Mark Diekhans

According to our database, Mark Diekhans authored at least 48 papers between 1999 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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 Hitz, Emilio Righi, Roderic Guigó, Barbara J. Wold, Alvis Brazma, Julia Burchard, Joe Capka, Michael Cherry, Laura Clarke, Brian Craft, Manolis Dermitzakis, Mark Diekhans, John Dursi, Michael Sean Fitzsimons, Zac Flaming, Romina Garrido, Alfred Gil, Paul Godden, Matt Green, Mitch Guttman, Brian Haas, Max Haeussler, Bo Li, Sten Linnarsson, Adam Lipski, David Liu, Simonne Longerich, David Lougheed, Jonathan Manning, John C. Marioni, Christopher Meyer, Stephen B. Montgomery, Alyssa Morrow, Alfonso Muñoz-Pomer Fuentes, Jared L. Nedzel, David Nguyen, Kevin Osborn, Francis Ouellette, Irene Papatheodorou, Dmitri D. Pervouchine, Arun K. Ramani, Jordi Rambla, Bashir Sadjad, David Steinberg, Jeremiah Talkar, Timothy Tickle, Kathy Tzeng, Saman Vaisipour, Sean Watford, Barbara Wold, Zhenyu Zhang, Jing Zhu

Bioinform., April, 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, Beagan Nguy, Tiana Pereira, Parisa Nejad, Gerardo Perez, Brian J. Raney, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent

Nucleic Acids Res., January, 2023

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, Andrew E. Berry, Alexandra Bignell, Carles Boix, Ferriol Calvet Riera, Daniel Cerdán-Vélez, Fiona Cunningham, Claire Davidson, Sarah M. Donaldson, Cagatay Dursun, Reham Fatima, Stefano Giorgetti, Carlos García-Girón, Jose M. Gonzalez, Matthew Hardy, Peter W. Harrison, Thibaut Hourlier, Zoe Hollis, Toby Hunt, Benjamin James, Yunzhe Jiang, Rory Johnson, Mike P. Kay, Julien Lagarde, Fergal J. Martin, Laura Martínez Gómez, Surag Nair, Pengyu Ni, Fernando Pozo, Vivek Ramalingam, Magali Ruffier, Bianca M. Schmitt, Jacob M. Schreiber, Emily Steed, Marie-Marthe Suner, Dulika Sumathipala, Irina Sycheva, Barbara Uszczynska-Ratajczak, Elizabeth Wass, Yucheng T. Yang, Andrew D. Yates, Zahoor Zafrulla, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Anshul Kundaje, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., January, 2023

2022

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, Beagan Nguy, Tiana Pereira, Gerardo Perez, Brian J. Raney, Kate R. Rosenbloom, Daniel Schmelter, Matthew L. Speir, Brittney D. Wick, Ann S. Zweig, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent

Nucleic Acids Res., 2022

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, Alastair C. Fyfe, Jason D. Fernandes, Mark Diekhans, Hiram Clawson, Jonathan Casper, Anna Benet-Pagès, Galt P. Barber, David Haussler, Robert M. Kuhn, Maximilian Haeussler, W. James Kent

Nucleic Acids Res., 2021

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, Carles Boix, Silvia Carbonell Sala, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Kevin L. Howe, Toby Hunt, Osagie G. Izuogu, Rory Johnson, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Ferriol Calvet Riera, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Maxim Y. Wolf, Jinrui Xu, Yucheng T. Yang, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2021

2020

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, Daniel Schmelter, Matthew L. Speir, Ann S. Zweig, David Haussler, Maximilian Haeussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 2020

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, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 2019

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, Alexandra Bignell, Silvia Carbonell Sala, Jacqueline Chrast, Fiona Cunningham, Tomás Di Domenico, Sarah M. Donaldson, Ian T. Fiddes, Carlos García-Girón, Jose M. Gonzalez, Tiago Grego, Matthew Hardy, Thibaut Hourlier, Toby Hunt, Osagie G. Izuogu, Julien Lagarde, Fergal J. Martin, Laura Martínez, Shamika Mohanan, Paul Muir, Fabio C. P. Navarro, Anne Parker, Baikang Pei, Fernando Pozo, Magali Ruffier, Bianca M. Schmitt, Eloise Stapleton, Marie-Marthe Suner, Irina Sycheva, Barbara Uszczynska-Ratajczak, Jinrui Xu, Andrew D. Yates, Daniel R. Zerbino, Yan Zhang, Bronwen L. Aken, Jyoti Choudhary, Mark Gerstein, Roderic Guigó, Tim J. P. Hubbard, Manolis Kellis, Benedict Paten, Alexandre Reymond, Michael L. Tress, Paul Flicek

