Using the Fisher Kernel Method to Detect Remote Protein Homologies. - Tommi S. Jaakkola; Mark Diekhans; David Haussler (ISMB, 1999)

A Discriminative Framework for Detecting Remote Protein Homologies. - Tommi S. Jaakkola; Mark Diekhans; David Haussler (J. Comput. Biol., 2000)

Sequence Analysis With the Kestrel SIMD Parallel Processor. - Leslie Grate; Mark Diekhans; David M. Dahle; Richard Hughey (Pacific Symposium on Biocomputing, 2001)

Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments. - Krishna M. Roskin; Mark Diekhans; David Haussler (RECOMB, 2003)

The UCSC Genome Browser Database. - Donna Karolchik; Robert Baertsch; Mark Diekhans; Terrence S. Furey; Angela S. Hinrichs; Yontao Lu; Krishna M. Roskin; Matt Schwartz; Charles W. Sugnet; Daryl J. Thomas; Ryan J. Weber; David Haussler; et al. (Nucleic Acids Res., 2003)

Score Functions for Determining Regional Conservation in Two-Species Local Alignments. - Krishna M. Roskin; Mark Diekhans; David Haussler (J. Comput. Biol., 2004)

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources. - Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J. Thomas; Ursula Pieper 001; Narayanan Eswar; David Haussler; Andrej Sali (Bioinform., 2005)

The UCSC Proteome Browser. - Fan Hsu; Tom H. Pringle; Robert M. Kuhn; Donna Karolchik; Mark Diekhans; David Haussler; W. James Kent (Nucleic Acids Res., 2005)

The UCSC Kestrel Parallel Processor. - Andrea Di Blas; David M. Dahle; Mark Diekhans; Leslie Grate; Jeffrey D. Hirschberg; Kevin Karplus; Hansjörg Keller; Mark Kendrick; Francisco J. Mesa-Martinez; David Pease; Eric Rice; Angela Schultz; et al. (IEEE Trans. Parallel Distributed Syst., 2005)

The UCSC Known Genes. - Fan Hsu; W. James Kent; Hiram Clawson; Robert M. Kuhn; Mark Diekhans; David Haussler (Bioinform., 2006)

The UCSC Genome Browser Database: update 2006. - Angela S. Hinrichs; Donna Karolchik; Robert Baertsch; Galt P. Barber; Gill Bejerano; Hiram Clawson; Mark Diekhans; Terrence S. Furey; Rachel A. Harte; Fan Hsu; Jennifer Hillman-Jackson; Robert M. Kuhn; et al. (Nucleic Acids Res., 2006)

The UCSC genome browser database: update 2007. - Robert M. Kuhn; Donna Karolchik; Ann S. Zweig; Heather Trumbower; Daryl J. Thomas; Archana Thakkapallayil; Charles W. Sugnet; Mario Stanke; Kayla E. Smith; Adam C. Siepel; Kate R. Rosenbloom; Brooke L. Rhead; et al. (Nucleic Acids Res., 2007)

Comparative Genomics Search for Losses of Long-Established Genes on the Human Lineage. - Jingchun Zhu; J. Zachary Sanborn; Mark Diekhans; Craig B. Lowe; Tom H. Pringle; David Haussler (PLoS Comput. Biol., 2007)

Using native and syntenically mapped cDNA alignments to improve de novo gene finding. - Mario Stanke; Mark Diekhans; Robert Baertsch; David Haussler (Bioinform., 2008)

The UCSC Genome Browser Database: 2008 update. - Donna Karolchik; Robert M. Kuhn; Robert Baertsch; Galt P. Barber; Hiram Clawson; Mark Diekhans; Belinda Giardine; Rachel A. Harte; Angela S. Hinrichs; Fan Hsu; Kord M. Kober; Webb Miller; et al. (Nucleic Acids Res., 2008)

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures. - Michael C. Ryan; Mark Diekhans; Stephanie Lien; Yun Liu 013; Rachel Karchin (Bioinform., 2009)

The UCSC Genome Browser Database: update 2009. - Robert M. Kuhn; Donna Karolchik; Ann S. Zweig; Ting Wang 032; Kayla E. Smith; Kate R. Rosenbloom; Brooke L. Rhead; Brian J. Raney; Andy Pohl; Michael Pheasant; Laurence R. Meyer; Fan Hsu; et al. (Nucleic Acids Res., 2009)

The UCSC Genome Browser database: update 2010. - Brooke L. Rhead; Donna Karolchik; Robert M. Kuhn; Angie S. Hinrichs; Ann S. Zweig; Pauline A. Fujita; Mark Diekhans; Kayla E. Smith; Kate R. Rosenbloom; Brian J. Raney; Andy Pohl; Michael Pheasant; et al. (Nucleic Acids Res., 2010)

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer. - Wing Chung Wong; Dewey Kim; Hannah Carter; Mark Diekhans; Michael C. Ryan; Rachel Karchin (Bioinform., 2011)

Cactus Graphs for Genome Comparisons. - Benedict Paten; Mark Diekhans; Dent Earl; John St. John; Jian Ma 004; Bernard B. Suh; David Haussler (J. Comput. Biol., 2011)

