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@article{DBLP:journals/nar/NassarBBCCDFGHLLMNPNPRSSWZHKHK23,
author = {Luis R. Nassar and
Galt P. Barber and
Anna Benet{-}Pag{\`{e}}s and
Jonathan Casper and
Hiram Clawson and
Mark Diekhans and
Clayton M. Fischer and
Jairo Navarro Gonzalez and
Angie S. Hinrichs and
Brian T. Lee and
Christopher M. Lee and
Pranav Muthuraman and
Beagan Nguy and
Tiana Pereira and
Parisa Nejad and
Gerardo Perez and
Brian J. Raney and
Daniel Schmelter and
Matthew L. Speir and
Brittney D. Wick and
Ann S. Zweig and
David Haussler and
Robert M. Kuhn and
Maximilian Haeussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2023 update},
journal = {Nucleic Acids Res.},
volume = {51},
number = {{D1}},
pages = {1188--1195},
year = {2023},
url = {https://doi.org/10.1093/nar/gkac1072},
doi = {10.1093/NAR/GKAC1072},
timestamp = {Fri, 18 Aug 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/NassarBBCCDFGHLLMNPNPRSSWZHKHK23.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LeeBBCCDFGHLMNN22,
author = {Brian T. Lee and
Galt P. Barber and
Anna Benet{-}Pag{\`{e}}s and
Jonathan Casper and
Hiram Clawson and
Mark Diekhans and
Clayton M. Fischer and
Jairo Navarro Gonzalez and
Angie S. Hinrichs and
Christopher M. Lee and
Pranav Muthuraman and
Luis R. Nassar and
Beagan Nguy and
Tiana Pereira and
Gerardo Perez and
Brian J. Raney and
Kate R. Rosenbloom and
Daniel Schmelter and
Matthew L. Speir and
Brittney D. Wick and
Ann S. Zweig and
David Haussler and
Robert M. Kuhn and
Maximilian Haeussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2022 update},
journal = {Nucleic Acids Res.},
volume = {50},
number = {{D1}},
pages = {1115--1122},
year = {2022},
url = {https://doi.org/10.1093/nar/gkab959},
doi = {10.1093/NAR/GKAB959},
timestamp = {Sun, 15 Jan 2023 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/LeeBBCCDFGHLMNN22.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/SpeirBMMNPPRSKH21,
author = {Matthew L. Speir and
Aparna Bhaduri and
Nikolay S. Markov and
Pablo A. Moreno and
Tomasz J. Nowakowski and
Irene Papatheodorou and
Alex A. Pollen and
Brian J. Raney and
Lucas Seninge and
W. James Kent and
Maximilian Haeussler},
title = {{UCSC} Cell Browser: visualize your single-cell data},
journal = {Bioinform.},
volume = {37},
number = {23},
pages = {4578--4580},
year = {2021},
url = {https://doi.org/10.1093/bioinformatics/btab503},
doi = {10.1093/BIOINFORMATICS/BTAB503},
timestamp = {Tue, 12 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/SpeirBMMNPPRSKH21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/GonzalezZSSRRPN21,
author = {Jairo Navarro Gonzalez and
Ann S. Zweig and
Matthew L. Speir and
Daniel Schmelter and
Kate R. Rosenbloom and
Brian J. Raney and
Conner C. Powell and
Luis R. Nassar and
Nathan D. Maulding and
Christopher M. Lee and
Brian T. Lee and
Angie S. Hinrichs and
Alastair C. Fyfe and
Jason D. Fernandes and
Mark Diekhans and
Hiram Clawson and
Jonathan Casper and
Anna Benet{-}Pag{\`{e}}s and
Galt P. Barber and
David Haussler and
Robert M. Kuhn and
Maximilian Haeussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2021 update},
journal = {Nucleic Acids Res.},
volume = {49},
number = {Database-Issue},
pages = {D1046--D1057},
year = {2021},
url = {https://doi.org/10.1093/nar/gkaa1070},
doi = {10.1093/NAR/GKAA1070},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/GonzalezZSSRRPN21.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/LeeBCCDGHLNPRRS20,
author = {Christopher M. Lee and
Galt P. Barber and
Jonathan Casper and
Hiram Clawson and
Mark Diekhans and
Jairo Navarro Gonzalez and
Angie S. Hinrichs and
Brian T. Lee and
Luis R. Nassar and
Conner C. Powell and
Brian J. Raney and
Kate R. Rosenbloom and
Daniel Schmelter and
Matthew L. Speir and
Ann S. Zweig and
David Haussler and
Maximilian Haeussler and
Robert M. Kuhn and
W. James Kent},
title = {{UCSC} Genome Browser enters 20th year},
