pradipta ray


Peer reviewed publications

For a comprehensive list of publications, please see my Google scholar account.

For archival copies of
high impact or relevant
publications, theses and
preprints, see here :


A Genetic Locus on Chromosome 2q24 Predicting Peripheral Neuropathy Risk in Type 2 Diabetes: Results From the ACCORD and BARI 2D Studies. Diabetes, 2019. Biology: Diabetes Algorithmics: RNA-seq meta-analysis Type: Genome-wide association study
Recent advances toward understanding the mysteries of the acute to chronic pain transition. Curr Opinion in Physiology, 2019. Biology: Sensory Neurobiology Algorithmics: Review Type: Review
Differences between dorsal root and trigeminal ganglion nociceptors in mice revealed by translational profiling. J Neurosci, 2019. Biology: Sensory Neurobiology Algorithmics: Translatome normalization against transcriptome Type: Biomarker discovery, resource
Transcriptome analysis of the human tibial nerve identifies sexually dimorphic expression of genes involved in pain, inflammation and neuro-immunity. Frontiers in Molecular Neuroscience, 2019. Biology: Sensory Neurobiology Algorithmics: Large scale statistical hypotheses testing for small effect sizes Type: Biomarker discovery, resource
Electrophysiologic and transcriptomic correlates of neuropathic pain in human primary sensory neurons. Brain, 2019. Biology: Sensory Neurobiology Algorithmics: Identification of discriminative features in low signal:noise scenario Type: Discriminative features and predictive models for identifying clinical states
Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain. J Neurosci, 2019. Biology: Sensory Neurobiology Algorithmics: Translatome normalization against transcriptome Type: Perturbation studies (for mechanism discovery)
Angiotensin II triggers peripheral macrophage-to-sensory neuron redox crosstalk to elicit pain. J Neurosci, 2018 Biology: Sensory Neurobiology Algorithmics: RNA-seq meta-analysis Type: Perturbation studies (for mechanism discovery)
Comparative transcriptome profiling of the human and mouse dorsal root ganglia: an RNA-seq–based resource for pain and sensory neuroscience research. PAIN, 2018 Biology: Sensory Neurobiology Algorithmics: Cross-species transcriptome normalization, creation of appropriate diversity index Type: Algorithm development, biomarker discovery, resource
Sigma 2 Receptor/Tmem97 Agonists Produce Long Lasting Antineuropathic Pain Effects in Mice. ACS Chem Neurosci, 2017 Biology: Sensory Neurobiology Algorithmics: RNA-seq meta-analysis Type: Perturbation studies (for mechanism discovery)
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. OUP Bioinfo, 2017 Biology: Epigenetics, gene regulation Algorithmics: Max-margin based classification for epigenetic signal prediction / imputation, feature engineering using genome - epigenome and epigenome - epigenome association testing Type: Algorithm development, association study
Group II mGluRs suppress hyperexcitability in mouse and human nociceptors. PAIN, 2016 Biology: Sensory neurobiology Algorithmics: RNA-seq meta-analysis Type: Perturbation studies for mechanism discovery
Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, 2015 Biology: Epigenetics Algorithmics: Haplotype resolved relative abundance quantification Type: Association study
Integrative analysis of 111 reference human epigenomes. Nature, 2015 Biology: Epigenetics Algorithmics: Integrative analysis overview Type: Consortium overview paper
Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3: Genes | Genomes | Genetics, 2014 Biology: Epigenetics, Gene regulation Algorithmics: Transcriptome - epigenome association testing Type: Association study
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell, 2013 Biology: Development and Pluripotency, Epigenetics, Gene regulation Algorithmics: Lineage-restricted transcriptome and epigenome feature identification Type: Association study, biomarker discovery
Computational Methods for Analyzing the Architecture and Evolution of the Regulatory Genome. Ph D thesis, Carnegie Mellon, 2012 Biology: Development, Gene regulation Algorithmics: Estimation and inference on graphical models for transcription regulatory motif finding Type: PhD Thesis
DISCOVER: a feature-based discriminative method for motif search in complex genomes. OUP Bioinfo, 2009 Biology: Development, gene regulation Algorithmics: Motif finding using associated features, feature engineering Type: Algorithm development, tool development, association study
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PLoS CompBio, 2008 Biology: Development, gene regulation Algorithmics: Evolutionary footprinting based motif finding Type: Algorithm development, tool development
Baycis: a bayesian hierarchical hmm for cis-regulatory module decoding in metazoan genomes. Proceedings of RECOMB 2008, LNBI, 2008 Biology: Development, gene regulation Algorithmics: Motif finding Type: Algorithm development, tool development