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)

External control in a special class of probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (ACC, 2005)

Intervention in context-sensitive probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS. - Ranadip Pal; Aniruddha Datta; Albert J. Fornace Jr.; Michael L. Bittner; Edward R. Dougherty (Bioinform., 2005)

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

Optimal infinite-horizon control for probabilistic Boolean networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2006)

Control approaches for probabilistic gene regulatory networks - What approaches have been developed for addreassinig the issue of intervention? - Anirulddlha Datta; Ranadip Pal; Ashish Choudhary; Edward R. Dougherty (IEEE Signal Process. Mag., 2007)

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

Generating structure-function correlations by ICA- based mapping of activation patterns on co-registered fMRI and FA-DTI data. - Sunanda Mitra; M. O'Boyle; Enrique Corona; Bian Li; F. Afrin; Brian Nutter; M. Baker; Ranadip Pal; Bijoy K. Ghosh; Tanja Karp (ACSCC, 2008)

Robust Intervention in Probabilistic Boolean Networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2008)

Steady-state preserving reduction for genetic regulatory network models. - Ranadip Pal; Sonal Bhattacharya (CBMS, 2009)

Analyzing steady state probability distributions of Context-sensitive Probabilistic Boolean Networks. - Ranadip Pal (GENSiPS, 2009)

Quantification of data extraction noise in probabilistic Boolean Network modeling. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (GENSiPS, 2009)

Adaptive intervention in probabilistic boolean networks. - Ritwik Layek; Aniruddha Datta; Ranadip Pal; Edward R. Dougherty (Bioinform., 2009)

Bayesian robustness in the control of gene regulatory networks. - Ranadip Pal; Aniruddha Datta; Edward R. Dougherty (IEEE Trans. Signal Process., 2009)

Effect of coarse-scale modeling on control outcome of genetic regulatory networks. - Ranadip Pal; Sonal Bhattacharya (ACC, 2010)

Control of stochastic master equation models of genetic regulatory networks by approximating their average behavior. - Ranadip Pal; Mehmet Umut Caglar (GENSiPS, 2010)

Classification of Alzheimer's disease and mild cognitive impairment by pattern recognition of EEG power and coherence. - Kwaku Akrofi; Ranadip Pal; Mary C. Baker; Brian Nutter; Randolph W. Schiffer (ICASSP, 2010)

Classification of cognitive states using functional MRI data. - Ye Yang; Ranadip Pal; Michael O'Boyle (Image Processing, 2010)

Stationary and structural control in gene regulatory networks: basic concepts. - Edward R. Dougherty; Ranadip Pal; Xiaoning Qian; Michael L. Bittner; Aniruddha Datta (Int. J. Syst. Sci., 2010)

Context-sensitive probabilistic Boolean networks: steady-state properties, reduction, and steady-state approximation. - Ranadip Pal (IEEE Trans. Signal Process., 2010)

Characterizing the effect of coarse-scale PBN modeling on dynamics and intervention performance of genetic regulatory networks represented by stochastic master equation models. - Ranadip Pal; Sonal Bhattacharya (IEEE Trans. Signal Process., 2010)

Generation of intervention strategy for a Genetic Regulatory Network represented by a family of Markov Chains. - Noah Berlow; Ranadip Pal (EMBC, 2011)

A novel approach for tumor sensitivity prediction and combination therapy design for targeted drugs. - Noah Berlow; Ranadip Pal (GENSiPS, 2011)

A novel critical time analysis approach for genetic regulatory networks. - Sonal Bhattacharya; Ranadip Pal (GENSiPS, 2011)

Inference of a genetic regulatory network model from limited time series data. - Saad Haider; Ranadip Pal (GENSiPS, 2011)

Complexity reduction of stochastic master equation simulation based on Kronecker product analysis. - Mehmet Umut Caglar; Ranadip Pal (BCB, 2012)

Combination therapy design for targeted therapeutics from a drug-protein interaction perspective. - Saad Haider; Noah Berlow; Ranadip Pal; Lara E. Davis; Charles Keller (GENSiPS, 2012)

Anticancer drug sensitivity analysis: An integrated approach applied to Erlotinib sensitivity prediction in the CCLE database. - Ranadip Pal; Noah Berlow; Saad Haider (GENSiPS, 2012)

