Literature DB >> 16169926

Galaxy: a platform for interactive large-scale genome analysis.

Belinda Giardine1, Cathy Riemer, Ross C Hardison, Richard Burhans, Laura Elnitski, Prachi Shah, Yi Zhang, Daniel Blankenberg, Istvan Albert, James Taylor, Webb Miller, W James Kent, Anton Nekrutenko.   

Abstract

Accessing and analyzing the exponentially expanding genomic sequence and functional data pose a challenge for biomedical researchers. Here we describe an interactive system, Galaxy, that combines the power of existing genome annotation databases with a simple Web portal to enable users to search remote resources, combine data from independent queries, and visualize the results. The heart of Galaxy is a flexible history system that stores the queries from each user; performs operations such as intersections, unions, and subtractions; and links to other computational tools. Galaxy can be accessed at http://g2.bx.psu.edu.

Mesh：

Year:  2005        PMID： 16169926      PMCID： PMC1240089          DOI： 10.1101/gr.4086505

Source DB:  PubMed          Journal:  Genome Res        ISSN： 1088-9051            Impact factor:   9.043


  21 in total

1.  Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.

Authors:  Z Yang; R Nielsen
Journal:  Mol Biol Evol       Date:  2000-01       Impact factor: 16.240

2.  The human genome browser at UCSC.

Authors:  W James Kent; Charles W Sugnet; Terrence S Furey; Krishna M Roskin; Tom H Pringle; Alan M Zahler; David Haussler
Journal:  Genome Res       Date:  2002-06       Impact factor: 9.043

3.  Identification and characterization of multi-species conserved sequences.

Authors:  Elliott H Margulies; Mathieu Blanchette; David Haussler; Eric D Green
Journal:  Genome Res       Date:  2003-12       Impact factor: 9.043

4.  The UCSC Table Browser data retrieval tool.

Authors:  Donna Karolchik; Angela S Hinrichs; Terrence S Furey; Krishna M Roskin; Charles W Sugnet; David Haussler; W James Kent
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

5.  Ensembl 2004.

Authors:  E Birney; D Andrews; P Bevan; M Caccamo; G Cameron; Y Chen; L Clarke; G Coates; T Cox; J Cuff; V Curwen; T Cutts; T Down; R Durbin; E Eyras; X M Fernandez-Suarez; P Gane; B Gibbins; J Gilbert; M Hammond; H Hotz; V Iyer; A Kahari; K Jekosch; A Kasprzyk; D Keefe; S Keenan; H Lehvaslaiho; G McVicker; C Melsopp; P Meidl; E Mongin; R Pettett; S Potter; G Proctor; M Rae; S Searle; G Slater; D Smedley; J Smith; W Spooner; A Stabenau; J Stalker; R Storey; A Ureta-Vidal; C Woodwark; M Clamp; T Hubbard
Journal:  Nucleic Acids Res       Date:  2004-01-01       Impact factor: 16.971

6.  The EBI SRS server-new features.

Authors:  Evgeny M Zdobnov; Rodrigo Lopez; Rolf Apweiler; Thure Etzold
Journal:  Bioinformatics       Date:  2002-08       Impact factor: 6.937

7.  A high-resolution map of active promoters in the human genome.

Authors:  Tae Hoon Kim; Leah O Barrera; Ming Zheng; Chunxu Qu; Michael A Singer; Todd A Richmond; Yingnian Wu; Roland D Green; Bing Ren
Journal:  Nature       Date:  2005-06-29       Impact factor: 49.962

8.  Comparative analysis of the gene-dense ACHE/TFR2 region on human chromosome 7q22 with the orthologous region on mouse chromosome 5.

