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Mark Diekhans

Research Profile

Occupations

Genes & Molecular Sequences

Concepts & Ideas

Procedures

Living Beings

Mouse

Activities & Behaviors

Chemicals & Drugs

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Evolution, Molecular

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Publications

TOP 3
Christopher Douville; Hannah Carter; David N Cooper; Mark Diekhans; Rick Kim; Noushin Niknafs; Michael Ryan; Peter D Stenson; Rachel Karchin
CRAVAT: cancer-related analysis of variants toolkit.
Kate Rosenbloom; Cricket A Sloan; Steven P Wilder; Matthew C Wong; Ann S Zweig; Vanessa M Kirkup; Robert M Kuhn; Katrina Learned; Brian T Lee; Jeffrey C Long; Morgan Maddren; Venkat S Malladi; Galt P Barber; Mark Diekhans; Timothy R Dreszer; Ruihua Fang; Rachel A Harte; David Haussler; Steven G Heitner; Donna Karolchik; W James Kent
ENCODE data in the UCSC Genome Browser: year 5 update.
Mary Goldman; David Haussler; Singer Ma; Josh Stuart; Teresa Swatloski; Chris Wilks; Melissa Cline; Brian Craft; Mark Diekhans; Kyle Ellrott; Jingchun Zhu
The UCSC Cancer Genomics Browser: update 2013.

