R. Pal

发表

Control approaches for probabilistic gene regulatory networks - What approaches have been developed for addreassinig the issue of intervention?

Ashish Choudhury, Edward R. Dougherty, Ranadip Pal, 2007, IEEE Signal Processing Magazine.

Overview of predictive modeling based on genomic characterizations

R. Pal, 2017 .

Send Orders of Reprints at Reprints@benthamscience.net Integrated Analysis of Transcriptomic and Proteomic Data

R. Pal, Saad Haider, 2022 .

The HDAC3–SMARCA4–miR-27a axis promotes expression of the PAX3:FOXO1 fusion oncogene in rhabdomyosarcoma

Noah E. Berlow, Matthew N. Svalina, T. Perkins, 2018, Science Signaling.

Feature selection and extraction from heterogeneous genomic characterizations

R. Pal, 2017 .

Inference of dynamic biological networks based on perturbation data

R. Pal, 2017 .

Bayesian Robustness in the Control of Gene Regulatory Networks

A. Datta, E. Dougherty, R. Pal, 2007 .

Dynamics Preserving Size Reduction Mappings for

E. Dougherty, R. Pal, I. Ivanov, 2007 .

Synthesizing Boolean networks with a given attractor structure

A. Datta, A. Datta, R. Pal, 2006, 2006 IEEE International Workshop on Genomic Signal Processing and Statistics.

Optimal infinite horizon control for probabilistic Boolean networks

A. Datta, E. Dougherty, R. Pal, 2006, ACC.

Optimal Infinite-Horizon Control for

A. Datta, E. Dougherty, R. Pal, 2006 .

External control in a special class of probabilistic Boolean networks

A. Datta, E. Dougherty, M. Bittner, 2005, Proceedings of the 2005, American Control Conference, 2005..

Functionally-defined Therapeutic Targets in Diffuse Intrinsic Pontine Glioma

Nicholas J. Wang, Noah E. Berlow, Matthew N. Svalina, 2015, Nature Medicine.

Predictive modeling based on multivariate random forests

R. Pal, 2017 .

Chapter 2 – Data characterization

R. Pal, 2017 .

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

Noah E. Berlow, Matthew N. Svalina, Elaine C. Huang, 2019, BMC Cancer.

Target Inhibition Maps Based on Responses to Kinase Inhibitors.

Noah E. Berlow, R. Pal, 2017, Methods in molecular biology.

Modeling of drug diffusion in a solid tumor leading to tumor cell death

R. Pal, Souparno Ghosh, Aminur Rahman, 2018, Physical Review E.

Predictive modeling based on functional and genomic characterizations

R. Pal, 2017 .

Deep Functional and Molecular Characterization of a High-Risk Undifferentiated Pleomorphic Sarcoma

Noah E. Berlow, P. Spellman, R. Pal, 2020, Sarcoma.

Tumor growth models

R. Pal, 2017 .

2009 IEEE International Workshop on Genomic Signal Processing and Statistics, GENSiPS 2009, Minneapolis, MN, USA, May 17-21, 2009

Ganapati Panda, Aniruddha Datta, Edward R. Dougherty, 2009, GENSiPS.

91 FADS AND FALLACIES IN THE NAME OF SMALL-SAMPLE MICROARRAY CLASSIFICATION

Rabab K. Ward, Petar M. Djuric, Sergios Theodoridis, 2007 .

Chapter 4 – Validation methodologies

Ranadip Pal, R. Pal, 2017 .

A High-Throughput In Vitro Drug Screen in a Genetically Engineered Mouse Model of Diffuse Intrinsic Pontine Glioma Identifies BMS-754807 as a Promising Therapeutic Agent

Noah E. Berlow, R. Pal, I. Spasojević, 2015, PloS one.

Algorithms for Drug Sensitivity Prediction

Ranadip Pal, Raziur Rahman, Carlos De Niz, 2016, Algorithms.

Erratum: Functionally defined therapeutic targets in diffuse intrinsic pontine glioma

Ranadip Pal, Charles Keller, Nathalene Truffaux, 2015, Nature Medicine.

Potential Active Shooter Detection Based on Radar Micro-Doppler and Range-Doppler Analysis Using Artificial Neural Network

Yiran Li, Changzhi Li, Zhengyu Peng, 2019, IEEE Sensors Journal.

Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction

R. Pal, Souparno Ghosh, Omid Bazgir, 2020, Bioinform..

Evaluating the consistency of large-scale pharmacogenomic studies

Ranadip Pal, Kevin Matlock, Souparno Ghosh, 2019, Briefings Bioinform..

IntegratedMRF: random forest‐based framework for integrating prediction from different data types

Ranadip Pal, Raziur Rahman, John Otridge, 2017, Bioinform..

Integrated multiomics analysis identifies molecular landscape perturbations during hyperammonemia in skeletal muscle and myotubes

Saugato Rahman Dhruba, R. Pal, K. Esser, 2021, The Journal of biological chemistry.

An Ensemble Based Top Performing Approach for NCI-DREAM Drug Sensitivity Prediction Challenge

R. Pal, Qian Wan, 2014, PloS one.

Ijbcp International Journal of Basic & Clinical Pharmacology Multiple Myeloma: the Disease and Its Treatment

R. Pal, Meenakshi Gupta, D. Tikoo, 2022 .

Gene expression Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS

Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty, 2005 .

EXPERIMENTAL THERAPEUTICS AND PHARMACOLOGY

Tina N. Davis, Forrest M Kievit, Atique U. Ahmed, 2013 .

Evidence for an unanticipated relationship between undifferentiated pleomorphic sarcoma and embryonal rhabdomyosarcoma.

Benjamin R Arenkiel, Ranadip Pal, Qing-Rong Chen, 2011, Cancer cell.

Rhabdomyosarcoma: current challenges and their implications for developing therapies.

J. Khan, R. Pal, C. Keller, 2014, Cold Spring Harbor perspectives in medicine.

Developing Therapies Rhabdomyosarcoma : Current Challenges and Their Implications for

J. Khan, R. Pal, B. Stillman, 2014 .

An adaptive Src-PDGFRA-Raf axis in rhabdomyosarcoma.

R. Pal, C. Keller, J. Michalek, 2012, Biochemical and biophysical research communications.

Emerging Research in the Analysis and Modeling of Gene Regulatory Networks

Xiaoning Qian, Ranadip Pal, Ivan Ivanov, 2016 .

Analyzing drug sensitivity prediction based on dose response curve characteristics

Ranadip Pal, Raziur Rahman, R. Pal, 2016, 2016 IEEE-EMBS International Conference on Biomedical and Health Informatics (BHI).

Sequential feature selection and inference using multi‐variate random forests

Ranadip Pal, Souparno Ghosh, Raziur Rahman, 2018, Bioinform..

S1: Supplementary Information for Article: A copula based S1: Supplementary Information for Article: A copula based approach for design of multivariate random forests for drug approach for design of multivariate random forests for drug sensitivity prediction sensitivity prediction

Ranadip Pal, Souparno Ghosh, Saad Haider, 2015 .

Chapter 11 – Combination therapeutics

Ranadip Pal, R. Pal, 2017 .

A Diverse Stochastic Search Algorithm for Combination Therapeutics

Ranadip Pal, Mehmet Umut Caglar, R. Pal, 2014, BioMed research international.

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, R. Pal, 2010, IEEE Transactions on Signal Processing.

Context-Sensitive Probabilistic Boolean Networks: Steady-State Properties, Reduction, and Steady-State Approximation

Ranadip Pal, R. Pal, 2010, IEEE Transactions on Signal Processing.

Stochastic Model Simulation Using Kronecker Product Analysis and Zassenhaus Formula Approximation

Ranadip Pal, Mehmet Umut Caglar, R. Pal, 2013, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Complexity reduction of stochastic master equation simulation based on Kronecker product analysis

Ranadip Pal, Mehmet Umut Caglar, R. Pal, 2012, BCB.

A Kinase Inhibition Map Approach for Tumor Sensitivity Prediction and Combination Therapy Design for Targeted Drugs

Ranadip Pal, Noah Berlow, Noah E. Berlow, 2011, Pacific Symposium on Biocomputing.

Active Shooter Detection in Multiple-Person Scenario Using RF-Based Machine Vision

Yiran Li, Changzhi Li, Ranadip Pal, 2021, IEEE Sensors Journal.

Modeling and control of genetic regulatory networks

Ranadip Pal, R. Pal, 2009 .

Optimal infinite horizon control for probabilistic Boolean networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2006, 2006 American Control Conference.

Intervention in context-sensitive probabilistic Boolean networks

Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty, 2005, Bioinform..