The UCSC Genome Browser database: update 2011. - Pauline A. Fujita; Brooke L. Rhead; Ann S. Zweig; Angie S. Hinrichs; Donna Karolchik; Melissa S. Cline; Mary Goldman; Galt P. Barber; Hiram Clawson; António Coelho; Mark Diekhans; Timothy R. Dreszer; et al. (Nucleic Acids Res., 2011)

Tracking and coordinating an international curation effort for the CCDS Project. - Rachel A. Harte; Catherine M. Farrell; Jane E. Loveland; Marie-Marthe Suner; Laurens G. Wilming; Bronwen L. Aken; Daniel Barrell; Adam Frankish; Craig Wallin; Steve Searle; Mark Diekhans; Jennifer L. Harrow; et al. (Database J. Biol. Databases Curation, 2012)

The UCSC Genome Browser database: extensions and updates 2011. - Timothy R. Dreszer; Donna Karolchik; Ann S. Zweig; Angie S. Hinrichs; Brian J. Raney; Robert M. Kuhn; Laurence R. Meyer; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; et al. (Nucleic Acids Res., 2012)

ENCODE whole-genome data in the UCSC Genome Browser: update 2012. - Kate R. Rosenbloom; Timothy R. Dreszer; Jeffrey C. Long; Venkat S. Malladi; Cricket A. Sloan; Brian J. Raney; Melissa S. Cline; Donna Karolchik; Galt P. Barber; Hiram Clawson; Mark Diekhans; Pauline A. Fujita; et al. (Nucleic Acids Res., 2012)

CRAVAT: cancer-related analysis of variants toolkit. - Christopher Douville; Hannah Carter; Rick Kim; Noushin Niknafs; Mark Diekhans; Peter D. Stenson; David N. Cooper; Michael C. Ryan; Rachel Karchin (Bioinform., 2013)

The UCSC Cancer Genomics Browser: update 2013. - Mary Goldman; Brian Craft; Teresa Swatloski; Kyle Ellrott; Melissa S. Cline; Mark Diekhans; Singer Ma; Chris Wilks; Joshua M. Stuart; David Haussler; Jingchun Zhu (Nucleic Acids Res., 2013)

The UCSC Genome Browser database: extensions and updates 2013. - Laurence R. Meyer; Ann S. Zweig; Angie S. Hinrichs; Donna Karolchik; Robert M. Kuhn; Matthew C. Wong; Cricket A. Sloan; Kate R. Rosenbloom; Greg Roe; Brooke L. Rhead; Brian J. Raney; Andy Pohl; et al. (Nucleic Acids Res., 2013)

ENCODE Data in the UCSC Genome Browser: year 5 update. - Kate R. Rosenbloom; Cricket A. Sloan; Venkat S. Malladi; Timothy R. Dreszer; Katrina Learned; Vanessa Kirkup; Matthew C. Wong; Morgan Maddren; Ruihua Fang; Steven G. Heitner; Brian T. Lee; Galt P. Barber; et al. (Nucleic Acids Res., 2013)

The Cancer Genomics Hub (CGHub): overcoming cancer through the power of torrential data. - Christopher Wilks; Melissa S. Cline; Erich Weiler; Mark Diekhans; Brian Craft; Christy Martin; Daniel Murphy; Howdy Pierce; John Black; Donavan Nelson; Brian Litzinger; Thomas Hatton; et al. (Database J. Biol. Databases Curation, 2014)

Current status and new features of the Consensus Coding Sequence database. - Catherine M. Farrell; Nuala A. O'Leary; Rachel A. Harte; Jane E. Loveland; Laurens G. Wilming; Craig Wallin; Mark Diekhans; Daniel Barrell; Stephen M. J. Searle; Bronwen L. Aken; Susan M. Hiatt; Adam Frankish; et al. (Nucleic Acids Res., 2014)

The UCSC Genome Browser database: 2014 update. - Donna Karolchik; Galt P. Barber; Jonathan Casper; Hiram Clawson; Melissa S. Cline; Mark Diekhans; Timothy R. Dreszer; Pauline A. Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A. Harte; Steven G. Heitner; et al. (Nucleic Acids Res., 2014)

The NIH BD2K center for big data in translational genomics. - Benedict Paten; Mark Diekhans; Brian J. Druker; Stephen H. Friend; Justin Guinney; Nadine Gassner; Mitchell Guttman; W. James Kent; Patrick Mantey; Adam A. Margolin; Matt Massie; Adam M. Novak; et al. (J. Am. Medical Informatics Assoc., 2015)

The UCSC Cancer Genomics Browser: update 2015. - Mary Goldman; Brian Craft; Teresa Swatloski; Melissa S. Cline; Olena Morozova; Mark Diekhans; David Haussler; Jingchun Zhu (Nucleic Acids Res., 2015)

