GoMiner: a resource for biological interpretation of genomic and proteomic data
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* Corresponding author: John N Weinstein weinstein@dtpax2.ncifcrf.gov
Genome Biology 2003, 4:R28 doi:10.1186/gb-2003-4-4-r28
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BioMed Central: 94 citations
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Research article
Gareth Williams BMC Genomics 2012, 13:12 (10 January 2012) |
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Research article
Maximizing biomarker discovery by minimizing gene signatures Chang Chang, Junwei Wang, Chen Zhao, Jennifer Fostel, Weida Tong, Pierre R Bushel, Youping Deng, Lajos Pusztai, W Fraser Symmans, Tieliu Shi BMC Genomics 2011, 12(Suppl 5):S6 (23 December 2011) |
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Research article
Analysis of the dynamics of limb transcriptomes during mouse development Istvan Gyurján, Bernhard Sonderegger, Felix Naef, Denis Duboule BMC Developmental Biology 2011, 11:47 (29 July 2011) The transcriptome of mouse limb bud development at three different stages reveals the changes in gene expression underpinning major developmental events and the role of non-coding RNAs during this process.
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Proceedings
Martin Ehler, Vinodh N Rajapakse, Barry R Zeeberg, Brian P Brooks, Jacob Brown, Wojciech Czaja, Robert F Bonner BMC Proceedings 2011, 5(Suppl 2):S3 (28 April 2011) |
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Research article
Characterization of the apoptotic response of human leukemia cells to organosulfur compounds W Wei-Lynn Wong, Paul C Boutros, Amanda R Wasylishen, Kristal D Guckert, Erin M O'Brien, Rebecca Griffiths, Anna R Martirosyan, Christina Bros, Igor Jurisica, Richard F Langler, Linda Z Penn BMC Cancer 2010, 10:351 (2 July 2010) |
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Research article
An interaction-motif-based scoring function for protein-ligand docking Zhong-Ru Xie, Ming-Jing Hwang BMC Bioinformatics 2010, 11:298 (2 June 2010) |
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Research article
Xin He, Moushumi Sarma, Xu Ling, Brant Chee, Chengxiang Zhai, Bruce Schatz BMC Bioinformatics 2010, 11:272 (20 May 2010) |
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Research
Rachel A Heimeier, Biswajit Das, Daniel R Buchholz, Maria Fiorentino, Yun-Bo Shi Genome Biology 2010, 11:R55 (19 May 2010) The developmental transcriptome of the Xenopus laevis intestine, from embryo to adult, reveals insights into the regulation of gut development in all vertebrates. |
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Research
A human functional protein interaction network and its application to cancer data analysis Guanming Wu, Xin Feng, Lincoln Stein Genome Biology 2010, 11:R53 (19 May 2010) A high-quality human functional protein interaction network is constructed. Its utility is demonstrated in the identification of cancer candidate genes. |
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Research article
Ivy D Moffat, Paul C Boutros, Hanbo Chen, Allan B Okey, Raimo Pohjanvirta BMC Genomics 2010, 11:263 (26 April 2010) |
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Method
Gene ontology analysis for RNA-seq: accounting for selection bias Matthew D Young, Matthew J Wakefield, Gordon K Smyth, Alicia Oshlack Genome Biology 2010, 11:R14 (4 February 2010) GOseq is a method for GO analysis of RNA-seq data that takes into account the length bias inherent in RNA-seq |
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Research article
Laure Guenin, Mahatsangy Raharijaona, Rémi Houlgatte, Fawzia Baba-Aissa BMC Genomics 2010, 11:47 (19 January 2010) |
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Research article
Shaobing O Zhang, Sachin Mathur, Gaye Hattem, Olivier Tassy, Olivier Pourquié BMC Genomics 2010, 11:13 (7 January 2010) |
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Research article
Gene expression profiling in sinonasal adenocarcinoma Dominique Tripodi, Sylvia Quéméner, Karine Renaudin, Christophe Ferron, Olivier Malard, Isabelle Guisle-Marsollier, Véronique Sébille-Rivain, Christian Verger, Christian Géraut, Catherine Gratas-Rabbia-Ré BMC Medical Genomics 2009, 2:65 (10 November 2009) |
