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	Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research [My Copy] Bioinformatics, Vol. 21, No. 18. (15 September 2005), pp. 3674-3676. by Ana Conesa, Stefan Gotz, Juan M. Garcia-Gomez, Javier Terol, Manuel Talon, Montserrat Robles posted to b2gpaper2 blast2go my_papers tutorial by sgoetz on 2007-04-20 14:27:30 as along with 10 people seb1 Thaverkamp karinlag nlapalu bertelsen fbristow Garamonfok talponer imelda aconesa
	Annotation of Bacterial and Archaeal Genomes: Improving Accuracy and Consistency [My Copy] Chemical Reviews, Vol. 107, No. 8. (1 August 2007), pp. 3431-3447. by Ross Overbeek, Daniela Bartels, Veronika Vonstein, Folker Meyer posted to no-tag by sgoetz on 2009-09-10 18:56:31 as along with 2 people druvus wenhan
	The RAST Server: rapid annotations using subsystems technology. [My Copy] BMC genomics, Vol. 9, No. 1. (08 February 2008), 75. by Ramy K. Aziz, Daniela Bartels, Aaron A. Best, et al.Matthew DeJongh, Terrence Disz, Robert A. Edwards, Kevin Formsma, Svetlana Gerdes, Elizabeth M. Glass, Michael Kubal, Folker Meyer, Gary J. Olsen, Robert Olson, Andrei L. Osterman, Ross A. Overbeek, Leslie K. McNeil, Daniel Paarmann, Tobias Paczian, Bruce Parrello, Gordon D. Pusch, Claudia Reich, Rick Stevens, Olga Vassieva, Veronika Vonstein, Andreas Wilke, Olga Zagnitko posted to no-tag by sgoetz on 2009-09-10 18:55:56 as along with 10 people and 2 groups karinlag hexaquo azazello stefanorb coela Thaverkamp barriot druvus JeremyZucker klager Waikato - Erebus MetabolicModeling
	WIT: integrated system for high-throughput genome sequence analysis and metabolic reconstruction [My Copy] Nucl. Acids Res., Vol. 28, No. 1. (1 January 2000), pp. 123-125. by Ross Overbeek, Niels Larsen, Gordon D. Pusch, et al.Mark D'Souza, Evgeni S. Jr, Nikos Kyrpides, Michael Fonstein, Natalia Maltsev, Evgeni Selkov posted to no-tag by sgoetz on 2009-09-10 18:55:46 as
	The ERGOTM genome analysis and discovery system [My Copy] Nucl. Acids Res., Vol. 31, No. 1. (1 January 2003), pp. 164-171. by Ross Overbeek, Niels Larsen, Theresa Walunas, et al.Mark D'Souza, Gordon Pusch, Eugene Selkov, Konstantinos Liolios, Viktor Joukov, Denis Kaznadzey, Iain Anderson, Anamitra Bhattacharyya, Henry Burd, Warren Gardner, Paul Hanke, Vinayak Kapatral, Natalia Mikhailova, Olga Vasieva, Andrei Osterman, Veronika Vonstein, Michael Fonstein, Natalia Ivanova, Nikos Kyrpides posted to no-tag by sgoetz on 2009-09-10 18:54:47 as along with 1 person eweaver
	Membrane transporters and carbon metabolism implicated in chloride homeostasis differentiate salt stress responses in tolerant and sensitive Citrus rootstocks [My Copy] Functional & Integrative Genomics, Vol. 9, No. 3. (1 August 2009), pp. 293-309. by Javier Brumós, José Colmenero-Flores, Ana Conesa, et al.Pedro Izquierdo, Guadalupe Sánchez, Domingo Iglesias, María López-Climent, Aurelio Gómez-Cadenas, Manuel Talón posted to no-tag by sgoetz on 2009-08-12 16:37:34 as
	Babelomics: advanced functional profiling of transcriptomics, proteomics and genomics experiments [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W341-346. by Fatima Al-Shahrour, Jose Carbonell, Pablo Minguez, et al.Stefan Goetz, Ana Conesa, Joaquin Tarraga, Ignacio Medina, Eva Alloza, David Montaner, Joaquin Dopazo posted to no-tag by sgoetz on 2009-08-05 13:50:42 as along with 3 people bertelsen neils balicea
