Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences
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* Corresponding authors: Anton Nekrutenko anton@bx.psu.edu - James Taylor james.taylor@emory.edu
Genome Biology 2010, 11:R86 doi:10.1186/gb-2010-11-8-r86
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BioMed Central: 30 citations
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Review
Current challenges in de novo plant genome sequencing and assembly Michael C Schatz, Jan Witkowski, W Richard McCombie Genome Biology 2012, 13:243 (27 April 2012) Michael Schatz and colleagues assess challenges in de novo plant genome assembly and review the best practices for the plant community
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Methodology
Kun-hsiang Liu, Matthew McCormack, Jen Sheen Plant Methods 2012, 8:12 (30 March 2012) Next generation sequencing (NGS) is becoming a powerful tool for identifying mutations at the molecular level. This paper describes an innovation that has the potential to make the NGS approach accessible to many more laboratories. In the targeted parallel sequencing (TPSeq) method only genetically defined genomic regions are sequenced, making the process less expensive and the downstream bioinformatics more straightforward.
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Research article
Ashley M Driver, Francisco Penagaricano, Wen Huang, Khawaja R Ahmad, Katie S Hackbart, Milo C Witlbank, Hasan Khatib BMC Genomics 2012, 13:118 (28 March 2012) |
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Research
Primates and mouse NumtS in the UCSC Genome Browser Francesco Maria Calabrese, Domenico Simone, Marcella Attimonelli BMC Bioinformatics 2012, 13(Suppl 4):S15 (28 March 2012) |
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Research article
CodingMotif: exact determination of overrepresented nucleotide motifs in coding sequences Yang Ding, William A Lorenz, Jeffrey H Chuang BMC Bioinformatics 2012, 13:32 (14 February 2012) |
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Proceedings
Hatice Osmanbeyoglu, Ryan J Hartmaier, Steffi Oesterreich, Xinghua Lu BMC Genomics 2012, 13(Suppl 1):S1 (17 January 2012) |
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Methodology article
Identifying elemental genomic track types and representing them uniformly Sveinung Gundersen, Matúš Kalaš, Osman Abul, Arnoldo Frigessi, Eivind Hovig, Geir Sandve BMC Bioinformatics 2011, 12:494 (30 December 2011) |
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Data Note
Francesco M Mancuso, Magda Montfort, Anna Carreras, Andreu Alibés, Guglielmo Roma BMC Research Notes 2011, 4:546 (19 December 2011) |
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Software
openBIS: a flexible framework for managing and analyzing complex data in biology research Angela Bauch, Izabela Adamczyk, Piotr Buczek, Franz-Josef Elmer, Kaloyan Enimanev, Pawel Glyzewski, Manuel Kohler, Tomasz Pylak, Andreas Quandt, Chandrasekhar Ramakrishnan, Christian Beisel, Lars Malmström, Ruedi Aebersold, Bernd Rinn BMC Bioinformatics 2011, 12:468 (8 December 2011) |
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Research article
A co-ordinated interaction between CTCF and ER in breast cancer cells Caryn S Ross-Innes, Gordon D Brown, Jason S Carroll BMC Genomics 2011, 12:593 (5 December 2011) |
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Poster presentation
Spectral classification of short numerical exon and intron sequences Benjamin YM Kwan, Jennifer YY Kwan, Hon Kwan BMC Bioinformatics 2011, 12(Suppl 11):A13 (21 November 2011) |
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Oral presentation
Oqtans: a Galaxy-integrated workflow for quantitative transcriptome analysis from NGS Data Sebastian J Schultheiss, Géraldine Jean, Jonas Behr, Regina Bohnert, Philipp Drewe, Nico Görnitz, André Kahles, Pramod Mudrakarta, Vipin T Sreedharan, Georg Zeller, Gunnar Rätsch BMC Bioinformatics 2011, 12(Suppl 11):A7 (21 November 2011) |
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Software
Exploratory analysis of genomic segmentations with Segtools Orion J Buske, Michael M Hoffman, Nadia Ponts, Karine G Le Roch, William Noble BMC Bioinformatics 2011, 12:415 (26 October 2011) |
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Software
Chipster: user-friendly analysis software for microarray and other high-throughput data M Aleksi Kallio, Jarno T Tuimala, Taavi Hupponen, Petri Klemelä, Massimiliano Gentile, Ilari Scheinin, Mikko Koski, Janne Käki, Eija I Korpelainen BMC Genomics 2011, 12:507 (14 October 2011) |
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Review
Identification of cis-regulatory sequence variations in individual genome sequences Rebecca Worsley-Hunt, Virginie Bernard, Wyeth W Wasserman Genome Medicine 2011, 3:65 (10 October 2011) Wasserman and colleagues review existing methods and software for predicting the impact of cis-regulatory mutations on disease gene transcription and RNA processing.