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Research article
Alissar Nehmé, Edward K Lobenhofer, W Daniel Stamer, Jeffrey L Edelman BMC Medical Genomics 2009, 2:58 (10 September 2009) |
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Research
Nicoletta Bivi, Milena Romanello, Richard Harrison, Ian Clarke, David C Hoyle, Luigi Moro, Fulvia Ortolani, Antonella Bonetti, Franco Quadrifoglio, Gianluca Tell, Daniela Delneri Genome Biology 2009, 10:R93 (10 September 2009) Growth competition assays using barcoded yeast deletion-mutants reveal the molecular targets of nitrogen containing bisphosphonates used for the treatment of bone cancers and osteoporosis. |
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Software
SNAD: sequence name annotation-based designer Igor A Sidorov, Denis A Reshetov, Alexander E Gorbalenya BMC Bioinformatics 2009, 10:251 (14 August 2009) |
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Research article
John A Lewis, Maria Szilagyi, Elizabeth Gehman, William E Dennis, David A Jackson BMC Genomics 2009, 10:202 (29 April 2009) |
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Research article
Gene set internal coherence in the context of functional profiling David Montaner, Pablo Minguez, Fátima Al-Shahrour, Joaquín Dopazo BMC Genomics 2009, 10:197 (27 April 2009) |
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Method
Reuben Thomas, Julia M Gohlke, Geffrey F Stopper, Frederick M Parham, Christopher J Portier Genome Biology 2009, 10:R44 (24 April 2009) A method is proposed that finds enriched pathways relevant to a studied condition, using molecular and network data. |
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Research
Early cellular signaling responses to axonal injury Thomas J Lukas, Ai Wang, Ming Yuan, Arthur H Neufeld Cell Communication and Signaling 2009, 7:5 (13 March 2009) |
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Methodology
GO Explorer: A gene-ontology tool to aid in the interpretation of shotgun proteomics data Paulo C Carvalho, Juliana SG Fischer, Emily I Chen, Gilberto B Domont, Maria GC Carvalho, Wim M Degrave, John R Yates, Valmir C Barbosa Proteome Science 2009, 7:6 (24 February 2009) |
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Research article
Using cell fate attractors to uncover transcriptional regulation of HL60 neutrophil differentiation Albert C Huang, Limei Hu, Stuart A Kauffman, Wei Zhang, Ilya Shmulevich BMC Systems Biology 2009, 3:20 (18 February 2009) |
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Software
GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists Eran Eden, Roy Navon, Israel Steinfeld, Doron Lipson, Zohar Yakhini BMC Bioinformatics 2009, 10:48 (3 February 2009) |
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Research
A protein interaction based model for schizophrenia study Pei-Chun Hsu, Ueng-Cheng Yang, Kuan-Hui Shih, Chih-Min Liu, Yu-Li Liu, Hai-Gwo Hwu BMC Bioinformatics 2008, 9(Suppl 12):S23 (12 December 2008) |
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Research article
Protein evolution in deep sea bacteria: an analysis of amino acids substitution rates Stefano Campanaro, Laura Treu, Giorgio Valle BMC Evolutionary Biology 2008, 8:313 (13 November 2008) |
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Research article
Paul C Boutros, Rui Yan, Ivy D Moffat, Raimo Pohjanvirta, Allan B Okey BMC Genomics 2008, 9:419 (16 September 2008) |
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Research
Bhavana Prasher, Sapna Negi, Shilpi Aggarwal, Amit K Mandal, Tav P Sethi, Shailaja R Deshmukh, Sudha G Purohit, Shantanu Sengupta, Sangeeta Khanna, Farhan Mohammad, Gaurav Garg, Samir K Brahmachari, Mitali Mukerji Journal of Translational Medicine 2008, 6:48 (9 September 2008) Differences in genome wide expression levels and biochemical and hematological parameters have been demonstrated between the constitutional types fundamental to the practice of Ayurveda, an ancient Indian method of holistic health care.
