pradipta ray


Peer reviewed publications

(1542 citations based on Google Scholar, co first authors underlined jointly)

Sigma 2 receptor / Tmem97 agonists produce long lasting anti-neuropathic pain effects in mice J Sahn, G Mejia, P Ray, S Martin, TJ Price, ACS Chemical Neuroscience. In press, 2017 GScholar

DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes Milos Pavlovic, Pradipta Ray, Kristina Pavlovic, Aaron Kotamarti, Min Chen, Michael Q. Zhang, OUP Bioinformatics, In press, 2017 Journal URL

Group II mGluRs suppress hyperexcitability in mouse and human nociceptors Steve Davidson, Judith P Golden, Bryan A Copits, Pradipta R Ray, Sherri K Vogt, Manouela V Valtcheva, Robert E Schmidt, Andrea Ghetti, Theodore J Price, Robert W Gereau IV, Pain 157 (9), 2081-2088, 2016 GScholar

Integrative analysis of 111 reference human epigenomes Anshul Kundaje, Wouter Meuleman, Jason Ernst, Misha Bilenky, Angela Yen, Alireza Heravi-Moussavi, Pouya Kheradpour, Zhizhuo Zhang, Jianrong Wang, Michael J Ziller, Viren Amin, John W Whitaker, Matthew D Schultz, Lucas D Ward, Abhishek Sarkar, Gerald Quon, Richard S Sandstrom, Matthew L Eaton, Yi-Chieh Wu, Andreas R Pfenning, Xinchen Wang, Melina Claussnitzer, Yaping Liu, Cristian Coarfa, R Alan Harris, Noam Shoresh, Charles B Epstein, Elizabeta Gjoneska, Danny Leung, Wei Xie, R David Hawkins, Ryan Lister, Chibo Hong, Philippe Gascard, Andrew J Mungall, Richard Moore, Eric Chuah, Angela Tam, Theresa K Canfield, R Scott Hansen, Rajinder Kaul, Peter J Sabo, Mukul S Bansal, Annaick Carles, Jesse R Dixon, Kai-How Farh, Soheil Feizi, Rosa Karlic, Ah-Ram Kim, Ashwinikumar Kulkarni, Daofeng Li, Rebecca Lowdon, GiNell Elliott, Tim R Mercer, Shane J Neph, Vitor Onuchic, Paz Polak, Nisha Rajagopal, Pradipta Ray, Richard C Sallari, Kyle T Siebenthall, Nicholas A Sinnott-Armstrong, Michael Stevens, Robert E Thurman, Jie Wu, Bo Zhang, Xin Zhou, Arthur E Beaudet, Laurie A Boyer, Philip L De Jager, Peggy J Farnham, Susan J Fisher, David Haussler, Steven JM Jones, Wei Li, Marco A Marra, Michael T McManus, Shamil Sunyaev, James A Thomson, Thea D Tlsty, Li-Huei Tsai, Wei Wang, Robert A Waterland, Michael Q Zhang, Lisa H Chadwick, Bradley E Bernstein, Joseph F Costello, Joseph R Ecker, Martin Hirst, Alexander Meissner, Aleksandar Milosavljevic, Bing Ren, John A Stamatoyannopoulos, Ting Wang, Manolis Kellis, Roadmap Epigenomics Consortium, Nature 518 (7539), 317-330, 2015 GScholar

Integrative analysis of haplotype-resolved epigenomes across human tissues Danny Leung, Inkyung Jung, Nisha Rajagopal, Anthony Schmitt, Siddarth Selvaraj, Ah Young Lee, Chia-An Yen, Shin Lin, Yiing Lin, Yunjiang Qiu, Wei Xie, Feng Yue, Manoj Hariharan, Pradipta Ray, Samantha Kuan, Lee Edsall, Hongbo Yang, Neil C Chi, Michael Q Zhang, Joseph R Ecker, Bing Ren, Nature 518 (7539), 350-354, 2015 GScholar

SCT promoter methylation is a highly discriminative biomarker for lung and many other cancers A Sathe, YA Zhang, X Ma, P Ray, D Cadinu, YW Wang, X Yao, X Liu, et al, IEEE Life Sciences Letters 1 (3), 30-33, 2015 GScholar

Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies N Rajagopal, J Ernst, P Ray, J Wu, M Zhang, M Kellis, B Ren, G3: Genes| Genomes| Genetics 4 (11), 2051-2063, 2014 GScholar

Epigenomic analysis of multilineage differentiation of human embryonic stem cells Xie, Wei; Lister, Ryan; Schultz, Matt; Rajagopal, Nisha; Hou, Zhonggang; Ray, Pradipta; Whitaker, John; Tian, Shulan; Hawkins, R. David; Leung, Danny; Wang, Tao; Yang, Hongbo; Swanson, Scott A.; Zhu, Yun; Lee, Ah Young; Kim, Audrey; Nery, Joseph; Urich, Mark A.; Kuan, Samantha; Yen, Chia-an; Klugman, Sarit; Yu; Pengzhi; Suknuntha, Kran; Propson, Nicholas E.; Chen, Huaming; Edsall, Lee E.; Wagner, Ulrich; Li, Yan; Ye, Zhen; Kulkarni, Ashwinikumar; Xuan, Zhenyu; Chung, Wen-yu; Chi, Neil C.; Antosiewicz -Bourget, Jessica; Slukvin, Igor; Stewart, Ron; Stamatoyannopoulos, John A.; Zhang, Michael Q.; Wang, Wei; Thomson, James A.; Ecker, Joseph R.; and Ren, Bing, Cell 153 (5), 1134-1148, 2013 GScholar

DISCOVER: a feature-based discriminative method for motif search in complex genomes W Fu, P Ray, EP Xing, Bioinformatics 25 (12), i321-i329, 2009 GScholar

CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing P Ray, S Shringarpure, M Kolar, EP Xing, PLoS Comput Biol 4 (6), e1000090, 2008 GScholar

Baycis: a bayesian hierarchical hmm for cis-regulatory module decoding in metazoan genomes T Lin, P Ray, GK Sandve, S Uguroglu, EP Xing, Proceedings of the 12th annual international conference on Research in Computational Biology Singapore, Springer (LNCS, volume 4955) 2008. GScholar

Selected publications on Natural Language Processing pre-2005:

Isolated-word Error Correction for Partially Phonemic Languages using Phonetic Cues B Bansal, M Choudhury, P R Ray, S Sarkar, A Basu, Proceedings of Fifth International Conference on Knowledge based Computer Systems (KBCS 2004), 2004 GScholar

Part of speech tagging and local word grouping techniques for natural language parsing in Hindi P R Ray, V Harish, S Sarkar, A Basu, Proceedings of the 1st International Conference on Natural Language Processing (ICON 2003), 2003 GScholar

Thesis

Computational Methods for Analyzing the Architecture and Evolution of the Regulatory Genome P Ray, Ph D thesis, Carnegie Mellon University (CMU-LTI-12-018) Link

Scientific presentations

Podium talks

Analyzing human and mouse dorsal root ganglia transcriptomes : uncovering the molecular biology of pain and putative therapeutic targets using information theory 1st Texas Pain Research Consortium Conference, Richardson TX, 2015 Abstract published digitally

DIRECTION: An Integrative Toolkit for Classification of Epigenetic Marks - A study on DNA 5-hmC + 5-mC marks in H1 and derived lineages Epigenomics 2013: A roadmap to the living genome, Boston, 2013 Extended abstract published in Proceedings of Epigenomics 2013: A roadmap to the living genome

DISCOVER: a feature-based discriminative method for motif search in complex genomes 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB), Stockholm, 2009 Full paper published in OUP Bioinformatics

Baycis: a bayesian hierarchical hmm for cis-regulatory module decoding in metazoan genomes 12th annual international conference on Research in Computational Biology (RECOMB), Singapore, 2008 Full paper published in Springer Lecture Notes in Computer Science / Bioinformatics

Recent posters (since last calendar year)

Ray P, Megat S, Barragan-Iglesias P, Lou T-F, Wangzhou A, Burton M, Moy J, Dussor G, Campbell Z, Price TJ A Genome-wide Snapshot of in Vivo and in Vitro Transcriptional and Translational Changes Underlying Pain Plasticity in Mouse Models Gulf Coast Consortium 7th Annual Symposium on Translational Pain Research April 7, 2017 Abstract published in conference proceedings. Confeence URL

