Literature DB >> 19204697

Understanding genome browsing.

Melissa S Cline1, W James Kent.   

Abstract

Mesh:

Year:  2009        PMID: 19204697     DOI: 10.1038/nbt0209-153

Source DB:  PubMed          Journal:  Nat Biotechnol        ISSN: 1087-0156            Impact factor:   54.908


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  16 in total

1.  dbSNP: the NCBI database of genetic variation.

Authors:  S T Sherry; M H Ward; M Kholodov; J Baker; L Phan; E M Smigielski; K Sirotkin
Journal:  Nucleic Acids Res       Date:  2001-01-01       Impact factor: 16.971

2.  The magical number seven plus or minus two: some limits on our capacity for processing information.

Authors:  G A MILLER
Journal:  Psychol Rev       Date:  1956-03       Impact factor: 8.934

3.  Widespread mRNA polyadenylation events in introns indicate dynamic interplay between polyadenylation and splicing.

Authors:  Bin Tian; Zhenhua Pan; Ju Youn Lee
Journal:  Genome Res       Date:  2007-01-08       Impact factor: 9.043

4.  Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.

Authors:  Adam Siepel; Gill Bejerano; Jakob S Pedersen; Angie S Hinrichs; Minmei Hou; Kate Rosenbloom; Hiram Clawson; John Spieth; Ladeana W Hillier; Stephen Richards; George M Weinstock; Richard K Wilson; Richard A Gibbs; W James Kent; Webb Miller; David Haussler
Journal:  Genome Res       Date:  2005-07-15       Impact factor: 9.043

5.  Computational detection and location of transcription start sites in mammalian genomic DNA.

Authors:  Thomas A Down; Tim J P Hubbard
Journal:  Genome Res       Date:  2002-03       Impact factor: 9.043

6.  The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

Authors:  Daniela S Gerhard; Lukas Wagner; Elise A Feingold; Carolyn M Shenmen; Lynette H Grouse; Greg Schuler; Steven L Klein; Susan Old; Rebekah Rasooly; Peter Good; Mark Guyer; Allison M Peck; Jeffery G Derge; David Lipman; Francis S Collins; Wonhee Jang; Steven Sherry; Mike Feolo; Leonie Misquitta; Eduardo Lee; Kirill Rotmistrovsky; Susan F Greenhut; Carl F Schaefer; Kenneth Buetow; Tom I Bonner; David Haussler; Jim Kent; Mark Kiekhaus; Terry Furey; Michael Brent; Christa Prange; Kirsten Schreiber; Nicole Shapiro; Narayan K Bhat; Ralph F Hopkins; Florence Hsie; Tom Driscoll; M Bento Soares; Tom L Casavant; Todd E Scheetz; Michael J Brown-stein; Ted B Usdin; Shiraki Toshiyuki; Piero Carninci; Yulan Piao; Dawood B Dudekula; Minoru S H Ko; Koichi Kawakami; Yutaka Suzuki; Sumio Sugano; C E Gruber; M R Smith; Blake Simmons; Troy Moore; Richard Waterman; Stephen L Johnson; Yijun Ruan; Chia Lin Wei; S Mathavan; Preethi H Gunaratne; Jiaqian Wu; Angela M Garcia; Stephen W Hulyk; Edwin Fuh; Ye Yuan; Anna Sneed; Carla Kowis; Anne Hodgson; Donna M Muzny; John McPherson; Richard A Gibbs; Jessica Fahey; Erin Helton; Mark Ketteman; Anuradha Madan; Stephanie Rodrigues; Amy Sanchez; Michelle Whiting; Anup Madari; Alice C Young; Keith D Wetherby; Steven J Granite; Peggy N Kwong; Charles P Brinkley; Russell L Pearson; Gerard G Bouffard; Robert W Blakesly; Eric D Green; Mark C Dickson; Alex C Rodriguez; Jane Grimwood; Jeremy Schmutz; Richard M Myers; Yaron S N Butterfield; Malachi Griffith; Obi L Griffith; Martin I Krzywinski; Nancy Liao; Ryan Morin; Ryan Morrin; Diana Palmquist; Anca S Petrescu; Ursula Skalska; Duane E Smailus; Jeff M Stott; Angelique Schnerch; Jacqueline E Schein; Steven J M Jones; Robert A Holt; Agnes Baross; Marco A Marra; Sandra Clifton; Kathryn A Makowski; Stephanie Bosak; Joel Malek
Journal:  Genome Res       Date:  2004-10       Impact factor: 9.043

7.  Whole-genome maps of USF1 and USF2 binding and histone H3 acetylation reveal new aspects of promoter structure and candidate genes for common human disorders.

