My NCBISign In
GOToolBox: functional analysis of gene datasets based on Gene Ontology
David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq
Genome Biol. 2004; 5(12): R101. Published online 2004 November 26. doi: 10.1186/gb-2004-5-12-r101
PMCID:
PMC545796
Abstract Full Text PDF–2.2M

Is Cited by the Following 93 Articles in this Archive:

Comparative SILAC Proteomic Analysis of Trypanosoma brucei Bloodstream and Procyclic Lifecycle Stages
Michael D. Urbaniak, M. Lucia S Guther, Michael A. J. Ferguson
PLoS One. 2012; 7(5): e36619. Published online 2012 May 4. doi: 10.1371/journal.pone.0036619
PMCID:
PMC3344917
Abstract Full Text PDF–2.2M Supplementary Material
Yeast Toxicogenomics: Genome-Wide Responses to Chemical Stresses with Impact in Environmental Health, Pharmacology, and Biotechnology
Sandra C. dos Santos, Miguel Cacho Teixeira, Tânia R. Cabrito, Isabel Sá-Correia
Front Genet. 2012; 3: 63. Prepublished online 2012 March 9. Published online 2012 April 19. doi: 10.3389/fgene.2012.00063
PMCID:
PMC3329712
Abstract Full Text PDF–3.0M
Genomic Targets of Brachyury (T) in Differentiating Mouse Embryonic Stem Cells
Amanda L. Evans, Tiago Faial, Michael J. Gilchrist, Thomas Down, Ludovic Vallier, Roger A. Pedersen, Fiona C. Wardle, James C. Smith
PLoS One. 2012; 7(3): e33346. Published online 2012 March 30. doi: 10.1371/journal.pone.0033346
PMCID:
PMC3316570
Abstract Full Text PDF–1.7M Supplementary Material
Ten Years of Pathway Analysis: Current Approaches and Outstanding Challenges
Purvesh Khatri, Marina Sirota, Atul J. Butte
PLoS Comput Biol. 2012 February; 8(2): e1002375. Published online 2012 February 23. doi: 10.1371/journal.pcbi.1002375
PMCID:
PMC3285573
Abstract Full Text PDF–663K Supplementary Material
Comprehensive analysis of tobacco pollen transcriptome unveils common pathways in polar cell expansion and underlying heterochronic shift during spermatogenesis
Said Hafidh, Katarína Breznenová, Petr Růžička, Jana Feciková, Věra Čapková, David Honys
BMC Plant Biol. 2012; 12: 24. Published online 2012 February 16. doi: 10.1186/1471-2229-12-24
PMCID:
PMC3305590
Abstract Full Text PDF–8.6M Supplementary Material
Old and new functions of proneural factors revealed by the genome-wide characterization of their transcriptional targets
Diogo S Castro, François Guillemot
Cell Cycle. 2011 December 1; 10(23): 4026–4031. Published online 2011 December 1. doi: 10.4161/cc.10.23.18578
PMCID:
PMC3272285
Free in PMC on 2012/12/01
SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus
Steven G Hussey, Eshchar Mizrachi, Antanas V Spokevicius, Gerd Bossinger, Dave K Berger, Alexander A Myburg
BMC Plant Biol. 2011; 11: 173. Published online 2011 December 1. doi: 10.1186/1471-2229-11-173
PMCID:
PMC3289092
Abstract Full Text PDF–1.1M Supplementary Material
Drosophila CLOCK target gene characterization: implications for circadian tissue-specific gene expression
Katharine Compton Abruzzi, Joseph Rodriguez, Jerome S. Menet, Jennifer Desrochers, Abigail Zadina, Weifei Luo, Sasha Tkachev, Michael Rosbash
Genes Dev. 2011 November 15; 25(22): 2374–2386. doi: 10.1101/gad.178079.111
PMCID:
PMC3222903
Abstract Full Text PDF–1.8M
Nutrigenomics in honey bees: digital gene expression analysis of pollen's nutritive effects on healthy and varroa-parasitized bees
Cédric Alaux, Christelle Dantec, Hughes Parrinello, Yves Le Conte
BMC Genomics. 2011; 12: 496. Published online 2011 October 10. doi: 10.1186/1471-2164-12-496
PMCID:
PMC3209670
Abstract Full Text PDF–2.3M Supplementary Material
The habitat disruption induces immune-suppression and oxidative stress in honey bees
Tomomi Morimoto, Yuriko Kojima, Taku Toki, Yayoi Komeda, Mikio Yoshiyama, Kiyoshi Kimura, Keijiro Nirasawa, Tatsuhiko Kadowaki
Ecol Evol. 2011 October; 1(2): 201–217. doi: 10.1002/ece3.21
PMCID:
PMC3287300
Abstract Full Text PDF–1.3M Supplementary Material
Functional Integrative Levels in the Human Interactome Recapitulate Organ Organization
