Literature DB >> 18514479

UCSC genome browser tutorial.

Ann S Zweig1, Donna Karolchik, Robert M Kuhn, David Haussler, W James Kent.   

Abstract

The University of California Santa Cruz (UCSC) Genome Bioinformatics website consists of a suite of free, open-source, on-line tools that can be used to browse, analyze, and query genomic data. These tools are available to anyone who has an Internet browser and an interest in genomics. The website provides a quick and easy-to-use visual display of genomic data. It places annotation tracks beneath genome coordinate positions, allowing rapid visual correlation of different types of information. Many of the annotation tracks are submitted by scientists worldwide; the others are computed by the UCSC Genome Bioinformatics group from publicly available sequence data. It also allows users to upload and display their own experimental results or annotation sets by creating a custom track. The suite of tools, downloadable data files, and links to documentation and other information can be found at http://genome.ucsc.edu/.

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Mesh:

Year:  2008        PMID: 18514479     DOI: 10.1016/j.ygeno.2008.02.003

Source DB:  PubMed          Journal:  Genomics        ISSN: 0888-7543            Impact factor:   5.736


  46 in total

1.  The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.

Authors:  Kim D Pruitt; Jennifer Harrow; Rachel A Harte; Craig Wallin; Mark Diekhans; Donna R Maglott; Steve Searle; Catherine M Farrell; Jane E Loveland; Barbara J Ruef; Elizabeth Hart; Marie-Marthe Suner; Melissa J Landrum; Bronwen Aken; Sarah Ayling; Robert Baertsch; Julio Fernandez-Banet; Joshua L Cherry; Val Curwen; Michael Dicuccio; Manolis Kellis; Jennifer Lee; Michael F Lin; Michael Schuster; Andrew Shkeda; Clara Amid; Garth Brown; Oksana Dukhanina; Adam Frankish; Jennifer Hart; Bonnie L Maidak; Jonathan Mudge; Michael R Murphy; Terence Murphy; Jeena Rajan; Bhanu Rajput; Lillian D Riddick; Catherine Snow; Charles Steward; David Webb; Janet A Weber; Laurens Wilming; Wenyu Wu; Ewan Birney; David Haussler; Tim Hubbard; James Ostell; Richard Durbin; David Lipman
Journal:  Genome Res       Date:  2009-06-04       Impact factor: 9.043

2.  SCN8A encephalopathy: Research progress and prospects.

Authors:  Miriam H Meisler; Guy Helman; Michael F Hammer; Brandy E Fureman; William D Gaillard; Alan L Goldin; Shinichi Hirose; Atsushi Ishii; Barbara L Kroner; Christoph Lossin; Heather C Mefford; Jack M Parent; Manoj Patel; John Schreiber; Randall Stewart; Vicky Whittemore; Karen Wilcox; Jacy L Wagnon; Phillip L Pearl; Adeline Vanderver; Ingrid E Scheffer
Journal:  Epilepsia       Date:  2016-06-08       Impact factor: 5.864

3.  MicroRNA let-7 establishes expression of beta2-adrenergic receptors and dynamically down-regulates agonist-promoted down-regulation.

Authors:  Wayne C H Wang; Aster H Juan; Alfredo Panebra; Stephen B Liggett
Journal:  Proc Natl Acad Sci U S A       Date:  2011-03-29       Impact factor: 11.205

4.  An integrative proteogenomics approach reveals peptides encoded by annotated lincRNA in the mouse kidney inner medulla.

Authors:  Cameron T Flower; Lihe Chen; Hyun Jun Jung; Viswanathan Raghuram; Mark A Knepper; Chin-Rang Yang
Journal:  Physiol Genomics       Date:  2020-08-31       Impact factor: 3.107

5.  A scalable SCENIC workflow for single-cell gene regulatory network analysis.

Authors:  Bram Van de Sande; Christopher Flerin; Kristofer Davie; Maxime De Waegeneer; Gert Hulselmans; Sara Aibar; Ruth Seurinck; Wouter Saelens; Robrecht Cannoodt; Quentin Rouchon; Toni Verbeiren; Dries De Maeyer; Joke Reumers; Yvan Saeys; Stein Aerts
Journal:  Nat Protoc       Date:  2020-06-19       Impact factor: 13.491

6.  Recoding RNA editing of AZIN1 predisposes to hepatocellular carcinoma.

Authors:  Leilei Chen; Yan Li; Chi Ho Lin; Tim Hon Man Chan; Raymond Kwok Kei Chow; Yangyang Song; Ming Liu; Yun-Fei Yuan; Li Fu; Kar Lok Kong; Lihua Qi; Yan Li; Na Zhang; Amy Hin Yan Tong; Dora Lai-Wan Kwong; Kwan Man; Chung Mau Lo; Si Lok; Daniel G Tenen; Xin-Yuan Guan
Journal:  Nat Med       Date:  2013-01-06       Impact factor: 53.440

7.  Teaching bioinformatics and neuroinformatics by using free web-based tools.

Authors:  William Grisham; Natalie A Schottler; Joanne Valli-Marill; Lisa Beck; Jackson Beatty
Journal:  CBE Life Sci Educ       Date:  2010       Impact factor: 3.325

Review 8.  Analysis of complex disease association and linkage studies using the University of California Santa Cruz Genome Browser.

Authors:  Tianyuan Wang; Terrence S Furey
Journal:  Circ Cardiovasc Genet       Date:  2009-04

9.  TTS mapping: integrative WEB tool for analysis of triplex formation target DNA sequences, G-quadruplets and non-protein coding regulatory DNA elements in the human genome.

Authors:  Piroon Jenjaroenpun; Vladimir A Kuznetsov
Journal:  BMC Genomics       Date:  2009-12-03       Impact factor: 3.969

10.  Organization of developmental enhancers in the Drosophila embryo.

Authors:  Dmitri Papatsenko; Yury Goltsev; Michael Levine
Journal:  Nucleic Acids Res       Date:  2009-08-03       Impact factor: 16.971

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