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All Publications

2013: Christopher Douville; Hannah Carter; David N Cooper; Mark Diekhans; Rick Kim; Noushin Niknafs; Michael Ryan; Peter D Stenson; Rachel Karchin
CRAVAT: cancer-related analysis of variants toolkit.
Bioinformatics (Oxford, England) 2013;29(5):647-8.
2013: Kate Rosenbloom; Cricket A Sloan; Steven P Wilder; Matthew C Wong; Ann S Zweig; Vanessa M Kirkup; Robert M Kuhn; Katrina Learned; Brian T Lee; Jeffrey C Long; Morgan Maddren; Venkat S Malladi; Galt P Barber; Mark Diekhans; Timothy R Dreszer; Ruihua Fang; Rachel A Harte; David Haussler; Steven G Heitner; Donna Karolchik; W James Kent
ENCODE data in the UCSC Genome Browser: year 5 update.
Nucleic acids research 2013;41(Database issue):D56-63.
2013: Mary Goldman; David Haussler; Singer Ma; Josh Stuart; Teresa Swatloski; Chris Wilks; Melissa Cline; Brian Craft; Mark Diekhans; Kyle Ellrott; Jingchun Zhu
The UCSC Cancer Genomics Browser: update 2013.
Nucleic acids research 2013;41(Database issue):D949-54.
2012: Baikang Pei; Alexandre Reymond; Cristina Sisu; Andrea Tanzer; Suganthi Balasubramanian; Mark Diekhans; Adam Frankish; Lukas Habegger; Jennifer Harrow; Rachel Harte; Cédric Howald; Tim J Hubbard; Xinmeng Jasmine Mu; Mark B Gerstein
The GENCODE pseudogene resource.
Genome biology 2012;13(9):R51.
2012: Rachel A Harte; Jane E Loveland; Bronwen Aken; Daniel Barrell; Mark Diekhans; Catherine M Farrell; Adam Frankish; Jennifer Harrow; Steve Searle; Marie-Marthe Suner; Craig Wallin; Laurens G Wilming; Kim D Pruitt
Tracking and coordinating an international curation effort for the CCDS Project.
Database : the journal of biological databases and curation 2012;2012():bas008.
2011: Benedict Paten; Daniel Zerbino; Mark Diekhans; Dent Earl; Ngan Nguyen; David Haussler
Cactus: Algorithms for genome multiple sequence alignment.
Genome research 2011;21(9):1512-28.
2011: Wing Chung Wong; Hannah Carter; Mark Diekhans; Dewey Kim; Michael C Ryan; Rachel Karchin
CHASM and SNVBox: toolkit for detecting biologically important single nucleotide mutations in cancer.
Bioinformatics (Oxford, England) 2011;27(15):2147-8.
2011: Benedict Paten; Mark Diekhans; Dent Earl; John St John; Jian Ma; Bernard Suh; David Haussler
Cactus graphs for genome comparisons.
Journal of computational biology : a journal of computational molecular cell biology 2011;18(3):469-81.
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; Antonio 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 Rosenbloom; Kayla E Smith; David Haussler; W James Kent
The UCSC Genome Browser database: update 2011.
Nucleic acids research 2011;39(Database issue):D876-82.
2010: Brooke L Rhead; Donna Karolchik; Robert M Kuhn; Angie S Hinrichs; Ann S Zweig; Pauline A Fujita; Mark Diekhans; Kayla E Smith; Kate 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
The UCSC Genome Browser database: update 2010.
Nucleic acids research 2010;38(Database issue):D613-9.
2009: Michael Ryan; Mark Diekhans; Stephanie Lien; Yun Liu; Rachel Karchin
LS-SNP/PDB: annotated non-synonymous SNPs mapped to Protein Data Bank structures.
Bioinformatics (Oxford, England) 2009;25(11):1431-2.
2008: Mario Stanke; Mark Diekhans; Robert Baertsch; David Haussler
Using native and syntenically mapped cDNA alignments to improve de novo gene finding.
Bioinformatics (Oxford, England) 2008;24(5):637-44.
2008: Robert Baertsch; Mark Diekhans; W James Kent; David Haussler; Jürgen Brosius
Retrocopy contributions to the evolution of the human genome.
BMC genomics 2008;9():466.
2008: Donna Karolchik; Robert M Kuhn; Robert Baertsch; Galt P Barber; Hiram Clawson; Mark Diekhans; Belinda Giardine; Rachel A Harte; Angie S Hinrichs; Fan Hsu; K M Kober; Webb Miller; Jan Skov Pedersen; Andy Pohl; Brian J Raney; Brooke L Rhead; Kate Rosenbloom; Kayla E Smith; M Stanke; A Thakkapallayil; Heather Trumbower; T Wang; Ann S Zweig; David Haussler; W James Kent
The UCSC Genome Browser Database: 2008 update.
Nucleic acids research 2008;36(Database issue):D773-9.
2007: Jingchun Zhu; J Zachary Sanborn; Mark Diekhans; Craig B Lowe; Tom H Pringle; David Haussler
Comparative genomics search for losses of long-established genes on the human lineage.
PLoS computational biology 2007;3(12):e247.
2007: Adam Siepel; Mark Diekhans; Brona Brejová; Laura Langton; Michael Stevens; Charles L G Comstock; Colleen Davis; Brent Ewing; Shelly Oommen; Christopher Lau; Hung-Chun Yu; Jianfeng Li; Bruce A Roe; Phil Green; Daniela S Gerhard; Gary Temple; David Haussler; Michael R Brent
Targeted discovery of novel human exons by comparative genomics.
Genome research 2007;17(12):1763-73.
2007: Webb Miller; Kate Rosenbloom; Ross C Hardison; Minmei Hou; James TAYLOR; Brian J Raney; Richard Burhans; David C King; Robert Baertsch; Daniel Blankenberg; Sergei L Kosakovsky Pond; Anton Nekrutenko; Belinda Giardine; Robert S Harris; Svitlana Tyekucheva; Mark Diekhans; Tom H Pringle; William J Murphy; Arthur Lesk; George Weinstock; Kerstin Lindblad-Toh; Richard A Gibbs; Eric S Lander; Adam Siepel; David Haussler; W James Kent
28-way vertebrate alignment and conservation track in the UCSC Genome Browser.
