Bioinform., 2009

Fewer permutations, more accurate <i>P</i>-values.

Theo A. Knijnenburg, Lodewyk F. A. Wessels, Marcel J. T. Reinders, Ilya Shmulevich

Bioinform., 2009

Critical Boolean networks require minimal intervention rate.

Golnaz Vahedi, Ilya Shmulevich, Wenbin Liu, Edward R. Dougherty

Proceedings of the 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 2009

2008

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.

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

PLoS Comput. Biol., 2008

Learning the structure of dynamic Bayesian networks from time series and steady state measurements.

Harri Lähdesmäki, Ilya Shmulevich

Mach. Learn., 2008

Introduction to the Issue on Genomic and Proteomic Signal Processing.

Dan Schonfeld, John Goutsias, Ilya Shmulevich, Ioan Tabus, Ahmed H. Tewfik

IEEE J. Sel. Top. Signal Process., 2008

Inference of Boolean Networks Using Sensitivity Regularization.

Wenbin Liu, Harri Lähdesmäki, Edward R. Dougherty, Ilya Shmulevich

EURASIP J. Bioinform. Syst. Biol., 2008

Set-based complexity and biological information

David J. Galas, Matti Nykter, Gregory W. Carter, Nathan D. Price, Ilya Shmulevich

CoRR, 2008

Systems biology driven software design for the research enterprise.

John Boyle, Christopher C. Cavnor, Sarah A. Killcoyne, Ilya Shmulevich

BMC Bioinform., 2008

2007

Simcluster: clustering enumeration gene expression data on the simplex space.

Ricardo Z. N. Vêncio, Leonardo Varuzza, Carlos A. de B. Pereira, Helena Paula Brentani, Ilya Shmulevich

BMC Bioinform., 2007

ProbCD: enrichment analysis accounting for categorization uncertainty.

Ricardo Z. N. Vêncio, Ilya Shmulevich

BMC Bioinform., 2007

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.

Miika Ahdesmäki, Harri Lähdesmäki, Andrew Gracey, Ilya Shmulevich, Olli Yli-Harja

BMC Bioinform., 2007

2006

Nonlinear modeling of protein expressions in protein arrays.

Ioan Tabus, Andrea Hategan, Cristian Mircean, Jorma Rissanen, Ilya Shmulevich, Wei Zhang, Jaakko Astola

IEEE Trans. Signal Process., 2006

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks.

Harri Lähdesmäki, Sampsa Hautaniemi, Ilya Shmulevich, Olli Yli-Harja

Signal Process., 2006

Extraction of the Number of Peroxisomes in Yeast Cells by Automated Image Analysis.

Antti Niemistö, Jyrki Selinummi, Ramsey Saleem, Ilya Shmulevich, John D. Aitchison, Olli Yli-Harja

Proceedings of the 28th International Conference of the IEEE Engineering in Medicine and Biology Society, 2006

2005

Robust quantification of in vitro angiogenesis through image analysis.

Antti Niemistö, Valerie Dunmire, Olli Yli-Harja, Wei Zhang, Ilya Shmulevich

IEEE Trans. Medical Imaging, 2005

Steady-state probabilities for attractors in probabilistic Boolean networks.

Marcel Brun, Edward R. Dougherty, Ilya Shmulevich

Signal Process., 2005

The Role of Redundancy in the Robustness of Random Boolean Networks

Carlos Gershenson, Stuart A. Kauffman, Ilya Shmulevich

CoRR, 2005

Noise in a small genetic circuit that undergoes bifurcation.

Trent Toulouse, Ping Ao, Ilya Shmulevich, Stuart A. Kauffman

Complex., 2005

<i>In silico </i>microdissection of microarray data from heterogeneous cell populations.

Harri Lähdesmäki, Ilya Shmulevich, Valerie Dunmire, Olli Yli-Harja, Wei Zhang

BMC Bioinform., 2005

Robust estimation of protein expression ratios with lysate microarray technology.