	GEPAS, a web-based tool for microarray data analysis and interpretation [My Copy] Nucl. Acids Res., Vol. 36, No. suppl_2. (1 July 2008), pp. W308-314. by Joaquin Tarraga, Ignacio Medina, Jose Carbonell, et al.Jaime Huerta-Cepas, Pablo Minguez, Eva Alloza, Fatima Al-Shahrour, Susana Vegas-Azcarate, Stefan Goetz, Pablo Escobar, Francisco Garcia-Garcia, Ana Conesa, David Montaner, Joaquin Dopazo posted to no-tag by sgoetz on 2009-08-05 13:46:50 as along with 4 people rdiaz jfr guhjy GeeSharpMinor
	SNOW, a web-based tool for the statistical analysis of protein-protein interaction networks [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_2. (1 July 2009), pp. W109-114. by Pablo Minguez, Stefan Gotz, David Montaner, Fatima Al-Shahrour, Joaquin Dopazo posted to no-tag by sgoetz on 2009-08-05 13:35:47 as along with 9 people guhjy yaredo Scis0000002 kiekyon daforerog renatomilani sjcockell kshameer neils
	PROGRAM DESCRIPTION Strategies for Biological Annotation of Mammalian Systems: Implementing Gene Ontologies in Mouse Genome Informatics [My Copy] Genomics, Vol. 74, No. 1. (15 May 2001), pp. 121-128. by D. Hill posted to no-tag by sgoetz on 2009-07-27 20:05:29 as
	The GOA database in 2009--an integrated Gene Ontology Annotation resource [My Copy] Nucl. Acids Res., Vol. 37, No. suppl_1. (1 January 2009), pp. D396-403. by Daniel Barrell, Emily Dimmer, Rachael P. Huntley, David Binns, Claire O'Donovan, Rolf Apweiler posted to no-tag by sgoetz on 2009-07-27 19:53:27 as along with 5 people and 1 group MarcoAlvarez avilella guhjy lptolik paszkows Ensembl Compara citations
	Predicting gene function by conserved co-expression [My Copy] Trends in Genetics, Vol. 19, No. 5. (May 2003), pp. 238-242. by V. Vannoort, B. Snel, M. Huynen posted to no-tag by sgoetz on 2009-07-27 12:41:06 as
	Identifying functional links between genes using conserved chromosomal proximity [My Copy] Trends in Genetics, Vol. 18, No. 4. (1 April 2002), pp. 176-179. by I. Yanai posted to no-tag by sgoetz on 2009-07-27 12:37:36 as
	Probabilistic protein function prediction from heterogeneous genome-wide data. [My Copy] PloS one, Vol. 2, No. 3. (2007), e337. by Naoki Nariai, Eric D. Kolaczyk, Simon Kasif posted to no-tag by sgoetz on 2009-07-27 12:23:03 as along with 5 people cjm cerca ptrobajo wilbur tmmurali
	Structure-based function prediction: approaches and applications [My Copy] Brief Funct Genomic Proteomic, Vol. 7, No. 4. (1 July 2008), pp. 291-302. by Pier F. Gherardini, Manuela Helmer-Citterich posted to no-tag by sgoetz on 2009-07-23 19:52:56 as along with 6 people dansullivanblk flbarroso MarcoAlvarez dgront jameswasmuth pansapiens
	Protein molecular function prediction by Bayesian phylogenomics. [My Copy] PLoS computational biology, Vol. 1, No. 5. (7 October 2005) by B. E. Engelhardt, M. I. Jordan, K. E. Muratore, S. E. Brenner posted to phylogenomics by sgoetz on 2009-07-23 18:26:46 as along with 9 people and 4 groups engelhardt kentsis ana eoghanharr Einat dlr marcius sriram_s bootsy structural_bioinformatics Bioinformatics BioinfoCIPF SGU-CIPF
	Automated functional classification of experimental and predicted protein structures. [My Copy] BMC bioinformatics, Vol. 7 (02 June 2006), 278. by K. Wang, R. Samudrala posted to no-tag by sgoetz on 2009-07-09 16:22:53 as along with 1 person dimka
	Functional Classification Using Phylogenomic Inference [My Copy] PLoS Comput Biol, Vol. 2, No. 6. (30 June 2006), e77. by Duncan Brown, Kimmen Sjölander posted to phylogenomics by sgoetz on 2009-07-09 15:50:43 as along with 5 people and 2 groups sharpton druvus giovenko marcius jhc BioinfoCIPF SGU-CIPF