Selected articles from the IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS'2011)

Yufei Huang, Ranadip Pal, Yidong Chen, 2012, BMC Genomics.

An Integrated Approach to Anti-Cancer Drug Sensitivity Prediction

Qian Wan, Ranadip Pal, Noah Berlow, 2014, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

A new approach for prediction of tumor sensitivity to targeted drugs based on functional data

Emma L. Cantor, Noah E. Berlow, R. Pal, 2013, BMC Bioinformatics.

Predictive Modeling of Anti-Cancer Drug Sensitivity from Genetic Characterizations.

Ranadip Pal, Raziur Rahman, R. Pal, 2018, Methods in molecular biology.

Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma

Ranadip Pal, Carol J. Bult, Charles Keller, 2018, BMC Cancer.

Full Title: Probabilistic modeling of personalized drug combinations from integrated chemical screen and molecular data in sarcoma Short Title: Predictive Algorithms for Personalized Drug Combinations

Noah E. Berlow, Matthew N. Svalina, Elaine C. Huang, 2018 .

Combination therapy design for maximizing sensitivity and minimizing toxicity

Ranadip Pal, Kevin Matlock, Noah Berlow, 2016, BMC Bioinformatics.

A mathematical framework for analyzing drug combination toxicity for personalized medicine applications

R. Pal, Raziur Rahman, 2016, 2016 IEEE Healthcare Innovation Point-Of-Care Technologies Conference (HI-POCT).

Analysis of multivariate drug sensitivity dependence structure using copulas

Ranadip Pal, Saad Haider, R. Pal, 2014, 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP).

Inference of dynamic biological networks based on responses to drug perturbations

Ranadip Pal, Noah Berlow, Charles Keller, 2014, EURASIP J. Bioinform. Syst. Biol..

Inference of tumor inhibition pathways from drug perturbation data

Ranadip Pal, Saad Haider, R. Pal, 2013, 2013 IEEE Global Conference on Signal and Information Processing.

Quantifying the inference power of a drug screen for predictive analysis

Ranadip Pal, Noah Berlow, Charles Keller, 2013, 2013 IEEE International Workshop on Genomic Signal Processing and Statistics.

A new approach for prediction of tumor sensitivity to targeted drugs based on functional data

Ranadip Pal, Noah Berlow, Charles Keller, 2013, BMC Bioinformatics.

Anticancer drug sensitivity analysis: An integrated approach applied to Erlotinib sensitivity prediction in the CCLE database

Ranadip Pal, Noah Berlow, Saad Haider, 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Bayesian Robustness in the Control of Gene Regulatory Networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2007, IEEE Transactions on Signal Processing.

Robust Intervention in Probabilistic Boolean Networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2007, 2007 American Control Conference.

Robust Approaches for Genetic Regulatory Network Modeling and Intervention: A review of recent advances

Ranadip Pal, Mehmet Umut Caglar, Sonal Bhattacharya, 2012, IEEE Signal Processing Magazine.

Generation of intervention strategy for a Genetic Regulatory Network represented by a family of Markov Chains

Ranadip Pal, Noah Berlow, Noah E. Berlow, 2011, 2011 Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

ANALYZING THE EFFECTS OF COARSE-SCALE MODELING OF GENETIC REGULATORY NETWORKS

R. Pal, D. Hoover, 2011 .

Control of stochastic master equation models of genetic regulatory networks by approximating their average behavior

Ranadip Pal, Mehmet Umut Caglar, R. Pal, 2010, 2010 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Steady-state preserving reduction for genetic regulatory network models

Ranadip Pal, Sonal Bhattacharya, R. Pal, 2009, 2009 22nd IEEE International Symposium on Computer-Based Medical Systems.

Federated learning framework integrating REFINED CNN and Deep Regression Forests

R. Pal, Souparno Ghosh, Omid Bazgir, 2023, Bioinformatics advances.

REFINED (REpresentation of Features as Images with NEighborhood Dependencies): A novel feature representation for Convolutional Neural Networks

Saugato Rahman Dhruba, R. Pal, Souparno Ghosh, 2019, ArXiv.

Combination therapy design for maximizing sensitivity and minimizing toxicity

Noah E. Berlow, R. Pal, C. Keller, 2016, BMC Bioinformatics.

