Ben Langmead

The paper introduces rowbowt, a tool for pangenomic genotyping using a marker array to improve accuracy and efficiency over existing methods.

DeepMosaic detects mosaic single nucleotide variants without control samples using deep convolutional neural networks, achieving high accuracy and uncovering many variants missed by existing methods.

This paper introduces SLED, a splicing-based method to control gene expression in specific cell types, demonstrating its utility in targeting neurons, photoreceptors, and cancer cells.

The paper introduces H+, a scale-agnostic and group-balance invariant discordance metric for clustering, and provides scalable methods to compute it.

The paper evaluates brain somatic mosaicism in the adult human to identify rules governing cellular distribution during embryogenesis.

The paper introduces REPAC, a framework for analyzing alternative polyadenylation from RNA-sequencing data, showing it identifies APA changes in B cell activation and is faster than existing methods.

The paper introduces 2s-LCA, a method for joint analysis of multiple biological data sets, and applies it to human brain development data to identify shared gene expression patterns.

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

MONI is a pangenomics index that efficiently finds maximal exact matches by combining prefix-free parsing with threshold calculation, outperforming existing tools in speed and memory usage.

SPUMONI enables fast and accurate targeted nanopore sequencing using efficient pangenome indexes, outperforming minimap2 in speed and memory usage.

LevioSAM lifts SAM/BAM alignments between references using VCF files, achieving faster performance with multi-threading.

minicore provides fast and memory-efficient scRNA-seq clustering using various distance measures, achieving results on large datasets in minutes with minimal resources.

Megadepth efficiently quantifies coverage in BigWig and BAM files, outperforming existing tools in speed and memory usage.

The paper introduces a machine learning method to detect somatic L1 insertions in human brain tissue, revealing their widespread distribution in neurons and glia and potential role in neuropsychiatric diseases.

The paper introduces a reference flow alignment method that reduces reference bias using multiple population reference genomes, achieving similar accuracy to graph aligners with lower memory usage and faster speed.

The paper presents FC-R2, an expanded transcriptome atlas of over 109,000 genes, including lncRNAs, and demonstrates its utility in analyzing gene expression across normal and diseased human samples.

Vargas provides a heuristic-free read aligner that computes optimal alignments for linear and graph genomes, improving alignment accuracy by optimizing parameters in existing aligners.

The paper introduces an efficient method for constructing a complete index for pan-genomics read alignment, improving memory and time efficiency over existing methods.

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.

Dashing estimates genomic similarities quickly and accurately using HyperLogLog, outperforming MinHash-based methods for large datasets.

Kraken 2's minimizer-keyed compact hash table cuts memory 85% versus Kraken 1 and classifies over 5 times faster with comparable accuracy; translated search boosts viral sensitivity.

The paper analyzes whole-genome bisulfite sequencing data from two divergent mouse strains to address challenges in differential methylation analysis due to strain-specific CpG sites.

Samovar calls mosaic SNVs in single samples using linked-read data with accuracy comparable to trio or tumor/normal pair analyses.

The paper introduces a preprocessing algorithm called prefix-free parsing to efficiently build compressed Burrows-Wheeler Transform indexes for large genomic datasets.

FORGe prioritizes genetic variants for graph genomes to balance alignment accuracy and computational overhead.

The paper improves thread scaling in read aligners on multi-core processors by addressing architectural challenges and implementing changes in Bowtie, Bowtie 2, and HISAT.

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 introduces a framework for predicting mapping quality by simulating tandem reads with known origins and implements it in the tool Qtip.

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.