Mark Diekhans

Mark Diekhans

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Mark Diekhans

Mark Diekhans

Publications by authors named "Mark Diekhans"

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Whole-Genome Alignment and Comparative Annotation.

Annu Rev Anim Biosci 2019 Feb 31;7:41-64. Epub 2018 Oct 31.

UC Santa Cruz Genomics Institute, University of California, Santa Cruz, California 95064, USA; email:

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http://dx.doi.org/10.1146/annurev-animal-020518-115005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6450745PMC
February 2019

Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation.

Genome Res 2018 07 8;28(7):1029-1038. Epub 2018 Jun 8.

Genomics Institute, University of California Santa Cruz and Howard Hughes Medical Institute, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.233460.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6028123PMC
July 2018

Evaluating recovery potential of the northern white rhinoceros from cryopreserved somatic cells.

Genome Res 2018 06 24;28(6):780-788. Epub 2018 May 24.

San Diego Zoo Institute for Conservation Research, Escondido, California 92027, USA.

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http://dx.doi.org/10.1101/gr.227603.117DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5991516PMC
June 2018

Long-read sequence assembly of the gorilla genome.

Science 2016 Apr;352(6281):aae0344

Department of Genome Sciences, University of Washington School of Medicine, Seattle, WA 98195, USA. Howard Hughes Medical Institute, University of Washington, Seattle, WA 98195, USA.

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http://dx.doi.org/10.1126/science.aae0344DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4920363PMC
April 2016

The UCSC Cancer Genomics Browser: update 2015.

Nucleic Acids Res 2015 Jan 11;43(Database issue):D812-7. Epub 2014 Nov 11.

Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA

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http://dx.doi.org/10.1093/nar/gku1073DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4383911PMC
January 2015

Comparative analysis of pseudogenes across three phyla.

Proc Natl Acad Sci U S A 2014 Sep 25;111(37):13361-6. Epub 2014 Aug 25.

Program in Computational Biology and Bioinformatics and Department of Molecular Biophysics and Biochemistry, Yale University, New Haven, CT 06520; Department of Computer Science, Yale University, New Haven, CT 06511

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http://dx.doi.org/10.1073/pnas.1407293111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4169933PMC
September 2014

Current status and new features of the Consensus Coding Sequence database.

Nucleic Acids Res 2014 Jan 11;42(Database issue):D865-72. Epub 2013 Nov 11.

National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Building 38A, 8600 Rockville Pike, Bethesda, MD 20894, USA, Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA, Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge, CB10 1SA, UK and Howard Hughes Medical Institute, University of California Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1059DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3965069PMC
January 2014

The UCSC Genome Browser database: 2014 update.

Nucleic Acids Res 2014 Jan 21;42(Database issue):D764-70. Epub 2013 Nov 21.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), 1156 High Street, Santa Cruz, CA 95064, USA, Computational Biology Graduate Group, University of California Berkeley, Berkeley, CA 94720, USA, Department of Genetics, Stanford University School of Medicine, 3165 Porter Drive, Stanford, CA 94305, USA and Howard Hughes Medical Institute, Center for Biomolecular Science and Engineering, UCSC, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkt1168DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3964947PMC
January 2014

MuPIT interactive: webserver for mapping variant positions to annotated, interactive 3D structures.

Hum Genet 2013 Nov 23;132(11):1235-43. Epub 2013 Jun 23.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, 3400 N. Charles St., Baltimore, MD, USA.

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http://dx.doi.org/10.1007/s00439-013-1325-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3797853PMC
November 2013

CRAVAT: cancer-related analysis of variants toolkit.

Bioinformatics 2013 Mar 16;29(5):647-8. Epub 2013 Jan 16.

Department of Biomedical Engineering, Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD 21218, USA.

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http://dx.doi.org/10.1093/bioinformatics/btt017DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3582272PMC
March 2013

The UCSC Cancer Genomics Browser: update 2013.

Nucleic Acids Res 2013 Jan 29;41(Database issue):D949-54. Epub 2012 Oct 29.

