Abhinav Nellore

recountmethylation provides processed blood DNA methylation data and analysis tools, showing genetic ancestry and cell fractions explain most DNAm variation and validating DMPs between sexes.

The paper evaluates four MHC binding affinity prediction tools across different peptide sources and alleles, revealing inconsistencies in their predictions and training data quality.

The paper compares retained intron detection in short and long RNA-seq reads, finding significant disagreement among tools and poor precision/recall.

This study examines the association between HLA genotype and SARS-CoV-2 disease severity in 3,235 individuals, finding limited impact compared to demographic and clinical factors.

recount3 provides uniformly processed RNA-seq data and tools for querying and analyzing large-scale human and mouse expression and splicing data.

Pepsickle predicts proteasomal cleavage sites more accurately and quickly than existing tools, improving neoantigen identification for vaccine development.

The paper analyzes 35,360 DNAm array samples from GEO, identifies tissue sources, evaluates quality assessments, and provides a database with annotated data through an R/Bioconductor package.

ASCOT identifies key regulators of neuronal subtype-specific splicing by analyzing public RNA-Seq data and demonstrating the role of PTBP1, MSI1, and PCBP2 in rod photoreceptor splicing.

neoepiscope improves neoepitope prediction by incorporating germline context and somatic variant phasing, addressing limitations in existing tools.

The paper develops a linear model to estimate transcript-level abundances from reduced-representation RNA-seq data in recount2, evaluating it on simulated and real data.

Snaptron provides a search engine for querying and visualizing splicing patterns across 70,000 human RNA-seq samples and 146 million splice junctions.

The paper analyzes human RNA-seq data from the SRA to identify unannotated splicing junctions and their tissue-specific expression, creating a resource called intropolis.

The paper introduces derfinder, a tool for RNA-seq analysis that identifies differentially expressed regions at single base resolution without relying on gene annotations, showing it works well with incomplete annotations and large datasets.

This paper introduces a framework to correct RNA quality effects in differential expression analysis, showing improved replication rates in schizophrenia studies.

recount provides a large-scale, processed RNA-seq resource with tools for analysis, including differential expression and meta-analysis, using data from the Sequence Read Archive.

Rail-dbGaP enables secure analysis of dbGaP-protected RNA-seq data in the cloud using Amazon Elastic MapReduce, with a spliced aligner tool and protocol for compliance with NIH guidelines.

Rail-RNA efficiently and accurately aligns RNA-seq samples and generates coverage files, enabling population-level analysis of splicing and expression variation.