Ilya Shmulevich

According to our database1, Ilya Shmulevich authored at least 79 papers between 1998 and 2018.

Collaborative distances:



In proceedings 
PhD thesis 




Flexibility of Boolean Network Reservoir Computers in Approximating Arbitrary Recursive and Non-Recursive Binary Filters.
Entropy, 2018

Multiscale mutation clustering algorithm identifies pan-cancer mutational clusters associated with pathway-level changes in gene expression.
PLoS Computational Biology, 2017

Solving the influence maximization problem reveals regulatory organization of the yeast cell cycle.
PLoS Computational Biology, 2017

Literature-based discovery of new candidates for drug repurposing.
Briefings in Bioinformatics, 2017

Combining dependent P-values with an empirical adaptation of Brown's method.
Bioinformatics, 2016

Mapping dynamical states to structural classes for Boolean networks using a classification algorithm.
Proceedings of the 23rd European Signal Processing Conference, 2015

Biocellion: accelerating computer simulation of multicellular biological system models.
Bioinformatics, 2014

Fastbreak: a tool for analysis and visualization of structural variations in genomic data.
EURASIP J. Bioinformatics and Systems Biology, 2012

Trade-off between Responsiveness and Noise Suppression in Biomolecular System Responses to Environmental Cues.
PLoS Computational Biology, 2011

EPEPT: A web service for enhanced P-value estimation in permutation tests.
BMC Bioinformatics, 2011

Introduction to the special issue on information theory in molecular biology and neuroscience.
IEEE Trans. Information Theory, 2010

Biological information as set-based complexity.
IEEE Trans. Information Theory, 2010

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

Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites.
Bioinformatics, 2010

Probabilistic analysis of gene expression measurements from heterogeneous tissues.
Bioinformatics, 2010

An Integration Architecture Designed to Deal with the Issues of Biological Scope, Scale and Complexity.
Proceedings of the Data Integration in the Life Sciences, 7th International Conference, 2010

Howdah - A Flexible Pipeline Framework for Analyzing Genomic Data.
Proceedings of the Cloud Computing, Second International Conference, 2010

Probabilistic Boolean Networks - The Modeling and Control of Gene Regulatory Networks.
SIAM, ISBN: 978-0-89871-692-4, 2010

Boolean Modeling of Biological Networks.
Proceedings of the Encyclopedia of Complexity and Systems Science, 2009

Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation.
BMC Systems Biology, 2009

Adaptable data management for systems biology investigations.
BMC Bioinformatics, 2009

Fewer permutations, more accurate P-values.
Bioinformatics, 2009

Critical Boolean networks require minimal intervention rate.
Proceedings of the 2009 IEEE International Workshop on Genomic Signal Processing and Statistics, 2009

Uncovering a Macrophage Transcriptional Program by Integrating Evidence from Motif Scanning and Expression Dynamics.
PLoS Computational Biology, 2008

Learning the structure of dynamic Bayesian networks from time series and steady state measurements.
Machine Learning, 2008

Introduction to the Issue on Genomic and Proteomic Signal Processing.
J. Sel. Topics Signal Processing, 2008

Inference of Boolean Networks Using Sensitivity Regularization.
EURASIP J. Bioinformatics and Systems Biology, 2008

Set-based complexity and biological information
CoRR, 2008

Systems biology driven software design for the research enterprise.
BMC Bioinformatics, 2008

Simcluster: clustering enumeration gene expression data on the simplex space.
BMC Bioinformatics, 2007

ProbCD: enrichment analysis accounting for categorization uncertainty.
BMC Bioinformatics, 2007

Robust regression for periodicity detection in non-uniformly sampled time-course gene expression data.
BMC Bioinformatics, 2007

Nonlinear modeling of protein expressions in protein arrays.
IEEE Trans. Signal Processing, 2006

Relationships between probabilistic Boolean networks and dynamic Bayesian networks as models of gene regulatory networks.
Signal Processing, 2006

Robust quantification of in vitro angiogenesis through image analysis.
IEEE Trans. Med. Imaging, 2005

Steady-state probabilities for attractors in probabilistic Boolean networks.
Signal Processing, 2005

The Role of Redundancy in the Robustness of Random Boolean Networks
CoRR, 2005

Noise in a small genetic circuit that undergoes bifurcation.
Complexity, 2005

In silico microdissection of microarray data from heterogeneous cell populations.
BMC Bioinformatics, 2005