Ouissem Souiai, Emmanuelle Becker, Carlos Prieto, Alia Benkahla, Javier De Las Rivas, Christine Brun
PLoS One. 2011; 6(7): e22051. Published online 2011 July 20. doi: 10.1371/journal.pone.0022051
PMCID:
PMC3140469
Abstract Full Text PDF–821K Supplementary Material
High-throughput phenotyping using parallel sequencing of RNA interference targets in the African trypanosome
Sam Alsford, Daniel J. Turner, Samson O. Obado, Alejandro Sanchez-Flores, Lucy Glover, Matthew Berriman, Christiane Hertz-Fowler, David Horn
Genome Res. 2011 June; 21(6): 915–924. doi: 10.1101/gr.115089.110
PMCID:
PMC3106324
Abstract Full Text PDF–1.5M
BioProfiling.de: analytical web portal for high-throughput cell biology
Alexey V. Antonov
Nucleic Acids Res. 2011 July 1; 39(Web Server issue): W323–W327. Published online 2011 May 23. doi: 10.1093/nar/gkr372
PMCID:
PMC3125774
Abstract Full Text PDF–215K
Genome-wide CTCF distribution in vertebrates defines equivalent sites that can aid in the identification of disease-associated genes
David Martin, Cristina Pantoja, Ana Fernández Miñán, Christian Valdes-Quezada, Eduardo Moltó, Fuencisla Matesanz, Ozren Bogdanovic, Elisa de la Calle-Mustienes, Orlando Domínguez, Leila Taher, Mayra Furlan-Magaril, Antonio Alcina, Susana Cañón, María Fedetz, María A. Blasco, Paulo S. Pereira, Ivan Ovcharenko, Félix Recillas-Targa, Lluís Montoliu, Miguel Manzanares, Roderic Guigó, Manuel Serrano, Fernando Casares, José Luis Gómez-Skarmeta
Nat Struct Mol Biol. Author manuscript; available in PMC 2011 December 1.
Published in final edited form as: Nat Struct Mol Biol. 2011 June; 18(6): 708–714. Published online 2011 May 22. doi: 10.1038/nsmb.2059
PMCID:
PMC3196567
Abstract Full Text PDF–1.4M Supplementary Material
TAFFEL: Independent Enrichment Analysis of gene sets
Mitja I Kurki, Jussi Paananen, Markus Storvik, Seppo Ylä-Herttuala, Juha E Jääskeläinen, Mikael von und zu Fraunberg, Garry Wong, Petri Pehkonen
BMC Bioinformatics. 2011; 12: 171. Published online 2011 May 19. doi: 10.1186/1471-2105-12-171
PMCID:
PMC3120704
Abstract Full Text PDF–1.2M Supplementary Material
Functional Cohesion of Gene Sets Determined by Latent Semantic Indexing of PubMed Abstracts
Lijing Xu, Nicholas Furlotte, Yunyue Lin, Kevin Heinrich, Michael W. Berry, Ebenezer O. George, Ramin Homayouni
PLoS One. 2011; 6(4): e18851. Published online 2011 April 14. doi: 10.1371/journal.pone.0018851
PMCID:
PMC3077411
Abstract Full Text PDF–357K Supplementary Material
Transcriptomic Analysis in a Drosophila Model Identifies Previously Implicated and Novel Pathways in the Therapeutic Mechanism in Neuropsychiatric Disorders
Priyanka Singh, Farhan Mohammad, Abhay Sharma
Front Neurosci. 2011; 5: 161. Published online 2011 March 31. doi: 10.3389/fnins.2011.00161
PMCID:
PMC3071501
Abstract Full Text PDF–1.9M
An EST-based analysis identifies new genes and reveals distinctive gene expression features of Coffea arabica and Coffea canephora
Jorge MC Mondego, Ramon O Vidal, Marcelo F Carazzolle, Eric K Tokuda, Lucas P Parizzi, Gustavo GL Costa, Luiz FP Pereira, Alan C Andrade, Carlos A Colombo, Luiz GE Vieira, Gonçalo AG Pereira
BMC Plant Biol. 2011; 11: 30. Published online 2011 February 8. doi: 10.1186/1471-2229-11-30
PMCID:
PMC3045888
Abstract Full Text PDF–2.6M Supplementary Material
Exploiting Statistical Methodologies and Controlled Vocabularies for Prioritized Functional Analysis of Genomic Experiments: the StRAnGER Web Application
Aristotelis A. Chatziioannou, Panagiotis Moulos
Front Neurosci. 2011; 5: 8. Published online 2011 January 26. doi: 10.3389/fnins.2011.00008
PMCID:
PMC3032379
Abstract Full Text PDF–1.8M
Epigenetic Regulation of Learning and Memory by Drosophila EHMT/G9a
Jamie M. Kramer, Korinna Kochinke, Merel A. W. Oortveld, Hendrik Marks, Daniela Kramer, Eiko K. de Jong, Zoltan Asztalos, J. Timothy Westwood, Hendrik G. Stunnenberg, Marla B. Sokolowski, Krystyna Keleman, Huiqing Zhou, Hans van Bokhoven, Annette Schenck
PLoS Biol. 2011 January; 9(1): e1000569. Published online 2011 January 4. doi: 10.1371/journal.pbio.1000569