Center for Biomolecular Science and Engineering, University of California at Santa Cruz, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gks1008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531186PMC
January 2013

ENCODE data in the UCSC Genome Browser: year 5 update.

Nucleic Acids Res 2013 Jan 27;41(Database issue):D56-63. Epub 2012 Nov 27.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gks1172DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3531152PMC
January 2013

The GENCODE pseudogene resource.

Genome Biol 2012 Sep 26;13(9):R51. Epub 2012 Sep 26.

Program in Computational Biology and Bioinformatics, Yale University, New Haven, CT 06520, USA.

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http://dx.doi.org/10.1186/gb-2012-13-9-r51DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3491395PMC
September 2012

Tracking and coordinating an international curation effort for the CCDS Project.

Database (Oxford) 2012 20;2012:bas008. Epub 2012 Mar 20.

Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/database/bas008DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3308164PMC
June 2012

Cactus: Algorithms for genome multiple sequence alignment.

Genome Res 2011 Sep 10;21(9):1512-28. Epub 2011 Jun 10.

Center for Biomolecular Science and Engineering, University of California-Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1101/gr.123356.111DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3166836PMC
September 2011

CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.

Bioinformatics 2011 Aug 17;27(15):2147-8. Epub 2011 Jun 17.

Department of Biomedical Engineering and Institute for Computational Medicine, Johns Hopkins University, Baltimore, MD, USA.

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http://dx.doi.org/10.1093/bioinformatics/btr357DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3137226PMC
August 2011

Cactus graphs for genome comparisons.

J Comput Biol 2011 Mar;18(3):469-81

Center for Biomolecular Science and Engineering, University of California, Santa Cruz, California, USA.

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http://dx.doi.org/10.1089/cmb.2010.0252DOI Listing
March 2011

The completion of the Mammalian Gene Collection (MGC).

Authors:
Gary Temple Daniela S Gerhard Rebekah Rasooly Elise A Feingold Peter J Good Cristen Robinson Allison Mandich Jeffrey G Derge Jeanne Lewis Debonny Shoaf Francis S Collins Wonhee Jang Lukas Wagner Carolyn M Shenmen Leonie Misquitta Carl F Schaefer Kenneth H Buetow Tom I Bonner Linda Yankie Ming Ward Lon Phan Alex Astashyn Garth Brown Catherine Farrell Jennifer Hart Melissa Landrum Bonnie L Maidak Michael Murphy Terence Murphy Bhanu Rajput Lillian Riddick David Webb Janet Weber Wendy Wu Kim D Pruitt Donna Maglott Adam Siepel Brona Brejova Mark Diekhans Rachel Harte Robert Baertsch Jim Kent David Haussler Michael Brent Laura Langton Charles L G Comstock Michael Stevens Chaochun Wei Marijke J van Baren Kourosh Salehi-Ashtiani Ryan R Murray Lila Ghamsari Elizabeth Mello Chenwei Lin Christa Pennacchio Kirsten Schreiber Nicole Shapiro Amber Marsh Elizabeth Pardes Troy Moore Anita Lebeau Mike Muratet Blake Simmons David Kloske Stephanie Sieja James Hudson Praveen Sethupathy Michael Brownstein Narayan Bhat Joseph Lazar Howard Jacob Chris E Gruber Mark R Smith John McPherson Angela M Garcia Preethi H Gunaratne Jiaqian Wu Donna Muzny Richard A Gibbs Alice C Young Gerard G Bouffard Robert W Blakesley Jim Mullikin Eric D Green Mark C Dickson Alex C Rodriguez Jane Grimwood Jeremy Schmutz Richard M Myers Martin Hirst Thomas Zeng Kane Tse Michelle Moksa Merinda Deng Kevin Ma Diana Mah Johnson Pang Greg Taylor Eric Chuah Athena Deng Keith Fichter Anne Go Stephanie Lee Jing Wang Malachi Griffith Ryan Morin Richard A Moore Michael Mayo Sarah Munro Susan Wagner Steven J M Jones Robert A Holt Marco A Marra Sun Lu Shuwei Yang James Hartigan Marcus Graf Ralf Wagner Stanley Letovksy Jacqueline C Pulido Keith Robison Dominic Esposito James Hartley Vanessa E Wall Ralph F Hopkins Osamu Ohara Stefan Wiemann

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

Bioinformatics 2009 Jun 15;25(11):1431-2. Epub 2009 Apr 15.