Robust estimation of protein expression ratios with lysate microarray technology.
Bioinformatics, 2005

Spectral methods for testing membership in certain post classes and the class of forcing functions.
IEEE Signal Process. Lett., 2004

Correction of Misclassifications Using a Proximity-Based Estimation Method.
EURASIP J. Adv. Sig. Proc., 2004

Genomic Signal Processing: The Salient Issues.
EURASIP J. Adv. Sig. Proc., 2004

Growing genetic regulatory networks from seed genes.
Bioinformatics, 2004

Mappings between probabilistic Boolean networks.
Signal Processing, 2003

Genomic signal processing.
Signal Processing, 2003

On Learning Gene Regulatory Networks Under the Boolean Network Model.
Machine Learning, 2003

Stability-based cluster analysis applied to microarray data.
Proceedings of the Seventh International Symposium on Signal Processing and Its Applications, 2003

On the robustness of the class of stack filters.
IEEE Trans. Signal Processing, 2002

Kernel density estimation with adaptive varying window size.
Pattern Recognition Letters, 2002

Markov Random Field Modeling in Median Pyramidal Transform Domain for Denoising Applications.
Journal of Mathematical Imaging and Vision, 2002

On the distribution of the number of monotone Boolean functions relative to the number of lower units.
Discrete Mathematics, 2002

Binary analysis and optimization-based normalization of gene expression data.
Bioinformatics, 2002

ayesian automatic relevance determination algorithms for classifying gene expression data.
Bioinformatics, 2002

Probabilistic Boolean networks: a rule-based uncertainty model for gene regulatory networks.
Bioinformatics, 2002

Correction to "output distributionsof stack filters based on mirrored threshold decomposition".
IEEE Trans. Signal Processing, 2001

Output distributions of stack filters based on mirrored threshold decomposition.
IEEE Trans. Signal Processing, 2001

Block-median pyramidal transform: analysis and denoising applications.
IEEE Trans. Signal Processing, 2001

Complexity of the consistency problem for certain Post classes.
IEEE Trans. Systems, Man, and Cybernetics, Part B, 2001

Simplified implementation of the recursive median sieve.
Signal Processing, 2001

Breakdown probabilities of recursive stack filters.
Signal Processing, 2001

Perceptual Issues in Music Pattern Recognition: Complexity of Rhythm and Key Finding.
Computers and the Humanities, 2001

Almost all monotone Boolean functions are polynomially learnable using membership queries.
Inf. Process. Lett., 2001

EURASIP J. Adv. Sig. Proc., 2001

A New Image Similarity Measure Based on Ordinal Correlation.
Proceedings of the 2000 International Conference on Image Processing, 2000

Statistics of stack filters with mirrored threshold decomposition.
Proceedings of the IEEE International Conference on Acoustics, 2000

A tree of median pyramidal decompositions with an application to signal denoising.
Proceedings of the IEEE International Conference on Acoustics, 2000

Reliable learning using post classes.
Proceedings of the 10th European Signal Processing Conference, 2000

A framework for ordinal-based image correspondence.
Proceedings of the 10th European Signal Processing Conference, 2000

Reduction factors in finite automata with application to nonlinear filters.
Proceedings of the 10th European Signal Processing Conference, 2000

Output distributions of recursive stack filters.
IEEE Signal Process. Lett., 1999

Graph-based smoothing of class data with applications in musical key finding.
Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999

Optimization of stack filters using sample selection probabilities.
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.
Proceedings of the IEEE-EURASIP Workshop on Nonlinear Signal and Image Processing (NSIP'99), 1999

Image Denoising Using a Block-Median Pyramid.
Proceedings of the 1999 International Conference on Image Processing, 1999

On the Structure of Idempotent Monotone Boolean Functions.
Proceedings of the Noblesse Workshop on Non-Linear Model Based Image Analysis, 1998

Rhythm complexity measures for music pattern recognition.
Proceedings of the Second IEEE Workshop on Multimedia Signal Processing, 1998

A system for machine recognition of music patterns.
Proceedings of the 1998 IEEE International Conference on Acoustics, 1998

Generation of idempotent monotone Boolean functions.
Proceedings of the 9th European Signal Processing Conference, 1998