journal = {Nucleic Acids Res.},
volume = {48},
number = {Database-Issue},
pages = {D756--D761},
year = {2020},
url = {https://doi.org/10.1093/nar/gkz1012},
doi = {10.1093/NAR/GKZ1012},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/LeeBCCDGHLNPRRS20.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HaeusslerZTSRRL19,
author = {Maximilian Haeussler and
Ann S. Zweig and
Cath Tyner and
Matthew L. Speir and
Kate R. Rosenbloom and
Brian J. Raney and
Christopher M. Lee and
Brian T. Lee and
Angie S. Hinrichs and
Jairo Navarro Gonzalez and
David Gibson and
Mark Diekhans and
Hiram Clawson and
Jonathan Casper and
Galt P. Barber and
David Haussler and
Robert M. Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2019 update},
journal = {Nucleic Acids Res.},
volume = {47},
number = {Database-Issue},
pages = {D853--D858},
year = {2019},
url = {https://doi.org/10.1093/nar/gky1095},
doi = {10.1093/NAR/GKY1095},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HaeusslerZTSRRL19.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/CasperZVTSRRLLK18,
author = {Jonathan Casper and
Ann S. Zweig and
Chris Villarreal and
Cath Tyner and
Matthew L. Speir and
Kate R. Rosenbloom and
Brian J. Raney and
Christopher M. Lee and
Brian T. Lee and
Donna Karolchik and
Angie S. Hinrichs and
Maximilian Haeussler and
Luvina Guruvadoo and
Jairo Navarro Gonzalez and
David Gibson and
Ian T. Fiddes and
Christopher Eisenhart and
Mark Diekhans and
Hiram Clawson and
Galt P. Barber and
Joel Armstrong and
David Haussler and
Robert M. Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2018 update},
journal = {Nucleic Acids Res.},
volume = {46},
number = {Database-Issue},
pages = {D762--D769},
year = {2018},
url = {https://doi.org/10.1093/nar/gkx1020},
doi = {10.1093/NAR/GKX1020},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/CasperZVTSRRLLK18.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/TynerBCCDEFGGGH17,
author = {Cath Tyner and
Galt P. Barber and
Jonathan Casper and
Hiram Clawson and
Mark Diekhans and
Christopher Eisenhart and
Clayton M. Fischer and
David Gibson and
Jairo Navarro Gonzalez and
Luvina Guruvadoo and
Maximilian Haeussler and
Steven G. Heitner and
Angie S. Hinrichs and
Donna Karolchik and
Brian T. Lee and
Christopher M. Lee and
Parisa Nejad and
Brian J. Raney and
Kate R. Rosenbloom and
Matthew L. Speir and
Chris Villarreal and
John Vivian and
Ann S. Zweig and
David Haussler and
Michael Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2017 update},
journal = {Nucleic Acids Res.},
volume = {45},
number = {Database-Issue},
pages = {D626--D634},
year = {2017},
url = {https://doi.org/10.1093/nar/gkw1134},
doi = {10.1093/NAR/GKW1134},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/TynerBCCDEFGGGH17.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HinrichsRSRCKKR16,
author = {Angie S. Hinrichs and
Brian J. Raney and
Matthew L. Speir and
Brooke L. Rhead and
Jonathan Casper and
Donna Karolchik and
Robert M. Kuhn and
Kate R. Rosenbloom and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {{UCSC} Data Integrator and Variant Annotation Integrator},
journal = {Bioinform.},
volume = {32},
number = {9},
pages = {1430--1432},
year = {2016},
url = {https://doi.org/10.1093/bioinformatics/btv766},
doi = {10.1093/BIOINFORMATICS/BTV766},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/HinrichsRSRCKKR16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SpeirZRRPNLLKHH16,
author = {Matthew L. Speir and
Ann S. Zweig and
Kate R. Rosenbloom and
Brian J. Raney and
Benedict Paten and
Parisa Nejad and
Brian T. Lee and
Katrina Learned and
Donna Karolchik and
Angie S. Hinrichs and
Steven G. Heitner and
Rachel A. Harte and
Maximilian Haeussler and
Luvina Guruvadoo and
Pauline A. Fujita and
Christopher Eisenhart and
Mark Diekhans and
Hiram Clawson and
Jonathan Casper and
Galt P. Barber and
David Haussler and