Nucleic Acids Res., 2019

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, Claire Davidson, Tamara Goldfarb, Jose M. Gonzalez, Toby Hunt, John Jackson, Vinita S. Joardar, Mike P. Kay, Vamsi K. Kodali, Fergal J. Martin, Monica McAndrews, Kelly M. McGarvey, Michael R. Murphy, Bhanu Rajput, Sanjida H. Rangwala, Lillian D. Riddick, Ruth L. Seal, Marie-Marthe Suner, David Webb, Yunxia Sophia Zhu, Bronwen L. Aken, Elspeth A. Bruford, Carol J. Bult, Adam Frankish, Terence D. Murphy, Kim D. Pruitt

Nucleic Acids Res., 2018

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, Luvina Guruvadoo, Jairo Navarro Gonzalez, David Gibson, Ian T. Fiddes, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Galt P. Barber, Joel Armstrong, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 2018

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, Angie S. Hinrichs, Donna Karolchik, Brian T. Lee, Christopher M. Lee, Parisa Nejad, Brian J. Raney, Kate R. Rosenbloom, Matthew L. Speir, Chris Villarreal, John Vivian, Ann S. Zweig, David Haussler, Michael Kuhn, W. James Kent

Nucleic Acids Res., 2017

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

Proceedings of the Summit on Clinical Research Informatics, 2017

2016

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, Maximilian Haeussler, Luvina Guruvadoo, Pauline A. Fujita, Christopher Eisenhart, Mark Diekhans, Hiram Clawson, Jonathan Casper, Galt P. Barber, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 2016

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, Glenn Hickey, Angie S. Hinrichs, Robert Hubley, Donna Karolchik, Katrina Learned, Brian T. Lee, Chin H. Li, Karen H. Miga, Ngan Nguyen, Benedict Paten, Brian J. Raney, Arian F. A. Smit, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 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 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, Frank A. Nothaft, Lior Pachter, David A. Patterson, Maciej Smuga-Otto, Joshua M. Stuart, Laura J. van't Veer, Barbara J. Wold, David Haussler

J. Am. Medical Informatics Assoc., 2015

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, Angie S. Hinrichs, Katrina Learned, Brian T. Lee, Chin H. Li, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Cricket A. Sloan, Matthew L. Speir, Ann S. Zweig, David Haussler, Robert M. Kuhn, W. James Kent

Nucleic Acids Res., 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, Marie-Marthe Suner, Bhanu Rajput, Charles A. Steward, Garth R. Brown, Ruth Bennett, Michael R. Murphy, Wendy Wu, Mike P. Kay, Jennifer Hart, Jeena Rajan, Janet Weber, Catherine Snow, Lillian D. Riddick, Toby Hunt, David Webb, Mark Thomas, Pamela Tamez, Sanjida H. Rangwala, Kelly M. McGarvey, Shashikant Pujar, Andrei Shkeda, Jonathan M. Mudge, Jose M. Gonzalez, James G. R. Gilbert, Stephen J. Trevanion, Robert Baertsch, Jennifer L. Harrow, Tim J. P. Hubbard, James M. Ostell, David Haussler, Kim D. Pruitt

Nucleic Acids Res., 2014

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, Lori Maltbie, Michael Ainsworth, Patrick Allen, Linda Rosewood, Elizabeth Mitchell, Bradley Smith, Jim Warner, John Groboske, Haifang Telc, Daniel Wilson, Brian Sanford, Hannes Schmidt, David Haussler, Daniel Maltbie

Database J. Biol. Databases Curation, 2014

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, Rachel A. Harte, Mark Diekhans, Jeffrey C. Long, Steven P. Wilder, Ann S. Zweig, Donna Karolchik, Robert M. Kuhn, David Haussler, W. James Kent

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, Venkat S. Malladi, Chin H. Li, Brian T. Lee, Katrina Learned, Vanessa Kirkup, Fan Hsu, Steven G. Heitner, Rachel A. Harte, Maximilian Haeussler, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Timothy R. Dreszer, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent

Nucleic Acids Res., 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

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

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, Mary Goldman, Robert C. Gravell, Rachel A. Harte, Angie S. Hinrichs, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Morgan Maddren, Laurence R. Meyer, Andy Pohl, Brooke L. Rhead, Matthew C. Wong, Ann S. Zweig, David Haussler, W. James Kent

