Abhinav Nellore

发表

Cloud computing for genomic data analysis and collaboration

B. Langmead, Abhinav Nellore, Ben Langmead, 2018, Nature Reviews Genetics.

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

B. Langmead, K. Hansen, J. Leek, 2016, Genome Biology.

Putatively cancer-specific alternative splicing is shared across patients and present in developmental and other non-cancer cells

Sean K. Maden, Julianne K. David, Reid F. Thompson, 2019, bioRxiv.

Population-level distribution and putative immunogenicity of cancer neoepitopes

Adam A. Margolin, Reid F. Thompson, Kyle Ellrott, 2017, BMC Cancer.

Population-level distribution and putative immunogenicity of cancer neoepitopes

Reid F. Thompson, Kyle Ellrott, A. Margolin, 2017, bioRxiv.

Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

Julianne K. David, Reid F. Thompson, Abhinav Nellore, 2020, Genome Medicine.

ASCOT identifies key regulators of neuronal subtype-specific splicing

Brian S. Clark, B. Langmead, P. Leavey, 2020, Nature Communications.

ASCOT identifies key regulators of neuronal subtype-specific splicing

Brian S. Clark, B. Langmead, C. Wilks, 2018, Nature Communications.

A framework for RNA quality correction in differential expression analysis

J. Leek, R. Straub, J. Kleinman, 2016, bioRxiv.

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2016, bioRxiv.

Flexible expressed region analysis for RNA-seq with derfinder

Rafael A. Irizarry, Leonardo Collado-Torres, Alyssa C. Frazee, 2015, bioRxiv.

recountmethylation enables flexible analysis of public blood DNA methylation array data

Sean K. Maden, Reid F. Thompson, K. Hansen, 2022, bioRxiv.

Minimal observed impact of HLA genotype on hospitalization and severity of SARS‐CoV‐2 infection

Reid F. Thompson, Abhinav Nellore, J. Hollenbach, 2022, HLA.

Alternative splicing of MR1 regulates antigen presentation to MAIT cells

Abhinav Nellore, F. Tafesse, E. Karamooz, 2019, Scientific Reports.

Human leukocyte antigen susceptibility map for SARS-CoV-2 2

Sean K. Maden, Julianne K. David, Reid F. Thompson, 2020 .

Discordant results among MHC binding affinity prediction tools

Reid F. Thompson, Abhinav Nellore, Austin Nguyen, 2022, bioRxiv.

Human Leukocyte Antigen Susceptibility Map for Severe Acute Respiratory Syndrome Coronavirus 2

Abhinav Nellore, Sean K. Maden, Julianne K. David, 2020, Journal of Virology.

Retained introns in long RNA-seq reads are not reliably detected in sample-matched short reads

Sean K. Maden, Julianne K. David, Reid F. Thompson, 2022, bioRxiv.

Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

Julianne K. David, Reid F. Thompson, Abhinav Nellore, 2020, Genome Medicine.

neoepiscope improves neoepitope prediction with multi-variant phasing

Kyle Ellrott, Abhinav Nellore, Mary A Wood, 2018, bioRxiv.

Reproducible RNA-seq analysis using recount2

Jeffrey T Leek, Leonardo Collado-Torres, Abhinav Nellore, 2017, Nature Biotechnology.

recount3: summaries and queries for large-scale RNA-seq expression and splicing

Shijie C. Zheng, B. Langmead, K. Hansen, 2021, Genome Biology.

Human splicing diversity across the Sequence Read Archive

Siruo Wang, Leonardo Collado-Torres, Andrew E. Jaffe, 2016, bioRxiv.

Human leukocyte antigen susceptibility map for SARS-CoV-2

Sean K. Maden, Julianne K. David, Reid F. Thompson, 2020, medRxiv.

Pepsickle rapidly and accurately predicts proteasomal cleavage sites for improved neoantigen identification

Reid F. Thompson, Abhinav Nellore, Benjamin R. Weeder, 2021, bioRxiv.

Human splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive

B. Langmead, K. Hansen, J. Leek, 2016, Genome Biology.

Cloud computing for genomic data analysis and collaboration

Abhinav Nellore, Ben Langmead, B. Langmead, 2018, Nature Reviews Genetics.

qSVA framework for RNA quality correction in differential expression analysis

Jeffrey T Leek, Abhinav Nellore, Daniel R Weinberger, 2017, Proceedings of the National Academy of Sciences of the United States of America.

An Invertible Transform for Efficient String Matching in Labeled Digraphs

Abhinav Nellore, Austin Nguyen, Reid F. Thompson, 2019, CPM.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Rail-RNA: Scalable analysis of RNA-seq splicing and coverage

Leonardo Collado-Torres, Andrew E. Jaffe, Jeffrey T. Leek, 2015, bioRxiv.

Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Paul W. Bible, Lisa Federer, Allissa Dillman, 2015, bioRxiv.

recount workflow: Accessing over 70,000 human RNA-seq samples with Bioconductor

Leonardo Collado-Torres, Abhinav Nellore, Andrew E Jaffe, 2017, F1000Research.

Discordant results among major histocompatibility complex binding affinity prediction tools

Reid F. Thompson, Abhinav Nellore, Austin Nguyen, 2023, F1000Research.

RNA-seq transcript quantification from reduced-representation data in recount2

Leonardo Collado-Torres, Jeffrey T. Leek, Abhinav Nellore, 2018, bioRxiv.

recount: A large-scale resource of analysis-ready RNA-seq expression data

Leonardo Collado-Torres, Andrew E. Jaffe, Kasper Daniel Hansen, 2016, bioRxiv.

Snaptron: querying splicing patterns across tens of thousands of RNA-seq samples

Abhinav Nellore, Christopher Wilks, Ben Langmead, 2017, Bioinform..

Burden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival

Julianne K. David, Reid F. Thompson, Abhinav Nellore, 2019, Genome Medicine.

Minimal observed impact of HLA genotype on hospitalization and severity of SARS‐CoV‐2 infection

Abhinav Nellore, Austin Nguyen, A. Nellore, 2021, medRxiv.

Building Genomic Analysis Pipelines in a Hackathon Setting with Bioinformatician Teams: DNA-seq, Epigenomics, Metagenomics and RNA-seq

Claire L. Simpson, D. Chandramohan, Abhinav Nellore, 2015, bioRxiv.

qSVA framework for RNA quality correction in differential expression analysis

J. Leek, R. Straub, J. Kleinman, 2017, Proceedings of the National Academy of Sciences.