Robert M. Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2016 update},
journal = {Nucleic Acids Res.},
volume = {44},
number = {Database-Issue},
pages = {717--725},
year = {2016},
url = {https://doi.org/10.1093/nar/gkv1275},
doi = {10.1093/NAR/GKV1275},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SpeirZRRPNLLKHH16.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/biodb/MalladiEPRCDHHL15,
author = {Venkat S. Malladi and
Drew T. Erickson and
Nikhil R. Podduturi and
Laurence D. Rowe and
Esther T. Chan and
Jean M. Davidson and
Benjamin C. Hitz and
Marcus Ho and
Brian T. Lee and
Stuart R. Miyasato and
Greg R. Roe and
Matt Simison and
Cricket A. Sloan and
J. Seth Strattan and
Forrest Tanaka and
W. James Kent and
J. Michael Cherry and
Eurie L. Hong},
title = {Ontology application and use at the {ENCODE} {DCC}},
journal = {Database J. Biol. Databases Curation},
volume = {2015},
year = {2015},
url = {https://doi.org/10.1093/database/bav010},
doi = {10.1093/DATABASE/BAV010},
timestamp = {Tue, 07 May 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/biodb/MalladiEPRCDHHL15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HaeusslerRHCZKC15,
author = {Maximilian Haeussler and
Brian J. Raney and
Angie S. Hinrichs and
Hiram Clawson and
Ann S. Zweig and
Donna Karolchik and
Jonathan Casper and
Matthew L. Speir and
David Haussler and
W. James Kent},
title = {Navigating protected genomics data with {UCSC} Genome Browser in a
Box},
journal = {Bioinform.},
volume = {31},
number = {5},
pages = {764--766},
year = {2015},
url = {https://doi.org/10.1093/bioinformatics/btu712},
doi = {10.1093/BIOINFORMATICS/BTU712},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HaeusslerRHCZKC15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jamia/PatenDDFGGGKMMM15,
author = {Benedict Paten and
Mark Diekhans and
Brian J. Druker and
Stephen H. Friend and
Justin Guinney and
Nadine Gassner and
Mitchell Guttman and
W. James Kent and
Patrick Mantey and
Adam A. Margolin and
Matt Massie and
Adam M. Novak and
Frank A. Nothaft and
Lior Pachter and
David A. Patterson and
Maciej Smuga{-}Otto and
Joshua M. Stuart and
Laura J. van't Veer and
Barbara J. Wold and
David Haussler},
title = {The {NIH} {BD2K} center for big data in translational genomics},
journal = {J. Am. Medical Informatics Assoc.},
volume = {22},
number = {6},
pages = {1143--1147},
year = {2015},
url = {https://doi.org/10.1093/jamia/ocv047},
doi = {10.1093/JAMIA/OCV047},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/jamia/PatenDDFGGGKMMM15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/jcb/NguyenHZREAKHP15,
author = {Ngan Nguyen and
Glenn Hickey and
Daniel R. Zerbino and
Brian J. Raney and
Dent Earl and
Joel Armstrong and
W. James Kent and
David Haussler and
Benedict Paten},
title = {Building a Pan-Genome Reference for a Population},
journal = {J. Comput. Biol.},
volume = {22},
number = {5},
pages = {387--401},
year = {2015},
url = {https://doi.org/10.1089/cmb.2014.0146},
doi = {10.1089/CMB.2014.0146},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/jcb/NguyenHZREAKHP15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RosenbloomABCCDDFGHHHHHHKLLLMNPRSSZHKK15,
author = {Kate R. Rosenbloom and
Joel Armstrong and
Galt P. Barber and
Jonathan Casper and
Hiram Clawson and
Mark Diekhans and
Timothy R. Dreszer and
Pauline A. Fujita and
Luvina Guruvadoo and
Maximilian Haeussler and
Rachel A. Harte and
Steven G. Heitner and
Glenn Hickey and
Angie S. Hinrichs and
Robert Hubley and
Donna Karolchik and
Katrina Learned and
Brian T. Lee and
Chin H. Li and
Karen H. Miga and
Ngan Nguyen and
Benedict Paten and
Brian J. Raney and
Arian F. A. Smit and
Matthew L. Speir and
Ann S. Zweig and
David Haussler and
Robert M. Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2015 update},
journal = {Nucleic Acids Res.},
volume = {43},
number = {Database-Issue},
pages = {670--681},
year = {2015},
