David H. Haussler

The paper introduces Giraffe, a pangenome mapper that improves genotyping of SNVs, indels, and SVs in 5,202 human genomes using the vg toolkit.

The paper introduces Piphys, an open-source platform for neural recording that enables remote control and scalability through cloud-based software and low-cost hardware.

The paper introduces a daily-updated database of SARS-CoV-2 mutation-annotated trees and associated tools for querying and manipulating the data.

The paper introduces UShER, a method for ultrafast phylogenetic placement of SARS-CoV-2 sequences, enabling real-time genomic contact tracing and maintaining an updated reference phylogeny.

The paper reports a SARS-CoV-2 lineage with mutations from known variants of concern that is rejected by sequence repositories due to a deletion, suggesting underestimation of its frequency.

The paper evaluates the informativeness of reads in bulk RNA-Seq datasets and recommends using MEND reads for accurate gene expression quantification in pediatric cancer studies.

The paper identifies lab-specific recurrent mutations in SARS-CoV-2 sequences that affect phylogenetic inference and proposes tools to improve sequence quality and phylogeny comparison.

ProTECT identifies and ranks tumor neoepitopes from raw sequencing data for cancer immunotherapy, outperforming existing tools in efficiency and scalability.

The paper describes a SARS-CoV-2 genome browser that integrates molecular data from multiple sources for visualization and analysis.

The paper provides a user guide to five online tools for exploring and visualizing PCAWG data, demonstrating their integration with external resources to enhance cancer genomics research.

The paper presents an optimized PromethION nanopore sequencing method and new computational tools for efficient human genome assembly, achieving high accuracy and speed.

The UCSC Repeat Browser provides a tool for visualizing and analyzing repeat elements in the genome, enabling the study of evolutionary conflicts across species.

This paper genomically characterizes 261 pediatric cancer patient-derived xenograft models to guide rational clinical trial design and drug development.

The paper improves the Cactus multiple-genome aligner to handle large numbers of vertebrate genomes with high accuracy and better orthology resolution.

The paper uses chimpanzee cerebral organoids to identify human-specific genes in cortical development and finds increased PI3K/AKT/mTOR activation in human outer radial glia.

The paper benchmarks somatic structural variant detection methods using synthetic tumors and crowd-sourced submissions, finding that ensembles do not always outperform individual methods.

The paper introduces CAT, a toolkit for simultaneous clade and personal genome annotation, demonstrating its ability to discover novel genes and improve cross-species RNA expression analysis.

This paper introduces a new algorithm called the flow procedure for linearizing genome sequence graphs, which outperforms existing methods in key metrics.

The paper identifies human-specific NOTCH2NL genes linked to neurodevelopmental disorders and shows they affect cortical neurogenesis through Notch signaling.

The paper uses nanopore sequencing to assemble and characterize the centromeric region of a human Y chromosome, overcoming challenges posed by repetitive DNA.

This paper introduces genome graphs as an alternative to linear reference genomes, showing they improve read mapping and variant calling compared to the standard GRCh38 reference.