A Kinase Inhibition Map Approach for Tumor Sensitivity Prediction and Combination Therapy Design for Targeted Drugs. - Ranadip Pal; Noah Berlow (Pacific Symposium on Biocomputing, 2012)

Analyzing pathway design from drug perturbation experiments. - Noah Berlow; Ranadip Pal; Lara E. Davis; Charles Keller (SSP, 2012)

Robust Approaches for Genetic Regulatory Network Modeling and Intervention: A review of recent advances. - Ranadip Pal; Sonal Bhattacharya; Mehmet Umut Caglar (IEEE Signal Process. Mag., 2012)

Transient Dynamics of Reduced-Order Models of Genetic Regulatory Networks. - Ranadip Pal; Sonal Bhattacharya (IEEE ACM Trans. Comput. Biol. Bioinform., 2012)

Quantifying the inference power of a drug screen for predictive analysis. - Noah Berlow; Saad Haider; Ranadip Pal; Charles Keller (GENSiPS, 2013)

A multivariate random forest based framework for drug sensitivity prediction. - Qian Wan; Ranadip Pal (GENSiPS, 2013)

Inference of tumor inhibition pathways from drug perturbation data. - Saad Haider; Ranadip Pal (GlobalSIP, 2013)

A new approach for prediction of tumor sensitivity to targeted drugs based on functional data. - Noah Berlow; Lara E. Davis; Emma L. Cantor; Bernard Séguin; Charles Keller; Ranadip Pal (BMC Bioinform., 2013)

Stochastic Model Simulation Using Kronecker Product Analysis and Zassenhaus Formula Approximation. - Mehmet Umut Caglar; Ranadip Pal (IEEE ACM Trans. Comput. Biol. Bioinform., 2013)

Modeling and inference of genetic interactions. - Ranadip Pal (WIREs Data Mining Knowl. Discov., 2013)

Non-contact multi-radar smart probing of body orientation based on micro-Doppler signatures. - Yiran Li; Ranadip Pal; Changzhi Li (EMBC, 2014)

Gesture recognition for smart home applications using portable radar sensors. - Qian Wan; Yiran Li; Changzhi Li; Ranadip Pal (EMBC, 2014)

Analysis of multivariate drug sensitivity dependence structure using copulas. - Saad Haider; Ranadip Pal (GlobalSIP, 2014)

Multi-objective optimization of ensemble of regression trees using genetic algorithms. - Qian Wan; Ranadip Pal (GlobalSIP, 2014)

Inference of dynamic biological networks based on responses to drug perturbations. - Noah Berlow; Lara E. Davis; Charles Keller; Ranadip Pal (EURASIP J. Bioinform. Syst. Biol., 2014)

An Integrated Approach to Anti-Cancer Drug Sensitivity Prediction. - Noah Berlow; Saad Haider; Qian Wan; Mathew Geltzeiler; Lara E. Davis; Charles Keller; Ranadip Pal (IEEE ACM Trans. Comput. Biol. Bioinform., 2014)

Analyzing drug sensitivity prediction based on dose response curve characteristics. - Raziur Rahman; Ranadip Pal (BHI, 2016)

A descriptive model of resting-state networks using Markov chains. - Hua Xie; Ranadip Pal; Sunanda Mitra (EMBC, 2016)

Automated segmentation of MS lesions in FLAIR, DIR and T2-w MR images via an information theoretic approach. - Jason E. Hill; Kevin Matlock; Ranadip Pal; Brian Nutter; Sunanda Mitra (Image Processing, 2016)

Algorithms for Drug Sensitivity Prediction. - Carlos De Niz; Raziur Rahman; Xiangyuan Zhao; Ranadip Pal (Algorithms, 2016)

IntegratedMRF: random forest-based framework for integrating prediction from different data types. - Raziur Rahman; John Otridge; Ranadip Pal (Bioinform., 2017)

Combination therapy design for maximizing sensitivity and minimizing toxicity. - Kevin Matlock; Noah Berlow; Charles Keller; Ranadip Pal (BMC Bioinform., 2017)

Recursive Model for Dose-time Responses in Pharmacological Studies. - Aminur Rahman; Saugato Rahman Dhruba; Souparno Ghosh; Ranadip Pal (BCB, 2018)

