Qtip in Genome Biology

A new paper describing a tandem simulation framework for predicting mapping quality was published in Genome Biology.  The paper describes the free, open source Qtip software. Mapping qualities are important quantities in the world of next-gen sequencing analysis. A mapping quality quantifies the read aligner’s confidence that the reported alignment for a sequencing read is the correct…

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Published:August 14, 2017 View Post

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Catalyst Award

PI Langmead was among thirty-four early career faculty members selected this year to receive Johns Hopkins Catalyst Awards, an honor accompanied by a grant, mentoring opportunities, and institutional recognition.  The funds will be used to study data structures for metagenomics.

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Published:July 11, 2017 View Post

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Bowtie at 10K citations

The study describing the Bowtie read alignment tool has been cited over 10,000 times since it first appeared in March 2009, according to Google Scholar. The Langmead Lab continues its hard work improving and maintaining this open source software, with a new version of Bowtie (1.2.1) having been released this week and two new versions…

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Published:June 13, 2017 View Post

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“Genome Hunters”

The JHU Engineering Magazine has an article in its summer 2017 issue about the Computational Genomics faculty in the Computer Science department at JHU.

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Published:June 11, 2017 View Post

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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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