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Article
Open AccessRetained introns in long RNA-seq reads are not reliably detected in sample-matched short reads
There is growing interest in retained introns in a variety of disease contexts including cancer and aging. Many software tools have been developed to detect retained introns from short RNA-seq reads, but relia...
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Article
Open Accessrecount3: summaries and queries for large-scale RNA-seq expression and splicing
We present recount3, a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly processed by our new Monorail analysis pipeline. To facilitate access to th...
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Article
Open AccessAlternative splicing of MR1 regulates antigen presentation to MAIT cells
Mucosal Associated Invariant T (MAIT) cells can sense intracellular infection by a broad array of pathogens. These cells are activated upon encountering microbial antigen(s) displayed by MR1 on the surface of ...
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Article
Open AccessBurden of tumor mutations, neoepitopes, and other variants are weak predictors of cancer immunotherapy response and overall survival
Tumor mutational burden (TMB; the quantity of aberrant nucleotide sequences a given tumor may harbor) has been associated with response to immune checkpoint inhibitor therapy and is gaining broad acceptance as...
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Article
Open AccessASCOT identifies key regulators of neuronal subtype-specific splicing
Public archives of next-generation sequencing data are growing exponentially, but the difficulty of marshaling this data has led to its underutilization by scientists. Here, we present ASCOT, a resource that u...
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Article
Erratum: Cloud computing for genomic data analysis and collaboration
Nature Reviews Genetics doi:10.1038/nrg.2017.113 (2018) The above article originally stated “FireCloud and CGC rely on AWS and the Google Cloud Platform for computing and data storage. In addition to charges f...
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Open AccessPopulation-level distribution and putative immunogenicity of cancer neoepitopes
Tumor neoantigens are drivers of cancer immunotherapy response; however, current prediction tools produce many candidates requiring further prioritization. Additional filtration criteria and population-level u...
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Cloud computing for genomic data analysis and collaboration
Cloud computing is a paradigm whereby computational resources such as computers, storage and bandwidth can be rented on a pay-for-what-you-use basis.
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Reproducible RNA-seq analysis using recount2
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Open AccessHuman splicing diversity and the extent of unannotated splice junctions across human RNA-seq samples on the Sequence Read Archive
Gene annotations, such as those in GENCODE, are derived primarily from alignments of spliced cDNA sequences and protein sequences. The impact of RNA-seq data on annotation has been confined to major projects l...
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Article
Open AccessCHANCE: comprehensive software for quality control and validation of ChIP-seq data
ChIP-seq is a powerful method for obtaining genome-wide maps of protein-DNA interactions and epigenetic modifications. CHANCE (CHip-seq ANalytics and Confidence Estimation) is a standalone package for ChIP-seq...
