Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 The UCSC genome browser: what every molecular biologist should know.

Literature DB >> 19816931

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 query and display many useful features that make benchwork more efficient and drive new discoveries. The UCSC Genome Browser provides a wealth of data and tools that advance one's understanding of genomic context for many species, enable detailed understanding of data, and provide the ability to interrogate regions of interest. Researchers can also supplement the standard display with their own data to query and share 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.

Entities: Chemical Disease Gene Species

Mesh：

Year: 2009 PMID： 19816931 PMCID： PMC4996636 DOI： 10.1002/0471142727.mb1909s88

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

4 in total

1. A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.

Authors: Maria Chiara Di Bernardo; Dalemari Crowther-Swanepoel; Peter Broderick; Emily Webb; Gabrielle Sellick; Ruth Wild; Kate Sullivan; Jayaram Vijayakrishnan; Yufei Wang; Alan M Pittman; Nicola J Sunter; Andrew G Hall; Martin J S Dyer; Estella Matutes; Claire Dearden; Tryfonia Mainou-Fowler; Graham H Jackson; Geoffrey Summerfield; Robert J Harris; Andrew R Pettitt; Peter Hillmen; David J Allsup; James R Bailey; Guy Pratt; Chris Pepper; Chris Fegan; James M Allan; Daniel Catovsky; Richard S Houlston
Journal: Nat Genet Date: 2008-08-31 Impact factor: 38.330

2. The mammalian gene collection.

Authors: R L Strausberg; E A Feingold; R D Klausner; F S Collins
Journal: Science Date: 1999-10-15 Impact factor: 47.728

3. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

Authors: Ewan Birney; John A Stamatoyannopoulos; Anindya Dutta; Roderic Guigó; Thomas R Gingeras; Elliott H Margulies; Zhiping Weng; Michael Snyder; Emmanouil T Dermitzakis; Robert E Thurman; Michael S Kuehn; Christopher M Taylor; Shane Neph; Christoph M Koch; Saurabh Asthana; Ankit Malhotra; Ivan Adzhubei; Jason A Greenbaum; Robert M Andrews; Paul Flicek; Patrick J Boyle; Hua Cao; Nigel P Carter; Gayle K Clelland; Sean Davis; Nathan Day; Pawandeep Dhami; Shane C Dillon; Michael O Dorschner; Heike Fiegler; Paul G Giresi; Jeff Goldy; Michael Hawrylycz; Andrew Haydock; Richard Humbert; Keith D James; Brett E Johnson; Ericka M Johnson; Tristan T Frum; Elizabeth R Rosenzweig; Neerja Karnani; Kirsten Lee; Gregory C Lefebvre; Patrick A Navas; Fidencio Neri; Stephen C J Parker; Peter J Sabo; Richard Sandstrom; Anthony Shafer; David Vetrie; Molly Weaver; Sarah Wilcox; Man Yu; Francis S Collins; Job Dekker; Jason D Lieb; Thomas D Tullius; Gregory E Crawford; Shamil Sunyaev; William S Noble; Ian Dunham; France Denoeud; Alexandre Reymond; Philipp Kapranov; Joel Rozowsky; Deyou Zheng; Robert Castelo; Adam Frankish; Jennifer Harrow; Srinka Ghosh; Albin Sandelin; Ivo L Hofacker; Robert Baertsch; Damian Keefe; Sujit Dike; Jill Cheng; Heather A Hirsch; Edward A Sekinger; Julien Lagarde; Josep F Abril; Atif Shahab; Christoph Flamm; Claudia Fried; Jörg Hackermüller; Jana Hertel; Manja Lindemeyer; Kristin Missal; Andrea Tanzer; Stefan Washietl; Jan Korbel; Olof Emanuelsson; Jakob S Pedersen; Nancy Holroyd; Ruth Taylor; David Swarbreck; Nicholas Matthews; Mark C Dickson; Daryl J Thomas; Matthew T Weirauch; James Gilbert; Jorg Drenkow; Ian Bell; XiaoDong Zhao; K G Srinivasan; Wing-Kin Sung; Hong Sain Ooi; Kuo Ping Chiu; Sylvain Foissac; Tyler Alioto; Michael Brent; Lior Pachter; Michael L Tress; Alfonso Valencia; Siew Woh Choo; Chiou Yu Choo; Catherine Ucla; Caroline Manzano; Carine Wyss; Evelyn Cheung; Taane G Clark; James B Brown; Madhavan Ganesh; Sandeep Patel; Hari Tammana; Jacqueline Chrast; Charlotte N Henrichsen; Chikatoshi Kai; Jun Kawai; Ugrappa Nagalakshmi; Jiaqian Wu; Zheng Lian; Jin Lian; Peter Newburger; Xueqing Zhang; Peter Bickel; John S Mattick; Piero Carninci; Yoshihide Hayashizaki; Sherman Weissman; Tim Hubbard; Richard M Myers; Jane Rogers; Peter F Stadler; Todd M Lowe; Chia-Lin Wei; Yijun Ruan; Kevin Struhl; Mark Gerstein; Stylianos E Antonarakis; Yutao Fu; Eric D Green; Ulaş Karaöz; Adam Siepel; James Taylor; Laura A Liefer; Kris A Wetterstrand; Peter J Good; Elise A Feingold; Mark S Guyer; Gregory M Cooper; George Asimenos; Colin N Dewey; Minmei Hou; Sergey Nikolaev; Juan I Montoya-Burgos; Ari Löytynoja; Simon Whelan; Fabio Pardi; Tim Massingham; Haiyan Huang; Nancy R Zhang; Ian Holmes; James C Mullikin; Abel Ureta-Vidal; Benedict Paten; Michael Seringhaus; Deanna Church; Kate Rosenbloom; W James Kent; Eric A Stone; Serafim Batzoglou; Nick Goldman; Ross C Hardison; David Haussler; Webb Miller; Arend Sidow; Nathan D Trinklein; Zhengdong D Zhang; Leah Barrera; Rhona Stuart; David C King; Adam Ameur; Stefan Enroth; Mark C Bieda; Jonghwan Kim; Akshay A Bhinge; Nan Jiang; Jun Liu; Fei Yao; Vinsensius B Vega; Charlie W H Lee; Patrick Ng; Atif Shahab; Annie Yang; Zarmik Moqtaderi; Zhou Zhu; Xiaoqin Xu; Sharon Squazzo; Matthew J Oberley; David Inman; Michael A Singer; Todd A Richmond; Kyle J Munn; Alvaro Rada-Iglesias; Ola Wallerman; Jan Komorowski; Joanna C Fowler; Phillippe Couttet; Alexander W Bruce; Oliver M Dovey; Peter D Ellis; Cordelia F Langford; David A Nix; Ghia Euskirchen; Stephen Hartman; Alexander E Urban; Peter Kraus; Sara Van Calcar; Nate Heintzman; Tae Hoon Kim; Kun Wang; Chunxu Qu; Gary Hon; Rosa Luna; Christopher K Glass; M Geoff Rosenfeld; Shelley Force Aldred; Sara J Cooper; Anason Halees; Jane M Lin; Hennady P Shulha; Xiaoling Zhang; Mousheng Xu; Jaafar N S Haidar; Yong Yu; Yijun Ruan; Vishwanath R Iyer; Roland D Green; Claes Wadelius; Peggy J Farnham; Bing Ren; Rachel A Harte; Angie S Hinrichs; Heather Trumbower; Hiram Clawson; Jennifer Hillman-Jackson; Ann S Zweig; Kayla Smith; Archana Thakkapallayil; Galt Barber; Robert M Kuhn; Donna Karolchik; Lluis Armengol; Christine P Bird; Paul I W de Bakker; Andrew D Kern; Nuria Lopez-Bigas; Joel D Martin; Barbara E Stranger; Abigail Woodroffe; Eugene Davydov; Antigone Dimas; Eduardo Eyras; Ingileif B Hallgrímsdóttir; Julian Huppert; Michael C Zody; Gonçalo R Abecasis; Xavier Estivill; Gerard G Bouffard; Xiaobin Guan; Nancy F Hansen; Jacquelyn R Idol; Valerie V B Maduro; Baishali Maskeri; Jennifer C McDowell; Morgan Park; Pamela J Thomas; Alice C Young; Robert W Blakesley; Donna M Muzny; Erica Sodergren; David A Wheeler; Kim C Worley; Huaiyang Jiang; George M Weinstock; Richard A Gibbs; Tina Graves; Robert Fulton; Elaine R Mardis; Richard K Wilson; Michele Clamp; James Cuff; Sante Gnerre; David B Jaffe; Jean L Chang; Kerstin Lindblad-Toh; Eric S Lander; Maxim Koriabine; Mikhail Nefedov; Kazutoyo Osoegawa; Yuko Yoshinaga; Baoli Zhu; Pieter J de Jong
Journal: Nature Date: 2007-06-14 Impact factor: 49.962