Authors:  M D Wilson; C Riemer; D W Martindale; P Schnupf; A P Boright; T L Cheung; D M Hardy; S Schwartz; S W Scherer; L C Tsui; W Miller; B F Koop
Journal:  Nucleic Acids Res       Date:  2001-03-15       Impact factor: 16.971

9.  Identification and functional analysis of human transcriptional promoters.

Authors:  Nathan D Trinklein; Shelley J Force Aldred; Alok J Saldanha; Richard M Myers
Journal:  Genome Res       Date:  2003-02       Impact factor: 9.043

10.  Adaptive evolution drives divergence of a hybrid inviability gene between two species of Drosophila.

Authors:  Daven C Presgraves; Lakshmi Balagopalan; Susan M Abmayr; H Allen Orr
Journal:  Nature       Date:  2003-06-12       Impact factor: 49.962
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  993 in total

1.  A comprehensive pipeline for translational top-down proteomics from a single blood draw.

Authors:  Timothy K Toby; Luca Fornelli; Kristina Srzentić; Caroline J DeHart; Josh Levitsky; John Friedewald; Neil L Kelleher
Journal:  Nat Protoc       Date:  2019-01       Impact factor: 13.491

Review 2.  Software for systems biology: from tools to integrated platforms.

Authors:  Samik Ghosh; Yukiko Matsuoka; Yoshiyuki Asai; Kun-Yi Hsin; Hiroaki Kitano
Journal:  Nat Rev Genet       Date:  2011-11-03       Impact factor: 53.242

3.  Transcription factor binding predictions using TRAP for the analysis of ChIP-seq data and regulatory SNPs.

Authors:  Morgane Thomas-Chollier; Andrew Hufton; Matthias Heinig; Sean O'Keeffe; Nassim El Masri; Helge G Roider; Thomas Manke; Martin Vingron
Journal:  Nat Protoc       Date:  2011-11-03       Impact factor: 13.491

4.  msCompare: a framework for quantitative analysis of label-free LC-MS data for comparative candidate biomarker studies.

Authors:  Berend Hoekman; Rainer Breitling; Frank Suits; Rainer Bischoff; Peter Horvatovich
Journal:  Mol Cell Proteomics       Date:  2012-02-07       Impact factor: 5.911

5.  The amino acid composition of proteins from anaerobic halophilic bacteria of the order Halanaerobiales.

Authors:  Rahel Elevi Bardavid; Aharon Oren
Journal:  Extremophiles       Date:  2012-04-19       Impact factor: 2.395

6.  Fulcrum: condensing redundant reads from high-throughput sequencing studies.

Authors:  Matthew S Burriesci; Erik M Lehnert; John R Pringle
Journal:  Bioinformatics       Date:  2012-03-13       Impact factor: 6.937

7.  Changes in exon-intron structure during vertebrate evolution affect the splicing pattern of exons.

Authors:  Sahar Gelfman; David Burstein; Osnat Penn; Anna Savchenko; Maayan Amit; Schraga Schwartz; Tal Pupko; Gil Ast
Journal:  Genome Res       Date:  2011-10-05       Impact factor: 9.043

8.  Metabolomics of tomato xylem sap during bacterial wilt reveals Ralstonia solanacearum produces abundant putrescine, a metabolite that accelerates wilt disease.

Authors:  Tiffany M Lowe-Power; Connor G Hendrich; Edda von Roepenack-Lahaye; Bin Li; Dousheng Wu; Raka Mitra; Beth L Dalsing; Patrizia Ricca; Jacinth Naidoo; David Cook; Amy Jancewicz; Patrick Masson; Bart Thomma; Thomas Lahaye; Anthony J Michael; Caitilyn Allen
Journal:  Environ Microbiol       Date:  2017-12-22       Impact factor: 5.491

9.  Reduced infectivity of adenovirus type 5 particles and degradation of entering viral genomes associated with incomplete processing of the preterminal protein.

Authors:  Sayuri E Kato; Jasdave S Chahal; S J Flint
Journal:  J Virol       Date:  2012-10-03       Impact factor: 5.103

Review 10.  Identification and Quantification of Proteoforms by Mass Spectrometry.

Authors:  Leah V Schaffer; Robert J Millikin; Rachel M Miller; Lissa C Anderson; Ryan T Fellers; Ying Ge; Neil L Kelleher; Richard D LeDuc; Xiaowen Liu; Samuel H Payne; Liangliang Sun; Paul M Thomas; Trisha Tucholski; Zhe Wang; Si Wu; Zhijie Wu; Dahang Yu; Michael R Shortreed; Lloyd M Smith
Journal:  Proteomics       Date:  2019-05       Impact factor: 3.984
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