Nucleic Acids Res., 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, Andy Pohl, Venkat S. Malladi, Chin H. Li, Katrina Learned, Vanessa Kirkup, Fan Hsu, Rachel A. Harte, Luvina Guruvadoo, Mary Goldman, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Melissa S. Cline, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent

Nucleic Acids Res., 2012

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, Kim D. Pruitt

Database J. Biol. Databases Curation, 2012

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, Belinda Giardine, Rachel A. Harte, Jennifer Hillman-Jackson, Fan Hsu, Vanessa Kirkup, Robert M. Kuhn, Katrina Learned, Chin H. Li, Laurence R. Meyer, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Kayla E. Smith, David Haussler, W. James Kent

Nucleic Acids Res., 2011

Cactus Graphs for Genome Comparisons.

Benedict Paten, Mark Diekhans, Dent Earl, John St. John, Jian Ma, Bernard B. Suh, David Haussler

J. Comput. Biol., 2011

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

2010

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, Laurence R. Meyer, Katrina Learned, Fan Hsu, Jennifer Hillman-Jackson, Rachel A. Harte, Belinda Giardine, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent

Nucleic Acids Res., 2010

2009

The UCSC Genome Browser Database: update 2009.

Robert M. Kuhn, Donna Karolchik, Ann S. Zweig, Ting Wang, Kayla E. Smith, Kate R. Rosenbloom, Brooke L. Rhead, Brian J. Raney, Andy Pohl, Michael Pheasant, Laurence R. Meyer, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Belinda Giardine, Pauline A. Fujita, Mark Diekhans, Timothy R. Dreszer, Hiram Clawson, Galt P. Barber, David Haussler, W. James Kent

Nucleic Acids Res., 2009

LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.

Michael C. Ryan, Mark Diekhans, Stephanie Lien, Yun Liu, Rachel Karchin

Bioinform., 2009

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, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Brooke L. Rhead, Kate R. Rosenbloom, Kayla E. Smith, Mario Stanke, Archana Thakkapallayil, Heather Trumbower, Ting Wang, Ann S. Zweig, David Haussler, W. James Kent

Nucleic Acids Res., 2008

Using native and syntenically mapped cDNA alignments to improve <i>de novo</i> gene finding.

Mario Stanke, Mark Diekhans, Robert Baertsch, David Haussler

Bioinform., 2008

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

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, Brian J. Raney, Andy Pohl, Jakob Skou Pedersen, Fan Hsu, Angela S. Hinrichs, Rachel A. Harte, Mark Diekhans, Hiram Clawson, Gill Bejerano, Galt P. Barber, Robert Baertsch, David Haussler, W. James Kent

Nucleic Acids Res., 2007

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, Jakob Skou Pedersen, Andy Pohl, Brian J. Raney, Kate R. Rosenbloom, Adam C. Siepel, Kayla E. Smith, Charles W. Sugnet, A. Sultan-Qurraie, Daryl J. Thomas, Heather Trumbower, Ryan J. Weber, M. Weirauch, Ann S. Zweig, David Haussler, W. James Kent

Nucleic Acids Res., 2006

The UCSC Known Genes.

Fan Hsu, W. James Kent, Hiram Clawson, Robert M. Kuhn, Mark Diekhans, David Haussler

Bioinform., 2006

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, Don Speck, Richard Hughey

IEEE Trans. Parallel Distributed Syst., 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

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, Narayanan Eswar, David Haussler, Andrej Sali

Bioinform., 2005

2004

Score Functions for Determining Regional Conservation in Two-Species Local Alignments.

Krishna M. Roskin, Mark Diekhans, David Haussler

J. Comput. Biol., 2004

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, W. James Kent

Nucleic Acids Res., 2003

Scoring two-species local alignments to try to statistically separate neutrally evolving from selected DNA segments.

Krishna M. Roskin, Mark Diekhans, David Haussler

Proceedings of the Sventh Annual International Conference on Computational Biology, 2003

2001

Sequence Analysis With the Kestrel SIMD Parallel Processor.

Leslie Grate, Mark Diekhans, David M. Dahle, Richard Hughey

Proceedings of the 6th Pacific Symposium on Biocomputing, 2001

2000

A Discriminative Framework for Detecting Remote Protein Homologies.

Tommi S. Jaakkola, Mark Diekhans, David Haussler

J. Comput. Biol., 2000

1999

Using the Fisher Kernel Method to Detect Remote Protein Homologies.

Tommi S. Jaakkola, Mark Diekhans, David Haussler

Proceedings of the Seventh International Conference on Intelligent Systems for Molecular Biology, 1999