url = {https://doi.org/10.1093/nar/gku1177},
doi = {10.1093/NAR/GKU1177},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RosenbloomABCCDDFGHHHHHHKLLLMNPRSSZHKK15.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/RaneyDBCFWNPZKK14,
author = {Brian J. Raney and
Timothy R. Dreszer and
Galt P. Barber and
Hiram Clawson and
Pauline A. Fujita and
Ting Wang and
Ngan Nguyen and
Benedict Paten and
Ann S. Zweig and
Donna Karolchik and
W. James Kent},
title = {Track data hubs enable visualization of user-defined genome-wide annotations
on the {UCSC} Genome Browser},
journal = {Bioinform.},
volume = {30},
number = {7},
pages = {1003--1005},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btt637},
doi = {10.1093/BIOINFORMATICS/BTT637},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/RaneyDBCFWNPZKK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/NguyenHRACZKKHP14,
author = {Ngan Nguyen and
Glenn Hickey and
Brian J. Raney and
Joel Armstrong and
Hiram Clawson and
Ann S. Zweig and
Donna Karolchik and
William James Kent and
David Haussler and
Benedict Paten},
title = {Comparative assembly hubs: Web-accessible browsers for comparative
genomics},
journal = {Bioinform.},
volume = {30},
number = {23},
pages = {3293--3301},
year = {2014},
url = {https://doi.org/10.1093/bioinformatics/btu534},
doi = {10.1093/BIOINFORMATICS/BTU534},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/NguyenHRACZKKHP14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarolchikBCCCDDFGHHHHLLLRRRSSZHKK14,
author = {Donna Karolchik and
Galt P. Barber and
Jonathan Casper and
Hiram Clawson and
Melissa S. Cline and
Mark Diekhans and
Timothy R. Dreszer and
Pauline A. Fujita and
Luvina Guruvadoo and
Maximilian Haeussler and
Rachel A. Harte and
Steven G. Heitner and
Angie S. Hinrichs and
Katrina Learned and
Brian T. Lee and
Chin H. Li and
Brian J. Raney and
Brooke L. Rhead and
Kate R. Rosenbloom and
Cricket A. Sloan and
Matthew L. Speir and
Ann S. Zweig and
David Haussler and
Robert M. Kuhn and
W. James Kent},
title = {The {UCSC} Genome Browser database: 2014 update},
journal = {Nucleic Acids Res.},
volume = {42},
number = {Database-Issue},
pages = {764--770},
year = {2014},
url = {https://doi.org/10.1093/nar/gkt1168},
doi = {10.1093/NAR/GKT1168},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarolchikBCCCDDFGHHHHLLLRRRSSZHKK14.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bib/KuhnHK13,
author = {Robert M. Kuhn and
David Haussler and
W. James Kent},
title = {The {UCSC} genome browser and associated tools},
journal = {Briefings Bioinform.},
volume = {14},
number = {2},
pages = {144--161},
year = {2013},
url = {https://doi.org/10.1093/bib/bbs038},
doi = {10.1093/BIB/BBS038},
timestamp = {Thu, 04 Jun 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bib/KuhnHK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RosenbloomSMDLKWMFHLBHDLWZKKHK13,
author = {Kate R. Rosenbloom and
Cricket A. Sloan and
Venkat S. Malladi and
Timothy R. Dreszer and
Katrina Learned and
Vanessa Kirkup and
Matthew C. Wong and
Morgan Maddren and
Ruihua Fang and
Steven G. Heitner and
Brian T. Lee and
Galt P. Barber and
Rachel A. Harte and
Mark Diekhans and
Jeffrey C. Long and
Steven P. Wilder and
Ann S. Zweig and
Donna Karolchik and
Robert M. Kuhn and
David Haussler and
W. James Kent},
title = {{ENCODE} Data in the {UCSC} Genome Browser: year 5 update},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {56--63},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1172},
doi = {10.1093/NAR/GKS1172},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RosenbloomSMDLKWMFHLBHDLWZKKHK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/MeyerZHKKWSRRRRPMLLLKHHHHGGGFDDCCBHK13,
author = {Laurence R. Meyer and
Ann S. Zweig and
Angie S. Hinrichs and
Donna Karolchik and
Robert M. Kuhn and
Matthew C. Wong and
Cricket A. Sloan and
Kate R. Rosenbloom and
Greg Roe and
Brooke L. Rhead and
Brian J. Raney and
