recount2 in Nature Biotech

The recount2 study appeared today in Nature Biotechnology. recount2 provides processed and summarized expression data for over 70,000 human RNA-seq samples from the Sequence Read Archive (SRA), The Cancer Genome Atlas (TCGA), and The Genotype-Tissue Expression (GTEx) project. The associated Bioconductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed study consists of meta-…

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Published:April 11, 2017 View Post

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Intropolis in Genome Biology

Abhi Nellore and co-authors published a new study in Genome Biology that reveals splicing patterns across more than 20,000 publicly available human RNA sequencing datasets in the Sequence Read Archive. The study is also discussed in an accompanying research highlight (“The incredible complexity of RNA splicing“) by Christelle Robert and Mick Watson. Abhi was a…

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Published:December 30, 2016 View Post

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Rail-RNA in Bioinformatics

Our manuscript describing Rail-RNA, a cloud-enabled spliced aligner designed to analyze many samples at once, appeared in the journal Bioinformatics today. Rail-RNA eliminates redundant work across samples, making it more efficient as samples are added. For many samples, Rail-RNA is more accurate than annotation-assisted aligners. Rail-RNA is the basis for the Intropolis and ReCount projects, among others. Congrats to Abhi…

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Published:September 4, 2016 View Post

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Recount update & preprint

Today, with the Leek group and other collaborators at JHU, we released a new version of the recount resource.  recount provides processed and summarized expression data for nearly 60,000 human RNA-seq samples from the Sequence Read Archive (SRA). The associated Bioconductor package provides a convenient API for querying, downloading, and analyzing the data. Each processed study consists of meta- and phenotype…

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Published:August 8, 2016 View Post

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Agilent Early Career Award finalist

Agilent announced that Ben Langmead is a finalist for the 2016 Agilent Early Career Professor Award. The award recognizes an early-career scientist for contributions “to the development of advanced Big Data technologies aimed at making breakthroughs in life science research and imaging for clinical diagnostics.”

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Published:July 26, 2016 View Post

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Online course in Top 50

The online course Algorithms for DNA Sequencing, created by Ben Langmead and Jacob Pritt, was named by Class Central as one of the top 50 MOOCs of all time. You can see the student reviews on the Class Central page for the course.

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Published:July 24, 2016 View Post

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Boiler appears in NAR

Our manuscript describing Boiler, a novel and radically lossy tool for compressing RNA sequencing alignments, appeared in Nucleic Acids Research. Congrats to Jacob Pritt! Boiler software is available here: https://github.com/jpritt/boiler Experiments for the Boiler paper are described here: https://github.com/jpritt/boiler-experiments

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Published:June 14, 2016 View Post

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R01 grant from NIH/NIGMS

The Langmead Lab was awarded an R01 grant from NIH/NIGMS for “Hardening and Scaling Core Genomics Software.” The award will fund the lab’s work on efficient, scalable, open source software tools for analyzing sequencing data, including the Bowtie and Rail suites.

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Published:April 22, 2016 View Post

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Rail-dbGaP appears in Bioinformatics

The Rail-dbGaP paper, by Abhi Nellore and colleagues, appeared in Bioinformatics. Abstract: Public archives contain thousands of trillions of bases of valuable sequencing data. More than 40% of the Sequence Read Archive is human data protected by provisions such as dbGaP. To analyze dbGaP-protected data, researchers must typically work with IT administrators and signing officials…

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Published:April 22, 2016 View Post

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Benjamin Franklin award

Bioinformatics.org announced a Ben Langmead as the laureate of the 2016 Benjamin Franklin Award in the Life Sciences: http://www.bioinformatics.org/forums/forum.php?forum_id=11999 This is a humanitarian/bioethics award presented annually by bioinformatics.org to an individual who has, in his or her practice, promoted free and open access to the materials and methods used in the life sciences. The award…

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Published:March 1, 2016 View Post

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