Price TJ, Megat S, Barragan-Iglesias P, Lou T-F, Wangzhou A, Ray P , Moy J , Burton M, Campbell ZT TRAPs and footprints reveal the landscape of protein synthesis in DRG and TG nociceptors Gulf Coast Consortium 7th Annual Symposium on Translational Pain Research April 7, 2017 Abstract published in conference proceedings. Confeence URL

Torck, Andrew; Kim, Ji-Young; Zhang, Michael Q.; Dussor, Gregory; Price Theodore J.; Ray, Pradipta R. RNA-seq based transcriptome profiling of human and mouse dorsal root ganglia provides insight into potential new pain targets. 35th Annual Scientific Meeting of the American Pain Society Austin, TX, May 11-14, 2016 Abstract published in The Journal of Pain. Journal URL

Ray, Pradipta R.; Torck, Andrew; Zhang, Michael Q., Dussor, Gregory; Price, Theodore J. Searching for the transcriptomic footprint of chronic pain. 35th Annual Scientific Meeting of the American Pain Society Austin, TX, May 11-14, 2016 Abstract published in The Journal of Pain. Journal URL

Srivastava, Siddhartha; Potla, Subodh; Torck, Andrew, Zhang, Michael Q., Dussor, Gregory, Ray, Pradipta R.; Price, Theodore J. A potential role for eIF4A in regulation of nociceptor plasticity: a motif-based genome-wide search for eIF4A targets 35th Annual Scientific Meeting of the American Pain Society, Austin, TX, May 11-14, 2016 Abstract published in The Journal of Pain. Journal URL

Lam, Tiffany; Torck, Andrew; Dussor, Gregory; Price, Theodore J.; Ray, Pradipta R. A public resource to explore and compare the human and mouse dorsal root ganglion (DRG) transcriptome 35th Annual Scientific Meeting of the American Pain Society Austin, TX, May 11-14, 2016 Abstract published in The Journal of Pain. Journal URL

Moy, Jamie; Ray, Pradipta; Walters, Edgar T.; Pelletier, J.; Price, Theodore J. Exploring the potential for an evolutionarily conserved role for eIF4A in pain plasticity 35th Annual Scientific Meeting of the American Pain Society Austin, TX, May 11-14, 2016 Abstract published in The Journal of Pain. Journal URL

Price, Theodore J., Torck, Andrew; Ray, Pradipta R.; Hassler, Shayne ; Vagner, Josef; Dussor, Gregory; Boitano, Scott RNA-seq based transcriptome profiling of human and mouse dorsal root ganglion reveals a potential role for Protease Activated Receptor 3 (PAR3) in pain processing Experimental Biology San Diego, CA, April 2-6,2016 Abstract published in The FASEB Journal. Journal URL

Ray, Pradipta R.; Torck, Andrew; Lam, Tiffany; Zhang, Michael Q., Dussor, Gregory; Price, Theodore J. Comparative Whole-transcriptome Analyses of Human and Mouse Dorsal Root Ganglia Reveal Tissue-specific and Evolutionarily Conserved Transcript Profiles with Implications for Mechanistic and Translational Therapeutic Studies Gulf Coast Consortium Translational Pain Research 6th Annual Symposium Houston, TX, April 2-6, 2016 Abstract published in proceedings of the conference.

Torck, Andrew; Quigley, Lilyana; Zhang, Michael Q., Dussor, Gregory; Price, Theodore J.; Ray, Pradipta R. Novel meta-analysis of RNA-seq data across tissues and species reveal evolutionarily conserved gene expression and splicing patterns implicated in pain states in sensory tissues Intelligent Systems for Molecular Biology Orlando, FL, July 8-12, 2016 Abstract published in poster proceedings of the conference. Conference URL

Pavlovic, Milos; Ray, Pradipta; Zhang, Michael Q. Regions of invariant DNA methylation in human epigenomes in the context of methylation prediction, and functional significance Epigenomics 2016 Rio Grande, Puerto Rico, Jan 31-Feb 5, 2016 Abstract published in proceedings of the conference. Conference URL