Literature DB >> 24984850

The UCSC Genome Browser: What Every Molecular Biologist Should Know.

Mary E Mangan1, Jennifer M Williams, Robert M Kuhn, Warren C Lathe.   

Abstract

Electronic data resources can enable molecular biologists to quickly get information from around the world that a decade ago would have been buried in papers scattered throughout the library. The ability to access, query, and display these data makes benchwork much more efficient and drives new discoveries. Increasingly, mastery of software resources and corresponding data repositories is required to fully explore the volume of data generated in biomedical and agricultural research, because only small amounts of data are actually found in traditional publications. The UCSC Genome Browser provides a wealth of data and tools that advance understanding of genomic context for many species, enable detailed analysis of data, and provide the ability to interrogate regions of interest across disparate data sets from a wide variety of sources. Researchers can also supplement the standard display with their own data to query and share this with others. Effective use of these resources has become crucial to biological research today, and this unit describes some practical applications of the UCSC Genome Browser.
Copyright © 2014 John Wiley & Sons, Inc.

Entities:  

Keywords:  ENCODE; SNP; UCSC Genome Browser; comparative genomics; custom tracks; primers; variations

Mesh:

Year:  2014        PMID: 24984850      PMCID: PMC4142428          DOI: 10.1002/0471142727.mb1909s107

Source DB:  PubMed          Journal:  Curr Protoc Mol Biol        ISSN: 1934-3647


  14 in total

1.  Annotating genes and genomes with DNA sequences extracted from biomedical articles.

Authors:  Maximilian Haeussler; Martin Gerner; Casey M Bergman
Journal:  Bioinformatics       Date:  2011-02-16       Impact factor: 6.937

2.  miRcode: a map of putative microRNA target sites in the long non-coding transcriptome.

Authors:  Ashwini Jeggari; Debora S Marks; Erik Larsson
Journal:  Bioinformatics       Date:  2012-06-19       Impact factor: 6.937

3.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration.

Authors:  Helga Thorvaldsdóttir; James T Robinson; Jill P Mesirov
Journal:  Brief Bioinform       Date:  2012-04-19       Impact factor: 11.622

4.  Modernizing reference genome assemblies.

Authors:  Deanna M Church; Valerie A Schneider; Tina Graves; Katherine Auger; Fiona Cunningham; Nathan Bouk; Hsiu-Chuan Chen; Richa Agarwala; William M McLaren; Graham R S Ritchie; Derek Albracht; Milinn Kremitzki; Susan Rock; Holland Kotkiewicz; Colin Kremitzki; Aye Wollam; Lee Trani; Lucinda Fulton; Robert Fulton; Lucy Matthews; Siobhan Whitehead; Will Chow; James Torrance; Matthew Dunn; Glenn Harden; Glen Threadgold; Jonathan Wood; Joanna Collins; Paul Heath; Guy Griffiths; Sarah Pelan; Darren Grafham; Evan E Eichler; George Weinstock; Elaine R Mardis; Richard K Wilson; Kerstin Howe; Paul Flicek; Tim Hubbard
Journal:  PLoS Biol       Date:  2011-07-05       Impact factor: 8.029

5.  Ensembl 2013.

Authors:  Paul Flicek; Ikhlak Ahmed; M Ridwan Amode; Daniel Barrell; Kathryn Beal; Simon Brent; Denise Carvalho-Silva; Peter Clapham; Guy Coates; Susan Fairley; Stephen Fitzgerald; Laurent Gil; Carlos García-Girón; Leo Gordon; Thibaut Hourlier; Sarah Hunt; Thomas Juettemann; Andreas K Kähäri; Stephen Keenan; Monika Komorowska; Eugene Kulesha; Ian Longden; Thomas Maurel; William M McLaren; Matthieu Muffato; Rishi Nag; Bert Overduin; Miguel Pignatelli; Bethan Pritchard; Emily Pritchard; Harpreet Singh Riat; Graham R S Ritchie; Magali Ruffier; Michael Schuster; Daniel Sheppard; Daniel Sobral; Kieron Taylor; Anja Thormann; Stephen Trevanion; Simon White; Steven P Wilder; Bronwen L Aken; Ewan Birney; Fiona Cunningham; Ian Dunham; Jennifer Harrow; Javier Herrero; Tim J P Hubbard; Nathan Johnson; Rhoda Kinsella; Anne Parker; Giulietta Spudich; Andy Yates; Amonida Zadissa; Stephen M J Searle
Journal:  Nucleic Acids Res       Date:  2012-11-30       Impact factor: 16.971