	Assessment of protein set coherence using functional annotations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008) by Monica Chagoyen, Jose Carazo, Alberto P. Montano posted to funsim by sgoetz on 2009-05-18 11:41:55 as along with 8 people taguchi imina Keywan druvus grahamc lptolik barriot GeeSharpMinor
	GS2: an efficiently computable measure of GO-based similarity of gene sets [My Copy] Bioinformatics, Vol. 25, No. 9. (1 May 2009), pp. 1178-1184. by Troy Ruths, Derek Ruths, Luay Nakhleh posted to funsim by sgoetz on 2009-04-28 19:59:34 as along with 4 people MarcoAlvarez guhjy chrisamiller nuin
	Metrics for GO based protein semantic similarity: a systematic evaluation [My Copy] BMC Bioinformatics, Vol. 9, No. Suppl 5. (2008), S4. by Catia Pesquita, Daniel Faria, Hugo Bastos, Antonio Ferreira, Andre Falcao, Francisco Couto posted to funsim by sgoetz on 2009-04-28 19:21:59 as along with 6 people Borsti Keywan MarcoAlvarez yas mariakmejia guhjy
	Defining functional distances over gene ontology. [My Copy] BMC bioinformatics, Vol. 9, No. 1. (2008), 50. by A. del Pozo, F. Pazos, A. Valencia posted to funsim by sgoetz on 2009-04-28 19:14:39 as along with 10 people and 2 groups biomcgary MarcoAlvarez wilbur barry tny grahamc sobolevnrm barriot carlk guhjy Bioinformatics baker-group
	Gene Ontology term overlap as a measure of gene functional similarity [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (04 August 2008), 327. by Meeta Mistry, Paul Pavlidis posted to funsim by sgoetz on 2009-04-28 19:13:02 as along with 5 people MarcoAlvarez bertelsen ndiaz guhjy barriot
	Total ancestry measure: quantifying the similarity in tree-like classification, with genomic applications [My Copy] Bioinformatics, Vol. 23, No. 16. (15 August 2007), pp. 2163-2173. by Haiyuan Yu, Ronald Jansen, Gustavo Stolovitzky, Mark Gerstein posted to funsim by sgoetz on 2009-04-28 18:58:40 as along with 4 people mgomes carlk grahamc shigepong
	Defining functional distance using manifold embeddings of gene ontology annotations [My Copy] Proceedings of the National Academy of Sciences, Vol. 104, No. 27. (3 July 2007), pp. 11334-11339. by Gilad Lerman, Boris E. Shakhnovich posted to funsim by sgoetz on 2009-04-28 18:55:48 as
	A relation based measure of semantic similarity for Gene Ontology annotations [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 468. by Brendan Sheehan, Aaron Quigley, Benoit Gaudin, Simon Dobson posted to funsim by sgoetz on 2009-04-28 18:54:06 as along with 9 people and 1 group MarcoAlvarez stefanorb sobolevnrm guhjy pengchy Keywan davidecellai phoenixzxl lptolik baker-group
	Gene functional similarity search tool (GFSST) [My Copy] BMC Bioinformatics, Vol. 7, No. 1. (2006), 135. by Peisen Zhang, Jinghui Zhang, Huitao Sheng, James Russo, Brian Osborne, Kenneth Buetow posted to funsim by sgoetz on 2009-04-28 18:52:52 as
	Evaluation of GO-based functional similarity measures using S. cerevisiae protein interaction and expression profile data [My Copy] BMC Bioinformatics, Vol. 9, No. 1. (2008), 472. by Tao Xu, LinFang Du, Yan Zhou posted to funsim by sgoetz on 2009-04-28 18:34:28 as along with 7 people Borsti MarcoAlvarez cgaugain saket kshameer barriot phoenixzxl