Authors:  Alvaro Rada-Iglesias; Adam Ameur; Philipp Kapranov; Stefan Enroth; Jan Komorowski; Thomas R Gingeras; Claes Wadelius
Journal:  Genome Res       Date:  2008-01-29       Impact factor: 9.043

8.  Prediction of mammalian microRNA targets.

Authors:  Benjamin P Lewis; I-hung Shih; Matthew W Jones-Rhoades; David P Bartel; Christopher B Burge
Journal:  Cell       Date:  2003-12-26       Impact factor: 41.582

9.  NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.

Authors:  Kim D Pruitt; Tatiana Tatusova; Donna R Maglott
Journal:  Nucleic Acids Res       Date:  2006-11-27       Impact factor: 16.971

10.  A large-scale analysis of mRNA polyadenylation of human and mouse genes.

Authors:  Bin Tian; Jun Hu; Haibo Zhang; Carol S Lutz
Journal:  Nucleic Acids Res       Date:  2005-01-12       Impact factor: 16.971

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  11 in total

1.  JBrowse: a next-generation genome browser.

Authors:  Mitchell E Skinner; Andrew V Uzilov; Lincoln D Stein; Christopher J Mungall; Ian H Holmes
Journal:  Genome Res       Date:  2009-07-01       Impact factor: 9.043

Review 2.  Visualizing genomes: techniques and challenges.

Authors:  Cydney B Nielsen; Michael Cantor; Inna Dubchak; David Gordon; Ting Wang
Journal:  Nat Methods       Date:  2010-02-25       Impact factor: 28.547

3.  Tissue-restricted transcription from a conserved intragenic CpG island in the Klf1 gene in mice.

Authors:  Cherie M Southwood; Leonard Lipovich; Alexander Gow
Journal:  Biol Reprod       Date:  2012-11-01       Impact factor: 4.285

4.  The UCSC Genome Browser.

Authors:  Donna Karolchik; Angie S Hinrichs; W James Kent
Journal:  Curr Protoc Hum Genet       Date:  2011-10

5.  The UCSC Genome Browser.

Authors:  Donna Karolchik; Angie S Hinrichs; W James Kent
Journal:  Curr Protoc Bioinformatics       Date:  2009-12

6.  DiProGB: the dinucleotide properties genome browser.

Authors:  Maik Friedel; Swetlana Nikolajewa; Jürgen Sühnel; Thomas Wilhelm
Journal:  Bioinformatics       Date:  2009-07-15       Impact factor: 6.937

7.  Genome Maps, a new generation genome browser.

Authors:  Ignacio Medina; Francisco Salavert; Rubén Sanchez; Alejandro de Maria; Roberto Alonso; Pablo Escobar; Marta Bleda; Joaquín Dopazo
Journal:  Nucleic Acids Res       Date:  2013-06-08       Impact factor: 16.971

8.  Unraveling genomic variation from next generation sequencing data.

Authors:  Georgios A Pavlopoulos; Anastasis Oulas; Ernesto Iacucci; Alejandro Sifrim; Yves Moreau; Reinhard Schneider; Jan Aerts; Ioannis Iliopoulos
Journal:  BioData Min       Date:  2013-07-25       Impact factor: 2.522

9.  Genoviz Software Development Kit: Java tool kit for building genomics visualization applications.

Authors:  Gregg A Helt; John W Nicol; Ed Erwin; Eric Blossom; Steven G Blanchard; Stephen A Chervitz; Cyrus Harmon; Ann E Loraine
Journal:  BMC Bioinformatics       Date:  2009-08-25       Impact factor: 3.169

10.  CBS: an open platform that integrates predictive methods and epigenetics information to characterize conserved regulatory features in multiple Drosophila genomes.

Authors:  Enrique Blanco; Montserrat Corominas
Journal:  BMC Genomics       Date:  2012-12-10       Impact factor: 3.969

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