Cristian Mircean, Ilya Shmulevich, David Cogdell, Woonyoung Choi, Yu Jia, Ioan Tabus, Stanley R. Hamilton, Wei Zhang

Bioinform., 2005

2004

Spectral methods for testing membership in certain post classes and the class of forcing functions.

Ilya Shmulevich, Harri Lähdesmäki, Karen O. Egiazarian

IEEE Signal Process. Lett., 2004

Correction of Misclassifications Using a Proximity-Based Estimation Method.

Antti Niemistö, Ilya Shmulevich, Vladimir Vasilyevich Lukin, Alexander N. Dolia, Olli Yli-Harja

EURASIP J. Adv. Signal Process., 2004

Genomic Signal Processing: The Salient Issues.

Edward R. Dougherty, Ilya Shmulevich, Michael L. Bittner

EURASIP J. Adv. Signal Process., 2004

Growing genetic regulatory networks from seed genes.

Ronaldo Fumio Hashimoto, Seungchan Kim, Ilya Shmulevich, Wei Zhang, Michael L. Bittner, Edward R. Dougherty

Bioinform., 2004

2003

Mappings between probabilistic Boolean networks.

Edward R. Dougherty, Ilya Shmulevich

Signal Process., 2003

Genomic signal processing.

Jaakko Astola, Edward R. Dougherty, Ilya Shmulevich, Ioan Tabus

Signal Process., 2003

On Learning Gene Regulatory Networks Under the Boolean Network Model.

Harri Lähdesmäki, Ilya Shmulevich, Olli Yli-Harja

Mach. Learn., 2003

Stability-based cluster analysis applied to microarray data.

Ciprian Doru Giurcaneanu, Ioan Tabus, Ilya Shmulevich, Wei Zhang

Proceedings of the Seventh International Symposium on Signal Processing and Its Applications, 2003

2002

On the robustness of the class of stack filters.

Ilya Shmulevich, Olli Yli-Harja, Jaakko Astola, Aleksey D. Korshunov

IEEE Trans. Signal Process., 2002

Kernel density estimation with adaptive varying window size.

Vladimir Katkovnik, Ilya Shmulevich

Pattern Recognit. Lett., 2002

From Boolean to probabilistic Boolean networks as models of genetic regulatory networks.

Ilya Shmulevich, Edward R. Dougherty, Wei Zhang

Proc. IEEE, 2002

Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications.

Ilya Gluhovsky, Vladimir P. Melnik, Ilya Shmulevich

J. Math. Imaging Vis., 2002

On the distribution of the number of monotone Boolean functions relative to the number of lower units.

Aleksey D. Korshunov, Ilya Shmulevich

Discret. Math., 2002

Binary analysis and optimization-based normalization of gene expression data.

Ilya Shmulevich, Wei Zhang

Bioinform., 2002

ayesian automatic relevance determination algorithms for classifying gene expression data.

Ilya Shmulevich, Edward R. Dougherty, Wei Zhang

Bioinform., 2002

Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks.

Ilya Shmulevich, Edward R. Dougherty, Seungchan Kim, Wei Zhang

Bioinform., 2002

2001

Correction to "output distributionsof stack filters based on mirrored threshold decomposition".

Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce

IEEE Trans. Signal Process., 2001

Output distributions of stack filters based on mirrored threshold decomposition.

Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce

IEEE Trans. Signal Process., 2001

Block-median pyramidal transform: analysis and denoising applications.

Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola

IEEE Trans. Signal Process., 2001

Complexity of the consistency problem for certain Post classes.

Ilya Shmulevich, Moncef Gabbouj, Jaakko Astola

IEEE Trans. Syst. Man Cybern. Part B, 2001

Spectral design of weighted median filters admitting negative weights.

Ilya Shmulevich, Gonzalo R. Arce

IEEE Signal Process. Lett., 2001

Simplified implementation of the recursive median sieve.