Genome research 2007;17(12):1797-808.
2007: Robert M Kuhn; Donna Karolchik; Ann S Zweig; Heather Trumbower; Daryl J Thomas; A Thakkapallayil; Charles W Sugnet; M Stanke; Kayla E Smith; Adam Siepel; Kate Rosenbloom; Brooke L Rhead; Brian J Raney; Andy Pohl; Jan Skov Pedersen; Fan Hsu; Angie S Hinrichs; Rachel A Harte; Mark Diekhans; Hiram Clawson; Gill Bejerano; Galt P Barber; Robert Baertsch; David Haussler; W James Kent
The UCSC genome browser database: update 2007.
Nucleic acids research 2007;35(Database issue):D668-73.
2006: Fan Hsu; W James Kent; Hiram Clawson; Robert M Kuhn; Mark Diekhans; David Haussler
The UCSC Known Genes.
Bioinformatics (Oxford, England) 2006;22(9):1036-46.
2006: Peter Schattner; Mark Diekhans
Regions of extreme synonymous codon selection in mammalian genes.
Nucleic acids research 2006;34(6):1700-10.
2006: Angie S Hinrichs; Donna Karolchik; Robert Baertsch; Galt P Barber; Gill Bejerano; Hiram Clawson; Mark Diekhans; Terrence S Furey; Rachel A Harte; Fan Hsu; J Hillman-Jackson; Robert M Kuhn; Jan Skov Pedersen; Andy Pohl; Brian J Raney; Kate Rosenbloom; Adam Siepel; Kayla E Smith; Charles W Sugnet; A Sultan-Qurraie; Daryl J Thomas; Heather Trumbower; RJ Weber; M Weirauch; Ann S Zweig; David Haussler; W James Kent
The UCSC Genome Browser Database: update 2006.
Nucleic acids research 2006;34(Database issue):D590-8.
2005: Rachel Karchin; Mark Diekhans; Libusha Kelly; Daryl J Thomas; Ursula Pieper; Narayanan Eswar; David Haussler; Andrej Sali
LS-SNP: large-scale annotation of coding non-synonymous SNPs based on multiple information sources.
Bioinformatics (Oxford, England) 2005;21(12):2814-20.
2005: Fan Hsu; Tom H Pringle; Robert M Kuhn; Donna Karolchik; Mark Diekhans; David Haussler; W James Kent
The UCSC Proteome Browser.
Nucleic acids research 2005;33(Database issue):D454-8.
2004: Terrence S Furey; Mark Diekhans; Yontao Lu; Tina Graves; Lachlan Oddy; Jennifer Randall-Maher; LaDeana W Hillier; Richard K Wilson; David Haussler
Analysis of human mRNAs with the reference genome sequence reveals potential errors, polymorphisms, and RNA editing.
Genome research 2004;14(10B):2034-40.
2004: Krishna M Roskin; Mark Diekhans; David Haussler
Score functions for determining regional conservation in two-species local alignments.
Journal of computational biology : a journal of computational molecular cell biology 2004;11(2-3):395-411.
2003: Ross C Hardison; Francesca Chiaromonte; Diana Kolbe; H Wang; Hanna Petrykowska; Laura Elnitski; Shan Yang; Belinda Giardine; Yi Zhang; Cathy Riemer; Scott Schwartz; David Haussler; Krishna M Roskin; RJ Weber; Mark Diekhans; W James Kent; Mitchell J Weiss; john welch; Webb Miller
Global predictions and tests of erythroid regulatory regions.
Cold Spring Harbor symposia on quantitative biology 2003;68():335-44.
2003: Francesca Chiaromonte; RJ Weber; Krishna M Roskin; Mark Diekhans; W James Kent; David Haussler
The share of human genomic DNA under selection estimated from human-mouse genomic alignments.
Cold Spring Harbor symposia on quantitative biology 2003;68():245-54.
2003: Kevin Karplus; Rachel Karchin; Jenny Draper; Jonathan Casper; Yael Mandel-Gutfreund; Mark Diekhans; Richard Hughey
Combining local-structure, fold-recognition, and new fold methods for protein structure prediction.
Proteins 2003;53 Suppl 6():491-6.
2003: Ross C Hardison; Krishna M Roskin; Shan Yang; Mark Diekhans; W James Kent; Ryan Weber; Laura Elnitski; Jia Li; Michael O'Connor; Diana Kolbe; Scott Schwartz; Terrence S Furey; Simon Whelan; Nick Goldman; Arian Smit; Webb Miller; Francesca Chiaromonte; David Haussler
Covariation in frequencies of substitution, deletion, transposition, and recombination during eutherian evolution.
Genome research 2003;13(1):13-26.
2003: Donna Karolchik; Robert Baertsch; Mark Diekhans; Terrence S Furey; Angie S Hinrichs; Y T Lu; Krishna M Roskin; M Schwartz; Charles W Sugnet; Daryl J Thomas; RJ Weber; David Haussler; W James Kent
The UCSC Genome Browser Database.
Nucleic acids research 2003;31(1):51-4.
2001: Kevin Karplus; Rachel Karchin; C Barrett; S Tu; Melissa Cline; Mark Diekhans; Leslie Grate; J Casper; Richard Hughey
What is the value added by human intervention in protein structure prediction?
Proteins 2001;Suppl 5():86-91.
2001: Leslie Grate; Mark Diekhans; D Dahle; Richard Hughey
Sequence analysis with the Kestrel SIMD parallel processor.
Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing 2001;():263-74.
2000: Tommi S Jaakkola; Mark Diekhans; David Haussler
A discriminative framework for detecting remote protein homologies.
Journal of computational biology : a journal of computational molecular cell biology 2000;7(1-2):95-114.
1999: Tommi S Jaakkola; Mark Diekhans; David Haussler
Using the Fisher kernel method to detect remote protein homologies.
Proceedings / ... International Conference on Intelligent Systems for Molecular Biology ; ISMB. International Conference on Intelligent Systems for Molecular Biology 1999;():149-58.
1999: Kevin Karplus; C Barrett; Melissa Cline; Mark Diekhans; Leslie Grate; Richard Hughey
Predicting protein structure using only sequence information.
Proteins 1999;Suppl 3():121-5.