pradipta ray

Peer reviewed publications

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

For archival copies of 15 high impact or relevant publications, theses and preprints, please see below.

Nociceptor translational profiling reveals the RagA-mTORC1 network as a critical generator of neuropathic pain. Biorxiv, 2018. Biology: Nociception & Pain Algorithmics: Translatome normalization against transcriptome Discovery (mechanism)
Angiotensin II triggers peripheral macrophage-to-sensory neuron redox crosstalk to elicit pain. J Neurosci, 2018 Biology: Nociception & Pain Algorithmics: RNA-seq meta-analysis Discovery (mechanism)
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: Nociception & Pain Algorithmics: Cross-species transcriptome normalization Algorithm development, resource
Sigma 2 Receptor/Tmem97 Agonists Produce Long Lasting Antineuropathic Pain Effects in Mice. ACS Chem Neurosci, 2017 Biology: Nociception & Pain Algorithmics: RNA-seq meta-analysis Discovery (mechanism)
DIRECTION: a machine learning framework for predicting and characterizing DNA methylation and hydroxymethylation in mammalian genomes. OUP Bioinfo, 2017 Biology: Epigenetics Algorithmics: Max margin based classification for data imputation Algorithm development, association study
Group II mGluRs suppress hyperexcitability in mouse and human nociceptors. PAIN, 2016 Biology: Nociception & Pain Algorithmics: RNA-seq meta-analysis Discovery (mechanism)
Integrative analysis of haplotype-resolved epigenomes across human tissues. Nature, 2015 Biology: Epigenetics Algorithmics: Haplotype resolved relative abundance quantification Association study
Integrative analysis of 111 reference human epigenomes. Nature, 2015 Biology: Epigenetics Algorithmics: NA Resource
SCT Promoter Methylation Is a Highly Discriminative Biomarker for Lung and Many Other Cancers. IEEE Life Science Letters, 2015 Biology: Cancer Algorithmics: Discriminative biomarker analysis Discovery (biomarker)
Distinct and predictive histone lysine acetylation patterns at promoters, enhancers, and gene bodies. G3: Genes | Genomes | Genetics, 2014 Biology: Epigenetics Algorithmics: Transcriptome - epigenome association testing Association study
Epigenomic analysis of multilineage differentiation of human embryonic stem cells. Cell, 2013 Biology: Pluripotency Algorithmics: Lineage-restricted transcriptome and epigenome feature identification Discovery (mechanism)
Computational Methods for Analyzing the Architecture and Evolution of the Regulatory Genome. Ph D thesis, Carnegie Mellon, 2012
DISCOVER: a feature-based discriminative method for motif search in complex genomes. OUP Bioinfo, 2009 Biology: Development Algorithmics: Motif finding using associated features, feature engineering Algorithm development, association study
CSMET: comparative genomic motif detection via multi-resolution phylogenetic shadowing. PLoS CompBio, 2008 Biology: Development Algorithmics: Evolutionary footprinting based motif finding Algorithm development
Baycis: a bayesian hierarchical hmm for cis-regulatory module decoding in metazoan genomes. Proceedings of RECOMB 2008, LNBI, 2008 Biology: Development Algorithmics: Motif finding Algorithm development