Andy Pohl and
Venkat S. Malladi and
Chin H. Li and
Brian T. Lee and
Katrina Learned and
Vanessa Kirkup and
Fan Hsu and
Steven G. Heitner and
Rachel A. Harte and
Maximilian Haeussler and
Luvina Guruvadoo and
Mary Goldman and
Belinda Giardine and
Pauline A. Fujita and
Timothy R. Dreszer and
Mark Diekhans and
Melissa S. Cline and
Hiram Clawson and
Galt P. Barber and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: extensions and updates 2013},
journal = {Nucleic Acids Res.},
volume = {41},
number = {Database-Issue},
pages = {64--69},
year = {2013},
url = {https://doi.org/10.1093/nar/gks1048},
doi = {10.1093/NAR/GKS1048},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/MeyerZHKKWSRRRRPMLLLKHHHHGGGFDDCCBHK13.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RosenbloomDLMSRCKBCDFGGHHKKLMMPRWZHK12,
author = {Kate R. Rosenbloom and
Timothy R. Dreszer and
Jeffrey C. Long and
Venkat S. Malladi and
Cricket A. Sloan and
Brian J. Raney and
Melissa S. Cline and
Donna Karolchik and
Galt P. Barber and
Hiram Clawson and
Mark Diekhans and
Pauline A. Fujita and
Mary Goldman and
Robert C. Gravell and
Rachel A. Harte and
Angie S. Hinrichs and
Vanessa Kirkup and
Robert M. Kuhn and
Katrina Learned and
Morgan Maddren and
Laurence R. Meyer and
Andy Pohl and
Brooke L. Rhead and
Matthew C. Wong and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {{ENCODE} whole-genome data in the {UCSC} Genome Browser: update 2012},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {912--917},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1012},
doi = {10.1093/NAR/GKR1012},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RosenbloomDLMSRCKBCDFGGHHKKLMMPRWZHK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/DreszerKZHRKMWSRRRPMLLKHHGGGFDCCBHK12,
author = {Timothy R. Dreszer and
Donna Karolchik and
Ann S. Zweig and
Angie S. Hinrichs and
Brian J. Raney and
Robert M. Kuhn and
Laurence R. Meyer and
Matthew C. Wong and
Cricket A. Sloan and
Kate R. Rosenbloom and
Greg Roe and
Brooke L. Rhead and
Andy Pohl and
Venkat S. Malladi and
Chin H. Li and
Katrina Learned and
Vanessa Kirkup and
Fan Hsu and
Rachel A. Harte and
Luvina Guruvadoo and
Mary Goldman and
Belinda Giardine and
Pauline A. Fujita and
Mark Diekhans and
Melissa S. Cline and
Hiram Clawson and
Galt P. Barber and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: extensions and updates 2011},
journal = {Nucleic Acids Res.},
volume = {40},
number = {Database-Issue},
pages = {918--923},
year = {2012},
url = {https://doi.org/10.1093/nar/gkr1055},
doi = {10.1093/NAR/GKR1055},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/DreszerKZHRKMWSRRRPMLLKHHGGGFDCCBHK12.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RaneyCRDLBMSMRSHCZKFRSPKKHK11,
author = {Brian J. Raney and
Melissa S. Cline and
Kate R. Rosenbloom and
Timothy R. Dreszer and
Katrina Learned and
Galt P. Barber and
Laurence R. Meyer and
Cricket A. Sloan and
Venkat S. Malladi and
Krishna M. Roskin and
Bernard B. Suh and
Angie S. Hinrichs and
Hiram Clawson and
Ann S. Zweig and
Vanessa Kirkup and
Pauline A. Fujita and
Brooke L. Rhead and
Kayla E. Smith and
Andy Pohl and
Robert M. Kuhn and
Donna Karolchik and
David Haussler and
W. James Kent},
title = {{ENCODE} whole-genome data in the {UCSC} genome browser {(2011} update)},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {871--875},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1017},
doi = {10.1093/NAR/GKQ1017},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RaneyCRDLBMSMRSHCZKFRSPKKHK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/FujitaRZHKCGBCCDDGHHHKKLLMPRRSHK11,
author = {Pauline A. Fujita and
Brooke L. Rhead and
Ann S. Zweig and
Angie S. Hinrichs and
Donna Karolchik and
Melissa S. Cline and
Mary Goldman and
Galt P. Barber and
Hiram Clawson and
Ant{\'{o}}nio Coelho and
Mark Diekhans and
Timothy R. Dreszer and
Belinda Giardine and
Rachel A. Harte and