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Research
Thomas J Lukas, Haixi Miao, Lin Chen, Sean M Riordan, Wenjun Li, Andrea M Crabb, Alexandria Wise, Pan Du, Simon M Lin, M Rosario Hernandez Genome Biology 2008, 9:R111 (9 July 2008) Comparison of gene expression in normal and glaucomatous eyes from Caucasian American and African American donors reveals differences that might reflect different susceptibility to glaucoma. |
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Method
Edward K Lobenhofer, J Todd Auman, Pamela E Blackshear, Gary A Boorman, Pierre R Bushel, Michael L Cunningham, Jennifer M Fostel, Kevin Gerrish, Alexandra N Heinloth, Richard D Irwin, David E Malarkey, B Alex Merrick, Stella O Sieber, Charles J Tucker, Sandra M Ward, Ralph E Wilson, Patrick Hurban, Raymond W Tennant, Richard S Paules Genome Biology 2008, 9:R100 (20 June 2008) Histopathology, clinical chemistry, hematology and gene expression data were collected from the rat liver and blood after treatment with eight known hepatotoxins. |
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Database
MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters Philip J Law, Clotilde Claudel-Renard, Fourie Joubert, Abraham I Louw, Dave K Berger BMC Genomics 2008, 9:105 (28 February 2008) |
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Methodology article
VennMaster: Area-proportional Euler diagrams for functional GO analysis of microarrays Hans A Kestler, André Müller, Johann M Kraus, Malte Buchholz, Thomas M Gress, Hongfang Liu, David W Kane, Barry R Zeeberg, John N Weinstein BMC Bioinformatics 2008, 9:67 (29 January 2008) |
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Software
Phillip G Febbo, Mike G Mulligan, David A Slonina, Kimberly Stegmaier, Dolores Di Vizio, Paul R Martinez, Massimo Loda, Stephen C Taylor BMC Genomics 2007, 8:461 (18 December 2007) |
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Research article
Pierre-Yves Rescan, Jerome Montfort, Cécile Rallière, Aurélie Le Cam, Diane Esquerré, Karine Hugot BMC Genomics 2007, 8:438 (28 November 2007) |
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Database
Brad T Sherman, Da Huang, Qina Tan, Yongjian Guo, Stephan Bour, David Liu, Robert Stephens, Michael W Baseler, H Clifford Lane, Richard A Lempicki BMC Bioinformatics 2007, 8:426 (2 November 2007) |
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Research article
Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D'Angelo, Giorgio Valle, Franca Anglani BMC Genomics 2007, 8:383 (22 October 2007) |
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Research article
Daniel Baron, Jérôme Montfort, Rémi Houlgatte, Alexis Fostier, Yann Guiguen BMC Genomics 2007, 8:357 (4 October 2007) |
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Research
Comparative proteome analysis of human epithelial ovarian cancer Jean-Philippe Gagné, Chantal Éthier, Pierre Gagné, Geneviève Mercier, Marie-Ève Bonicalzi, Anne-Marie Mes-Masson, Arnaud Droit, Eric Winstall, Maxim Isabelle, Guy G Poirier Proteome Science 2007, 5:16 (24 September 2007) |
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Method
Gabriel S Eichler, Mark Reimers, David Kane, John N Weinstein Genome Biology 2007, 8:R187 (10 September 2007) The LeFE algorithm has been developed to address the complex, non-linear regulation of gene expression. |
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Research article