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Software
Interactive metagenomic visualization in a Web browser Brian D Ondov, Nicholas H Bergman, Adam M Phillippy BMC Bioinformatics 2011, 12:385 (30 September 2011) |
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Technical Note
Agile parallel bioinformatics workflow management using Pwrake Hiroyuki Mishima, Kensaku Sasaki, Masahiro Tanaka, Osamu Tatebe, Koh-ichiro Yoshiura BMC Research Notes 2011, 4:331 (8 September 2011) |
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Research article
Rathi D Thiagarajan, Nicole Cloonan, Brooke B Gardiner, Tim R Mercer, Gabriel Kolle, Ehsan Nourbakhsh, Shivangi Wani, Dave Tang, Keerthana Krishnan, Kylie M Georgas, Bree A Rumballe, Han S Chiu, Jason A Steen, John S Mattick, Melissa H Little, Sean M Grimmond BMC Genomics 2011, 12:441 (5 September 2011) |
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Software
Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White, W Florian Fricke BMC Bioinformatics 2011, 12:356 (30 August 2011) Cloud Virtual Resource (CloVR) is a new desktop application for large-scale sequence analysis using remote computing resources that provides several automated pipelines for microbial genomics, including 16S, whole genome and metagenome sequence analysis.
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Opinion
The real cost of sequencing: higher than you think! Andrea Sboner, Xinmeng Mu, Dov Greenbaum, Raymond K Auerbach, Mark B Gerstein Genome Biology 2011, 12:125 (25 August 2011) The sharp decrease in the cost of 'data generation' has not been matched by a comparable decrease in the cost of the computational infrastructure required to mine the data
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Software
Cistrome: an integrative platform for transcriptional regulation studies Tao Liu, Jorge A Ortiz, Len Taing, Clifford A Meyer, Bernett Lee, Yong Zhang, Hyunjin Shin, Swee S Wong, Jian Ma, Ying Lei, Utz J Pape, Michael Poidinger, Yiwen Chen, Kevin Yeung, Myles Brown, Yaron Turpaz, X Shirley Liu Genome Biology 2011, 12:R83 (22 August 2011) A Galaxy-based web application for integrative analysis of ChIP data
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Introduction
Proceedings of the Tenth Annual UT-ORNL-KBRIN Bioinformatics Summit 2011 Eric C Rouchka, Robert M Flight, Ramin Homayouni BMC Bioinformatics 2011, 12(Suppl 7):A1 (5 August 2011) |
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Software
ExpressionPlot: a web-based framework for analysis of RNA-Seq and microarray gene expression data Brad A Friedman, Tom Maniatis Genome Biology 2011, 12:R69 (28 July 2011) A web-based RNA-seq and microarray analysis tool
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Software
Applications of the pipeline environment for visual informatics and genomics computations Ivo D Dinov, Federica Torri, Fabio Macciardi, Petros Petrosyan, Zhizhong Liu, Alen Zamanyan, Paul Eggert, Jonathan Pierce, Alex Genco, James A Knowles, Andrew P Clark, John D Van Horn, Joseph Ames, Carl Kesselman, Arthur W Toga BMC Bioinformatics 2011, 12:304 (26 July 2011) |
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Software
An integrated ChIP-seq analysis platform with customizable workflows Eugenia G Giannopoulou, Olivier Elemento BMC Bioinformatics 2011, 12:277 (7 July 2011) |
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Method
Metagenomic biomarker discovery and explanation Nicola Segata, Jacques Izard, Levi Waldron, Dirk Gevers, Larisa Miropolsky, Wendy S Garrett, Curtis Huttenhower Genome Biology 2011, 12:R60 (24 June 2011) A method for distinguishing microbial populations from metagenomic data is presented
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Research
Hiroki Goto, Benjamin Dickins, Enis Afgan, Ian M Paul, James Taylor, Kateryna D Makova, Anton Nekrutenko Genome Biology 2011, 12:R59 (23 June 2011) Analysis of 3 families with a Galaxy-based method for heteroplasmy identification suggests that within-individual mtDNA variation is infrequent
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Review
Microarrays, deep sequencing and the true measure of the transcriptome John H Malone, Brian Oliver BMC Biology 2011, 9:34 (31 May 2011) Global measures of gene expression can now be extracted either from microarrays or from RNA-seq, which do not always seem to give the same answer. Malone and Oliver review the advantages and limitations of each and conclude that, with some important exceptions, they tell the same story.
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Proceedings
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde, Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes, Engbert O de Brock, Ritsert C Jansen, Helen Parkinson BMC Bioinformatics 2010, 11(Suppl 12):S12 (21 December 2010) |
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Perspective
Tin Tan, Joo Tong, Asif M Khan, Mark de Silva, Kuan Lim, Shoba Ranganathan BMC Genomics 2010, 11(Suppl 4):S27 (2 December 2010) |