Gesture recognition for smart home applications using portable radar sensors

Yiran Li, Changzhi Li, Qian Wan, 2014, 2014 36th Annual International Conference of the IEEE Engineering in Medicine and Biology Society.

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, R. Pal, Xiaoning Qian, 2019, BMC Bioinformatics.

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, R. Pal, Xiaoning Qian, 2018, BMC Bioinformatics.

Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, R. Pal, Xiaoning Qian, 2020, BMC Genomics.

Recursive model for dose-time responses in pharmacological studies

Ranadip Pal, Souparno Ghosh, Saugato Rahman Dhruba, 2019, BMC Bioinformatics.

Structural Intervention and External Control for Markovian Regulatory Network Models

Xiaoning Qian, Ranadip Pal, R. Pal, 2019, Biotechnology.

Heterogeneity Aware Random Forest for Drug Sensitivity Prediction

Ranadip Pal, Kevin Matlock, Souparno Ghosh, 2017, Scientific Reports.

Application of transfer learning for cancer drug sensitivity prediction

Ranadip Pal, Kevin Matlock, Souparno Ghosh, 2018, BMC Bioinformatics.

Dynamics Preserving Size Reduction Mappings for Probabilistic Boolean Networks

Edward R. Dougherty, Ivan Ivanov, Ranadip Pal, 2007, IEEE Transactions on Signal Processing.

Generating Boolean networks with a prescribed attractor structure

Aniruddha Datta, Michael L. Bittner, Edward R. Dougherty, 2005, Bioinform..

A Bayesian connectivity-based approach to constructing probabilistic gene regulatory networks

Xiaobo Zhou, Xiaodong Wang, Michael L. Bittner, 2004, Bioinform..

A novel approach for tumor sensitivity prediction and combination therapy design for targeted drugs

Ranadip Pal, Noah Berlow, Noah E. Berlow, 2011, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Functional random forest with applications in dose-response predictions

R. Pal, Souparno Ghosh, Raziur Rahman, 2019, Scientific Reports.

Comparative non-cholinergic neurotoxic effects of paraoxon and diisopropyl fluorophosphate (DFP) on human neuroblastoma and astrocytoma cell lines.

A. Datta, R. Pal, J. Wild, 2007, Toxicology and applied pharmacology.

Investigation of model stacking for drug sensitivity prediction

Ranadip Pal, Kevin Matlock, Souparno Ghosh, 2017, BMC Bioinformatics.

Representation of features as images with neighborhood dependencies for compatibility with convolutional neural networks

R. Pal, Souparno Ghosh, Omid Bazgir, 2019, Nature Communications.

Adaptive intervention in Probabilistic Boolean Networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2009, 2009 American Control Conference.

Modeling and inference of genetic interactions

Ranadip Pal, R. Pal, 2013, WIREs Data Mining Knowl. Discov..

Preclinical rationale for entinostat in embryonal rhabdomyosarcoma

Noah E. Berlow, Matthew N. Svalina, T. Perkins, 2019, Skeletal Muscle.

Generating structure-function correlations by ICA- based mapping of activation patterns on co-registered fMRI and FA-DTI data

R. Pal, S. Mitra, T. Karp, 2008, 2008 42nd Asilomar Conference on Signals, Systems and Computers.

On the fast convergence modeling and accurate calculation of PV output energy for operation and planning studies

Seyed Hossein Hosseinian, Sajjad Abedi, Ranadip Pal, 2015 .

Integrated Analysis of Transcriptomic and Proteomic Data

R. Pal, Saad Haider, 2013, Current genomics.

Classification of Alzheimer's disease and mild cognitive impairment by pattern recognition of EEG power and coherence

Mary C. Baker, Kwaku Akrofi, Brian Nutter, 2010, 2010 IEEE International Conference on Acoustics, Speech and Signal Processing.

Chapter 12 – Online resources

R. Pal, 2017 .

Investigation of REFINED CNN ensemble learning for anti-cancer drug sensitivity prediction

Ranadip Pal, Souparno Ghosh, Omid Bazgir, 2020, Bioinform..

Heterogeneity Aware Random Forest for Drug Sensitivity Prediction

R. Pal, Souparno Ghosh, K. Matlock, 2017, Scientific Reports.

GENERATION OF STATIONARY CONTROL POLICIES WITH BEST EXPECTED PERFORMANCE FOR A FAMILY OF MARKOV CHAINS

Ranadip Pal, Noah Berlow, Noah E. Berlow, 2012 .