	A new measure for functional similarity of gene products based on Gene Ontology [My Copy] BMC Bioinformatics, Vol. 7 (15 June 2006), 302. by Andreas Schlicker, Francisco S. Domingues, Jorg Rahnenfuhrer, Thomas Lengauer posted to funsim by sgoetz on 2009-04-28 18:33:22 as along with 8 people and 1 group stefanorb MarcoAlvarez bsamal yas CitoJam gaudan iris_2001 macavity1g T_lab
	An Open Graph Visualization System and Its Applications to [My Copy] Software - Practice and Experience, Vol. 30 (1999), pp. 1203-1233. by Emden R. Gansner, Stephen C. North posted to no-tag by sgoetz on 2009-03-30 15:33:27 as
	A technique for drawing directed graphs [My Copy] IEEE Transactions on Software Engineering, Vol. 19 (1993), pp. 214-230. by Emden R. Gansner, Eleftherios Koutsofios, Stephen C. North, Kiem-Phong Vo posted to no-tag by sgoetz on 2009-03-30 15:32:43 as along with 1 person antonkratz
	Direct functional assessment of the composite phenotype through multivariate projection strategies [My Copy] Genomics, Vol. 92, No. 6. (13 December 2008), pp. 373-383. by A. Conesa, R. Bro, F. Garciagarcia, et al.J. Prats, S. Gotz, K. Kjeldahl, D. Montaner, J. Dopazo posted to no-tag by sgoetz on 2009-03-27 16:22:51 as along with 1 person guhjy
	Ontologies for molecular biology. [My Copy] Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing (1998), pp. 695-706. by S. Schulze-Kremer posted to no-tag by sgoetz on 2009-02-26 16:28:57 as along with 1 person mjbell
	MIPS: a database for protein sequences, homology data and yeast genome information. [My Copy] Nucleic Acids Res, Vol. 25, No. 1. (1 January 1997), pp. 28-30. by H. W. Mewes, K. Albermann, K. Heumann, S. Liebl, F. Pfeiffer posted to no-tag by sgoetz on 2009-02-26 16:25:52 as along with 2 people and 1 group irenas RMGraze dbk-lab
	Enzyme nomenclature 1992: recommendations of the Nomenclature Committee of the International Union of Biochemistry and Molecular Biology on the nomenclature and classification of enzymes [My Copy] (1992) by E. C. Webb posted to no-tag by sgoetz on 2009-02-26 16:14:55 as along with 1 person incovoma
	Distinguishing homologous from analogous proteins. [My Copy] Syst Zool, Vol. 19, No. 2. (June 1970), pp. 99-113. by W. M. Fitch posted to no-tag by sgoetz on 2009-02-25 20:46:02 as along with 3 people and 2 groups cgaugain ana barry structural_bioinformatics Bioinformatics
	Similar amino acid sequences: chance or common ancestry? [My Copy] Science, Vol. 214, No. 4517. (9 October 1981), pp. 149-159. by R. F. Doolittle posted to no-tag by sgoetz on 2009-02-24 18:38:37 as
	The relation between the divergence of sequence and structure in proteins. [My Copy] The EMBO journal, Vol. 5, No. 4. (April 1986), pp. 823-826. by C. Chothia, A. M. Lesk posted to no-tag by sgoetz on 2009-02-24 17:23:26 as along with 16 people and 6 groups edvin parnell dfdong martainn ucbcjbm bertelsen semin cen4ik ana pansapiens jwm Einat marcius xdeupi ffranca insectopalo structural_bioinformatics Radiation_Damage Stressosome Bioinformatics BioinfoCIPF SGU-CIPF
	Quantification of the variation in percentage identity for protein sequence alignments [My Copy] BMC Bioinformatics, Vol. 7 (19 September 2006), 415. by Ps G. Raghava, Geoffrey J. Barton posted to no-tag by sgoetz on 2009-01-30 19:40:13 as along with 7 people and 1 group thegoose pansapiens bicko dpollard rabio medic0747 sujaikumar EisenLab
	Enzyme function less conserved than anticipated. [My Copy] J Mol Biol, Vol. 318, No. 2. (26 April 2002), pp. 595-608. by B. Rost posted to no-tag by sgoetz on 2009-01-30 19:39:12 as along with 4 people JeremyZucker kuhn cjeans shung