An investigation of proteomic data for application in precision medicine. - Kevin Matlock; Saugato Rahman Dhruba; Moazzam Nazir; Ranadip Pal (BHI, 2018)

Dimensionality Reduction based Transfer Learning applied to Pharmacogenomics Databases. - Saugato Rahman Dhruba; Raziur Rahman; Kevin Matlock; Souparno Ghosh; Ranadip Pal (EMBC, 2018)

Adaptive Multi-task Elastic Net based feature selection from Pharmacogenomics Databases. - Raziur Rahman; Chamila Perera; Souparno Ghosh; Ranadip Pal (EMBC, 2018)

Sequential feature selection and inference using multi-variate random forests. - Joshua Mayer; Raziur Rahman; Souparno Ghosh; Ranadip Pal (Bioinform., 2018)

Application of transfer learning for cancer drug sensitivity prediction. - Saugato Rahman Dhruba; Raziur Rahman; Kevin Matlock; Souparno Ghosh; Ranadip Pal (BMC Bioinform., 2018)

Investigation of model stacking for drug sensitivity prediction. - Kevin Matlock; Carlos De Niz; Raziur Rahman; Souparno Ghosh; Ranadip Pal (BMC Bioinform., 2018)

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2018)

Deep Sequencing Data Analysis. - Bijoy K. Ghosh; Aniruddha Datta; Ranadip Pal (IEEE ACM Trans. Comput. Biol. Bioinform., 2018)

Evaluating the consistency of large-scale pharmacogenomic studies. - Raziur Rahman; Saugato Rahman Dhruba; Kevin Matlock; Carlos De Niz; Souparno Ghosh; Ranadip Pal (Briefings Bioinform., 2019)

Sstack: an R package for stacking with applications to scenarios involving sequential addition of samples and features. - Kevin Matlock; Raziur Rahman; Souparno Ghosh; Ranadip Pal (Bioinform., 2019)

Recursive model for dose-time responses in pharmacological studies. - Saugato Rahman Dhruba; Aminur Rahman; Raziur Rahman; Souparno Ghosh; Ranadip Pal (BMC Bioinform., 2019)

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC). - Byung-Jun Yoon; Xiaoning Qian; Tamer Kahveci; Ranadip Pal (BMC Bioinform., 2019)

REFINED (REpresentation of Features as Images with NEighborhood Dependencies): A novel feature representation for Convolutional Neural Networks. - Omid Bazgir; Ruibo Zhang; Saugato Rahman Dhruba; Raziur Rahman; Souparno Ghosh; Ranadip Pal (CoRR, 2019)

Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction. - Omid Bazgir; Souparno Ghosh; Ranadip Pal (Bioinform., 2021)

Predicting binding affinities of emerging variants of SARS-CoV-2 using spike protein sequencing data: observations, caveats and recommendations. - Ruibo Zhang; Souparno Ghosh; Ranadip Pal (Briefings Bioinform., 2022)

Efficient Normalized Conformal Prediction and Uncertainty Quantification for Anti-Cancer Drug Sensitivity Prediction with Deep Regression Forests. - Daniel Nolte; Souparno Ghosh; Ranadip Pal (EMBC, 2024)

Assessing Reusability of Deep Learning-Based Monotherapy Drug Response Prediction Models Trained with Omics Data. - Jamie C. Overbeek; Alexander Partin; Thomas S. Brettin; Nicholas Chia; Oleksandr Narykov; Priyanka Vasanthakumari; Andreas Wilke; Yitan Zhu; Austin Clyde; Sara Jones; Rohan Gnanaolivu; Yuanhang Liu; et al. (CoRR, 2024)

Benchmarking community drug response prediction models: datasets, models, tools, and metrics for cross-dataset generalization analysis. - Alexander Partin; Priyanka Vasanthakumari; Oleksandr Narykov; Andreas Wilke; Natasha Koussa; Sara E. Jones; Yitan Zhu; Jamie C. Overbeek; Rajeev Jain; Gayara Demini Fernando; Cesar Sanchez-Villalobos; Cristina Garcia-Cardona; et al. (CoRR, 2025)

AdapTor: Adaptive Topological Regression for quantitative structure-activity relationship modeling. - Yixiang Mao; Souparno Ghosh; Ranadip Pal (J. Cheminformatics, 2025)