Jennifer Hillman{-}Jackson and
Fan Hsu and
Vanessa Kirkup and
Robert M. Kuhn and
Katrina Learned and
Chin H. Li and
Laurence R. Meyer and
Andy Pohl and
Brian J. Raney and
Kate R. Rosenbloom and
Kayla E. Smith and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: update 2011},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {876--882},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq963},
doi = {10.1093/NAR/GKQ963},
timestamp = {Sat, 13 Apr 2024 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/FujitaRZHKCGBCCDDGHHHKKLLMPRRSHK11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/SanbornBCSKMVGSKKKSHZ11,
author = {J. Zachary Sanborn and
Stephen C. Benz and
Brian Craft and
Christopher Szeto and
Kord M. Kober and
Laurence R. Meyer and
Charles J. Vaske and
Mary Goldman and
Kayla E. Smith and
Robert M. Kuhn and
Donna Karolchik and
W. James Kent and
Joshua M. Stuart and
David Haussler and
Jingchun Zhu},
title = {The {UCSC} cancer genomics browser: update 2011},
journal = {Nucleic Acids Res.},
volume = {39},
number = {Database-Issue},
pages = {951--959},
year = {2011},
url = {https://doi.org/10.1093/nar/gkq1113},
doi = {10.1093/NAR/GKQ1113},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/SanbornBCSKMVGSKKKSHZ11.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/KentZBHK10,
author = {W. James Kent and
Ann S. Zweig and
Galt P. Barber and
Angie S. Hinrichs and
Donna Karolchik},
title = {BigWig and BigBed: enabling browsing of large distributed datasets},
journal = {Bioinform.},
volume = {26},
number = {17},
pages = {2204--2207},
year = {2010},
url = {https://doi.org/10.1093/bioinformatics/btq351},
doi = {10.1093/BIOINFORMATICS/BTQ351},
timestamp = {Mon, 02 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/bioinformatics/KentZBHK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RheadKKHZFDSRRPPMLHHHGDCBHK10,
author = {Brooke L. Rhead and
Donna Karolchik and
Robert M. Kuhn and
Angie S. Hinrichs and
Ann S. Zweig and
Pauline A. Fujita and
Mark Diekhans and
Kayla E. Smith and
Kate R. Rosenbloom and
Brian J. Raney and
Andy Pohl and
Michael Pheasant and
Laurence R. Meyer and
Katrina Learned and
Fan Hsu and
Jennifer Hillman{-}Jackson and
Rachel A. Harte and
Belinda Giardine and
Timothy R. Dreszer and
Hiram Clawson and
Galt P. Barber and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser database: update 2010},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {613--619},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp939},
doi = {10.1093/NAR/GKP939},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RheadKKHZFDSRRPPMLHHHGDCBHK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/RosenbloomDPBMPRWHZFLRSKKHK10,
author = {Kate R. Rosenbloom and
Timothy R. Dreszer and
Michael Pheasant and
Galt P. Barber and
Laurence R. Meyer and
Andy Pohl and
Brian J. Raney and
Ting Wang and
Angie S. Hinrichs and
Ann S. Zweig and
Pauline A. Fujita and
Katrina Learned and
Brooke L. Rhead and
Kayla E. Smith and
Robert M. Kuhn and
Donna Karolchik and
David Haussler and
W. James Kent},
title = {{ENCODE} whole-genome data in the {UCSC} Genome Browser},
journal = {Nucleic Acids Res.},
volume = {38},
number = {Database-Issue},
pages = {620--625},
year = {2010},
url = {https://doi.org/10.1093/nar/gkp961},
doi = {10.1093/NAR/GKP961},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/RosenbloomDPBMPRWHZFLRSKKHK10.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KuhnKZWSRRRPPMHHHGFDDCBHK09,
author = {Robert M. Kuhn and
Donna Karolchik and
Ann S. Zweig and
Ting Wang and
Kayla E. Smith and
Kate R. Rosenbloom and
Brooke L. Rhead and
Brian J. Raney and
Andy Pohl and
Michael Pheasant and
Laurence R. Meyer and
Fan Hsu and
Angela S. Hinrichs and
Rachel A. Harte and
Belinda Giardine and
Pauline A. Fujita and
Mark Diekhans and
Timothy R. Dreszer and
Hiram Clawson and
Galt P. Barber and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database: update 2009},