PMCID:
PMC3014924
Abstract Full Text PDF–2.7M Supplementary Material
IntelliGO: a new vector-based semantic similarity measure including annotation origin
Sidahmed Benabderrahmane, Malika Smail-Tabbone, Olivier Poch, Amedeo Napoli, Marie-Dominique Devignes
BMC Bioinformatics. 2010; 11: 588. Published online 2010 December 1. doi: 10.1186/1471-2105-11-588
PMCID:
PMC3098105
Abstract Full Text PDF–936K
Reversible Block of Mouse Neural Stem Cell Differentiation in the Absence of Dicer and MicroRNAs
Therese Andersson, Sabhi Rahman, Stephen N. Sansom, Jessica M. Alsiö, Masahiro Kaneda, James Smith, Donal O'Carroll, Alexander Tarakhovsky, Frederick J. Livesey
PLoS One. 2010; 5(10): e13453. Published online 2010 October 18. doi: 10.1371/journal.pone.0013453
PMCID:
PMC2956652
Abstract Full Text PDF–12M Supplementary Material
Genome-wide inference of regulatory networks in Streptomyces coelicolor
Marlene Castro-Melchor, Salim Charaniya, George Karypis, Eriko Takano, Wei-Shou Hu
BMC Genomics. 2010; 11: 578. Published online 2010 October 18. doi: 10.1186/1471-2164-11-578
PMCID:
PMC3224704
Abstract Full Text PDF–2.8M Supplementary Material
MiRNA–miRNA synergistic network: construction via co-regulating functional modules and disease miRNA topological features
Juan Xu, Chuan-Xing Li, Yong-Sheng Li, Jun-Ying Lv, Ye Ma, Ting-Ting Shao, Liang-De Xu, Ying-Ying Wang, Lei Du, Yun-Peng Zhang, Wei Jiang, Chun-Quan Li, Yun Xiao, Xia Li
Nucleic Acids Res. 2011 February; 39(3): 825–836. Published online 2010 October 6. doi: 10.1093/nar/gkq832
PMCID:
PMC3035454
Abstract Full Text PDF–8.2M Supplementary Material
A High-Throughput Data Mining of Single Nucleotide Polymorphisms in Coffea Species Expressed Sequence Tags Suggests Differential Homeologous Gene Expression in the Allotetraploid Coffea arabica
Ramon Oliveira Vidal, Jorge Maurício Costa Mondego, David Pot, Alinne Batista Ambrósio, Alan Carvalho Andrade, Luiz Filipe Protasio Pereira, Carlos Augusto Colombo, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira
Plant Physiol. 2010 November; 154(3): 1053–1066. Published online 2010 September 23. doi: 10.1104/pp.110.162438
PMCID:
PMC2971587
Abstract Full Text PDF–550K Supplementary Material
Ecological Adaptation of Diverse Honey Bee (Apis mellifera) Populations
Robert Parker, Andony P. Melathopoulos, Rick White, Stephen F. Pernal, M. Marta Guarna, Leonard J. Foster
PLoS One. 2010; 5(6): e11096. Published online 2010 June 15. doi: 10.1371/journal.pone.0011096
PMCID:
PMC2886107
Abstract Full Text PDF–1.3M Supplementary Material
R spider: a network-based analysis of gene lists by combining signaling and metabolic pathways from Reactome and KEGG databases
Alexey V. Antonov, Esther E. Schmidt, Sabine Dietmann, Maria Krestyaninova, Henning Hermjakob
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W78–W83. Published online 2010 June 2. doi: 10.1093/nar/gkq482
PMCID:
PMC2896180
Abstract Full Text PDF–2.7M
Revealing and avoiding bias in semantic similarity scores for protein pairs
Jing Wang, Xianxiao Zhou, Jing Zhu, Chenggui Zhou, Zheng Guo
BMC Bioinformatics. 2010; 11: 290. Published online 2010 May 28. doi: 10.1186/1471-2105-11-290
PMCID:
PMC2903568
Abstract Full Text PDF–2.0M
Identifying overrepresented concepts in gene lists from literature: a statistical approach based on Poisson mixture model
Xin He, Moushumi Sen Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz
BMC Bioinformatics. 2010; 11: 272. Published online 2010 May 20. doi: 10.1186/1471-2105-11-272
PMCID:
PMC2885378
Abstract Full Text PDF–1.6M Supplementary Material
Gene Expression Profiling and Network Analysis Reveals Lipid and Steroid Metabolism to Be the Most Favored by TNFα in HepG2 Cells
Amit K. Pandey, Neha Munjal, Malabika Datta
PLoS One. 2010; 5(2): e9063. Published online 2010 February 4. doi: 10.1371/journal.pone.0009063
PMCID:
PMC2816217
Abstract Full Text PDF–839K Supplementary Material
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