pradipta ray


Peer reviewed publications

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

For archival copies of 16 high impact or relevant publications, theses and preprints, please see below.

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