Ying Hao, Sumita Sood, George Triadafilopoulos, Jong Kim, Zheng Wang, Peyman Sahbaie, M Bishr Omary, Anson W Lowe BMC Gastroenterology 2007, 7:24 (27 June 2007) |
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Research
Yuxia Cui, Sandra J McBride, Windy A Boyd, Scott Alper, Jonathan H Freedman Genome Biology 2007, 8:R122 (25 June 2007) Global analysis of the transcriptional response to cadmium exposure in |
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Research article
CAG-encoded polyglutamine length polymorphism in the human genome Stefanie L Butland, Rebecca S Devon, Yong Huang, Carri-Lyn Mead, Alison M Meynert, Scott J Neal, Soo Lee, Anna Wilkinson, George S Yang, Macaire MS Yuen, Michael R Hayden, Robert A Holt, Blair R Leavitt, BF Francis Ouellette BMC Genomics 2007, 8:126 (22 May 2007) |
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Methodology article
Carina Strand, Johan Enell, Ingrid Hedenfalk, Mårten Fernö BMC Molecular Biology 2007, 8:38 (22 May 2007) |
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Method
Yingchun Liu, Markus Ringnér Genome Biology 2007, 8:R77 (11 May 2007) A strategy for identifying cell signaling pathways whose deregulation result in an observed expression signature is presented. |
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Research
Decline of nucleotide excision repair capacity in aging Caenorhabditis elegans Joel N Meyer, Windy A Boyd, Gregory A Azzam, Astrid C Haugen, Jonathan H Freedman, Bennett Van Houten Genome Biology 2007, 8:R70 (1 May 2007) Repair of UVC-induced DNA damage in |
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Database
Ari B Kahn, Michael C Ryan, Hongfang Liu, Barry R Zeeberg, D Curtis Jamison, John N Weinstein BMC Bioinformatics 2007, 8:75 (5 March 2007) |
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Software
FUNC: a package for detecting significant associations between gene sets and ontological annotations Kay Prüfer, Bjoern Muetzel, Hong-Hai Do, Gunter Weiss, Philipp Khaitovich, Erhard Rahm, Svante Pääbo, Michael Lachmann, Wolfgang Enard BMC Bioinformatics 2007, 8:41 (6 February 2007) |
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Research
Immune-mediated changes in actinic keratosis following topical treatment with imiquimod 5% cream Abel Torres, Leslie Storey, Makala Anders, Richard L Miller, Barbara J Bulbulian, Jizhong Jin, Shalini Raghavan, James Lee, Herbert B Slade, Woubalem Birmachu Journal of Translational Medicine 2007, 5:7 (26 January 2007) |
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Software
GO-2D: identifying 2-dimensional cellular-localized functional modules in Gene Ontology Jing Zhu, Jing Wang, Zheng Guo, Min Zhang, Da Yang, Yanhui Li, Dong Wang, Guohua Xiao BMC Genomics 2007, 8:30 (24 January 2007) |
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Review
Lyn-Marie Birkholtz, Olivier Bastien, Gordon Wells, Delphine Grando, Fourie Joubert, Vinod Kasam, Marc Zimmermann, Philippe Ortet, Nicolas Jacq, Nadia Saïdani, Sylvaine Roy, Martin Hofmann-Apitius, Vincent Breton, Abraham I Louw, Eric Maréchal Malaria Journal 2006, 5:110 (17 November 2006) A review of the different tools and strategies that have recently been developed to process the huge amount of data produced by the X-omic projects. This includes the comparison of protein sequences, high throughput reconstruction of molecular phylogenies, representation of biological processes, methods to integrate X-omic generated data following drug treatments and in silico prediction of protein structure and identification of specific ligand.
