A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks. - Xiaobo Zhou 001; Xiaodong Wang 001; Ranadip Pal; Ivan Ivanov 001; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2004)

Reduction Mappings between Probabilistic Boolean Networks. - Ivan Ivanov 001; Edward R. Dougherty (EURASIP J. Adv. Signal Process., 2004)

Generating Boolean networks with a prescribed attractor structure. - Ranadip Pal; Ivan Ivanov 001; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks. - Ivan Ivanov 001; Ranadip Pal; Edward R. Dougherty (IEEE Trans. Signal Process., 2007)

A CoD based reduction algorithm for Boolean and probabilistic Boolean networks. - Noushin Ghaffari; Ivan Ivanov 001; Edward R. Dougherty (GENSiPS, 2009)

Intervention in gene regulatory networks via greedy control policies based on long-run behavior. - Xiaoning Qian; Ivan Ivanov 001; Noushin Ghaffari; Edward R. Dougherty (BMC Syst. Biol., 2009)

Conditioning-based model for the regulatory activities of microRNAs in specific dietary contexts. - Chen Zhao; Ivan Ivanov 001; Manasvi Shah; Laurie A. Davidson; Robert S. Chapkin; Edward R. Dougherty (GENSiPS, 2010)

A CoD-based reduction algorithm for designing stationary control policies on Boolean networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (Bioinform., 2010)

State reduction for network intervention in probabilistic Boolean networks. - Xiaoning Qian; Noushin Ghaffari; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2010)

Selection policy-induced reduction mappings for Boolean networks. - Ivan Ivanov 001; Plamen Simeonov; Noushin Ghaffari; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2010)

Pathway analysis in the context of Bayesian networks - mathematical modeling of master and canalizing genes. - Chen Zhao; Ivan Ivanov 001; Michael L. Bittner; Edward R. Dougherty (GENSiPS, 2011)

A CoD-based stationary control policy for intervening in large gene regulatory networks. - Noushin Ghaffari; Ivan Ivanov 001; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2011)

Feature Selection for High-dimensional Integrated Data. - Charles Zheng; Scott Schwartz; Robert S. Chapkin; Raymond J. Carroll; Ivan Ivanov 001 (SDM, 2012)

Identifying mechanistic similarities in drug responses. - Chen Zhao; Jianping Hua; Michael L. Bittner; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2012)

Bayesian multivariate Poisson model for RNA-seq classification. - Jason M. Knight; Ivan Ivanov 001; Edward R. Dougherty (GENSiPS, 2013)

Optimal control of gene regulatory networks with uncertain intervention effects. - Mohammadmahdi R. Yousefi; Ivan Ivanov 001 (GlobalSIP, 2013)

Modeling the Next Generation Sequencing sample processing pipeline for the purposes of classification. - Noushin Ghaffari; Mohammadmahdi R. Yousefi; Charles D. Johnson; Ivan Ivanov 001; Edward R. Dougherty (BMC Bioinform., 2013)

MCMC implementation of the optimal Bayesian classifier for non-Gaussian models: model-based RNA-Seq classification. - Jason M. Knight; Ivan Ivanov 001; Edward R. Dougherty (BMC Bioinform., 2014)

Model-based study of the Effectiveness of Reporting Lists of Small Feature Sets using RNA-Seq Data. - Eunji Kim; Ivan Ivanov 001; Jianping Hua; Robert S. Chapkin; Edward R. Dougherty (BCB, 2016)

Detecting Multivariate Gene Interactions in RNA-Seq Data Using Optimal Bayesian Classification. - Jason M. Knight; Ivan Ivanov 001; Karen Triff; Robert S. Chapkin; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Quantifying the notions of canalizing and master genes in a gene regulatory network - a Boolean network modeling perspective. - Eunji Kim; Ivan Ivanov 001; Edward R. Dougherty (Bioinform., 2019)

Comparative Study of Synthetic Bulk RNA-Seq Generators. - Felitsiya Shakola; Dean Palejev; Ivan Ivanov 001 (IWBBIO (2), 2022)

Network Classification Based on Reducibility With Respect to the Stability of Canalizing Power of Genes in a Gene Regulatory Network - A Boolean Network Modeling Perspective. - Eunji Kim; Ivan Ivanov 001; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2022)