title: The UCSC Genome Browser database: 2015 update.
abstract: Launched in 2001 to showcase the draft human genome assembly, the UCSC Genome Browser database (http://genome.ucsc.edu) and associated tools continue to grow, providing a comprehensive resource of genome assemblies and annotations to scientists and students worldwide. Highlights of the past year include the release of a browser for the first new human genome reference assembly in 4 years in December 2013 (GRCh38, UCSC hg38), a watershed comparative genomics annotation (100-species multiple alignment and conservation) and a novel distribution mechanism for the browser (GBiB: Genome Browser in a Box). We created browsers for new species (Chinese hamster, elephant shark, minke whale), 'mined the web' for DNA sequences and expanded the browser display with stacked color graphs and region highlighting. As our user community increasingly adopts the UCSC track hub and assembly hub representations for sharing large-scale genomic annotation data sets and genome sequencing projects, our menu of public data hubs has tripled.
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA kate@soe.ucsc.edu.
authors.forename: Kate R
authors.initials: KR
authors.lastname: Rosenbloom
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Joel
authors.initials: J
authors.lastname: Armstrong
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Galt P
authors.initials: GP
authors.lastname: Barber
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Jonathan
authors.initials: J
authors.lastname: Casper
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Hiram
authors.initials: H
authors.lastname: Clawson
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Mark
authors.initials: M
authors.lastname: Diekhans
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Timothy R
authors.initials: TR
authors.lastname: Dreszer
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Pauline A
authors.initials: PA
authors.lastname: Fujita
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Luvina
authors.initials: L
authors.lastname: Guruvadoo
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Maximilian
authors.initials: M
authors.lastname: Haeussler
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Rachel A
authors.initials: RA
authors.lastname: Harte
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Steve
authors.initials: S
authors.lastname: Heitner
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Glenn
authors.initials: G
authors.lastname: Hickey
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Angie S
authors.initials: AS
authors.lastname: Hinrichs
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Robert
authors.initials: R
authors.lastname: Hubley
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Donna
authors.initials: D
authors.lastname: Karolchik
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Katrina
authors.initials: K
authors.lastname: Learned
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Brian T
authors.initials: BT
authors.lastname: Lee
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Chin H
authors.initials: CH
authors.lastname: Li
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Karen H
authors.initials: KH
authors.lastname: Miga
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Ngan
authors.initials: N
authors.lastname: Nguyen
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Benedict
authors.initials: B
authors.lastname: Paten
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Brian J
authors.initials: BJ
authors.lastname: Raney
authors.affiliation: Institute for Systems Biology, Seattle, WA 98109, USA.
authors.forename: Arian F A
authors.initials: AF
authors.lastname: Smit
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Matthew L
authors.initials: ML
authors.lastname: Speir
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Ann S
authors.initials: AS
authors.lastname: Zweig
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA Howard Hughes Medical Institute, UCSC, Santa Cruz, CA 95064, USA.
authors.forename: David
authors.initials: D
authors.lastname: Haussler
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Kuhn
authors.affiliation: Center for Biomolecular Science and Engineering, CBSE, UC Santa Cruz, 1156 High Street, Santa Cruz, CA 95064, USA.
authors.forename: W James
authors.initials: WJ
authors.lastname: Kent
mesh_terms: D000818:Animals; D006224:Cricetinae; D030561:Databases, Nucleic Acid; D004285:Dogs; D029043:Ebolavirus / Q000235:genetics; D015870:Gene Expression; D016678:Genome; D023281:Genomics; D020407:Internet; D051379:Mice; D058977:Molecular Sequence Annotation; D010641:Phenotype; D051381:Rats; D012984:Software