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Software
GeneTools – application for functional annotation and statistical hypothesis testing Vidar Beisvag, Frode KR Jünge, Hallgeir Bergum, Lars Jølsum, Stian Lydersen, Clara-Cecilie Günther, Heri Ramampiaro, Mette Langaas, Arne K Sandvik, Astrid Lægreid BMC Bioinformatics 2006, 7:470 (24 October 2006) |
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Research
David M Levine, David R Haynor, John C Castle, Sergey B Stepaniants, Matteo Pellegrini, Mao Mao, Jason M Johnson Genome Biology 2006, 7:R93 (17 October 2006) A comparison of five different measures of pathway expression and a public map of pathway expression in human tissues are presented. |
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Software
GOLEM: an interactive graph-based gene-ontology navigation and analysis tool Rachel SG Sealfon, Matthew A Hibbs, Curtis Huttenhower, Chad L Myers, Olga G Troyanskaya BMC Bioinformatics 2006, 7:443 (10 October 2006) |
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Proceedings
Hongmei Sun, Hong Fang, Tao Chen, Roger Perkins, Weida Tong BMC Bioinformatics 2006, 7(Suppl 2):S23 (26 September 2006) |
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Proceedings
Lei Guo, Hong Fang, Jim Collins, Xiao-hui Fan, Stacey Dial, Alex Wong, Kshama Mehta, Ernice Blann, Leming Shi, Weida Tong, Yvonne P Dragan BMC Bioinformatics 2006, 7(Suppl 2):S18 (26 September 2006) |
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Research article
Betti Giusti, Gabriella Fibbi, Francesca Margheri, Simona Serratì, Luciana Rossi, Filippo Poggi, Ilaria Lapini, Alberto Magi, Angela Del Rosso, Marina Cinelli, Serena Guiducci, Bashar Kahaleh, Laura Bazzichi, Stefano Bombardieri, Marco Matucci-Cerinic, Gian Gensini, Mario Del Rosso, Rosanna Abbate Arthritis Research & Therapy 2006, 8:R115 (19 July 2006) |
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Research article
A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model Patrícia Beldade, Stephen Rudd, Jonathan D Gruber, Anthony D Long BMC Genomics 2006, 7:130 (31 May 2006) The Expressed Sequence Tag (EST) collection for Bicyclus anynana is the largest to date for any butterfly species and provides a valuable resource for future evolutionary and genomic analysis.
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Research
Large-scale and high-confidence proteomic analysis of human seminal plasma Bartosz Pilch, Matthias Mann Genome Biology 2006, 7:R40 (18 May 2006) The high-confidence identification of 923 proteins in seminal fluid provides an inventory of proteins with potential roles in fertilization.
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Methodology article
Marc Aubry, Annabelle Monnier, Celine Chicault, Marie de Tayrac, Marie-Dominique Galibert, Anita Burgun, Jean Mosser BMC Bioinformatics 2006, 7:241 (4 May 2006) |
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Research article
Transcription profiles of non-immortalized breast cancer cell lines Mariana Fernandez-Cobo, James F Holland, Beatriz GT Pogo BMC Cancer 2006, 6:99 (20 April 2006) |
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Research article
Edward Dere, Darrell R Boverhof, Lyle D Burgoon, Timothy R Zacharewski BMC Genomics 2006, 7:80 (12 April 2006) Gene expression in hepatic cell lines in response to the dioxin TCDD shows significant differences from that of the mouse liver in vivo, highlighting the limitations of in vitro systems for modeling whole organism responses.
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Methodology article
Amplification of the Gene Ontology annotation of Affymetrix probe sets Enrique M Muro, Carolina Perez-Iratxeta, Miguel A Andrade-Navarro BMC Bioinformatics 2006, 7:159 (20 March 2006) |
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Software
Jason M Doherty, Lynn K Carmichael, Jason C Mills BMC Bioinformatics 2006, 7:151 (17 March 2006) |
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Research
Deciphering cellular states of innate tumor drug responses Esther Graudens, Virginie Boulanger, Cindy Mollard, Régine Mariage-Samson, Xavier Barlet, Guilaine Grémy, Christine Couillault, Malika Lajémi, Dominique Piatier-Tonneau, Patrick Zaborski, Eric Eveno, Charles Auffray, Sandrine Imbeaud Genome Biology 2006, 7:R19 (15 March 2006) Nearly 700 genes were identified that are differently expressed between tumors of patients with colorectal cancer who subsequently responded well to combined chemotherapy and those of patients who were resistant to the therapy.