journal = {Nucleic Acids Res.},
volume = {37},
number = {Database-Issue},
pages = {755--761},
year = {2009},
url = {https://doi.org/10.1093/nar/gkn875},
doi = {10.1093/NAR/GKN875},
timestamp = {Sat, 30 Sep 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KuhnKZWSRRRPPMHHHGFDDCBHK09.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarolchikKBBCDGHHHKMPPRRRSSTTWZHK08,
author = {Donna Karolchik and
Robert M. Kuhn and
Robert Baertsch and
Galt P. Barber and
Hiram Clawson and
Mark Diekhans and
Belinda Giardine and
Rachel A. Harte and
Angela S. Hinrichs and
Fan Hsu and
Kord M. Kober and
Webb Miller and
Jakob Skou Pedersen and
Andy Pohl and
Brian J. Raney and
Brooke L. Rhead and
Kate R. Rosenbloom and
Kayla E. Smith and
Mario Stanke and
Archana Thakkapallayil and
Heather Trumbower and
Ting Wang and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database: 2008 update},
journal = {Nucleic Acids Res.},
volume = {36},
number = {Database-Issue},
pages = {773--779},
year = {2008},
url = {https://doi.org/10.1093/nar/gkm966},
doi = {10.1093/NAR/GKM966},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarolchikKBBCDGHHHKMPPRRRSSTTWZHK08.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ThomasRCHTRKBHHKRSTZHK07,
author = {Daryl J. Thomas and
Kate R. Rosenbloom and
Hiram Clawson and
Angie S. Hinrichs and
Heather Trumbower and
Brian J. Raney and
Donna Karolchik and
Galt P. Barber and
Rachel A. Harte and
Jennifer Hillman{-}Jackson and
Robert M. Kuhn and
Brooke L. Rhead and
Kayla E. Smith and
Archana Thakkapallayil and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {The {ENCODE} Project at {UC} Santa Cruz},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {663--667},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl1017},
doi = {10.1093/NAR/GKL1017},
timestamp = {Thu, 14 Oct 2021 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ThomasRCHTRKBHHKRSTZHK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KuhnKZTTTSSSSRRRPPHHHDCBBBHK07,
author = {Robert M. Kuhn and
Donna Karolchik and
Ann S. Zweig and
Heather Trumbower and
Daryl J. Thomas and
Archana Thakkapallayil and
Charles W. Sugnet and
Mario Stanke and
Kayla E. Smith and
Adam C. Siepel and
Kate R. Rosenbloom and
Brooke L. Rhead and
Brian J. Raney and
Andy Pohl and
Jakob Skou Pedersen and
Fan Hsu and
Angela S. Hinrichs and
Rachel A. Harte and
Mark Diekhans and
Hiram Clawson and
Gill Bejerano and
Galt P. Barber and
Robert Baertsch and
David Haussler and
W. James Kent},
title = {The {UCSC} genome browser database: update 2007},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {668--673},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl928},
doi = {10.1093/NAR/GKL928},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KuhnKZTTTSSSSRRRPPHHHDCBBBHK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/ThomasTKRKHK07,
author = {Daryl J. Thomas and
Heather Trumbower and
Andrew D. Kern and
Brooke L. Rhead and
Robert M. Kuhn and
David Haussler and
W. James Kent},
title = {Variation resources at {UC} Santa Cruz},
journal = {Nucleic Acids Res.},
volume = {35},
number = {Database-Issue},
pages = {716--720},
year = {2007},
url = {https://doi.org/10.1093/nar/gkl953},
doi = {10.1093/NAR/GKL953},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/ThomasTKRKHK07.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/bioinformatics/HsuKCKDH06,
author = {Fan Hsu and
W. James Kent and
Hiram Clawson and
Robert M. Kuhn and
Mark Diekhans and
David Haussler},
title = {The {UCSC} Known Genes},
journal = {Bioinform.},
volume = {22},
number = {9},
pages = {1036--1046},
year = {2006},
url = {https://doi.org/10.1093/bioinformatics/btl048},
doi = {10.1093/BIOINFORMATICS/BTL048},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/bioinformatics/HsuKCKDH06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HinrichsKBBBCDFHHHKPPRRSSSSTTWWZHK06,