4. The UCSC Genome Browser Database: update 2009.

Authors: R M Kuhn; D Karolchik; A S Zweig; T Wang; K E Smith; K R Rosenbloom; B Rhead; B J Raney; A Pohl; M Pheasant; L Meyer; F Hsu; A S Hinrichs; R A Harte; B Giardine; P Fujita; M Diekhans; T Dreszer; H Clawson; G P Barber; D Haussler; W J Kent
Journal: Nucleic Acids Res Date: 2008-11-07 Impact factor: 16.971

4 in total

8 in total

Review 1. Annotating individual human genomes.

Authors: Ali Torkamani; Ashley A Scott-Van Zeeland; Eric J Topol; Nicholas J Schork
Journal: Genomics Date: 2011-08-02 Impact factor: 5.736

8. Human GPR42 is a transcribed multisite variant that exhibits copy number polymorphism and is functional when heterologously expressed.

Authors: Henry L Puhl; Yu-Jin Won; Van B Lu; Stephen R Ikeda
Journal: Sci Rep Date: 2015-08-11 Impact factor: 4.379

8 in total

The UCSC genome browser: what every molecular biologist should know.

1. A genome-wide association study identifies six susceptibility loci for chronic lymphocytic leukemia.

2. The mammalian gene collection.

3. Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project.

4. The UCSC Genome Browser Database: update 2009.

Review 1. Annotating individual human genomes.

2. A revised nomenclature for transcribed human endogenous retroviral loci.

3. Epigenome analysis of pluripotent stem cells.

Review 4. Genomic medicine and neurological disease.

5. GenoSets: visual analytic methods for comparative genomics.

6. Alternative polyadenylation allows differential negative feedback of human miRNA miR-579 on its host gene ZFR.

7. Clinical implications of human population differences in genome-wide rates of functional genotypes.

8. Human GPR42 is a transcribed multisite variant that exhibits copy number polymorphism and is functional when heterologously expressed.