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Software
GO-Diff: Mining functional differentiation between EST-based transcriptomes Zuozhou Chen, Weilin Wang, Xuefeng Ling, Jane Liu, Liangbiao Chen BMC Bioinformatics 2006, 7:72 (16 February 2006) |
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Research article
Jianyong Shou, Christopher M Bull, Li Li, Hui-Rong Qian, Tao Wei, Shuang Luo, Douglas Perkins, Patricia J Solenberg, Seng-Lai Tan, Xin-Yi Chen, Neal W Roehm, Jeffrey A Wolos, Jude E Onyia Arthritis Research & Therapy 2006, 8:R28 (10 January 2006) |
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Methodology article
Finding biological process modifications in cancer tissues by mining gene expression correlations Giacomo Gamberoni, Sergio Storari, Stefano Volinia BMC Bioinformatics 2006, 7:6 (9 January 2006) |
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Research
Primary and secondary transcriptional effects in the developing human Down syndrome brain and heart Rong Mao, Xiaowen Wang, Edward L Spitznagel, Laurence P Frelin, Jason C Ting, Huashi Ding, Jung-whan Kim, Ingo Ruczinski, Thomas J Downey, Jonathan Pevsner Genome Biology 2005, 6:R107 (16 December 2005) Microarray analysis of transcript levels in fetal cerebellum and heart tissues of Down syndrome patients showed a disruption only of chromosome 21 gene expression. |
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Research article
Markey C McNutt, Ron Tongbai, Wenwu Cui, Irene Collins, Wendy J Freebern, Idalia Montano, Cynthia M Haggerty, GVR Chandramouli, Kevin Gardner BMC Bioinformatics 2005, 6:259 (18 October 2005) |
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Research article
Laterally transferred elements and high pressure adaptation in Photobacterium profundum strains Stefano Campanaro, Alessandro Vezzi, Nicola Vitulo, Federico M Lauro, Michela D'Angelo, Francesca Simonato, Alessandro Cestaro, Giorgio Malacrida, Giulio Bertoloni, Giorgio Valle, Douglas H Bartlett BMC Genomics 2005, 6:122 (14 September 2005) The bacterium Photobacterium profundum has a large and flexible gene pool, in part acquired by horizontal gene transfer, and includes genes that are upregulated in piezophilic strains perhaps to assist in their survival in high-pressure deep-sea environments.
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Methodology article
Pathway level analysis of gene expression using singular value decomposition John Tomfohr, Jun Lu, Thomas B Kepler BMC Bioinformatics 2005, 6:225 (12 September 2005) |
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Software
L2L: a simple tool for discovering the hidden significance in microarray expression data John C Newman, Alan M Weiner Genome Biology 2005, 6:R81 (31 August 2005) A database with lists of differentially expressed genes from published microarray studies is presented together with an application for mining the database with the user’s own microarray data, allowing the identification of novel biological patterns in microarray data. |
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Research article
Dynamic covariation between gene expression and proteome characteristics Mansour Sharabiani, Markku Siermala, Tommi O Lehtinen, Mauno Vihinen BMC Bioinformatics 2005, 6:215 (30 August 2005) |
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Software
DynGO: a tool for visualizing and mining of Gene Ontology and its associations Hongfang Liu, Zhang-Zhi Hu, Cathy H Wu BMC Bioinformatics 2005, 6:201 (9 August 2005) |
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Proceedings
H Fang, W Tong, R Perkins, L Shi, H Hong, X Cao, Q Xie, SH Yim, JM Ward, HC Pitot, YP Dragan BMC Bioinformatics 2005, 6(Suppl 2):S6 (15 July 2005) |
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Software
Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W Kane, Mark Reimers, Robert M Stephens, David Bryant, Stanley K Burt, Eldad Elnekave, Danielle M Hari, Thomas A Wynn, Charlotte Cunningham-Rundles, Donn M Stewart, David Nelson, John N Weinstein BMC Bioinformatics 2005, 6:168 (5 July 2005) |
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Research article
Signal transduction pathway profiling of individual tumor samples Thomas Breslin, Morten Krogh, Carsten Peterson, Carl Troein BMC Bioinformatics 2005, 6:163 (29 June 2005) |
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Software
FACT – a framework for the functional interpretation of high-throughput experiments Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt, Peter Lichter BMC Bioinformatics 2005, 6:161 (28 June 2005) |
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Methodology article