Olli Yli-Harja, Pertti Koivisto, J. Andrew Bangham, Gavin C. Cawley, Richard W. Harvey, Ilya Shmulevich

Signal Process., 2001

Breakdown probabilities of recursive stack filters.

Pertti Koivisto, Olli Yli-Harja, Antti Niemistö, Ilya Shmulevich

Signal Process., 2001

Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding.

Ilya Shmulevich, Olli Yli-Harja, Edward J. Coyle, Dirk-Jan Povel, Kjell Lemström

Comput. Humanit., 2001

Almost all monotone Boolean functions are polynomially learnable using membership queries.

Ilya Shmulevich, Aleksey D. Korshunov, Jaakko Astola

Inf. Process. Lett., 2001

Editorial.

Kenneth E. Barner, Gonzalo R. Arce, Giovanni L. Sicuranza, Ilya Shmulevich

EURASIP J. Adv. Signal Process., 2001

2000

The use of sample selection probabilities for stack filter design.

Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian

IEEE Signal Process. Lett., 2000

A New Image Similarity Measure Based on Ordinal Correlation.

Bogdan Cramariuc, Ilya Shmulevich, Moncef Gabbouj, Asko Makela

Proceedings of the 2000 International Conference on Image Processing, 2000

Statistics of stack filters with mirrored threshold decomposition.

Ilya Shmulevich, José L. Paredes, Gonzalo R. Arce

Proceedings of the IEEE International Conference on Acoustics, 2000

A tree of median pyramidal decompositions with an application to signal denoising.

Vladimir P. Melnik, Karen O. Egiazarian, Ilya Shmulevich, Pauli Kuosmanen

Proceedings of the IEEE International Conference on Acoustics, 2000

Reliable learning using post classes.

Ilya Shmulevich, Moncef Gabbouj

Proceedings of the 10th European Signal Processing Conference, 2000

A framework for ordinal-based image correspondence.

Ilya Shmulevich, Bogdan Cramariuc, Moncef Gabbouj

Proceedings of the 10th European Signal Processing Conference, 2000

Reduction factors in finite automata with application to nonlinear filters.

Antti Niemistö, Olli Yli-Harja, Antti Valmari, Pertti Koivisto, Ilya Shmulevich

Proceedings of the 10th European Signal Processing Conference, 2000

1999

Output distributions of recursive stack filters.

Ilya Shmulevich, Olli Yli-Harja, Karen O. Egiazarian, Jaakko Astola

IEEE Signal Process. Lett., 1999

Graph-based smoothing of class data with applications in musical key finding.

Olli Yli-Harja, Ilya Shmulevich, Kjell Lemström

Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999

Optimization of stack filters using sample selection probabilities.

Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian

Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999

Combination of transform based denoising and stack filtering for non-Gaussian noise suppression.

Ilya Shmulevich, Vladimir P. Melnik, Karen O. Egiazarian

Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999

Image Denoising Using a Block-Median Pyramid.

Vladimir P. Melnik, Ilya Shmulevich, Karen O. Egiazarian, Jaakko Astola

Proceedings of the 1999 International Conference on Image Processing, 1999

1998

On the Structure of Idempotent Monotone Boolean Functions.

Ilya Shmulevich, Edward J. Coyle

Proceedings of the Noblesse Workshop on Non-Linear Model Based Image Analysis, 1998

Rhythm complexity measures for music pattern recognition.

Ilya Shmulevich, Dirk-Jan Povel

Proceedings of the Second IEEE Workshop on Multimedia Signal Processing, 1998

A system for machine recognition of music patterns.

Edward J. Coyle, Ilya Shmulevich

Proceedings of the 1998 IEEE International Conference on Acoustics, 1998

Generation of idempotent monotone Boolean functions.

Ilya Shmulevich

Proceedings of the 9th European Signal Processing Conference, 1998