Designing enhanced classifiers using prior process knowledge: Regularized maximum-likelihood. - Mohammad Shahrokh Esfahani; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (GENSiPS, 2011)

Probabilistic reconstruction of the tumor progression process in gene regulatory networks in the presence of uncertainty. - Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (BMC Bioinform., 2011)

OBGene: Optimal barcode generator for NGS experiments. - Esmaeil Atashpaz-Gargari; Mohammad Shahrokh Esfahani; Richard Metz; Charles D. Johnson (GENSiPS, 2012)

Sample-based prior probability construction using biological pathway knowledge. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (ACSSC, 2013)

Effect of separate sampling on classification and the minimax criterion. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (GENSiPS, 2013)

A Cooperative MARC Scheme Using Analogue Network Coding to Achieve Second-Order Diversity - Mohammad Shahrokh Esfahani; Masoumeh Nasiri-Kenari (CoRR, 2013)

Classifier design given an uncertainty class of feature distributions via regularized maximum likelihood and the incorporation of biological pathway knowledge in steady-state phenotype classification. - Mohammad Shahrokh Esfahani; Jason M. Knight; Amin Zollanvari; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2013)

Effect of separate sampling on classification accuracy. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (Bioinform., 2014)

Incorporation of Biological PathwayKnowledge in the Construction of Priorsfor Optimal Bayesian Classification. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Discrete optimal Bayesian classification with error-conditioned sequential sampling. - Ariana Broumand; Mohammad Shahrokh Esfahani; Byung-Jun Yoon; Edward R. Dougherty (Pattern Recognit., 2015)

An Optimization-Based Framework for the Transformation of Incomplete Biological Knowledge into a Probabilistic Structure and Its Application to the Utilization of Gene/Protein Signaling Pathways in Discrete Phenotype Classification. - Mohammad Shahrokh Esfahani; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2015)

A Bayesian framework for robust Kalman filtering under uncertain noise statistics. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Edward R. Dougherty (ACSSC, 2016)

Inference of Nonlinear ODE-Based Gene Regulatory Networks via Intrinsically Bayesian Robust Kalman Filtering. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Edward R. Dougherty (BCB, 2016)

Noninvasive Cancer Classification Using Diverse Genomic Features in Circulating Tumor DNA. - Mohammad Shahrokh Esfahani; Aaron M. Newman; Florian Scherer; Robert Tibshirani; Maximilian Diehn; Ash A. Alizadeh (BCB, 2016)

Bayesian Kalman filtering in the presence of unknown noise statistics using factor graphs. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (ACSSC, 2017)

Incorporating biological prior knowledge for Bayesian learning via maximal knowledge-driven information priors. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (BMC Bioinform., 2017)

Intrinsically Bayesian Robust Kalman Filter: An Innovation Process Approach. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani (IEEE Trans. Signal Process., 2017)

Optimal Bayesian Kalman Filtering With Prior Update. - Roozbeh Dehghannasiri; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE Trans. Signal Process., 2018)

Constructing Pathway-Based Priors within a Gaussian Mixture Model for Bayesian Regression and Classification. - Shahin Boluki; Mohammad Shahrokh Esfahani; Xiaoning Qian; Edward R. Dougherty (IEEE ACM Trans. Comput. Biol. Bioinform., 2019)