The UCSC Genome Browser database: 2015 update. - Kate R. Rosenbloom; Joel Armstrong; Galt P. Barber; Jonathan Casper; Hiram Clawson; Mark Diekhans; Timothy R. Dreszer; Pauline A. Fujita; Luvina Guruvadoo; Maximilian Haeussler; Rachel A. Harte; Steven G. Heitner; et al. (Nucleic Acids Res., 2015)

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; Steven G. Heitner; Rachel A. Harte; et al. (Nucleic Acids Res., 2016)

Count Everything: Secure Count Query Framework Across Big Data Centers. - Xiaoqian Jiang; Claudiu Farcas; Benedict Paten; Mark Diekhans; Paul Avillach; Wallace Wadge; David Haussler; Lucila Ohno-Machado; Ida Sim (CRI, 2017)

The UCSC Genome Browser database: 2017 update. - Cath Tyner; Galt P. Barber; Jonathan Casper; Hiram Clawson; Mark Diekhans; Christopher Eisenhart; Clayton M. Fischer; David Gibson; Jairo Navarro Gonzalez; Luvina Guruvadoo; Maximilian Haeussler; Steven G. Heitner; et al. (Nucleic Acids Res., 2017)

The UCSC Genome Browser database: 2018 update. - Jonathan Casper; Ann S. Zweig; Chris Villarreal; Cath Tyner; Matthew L. Speir; Kate R. Rosenbloom; Brian J. Raney; Christopher M. Lee; Brian T. Lee; Donna Karolchik; Angie S. Hinrichs; Maximilian Haeussler; et al. (Nucleic Acids Res., 2018)

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation. - Shashikant Pujar; Nuala A. O'Leary; Catherine M. Farrell; Jane E. Loveland; Jonathan M. Mudge; Craig Wallin; Carlos García-Girón; Mark Diekhans; If Barnes; Ruth Bennett; Andrew E. Berry; Eric Cox; et al. (Nucleic Acids Res., 2018)

GENCODE reference annotation for the human and mouse genomes. - Adam Frankish; Mark Diekhans; Anne-Maud Ferreira; Rory Johnson; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; et al. (Nucleic Acids Res., 2019)

The UCSC Genome Browser database: 2019 update. - Maximilian Haeussler; Ann S. Zweig; Cath Tyner; Matthew L. Speir; Kate R. Rosenbloom; Brian J. Raney; Christopher M. Lee; Brian T. Lee; Angie S. Hinrichs; Jairo Navarro Gonzalez; David Gibson; Mark Diekhans; et al. (Nucleic Acids Res., 2019)

UCSC Genome Browser enters 20th year. - Christopher M. Lee; Galt P. Barber; Jonathan Casper; Hiram Clawson; Mark Diekhans; Jairo Navarro Gonzalez; Angie S. Hinrichs; Brian T. Lee; Luis R. Nassar; Conner C. Powell; Brian J. Raney; Kate R. Rosenbloom; et al. (Nucleic Acids Res., 2020)

GENCODE 2021. - Adam Frankish; Mark Diekhans; Irwin Jungreis; Julien Lagarde; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Joel Armstrong; If Barnes; Andrew E. Berry; Alexandra Bignell; et al. (Nucleic Acids Res., 2021)

The UCSC Genome Browser database: 2021 update. - Jairo Navarro Gonzalez; Ann S. Zweig; Matthew L. Speir; Daniel Schmelter; Kate R. Rosenbloom; Brian J. Raney; Conner C. Powell; Luis R. Nassar; Nathan D. Maulding; Christopher M. Lee; Brian T. Lee; Angie S. Hinrichs; et al. (Nucleic Acids Res., 2021)

The UCSC Genome Browser database: 2022 update. - Brian T. Lee; Galt P. Barber; Anna Benet-Pagès; Jonathan Casper; Hiram Clawson; Mark Diekhans; Clayton M. Fischer; Jairo Navarro Gonzalez; Angie S. Hinrichs; Christopher M. Lee; Pranav Muthuraman; Luis R. Nassar; et al. (Nucleic Acids Res., 2022)

GENCODE: reference annotation for the human and mouse genomes in 2023. - Adam Frankish; Silvia Carbonell Sala; Mark Diekhans; Irwin Jungreis; Jane E. Loveland; Jonathan M. Mudge; Cristina Sisu; James C. Wright; Carme Arnan; If Barnes; Abhimanyu Banerjee; Ruth Bennett; et al. (Nucleic Acids Res., 2023)

The UCSC Genome Browser database: 2023 update. - Luis R. Nassar; Galt P. Barber; Anna Benet-Pagès; Jonathan Casper; Hiram Clawson; Mark Diekhans; Clayton M. Fischer; Jairo Navarro Gonzalez; Angie S. Hinrichs; Brian T. Lee; Christopher M. Lee; Pranav Muthuraman; et al. (Nucleic Acids Res., 2023)

RNAget: an API to securely retrieve RNA quantifications. - Sean Upchurch; Emilio Palumbo; Jeremy Adams; David Bujold; Guillaume Bourque; Jared Nedzel; Keenan Graham; Meenakshi S. Kagda; Pedro Assis; Benjamin C. Hitz; Emilio Righi; Roderic Guigó; et al. (Bioinform., 2023)