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

Authors:  Kate R Rosenbloom; Cricket A Sloan; Venkat S Malladi; Timothy R Dreszer; Katrina Learned; Vanessa M 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
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

7.  Database resources of the National Center for Biotechnology Information.

Authors: 
Journal:  Nucleic Acids Res       Date:  2012-11-27       Impact factor: 16.971

8.  Using GBrowse 2.0 to visualize and share next-generation sequence data.

Authors:  Lincoln D Stein
Journal:  Brief Bioinform       Date:  2013-02-01       Impact factor: 11.622

9.  The UCSC genome browser and associated tools.

Authors:  Robert M Kuhn; David Haussler; W James Kent
Journal:  Brief Bioinform       Date:  2012-08-20       Impact factor: 11.622

10.  The UCSC Genome Browser database: extensions and updates 2013.

Authors:  Laurence R Meyer; Ann S Zweig; Angie S Hinrichs; Donna Karolchik; Robert M Kuhn; Matthew Wong; Cricket A Sloan; Kate R Rosenbloom; Greg Roe; Brooke Rhead; Brian J Raney; Andy Pohl; Venkat S Malladi; Chin H Li; Brian T Lee; Katrina Learned; Vanessa Kirkup; Fan Hsu; Steve Heitner; Rachel A Harte; Maximilian Haeussler; Luvina Guruvadoo; Mary Goldman; Belinda M Giardine; Pauline A Fujita; Timothy R Dreszer; Mark Diekhans; Melissa S Cline; Hiram Clawson; Galt P Barber; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2012-11-15       Impact factor: 16.971

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  7 in total

1.  CMPD: cancer mutant proteome database.

Authors:  Po-Jung Huang; Chi-Ching Lee; Bertrand Chin-Ming Tan; Yuan-Ming Yeh; Lichieh Julie Chu; Ting-Wen Chen; Kai-Ping Chang; Cheng-Yang Lee; Ruei-Chi Gan; Hsuan Liu; Petrus Tang
Journal:  Nucleic Acids Res       Date:  2014-11-14       Impact factor: 19.160

2.  The acquisition of novel N-glycosylation sites in conserved proteins during human evolution.

Authors:  Dong Seon Kim; Yoonsoo Hahn
Journal:  BMC Bioinformatics       Date:  2015-01-28       Impact factor: 3.169

3.  CardioTF, a database of deconstructing transcriptional circuits in the heart system.

Authors:  Yisong Zhen
Journal:  PeerJ       Date:  2016-08-23       Impact factor: 2.984

4.  Sex-Dependent Changes in miRNA Expression in the Bed Nucleus of the Stria Terminalis Following Stress.

Authors:  Maria Mavrikaki; Lorena Pantano; David Potter; Maximilian A Rogers-Grazado; Eleni Anastasiadou; Frank J Slack; Sami S Amr; Kerry J Ressler; Nikolaos P Daskalakis; Elena Chartoff
Journal:  Front Mol Neurosci       Date:  2019-10-04       Impact factor: 5.639

Review 5.  The Role of Single-Nucleotide Polymorphisms in the Function of Candidate Tumor Suppressor ALDH1L1.

Authors:  Sergey A Krupenko; David A Horita
Journal:  Front Genet       Date:  2019-10-30       Impact factor: 4.599

Review 6.  MicroRNAs and the Diagnosis of Childhood Acute Lymphoblastic Leukemia: Systematic Review, Meta-Analysis and Re-Analysis with Novel Small RNA-Seq Tools.

Authors:  Ioannis Kyriakidis; Konstantinos Kyriakidis; Aspasia Tsezou
Journal:  Cancers (Basel)       Date:  2022-08-17       Impact factor: 6.575

7.  Developing the eHistology Atlas.

Authors:  Lorna Richardson; Liz Graham; Julie Moss; Nick Burton; Yogmatee Roochun; Chris Armit; Richard A Baldock
Journal:  Database (Oxford)       Date:  2015-10-24       Impact factor: 3.451

  7 in total

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