Author

David Haussler

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 3 Genomics· 1

Signature Assays, Organisms & Methods

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Research Focus:database / resource· 2 Approach:experimental assay· 2 Assay:whole-genome sequencing· 2 Research Focus:batch correction / integration· 1 Approach:benchmark study· 1 Research Focus:benchmarking· 1 Assay:bulk RNA-seq· 1 Organism:human· 1

Frequent Co-Authors

Benedict PateniD· 4 shared Hiram ClawsoniD· 3 shared Glenn HickeyiD· 2 shared Mark DiekhansiD· 2 shared Maximilian HaeussleriD· 2 shared W. James Kent· 2 shared Aaron E. Darling· 1 shared Adam FrankishiD· 1 shared

Activity by Year

2014-2026 · peak 1/yr

Co-Author Collaboration Network

10 top collaborators · 30 mutual co-author links

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4 shared papersBioinformatics

Benedict PatenORCID

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Author profile →

4 papers

Recent·Most cited

GBZ-base and GAF-base: Indexed pangenome file formats

Jouni Sirén, Benedict Paten, Derek Albracht, Ivan A Alexandrov, Jamie Allen, Alawi A Alsheikh-Ali, Nicolas Altemose, Casey Andrews, Dmitry Antipov, Lucinda Antonacci-Fulton, Mobin Asri, Marcelo Ayllon, Jennifer R Balacco, Floris P Barthel, Edward A Belter, , Sergey Koren

The paper introduces GBZ-base and GAF-base, indexed pangenome file formats for efficient subgraph and alignment extraction.

Bioinformatics · Oct 24, 2026Peer-reviewedBioinformatics

Rapid and efficient analysis of 20,000 RNA-seq samples with Toil

John Vivian, Arjun Rao, Frank Austin Nothaft, Christopher Ketchum, Joel Armstrong, Adam Novak, Jacob Pfeil, Jake Narkizian, Alden D. Deran, Audrey Musselman-Brown, Hannes Schmidt, Peter Amstutz, Brian Craft, Mary Goldman, Kate Rosenbloom, , Benedict Paten

The paper demonstrates Toil's ability to efficiently process 20,000 RNA-seq samples to create a batch-effect-free meta-analysis across five datasets.

bioRxiv · Jul 7, 2016Bioinformatics

The UCSC Genome Browser database: 2016 update

Matthew L. Speir, Ann S. Zweig, Kate R. Rosenbloom, Brian J. Raney, Benedict Paten, Parisa Nejad, Brian T. Lee, Katrina Learned, Donna Karolchik, Angie S. Hinrichs, Steve Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, , W. James Kent

The paper updates the UCSC Genome Browser with new features and data sets, including improved human genome assembly hg38/GRCh38 and new tools for data integration.

bioRxiv · Nov 6, 2015Genomics

Alignathon: A competitive assessment of whole genome alignment methods.

Dent Earl, Ngan K Nguyen, Glenn Hickey, Robert S. Harris, Stephen Fitzgerald, Kathryn Beal, Igor Seledtsov, Vladimir Molodtsov, Brian Raney, Hiram Clawson, Jaebum Kim, Carsten Kemena, Jia-Ming Chang, Ionas Erb, Alexander Poliakov, , Benedict Paten

The paper organizes a competitive evaluation of whole genome alignment methods using simulated and real datasets, finding significant accuracy differences between tools and performance variations across evolutionary distances.

Genome Research · Oct 1, 2014Peer-reviewedBioinformatics