	Percent Sequence Identity: The Need to Be Explicit [My Copy] Structure, Vol. 12, No. 5. (May 2004), pp. 737-738. by Alex C. May posted to no-tag by sgoetz on 2009-01-30 19:33:25 as along with 2 people Julien_Fayolle dimka
	The ASTRAL Compendium in 2004. [My Copy] Nucleic acids research, Vol. 32, No. Database issue. (1 January 2004) by John-Marc M. Chandonia, Gary Hon, Nigel S. Walker, et al.Loredana Lo Conte, Patrice Koehl, Michael Levitt, Steven E. Brenner posted to no-tag by sgoetz on 2009-01-30 19:33:06 as along with 8 people bicko shacko chad_davis sriram_s aengisch rabio siebertm saunders
	Evolution of function in protein superfamilies, from a structural perspective [My Copy] Journal of Molecular Biology, Vol. 307, No. 4. (6 April 2001), pp. 1113-1143. by Annabel E. Todd, Christine A. Orengo, Janet M. Thornton posted to no-tag by sgoetz on 2009-01-30 19:18:17 as along with 10 people and 2 groups ucbcjbm flbarroso yuslinaz ana kuhn tny sriram_s cdallett uz_labu_laimi sim82 structural_bioinformatics Bioinformatics
	Assessing annotation transfer for genomics: quantifying the relations between protein sequence, structure and function through traditional and probabilistic scores [My Copy] Journal of Molecular Biology, Vol. 297, No. 1. (17 March 2000), pp. 233-249. by Cyrus A. Wilson, Julia Kreychman, Mark Gerstein posted to no-tag by sgoetz on 2009-01-30 19:17:25 as along with 2 people and 1 group JeremyZucker lfriedl kdl
	Practical limits of function prediction. [My Copy] Proteins, Vol. 41, No. 1. (1 October 2000), pp. 98-107. by D. Devos, A. Valencia posted to no-tag by sgoetz on 2009-01-30 19:08:58 as along with 5 people MarcoAlvarez shung tjimenez bayesian bootsy
	Intrinsic errors in genome annotation [My Copy] Trends in Genetics, Vol. 17, No. 8. (01 August 2001), pp. 429-431. by Damien Devos, Alfonso Valencia posted to no-tag by sgoetz on 2009-01-30 19:07:59 as along with 1 person ziquje
	Profiling gene expression using onto-express. [My Copy] Genomics, Vol. 79, No. 2. (February 2002), pp. 266-270. by P. Khatri, S. Draghici, G. C. Ostermeier, S. A. Krawetz posted to khatri2002profiling by sgoetz on 2008-12-13 13:45:28 as along with 2 people and 3 groups beapen klo Atopic_and_Seborrhoeic_Dermatitis Skin_Deep Applied_Bimatics
	A prediction-based resampling method for estimating the number of clusters in a dataset. [My Copy] Genome biology, Vol. 3, No. 7. (25 June 2002) by S. Dudoit, J. Fridlyand posted to no-tag by sgoetz on 2008-12-13 13:42:29 as along with 3 people isimpson sba amargoli
	Exploring the new world of the genome with DNA microarrays. [My Copy] Nat Genet, Vol. 21, No. 1 Suppl. (January 1999), pp. 33-37. by P. O. Brown, D. Botstein posted to brown1999exploring by sgoetz on 2008-12-13 13:41:11 as along with 4 people and 1 group frohike pengchy stsaft jeremymiller GeschwindLab
	Quantitative monitoring of gene expression patterns with a complementary DNA microarray. [My Copy] Science (New York, N.Y.), Vol. 270, No. 5235. (20 October 1995), pp. 467-470. by M. Schena, D. Shalon, R. W. Davis, P. O. Brown posted to no-tag by sgoetz on 2008-12-13 13:36:00 as along with 13 people and 1 group daforerog mqbphcw3 winterschlaefer jangamannie dragonrez Dax42 stsaft fisherp jeremymiller tvdbulck talponer frohike shikin GeschwindLab

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