LANGMEAD LAB @ JHU

Daniel Baker successfully completed his Ph.D. defense on 12/17. His thesis is titled “Applied Randomized Algorithms for Efficient Genomic Analysis” and spans his work on genomic sketching, coreset clustering, efficient single-cell clustering under various distance measures, as well as other projects. After graduation, Daniel will join Pacific Biosciences as a Senior Scientist. Huge congrats to…

Taher Mun successfully completed his Ph.D. defense on 12/16. His thesis is titled “Using Pan-Genomic Data Structures to Incorporate Diversity Into Genomic Analyses” and spans his work on the r-index, reference flow, liftover of alignments, and the novel “marker array” structure to perform genotyping. After graduation, Taher will join Illumina, Inc. in San Diego, CA…

The publication describing the recount3 project (and related projects like Snaptron and the associated recount3 and snapcount Bioconductor packages) is out in the journal Genome Biology. This was a huge effort involving many researchers at Johns Hopkins University and beyond. But a very large share of the credit goes to Langmead-lab student Chris Wilks, who…

A team led by Ph.D. student Omar Ahmed just published a journal paper in iScience describing a novel method and new software tool called SPUMONI.  SPUMONI can rapidly match sequencing reads to a pan-genome index, i.e. an index consisting of many strains or individuals.  At SPUMONI’s core is a novel algorithm for computing “matching statistics” against an…

Students Taher Mun and Nae-Chyun Chen published an Application Note in the journal Bioinformatics describing a new tool called levioSAM. As more population genetics datasets and population-specific references become available, the task of translating (“lifting”) read alignments from one reference coordinate system to another is becoming more common. LevioSAM is a tool for lifting SAM/BAM…

We posted a preprint today describing the new recount3 resource.  This effort was led by (now graduated) Ph.D. student Chris Wilks and spanned multiple research groups including our group, Kasper Hansen’s group and Leonardo Collado Torres’ group. recount3 is a resource consisting of over 750,000 publicly available human and mouse RNA sequencing (RNA-seq) samples uniformly…

Ph.D. student Daniel Baker posted a preprint describing a new software library called Minicore for fast k-means clustering of single-cell RNA sequencing (scRNA-seq) data.  Minicore works with sparse count data — which is the form scRNA-seq data usually starts in —  as well as with dense data from after dimensionality reduction. Minicore uses a novel vectorized weighted…

A team led by Ph.D. student Omar Ahmed posted a preprint describing a novel method and new software tool called SPUMONI.  SPUMONI can rapidly match sequencing reads to a pan-genome index, i.e. an index consisting of many strains or individuals.  At SPUMONI’s core is a novel algorithm for computing “matching statistics” against an efficient kind…

A team led by (now graduated) Ph.D. student Chris Wilks published a new study in the journal Bioinformatics describing the software tool Megadepth.  Megadepth is a fast tool for quantifying alignments and coverage for BigWig and BAM/CRAM input files — i.e. summing or averaging the depth of coverage over genomic intervals.  It uses substantially less…

The Langmead Lab is starting the new year with two new funded projects. One is an R01 from NIH/NHGRI funding our work on addressing reference bias with personal and panel references. This is joint work with Christina Boucher at University of Florida and Travis Gagie at Dalhousie University. Our recent paper on the Reference Flow…