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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
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 Is Cited by the Following 84 Articles in this Archive:
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
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
Gene ontology analysis for RNA-seq: accounting for selection bias
Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack
Genome Biol. 2010; 11(2): R14. Published online 2010 February 4. doi: 10.1186/gb-2010-11-2-r14
PMCID:
PMC2872874
Abstract Full Text PDF–1.4M Supplementary Material
Graph ranking for exploratory gene data analysis
Cuilan Gao, Xin Dang, Yixin Chen, Dawn Wilkins
BMC Bioinformatics. 2009; 10(Suppl 11): S19. Published online 2009 October 8. doi: 10.1186/1471-2105-10-S11-S19
PMCID:
PMC3226190
Abstract Full Text PDF–1.1M
Transcriptomic Profiling of the Saccharomyces cerevisiae Response to Quinine Reveals a Glucose Limitation Response Attributable to Drug-Induced Inhibition of Glucose Uptake
Sandra C. dos Santos, Sandra Tenreiro, Margarida Palma, Jorg Becker, Isabel Sá-Correia
Antimicrob Agents Chemother. 2009 December; 53(12): 5213–5223. Published online 2009 October 5. doi: 10.1128/AAC.00794-09
PMCID:
PMC2786357
Abstract Full Text PDF–866K Supplementary Material
Honey bee aggression supports a link between gene regulation and behavioral evolution
Cédric Alaux, Saurabh Sinha, Linda Hasadsri, Greg J. Hunt, Ernesto Guzmán-Novoa, Gloria DeGrandi-Hoffman, José Luis Uribe-Rubio, Bruce R. Southey, Sandra Rodriguez-Zas, Gene E. Robinson
Proc Natl Acad Sci U S A. 2009 September 8; 106(36): 15400–15405. Published online 2009 August 21. doi: 10.1073/pnas.0907043106
PMCID:
PMC2730357
Abstract Full Text PDF–482K Supplementary Material
Modulatory Communication Signal Performance Is Associated with a Distinct Neurogenomic State in Honey Bees
Cédric Alaux, Nhi Duong, Stanley S. Schneider, Bruce R. Southey, Sandra Rodriguez-Zas, Gene E. Robinson
PLoS One. 2009; 4(8): e6694. Published online 2009 August 20. doi: 10.1371/journal.pone.0006694
PMCID:
PMC2725773
Abstract Full Text PDF–401K Supplementary Material
Genome-Wide Identification of Saccharomyces cerevisiae Genes Required for Maximal Tolerance to Ethanol
Miguel C. Teixeira, Luís R. Raposo, Nuno P. Mira, Artur B. Lourenço, Isabel Sá-Correia
Appl Environ Microbiol. 2009 September; 75(18): 5761–5772. Published online 2009 July 24. doi: 10.1128/AEM.00845-09
PMCID:
PMC2747848
Abstract Full Text PDF–848K Supplementary Material
Evidence of genome-wide G4 DNA-mediated gene expression in human cancer cells
Anjali Verma, Vinod Kumar Yadav, Richa Basundra, Akinchan Kumar, Shantanu Chowdhury
Nucleic Acids Res. 2009 July; 37(13): 4194–4204. Published online 2009 July. doi: 10.1093/nar/gkn1076
PMCID:
PMC2715224
Abstract Full Text PDF–4.8M Supplementary Material
A polynomial time biclustering algorithm for finding approximate expression patterns in gene expression time series
Sara C Madeira, Arlindo L Oliveira
Algorithms Mol Biol. 2009; 4: 8. Published online 2009 June 4. doi: 10.1186/1748-7188-4-8
PMCID:
PMC2709627
Abstract Full Text PDF–4.8M Supplementary Material
A gene regulatory network directed by zebrafish No tail accounts for its roles in mesoderm formation
Rosalind H. Morley, Kim Lachani, Damian Keefe, Michael J. Gilchrist, Paul Flicek, James C. Smith, Fiona C. Wardle
Proc Natl Acad Sci U S A. 2009 March 10; 106(10): 3829–3834. Published online 2009 February 18. doi: 10.1073/pnas.0808382106
PMCID:
PMC2656165
Abstract Full Text PDF–952K Supplementary Material
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