author = {Angela S. Hinrichs and
Donna Karolchik and
Robert Baertsch and
Galt P. Barber and
Gill Bejerano and
Hiram Clawson and
Mark Diekhans and
Terrence S. Furey and
Rachel A. Harte and
Fan Hsu and
Jennifer Hillman{-}Jackson and
Robert M. Kuhn and
Jakob Skou Pedersen and
Andy Pohl and
Brian J. Raney and
Kate R. Rosenbloom and
Adam C. Siepel and
Kayla E. Smith and
Charles W. Sugnet and
A. Sultan{-}Qurraie and
Daryl J. Thomas and
Heather Trumbower and
Ryan J. Weber and
M. Weirauch and
Ann S. Zweig and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database: update 2006},
journal = {Nucleic Acids Res.},
volume = {34},
number = {Database-Issue},
pages = {590--598},
year = {2006},
url = {https://doi.org/10.1093/nar/gkj144},
doi = {10.1093/NAR/GKJ144},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HinrichsKBBBCDFHHHKPPRRSSSSTTWWZHK06.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/HsuPKKDHK05,
author = {Fan Hsu and
Tom H. Pringle and
Robert M. Kuhn and
Donna Karolchik and
Mark Diekhans and
David Haussler and
W. James Kent},
title = {The {UCSC} Proteome Browser},
journal = {Nucleic Acids Res.},
volume = {33},
number = {Database-Issue},
pages = {454--458},
year = {2005},
url = {https://doi.org/10.1093/nar/gki100},
doi = {10.1093/NAR/GKI100},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/HsuPKKDHK05.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarolchikHFRSHK04,
author = {Donna Karolchik and
Angela S. Hinrichs and
Terrence S. Furey and
Krishna M. Roskin and
Charles W. Sugnet and
David Haussler and
W. James Kent},
title = {The {UCSC} Table Browser data retrieval tool},
journal = {Nucleic Acids Res.},
volume = {32},
number = {Database-Issue},
pages = {493--496},
year = {2004},
url = {https://doi.org/10.1093/nar/gkh103},
doi = {10.1093/NAR/GKH103},
timestamp = {Sun, 17 May 2020 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarolchikHFRSHK04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@inproceedings{DBLP:conf/psb/SugnetKAH04,
author = {Charles W. Sugnet and
W. James Kent and
Manuel Ares and
David Haussler},
editor = {Russ B. Altman and
A. Keith Dunker and
Lawrence Hunter and
Tiffany A. Jung and
Teri E. Klein},
title = {Transcriptome and Genome Conservation of Alternative Splicing Events
in Humans and Mice},
booktitle = {Biocomputing 2004, Proceedings of the Pacific Symposium, Hawaii, USA,
6-10 January 2004},
pages = {66--77},
publisher = {World Scientific},
year = {2004},
url = {http://psb.stanford.edu/psb-online/proceedings/psb04/sugnet.pdf},
timestamp = {Thu, 12 Mar 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/conf/psb/SugnetKAH04.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KarolchikBDFHLRSSTWHK03,
author = {Donna Karolchik and
Robert Baertsch and
Mark Diekhans and
Terrence S. Furey and
Angela S. Hinrichs and
Yontao Lu and
Krishna M. Roskin and
Matt Schwartz and
Charles W. Sugnet and
Daryl J. Thomas and
Ryan J. Weber and
David Haussler and
W. James Kent},
title = {The {UCSC} Genome Browser Database},
journal = {Nucleic Acids Res.},
volume = {31},
number = {1},
pages = {51--54},
year = {2003},
url = {https://doi.org/10.1093/nar/gkg129},
doi = {10.1093/NAR/GKG129},
timestamp = {Mon, 26 Jun 2023 01:00:00 +0200},
biburl = {https://dblp.org/rec/journals/nar/KarolchikBDFHLRSSTWHK03.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
@article{DBLP:journals/nar/KentZ00,
author = {W. James Kent and
Alan M. Zahler},
title = {The Intronerator: exploring introns and alternative splicing in Caenorhabditis
elegans},
journal = {Nucleic Acids Res.},
volume = {28},
number = {1},
pages = {91--93},
year = {2000},
url = {https://doi.org/10.1093/nar/28.1.91},
doi = {10.1093/NAR/28.1.91},
timestamp = {Mon, 26 Oct 2020 00:00:00 +0100},
biburl = {https://dblp.org/rec/journals/nar/KentZ00.bib},
bibsource = {dblp computer science bibliography, https://dblp.org}
}
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