Department of Bioinformatics, George Mason University, Fairfax, VA, USA.

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http://dx.doi.org/10.1093/bioinformatics/btp242DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6276889PMC
June 2009

Retrocopy contributions to the evolution of the human genome.

BMC Genomics 2008 Oct 8;9:466. Epub 2008 Oct 8.

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1186/1471-2164-9-466DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2584115PMC
October 2008

Using native and syntenically mapped cDNA alignments to improve de novo gene finding.

Bioinformatics 2008 Mar 24;24(5):637-44. Epub 2008 Jan 24.

Center for Biomolecular Science and Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btn013DOI Listing
March 2008

Comparative genomics search for losses of long-established genes on the human lineage.

PLoS Comput Biol 2007 Dec;3(12):e247

Center for Biomolecular Science and Engineering, University of California Santa Cruz, Santa Cruz, California, United States of America.

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http://dx.doi.org/10.1371/journal.pcbi.0030247DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2134963PMC
December 2007

The UCSC Known Genes.

Bioinformatics 2006 May 24;22(9):1036-46. Epub 2006 Feb 24.

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz Santa Cruz, CA 95064, USA.

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https://academic.oup.com/bioinformatics/article-lookup/doi/1
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http://dx.doi.org/10.1093/bioinformatics/btl048DOI Listing
May 2006

Regions of extreme synonymous codon selection in mammalian genes.

Nucleic Acids Res 2006 23;34(6):1700-10. Epub 2006 Mar 23.

Department of Biomolecular Engineering, University of California Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1093/nar/gkl095DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC1410912PMC
April 2006

LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.

Bioinformatics 2005 Jun 12;21(12):2814-20. Epub 2005 Apr 12.

Department of Biopharmaceutical Sciences, University of California at San Francisco, San Francisco, CA 94143, USA.

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http://dx.doi.org/10.1093/bioinformatics/bti442DOI Listing
June 2005

The UCSC Proteome Browser.

Nucleic Acids Res 2005 Jan;33(Database issue):D454-8

Center for Biomolecular Science and Engineering, School of Engineering, University of California Santa Cruz (UCSC), Santa Cruz, CA 95064, USA.

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https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/
Publisher Site
http://dx.doi.org/10.1093/nar/gki100DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC540054PMC
January 2005

Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.

Genome Res 2004 Oct;14(10B):2034-40

Center for Biomolecular Science and Engineering, Department of Computer Science, University of California, Santa Cruz, Santa Cruz, California 95064, USA.

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http://dx.doi.org/10.1101/gr.2467904DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC528917PMC
October 2004

Score functions for determining regional conservation in two-species local alignments.

J Comput Biol 2004 ;11(2-3):395-411

Howard Hughes Medical Institute, Baskin School of Engineering, University of California, 1156 High Street, Santa Cruz, CA 95064, USA.

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http://dx.doi.org/10.1089/1066527041410328DOI Listing
August 2004

Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.

Proteins 2003 ;53 Suppl 6:491-6

Computer Engineering Department, University of California, Santa Cruz 95064, USA.

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http://dx.doi.org/10.1002/prot.10540DOI Listing
January 2004

Initial sequencing and comparative analysis of the mouse genome.