PAGE: Parametric Analysis of Gene Set Enrichment Seon-Young Kim, David J Volsky BMC Bioinformatics 2005, 6:144 (8 June 2005) |
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Research article
Pascale Anderle, Thierry Sengstag, David M Mutch, Martin Rumbo, Viviane Praz, Robert Mansourian, Mauro Delorenzi, Gary Williamson, Matthew-Alan Roberts BMC Genomics 2005, 6:69 (10 May 2005) |
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Methodology article
Towards precise classification of cancers based on robust gene functional expression profiles Zheng Guo, Tianwen Zhang, Xia Li, Qi Wang, Jianzhen Xu, Hui Yu, Jing Zhu, Haiyun Wang, Chenguang Wang, Eric J Topol, Qing Wang, Shaoqi Rao BMC Bioinformatics 2005, 6:58 (17 March 2005) |
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Research article
Gene expression in the brain and kidney of rainbow trout in response to handling stress Aleksei Krasnov, Heikki Koskinen, Petri Pehkonen, Caird E Rexroad, Sergey Afanasyev, Hannu Mölsä BMC Genomics 2005, 6:3 (6 January 2005) |
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Methodology article
Comparing functional annotation analyses with Catmap Thomas Breslin, Patrik Edén, Morten Krogh BMC Bioinformatics 2004, 5:193 (9 December 2004) |
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Software
GOToolBox: functional analysis of gene datasets based on Gene Ontology David Martin, Christine Brun, Elisabeth Remy, Pierre Mouren, Denis Thieffry, Bernard Jacq Genome Biology 2004, 5:R101 (26 November 2004) Tools are presented to identify Gene Ontology terms that are over- or under-represented in a dataset, to cluster genes by function and to find genes with similar annotations. |
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Research article
Iterative class discovery and feature selection using Minimal Spanning Trees Sudhir Varma, Richard Simon BMC Bioinformatics 2004, 5:126 (8 September 2004) |
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Research article
Handling multiple testing while interpreting microarrays with the Gene Ontology Database Michael V Osier, Hongyu Zhao, Kei-Hoi Cheung BMC Bioinformatics 2004, 5:124 (6 September 2004) |
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Methodology article
Graph-based iterative Group Analysis enhances microarray interpretation Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:100 (23 July 2004) Graph-based iterative Group Analysis (GiGA), a graph-based approach to identify biologically relevant changes in expression data, visually enhances microarray interpretation.
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Research
System-based proteomic analysis of the interferon response in human liver cells Wei Yan, Hookeun Lee, Eugene C Yi, David Reiss, Paul Shannon, Bartlomiej K Kwieciszewski, Carlos Coito, Xiao-jun Li, Andrew Keller, Jimmy Eng, Timothy Galitski, David R Goodlett, Ruedi Aebersold, Michael G Katze Genome Biology 2004, 5:R54 (22 July 2004) A global quantitative proteomic analysis in a human hepatoma cell line in the presence and absence of interferon treatment using the isotope coded affinity tag method and tandem mass spectrometry identified several novel regulatory components of the interferon response. |
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Software
Visualization and analysis of microarray and gene ontology data with treemaps Eric H Baehrecke, Niem Dang, Ketan Babaria, Ben Shneiderman BMC Bioinformatics 2004, 5:84 (28 June 2004) |
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Correspondence
Barry R Zeeberg, Joseph Riss, David W Kane, Kimberly J Bussey, Edward Uchio, W Marston Linehan, J Carl Barrett, John N Weinstein BMC Bioinformatics 2004, 5:80 (23 June 2004) |
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Methodology article
Rainer Breitling, Anna Amtmann, Pawel Herzyk BMC Bioinformatics 2004, 5:34 (29 March 2004) |
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Software
Bing Zhang, Denise Schmoyer, Stefan Kirov, Jay Snoddy BMC Bioinformatics 2004, 5:16 (18 February 2004) |
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Commentary
Changing paradigm through a genome-based approach to clinical and basic immunology Ena Wang, András Falus Journal of Translational Medicine 2004, 2:2 (17 January 2004) |
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Software
Identifying biological themes within lists of genes with EASE Douglas A Hosack, Glynn Dennis, Brad T Sherman, H Lane, Richard A Lempicki Genome Biology 2003, 4:R70 (11 September 2003) EASE is a customizable software application for rapid biological interpretation of gene lists that result from the analysis of microarray, proteomics, SAGE and other high-throughput genomic data. |