Controlpproaches for Probabilistic Gene Regulatory Networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2007 .

Intervention in Probabilistic Gene Regulatory Networks

Aniruddha Datta, Edward R. Dougherty, Ranadip Pal, 2006 .

Functional random forest with applications in dose-response predictions

Ranadip Pal, Souparno Ghosh, Saugato Rahman Dhruba, 2019, Scientific Reports.

An investigation of proteomic data for application in precision medicine

Ranadip Pal, Kevin Matlock, Saugato Rahman Dhruba, 2018, 2018 IEEE EMBS International Conference on Biomedical & Health Informatics (BHI).

Efficient Normalized Conformal Prediction and Uncertainty Quantification for Anti-Cancer Drug Sensitivity Prediction with Deep Regression Forests

R. Pal, Souparno Ghosh, Daniel Nolte, 2024, ArXiv.

A Modified Neighborhood Hypothesis Test for Population Mean in Functional Data

R. Pal, Souparno Ghosh, Leif Ellingson, 2023, Journal of Agricultural, Biological and Environmental Statistics.

Design of Probabilistic Random Forests with Applications to Anticancer Drug Sensitivity Prediction

Ranadip Pal, Souparno Ghosh, Saad Haider, 2015, Cancer informatics.

Multi-objective optimization of ensemble of regression trees using genetic algorithms

Qian Wan, Ranadip Pal, R. Pal, 2014, 2014 IEEE Global Conference on Signal and Information Processing (GlobalSIP).

A multivariate random forest based framework for drug sensitivity prediction

Qian Wan, Ranadip Pal, R. Pal, 2013, 2013 IEEE International Workshop on Genomic Signal Processing and Statistics.

Predictive modeling based on random forests

Ranadip Pal, R. Pal, 2017 .

Chapter 13 – Challenges

Ranadip Pal, R. Pal, 2017 .

Analyzing pathway design from drug perturbation experiments

Ranadip Pal, Noah Berlow, Charles Keller, 2012, 2012 IEEE Statistical Signal Processing Workshop (SSP).

Combination therapy design for targeted therapeutics from a drug-protein interaction perspective

Ranadip Pal, Noah Berlow, Charles Keller, 2012, Proceedings 2012 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Transient Dynamics of Reduced-Order Models of Genetic Regulatory Networks

Ranadip Pal, Sonal Bhattacharya, R. Pal, 2012, IEEE/ACM Transactions on Computational Biology and Bioinformatics.

Generating Boolean networks with a prescribed attractor structure

A. Datta, R. Pal, Edward R. Dougherty, 2005, Bioinform..

A novel critical time analysis approach for genetic regulatory networks

Ranadip Pal, Sonal Bhattacharya, R. Pal, 2011, 2011 IEEE International Workshop on Genomic Signal Processing and Statistics (GENSIPS).

Effect of coarse-scale modeling on control outcome of genetic regulatory networks

S Bhattacharya, R Pal, R. Pal, 2010, Proceedings of the 2010 American Control Conference.

Selected Research Articles from the 2019 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, R. Pal, Xiaoning Qian, 2020, BMC Genomics.

Boolean network inference from time series data incorporating prior biological knowledge

Ranadip Pal, Saad Haider, R. Pal, 2012, BMC Genomics.

Selected research articles from the 2018 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, Xiaoning Qian, Byung-Jun Yoon, 2019, BMC Bioinformatics.

Selected research articles from the 2017 International Workshop on Computational Network Biology: Modeling, Analysis, and Control (CNB-MAC)

Tamer Kahveci, Xiaoning Qian, Byung-Jun Yoon, 2018, BMC Bioinformatics.

Boolean relationships among genes responsive to ionizing radiation in the NCI 60 ACDS

A. Datta, A. Fornace, R. Pal, 2005, Bioinform..

Adaptive Multi-task Elastic Net based feature selection from Pharmacogenomics Databases

Ranadip Pal, Souparno Ghosh, Raziur Rahman, 2018, 2018 40th Annual International Conference of the IEEE Engineering in Medicine and Biology Society (EMBC).

Automated segmentation of MS lesions in FLAIR, DIR and T2-w MR images via an information theoretic approach

Sunanda Mitra, Brian Nutter, Ranadip Pal, 2016, SPIE Medical Imaging.