Authors:
Robert H Waterston Kerstin Lindblad-Toh Ewan Birney Jane Rogers Josep F Abril Pankaj Agarwal Richa Agarwala Rachel Ainscough Marina Alexandersson Peter An Stylianos E Antonarakis John Attwood Robert Baertsch Jonathon Bailey Karen Barlow Stephan Beck Eric Berry Bruce Birren Toby Bloom Peer Bork Marc Botcherby Nicolas Bray Michael R Brent Daniel G Brown Stephen D Brown Carol Bult John Burton Jonathan Butler Robert D Campbell Piero Carninci Simon Cawley Francesca Chiaromonte Asif T Chinwalla Deanna M Church Michele Clamp Christopher Clee Francis S Collins Lisa L Cook Richard R Copley Alan Coulson Olivier Couronne James Cuff Val Curwen Tim Cutts Mark Daly Robert David Joy Davies Kimberly D Delehaunty Justin Deri Emmanouil T Dermitzakis Colin Dewey Nicholas J Dickens Mark Diekhans Sheila Dodge Inna Dubchak Diane M Dunn Sean R Eddy Laura Elnitski Richard D Emes Pallavi Eswara Eduardo Eyras Adam Felsenfeld Ginger A Fewell Paul Flicek Karen Foley Wayne N Frankel Lucinda A Fulton Robert S Fulton Terrence S Furey Diane Gage Richard A Gibbs Gustavo Glusman Sante Gnerre Nick Goldman Leo Goodstadt Darren Grafham Tina A Graves Eric D Green Simon Gregory Roderic Guigó Mark Guyer Ross C Hardison David Haussler Yoshihide Hayashizaki LaDeana W Hillier Angela Hinrichs Wratko Hlavina Timothy Holzer Fan Hsu Axin Hua Tim Hubbard Adrienne Hunt Ian Jackson David B Jaffe L Steven Johnson Matthew Jones Thomas A Jones Ann Joy Michael Kamal Elinor K Karlsson Donna Karolchik Arkadiusz Kasprzyk Jun Kawai Evan Keibler Cristyn Kells W James Kent Andrew Kirby Diana L Kolbe Ian Korf Raju S Kucherlapati Edward J Kulbokas David Kulp Tom Landers J P Leger Steven Leonard Ivica Letunic Rosie Levine Jia Li Ming Li Christine Lloyd Susan Lucas Bin Ma Donna R Maglott Elaine R Mardis Lucy Matthews Evan Mauceli John H Mayer Megan McCarthy W Richard McCombie Stuart McLaren Kirsten McLay John D McPherson Jim Meldrim Beverley Meredith Jill P Mesirov Webb Miller Tracie L Miner Emmanuel Mongin Kate T Montgomery Michael Morgan Richard Mott James C Mullikin Donna M Muzny William E Nash Joanne O Nelson Michael N Nhan Robert Nicol Zemin Ning Chad Nusbaum Michael J O'Connor Yasushi Okazaki Karen Oliver Emma Overton-Larty Lior Pachter Genís Parra Kymberlie H Pepin Jane Peterson Pavel Pevzner Robert Plumb Craig S Pohl Alex Poliakov Tracy C Ponce Chris P Ponting Simon Potter Michael Quail Alexandre Reymond Bruce A Roe Krishna M Roskin Edward M Rubin Alistair G Rust Ralph Santos Victor Sapojnikov Brian Schultz Jörg Schultz Matthias S Schwartz Scott Schwartz Carol Scott Steven Seaman Steve Searle Ted Sharpe Andrew Sheridan Ratna Shownkeen Sarah Sims Jonathan B Singer Guy Slater Arian Smit Douglas R Smith Brian Spencer Arne Stabenau Nicole Stange-Thomann Charles Sugnet Mikita Suyama Glenn Tesler Johanna Thompson David Torrents Evanne Trevaskis John Tromp Catherine Ucla Abel Ureta-Vidal Jade P Vinson Andrew C Von Niederhausern Claire M Wade Melanie Wall Ryan J Weber Robert B Weiss Michael C Wendl Anthony P West Kris Wetterstrand Raymond Wheeler Simon Whelan Jamey Wierzbowski David Willey Sophie Williams Richard K Wilson Eitan Winter Kim C Worley Dudley Wyman Shan Yang Shiaw-Pyng Yang Evgeny M Zdobnov Michael C Zody Eric S Lander

Nature 2002 Dec;420(6915):520-62

Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA.

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http://dx.doi.org/10.1038/nature01262DOI Listing
December 2002