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	Multi-RELIEF: a method to recognize specificity determining residues from multiple sequence alignments using a Machine-Learning approach for feature weighting [My Copy] Bioinformatics, Vol. 24, No. 1. (1 January 2008), pp. 18-25. by Kai Ye, Anton, Jaap Heringa, Adriaan P. Ijzerman, Elena Marchiori posted to families motif_discovery software by jameswasmuth on 2009-03-16 19:36:14 as along with 2 people idonaldson h-chi
	Sequence comparison by sequence harmony identifies subtype-specific functional sites. [My Copy] Nucleic acids research, Vol. 34, No. 22. (December 2006), pp. 6540-6548. by Walter Pirovano, K. Anton Feenstra, Jaap Heringa posted to families motif_discovery software by jameswasmuth on 2009-03-16 19:33:31 as along with 4 people and 2 groups mgomes marcius sriram_s marti BioinfoCIPF SGU-CIPF
	Comparative analysis of protein domain organization. [My Copy] Genome Res, Vol. 14, No. 3. (March 2004), pp. 343-353. by Y. Ye, A. Godzik posted to domains by jameswasmuth on 2008-10-24 19:02:08 as along with 4 people wiedenhoeft Schmidtc tny gulkur
	Modeling the evolution of protein domain architectures using maximum parsimony. [My Copy] Journal of molecular biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315. by Jessica H. Fong, Lewis Y. Geer, Anna R. Panchenko, Stephen H. Bryant posted to domains by jameswasmuth on 2008-10-24 19:01:01 as along with 10 people and 3 groups swp09 martainn calderonv wiedenhoeft icases marcius tny choonpeng redelings zwang BioinfoCIPF SGU-CIPF TNT
	Coevolution in defining the functional specificity [My Copy] Proteins: Structure, Function, and Bioinformatics, Vol. 75, No. 1. (April 2009), pp. 231-240. by Saikat Chakrabarti, Anna R. Panchenko posted to families motif_discovery by jameswasmuth on 2009-03-16 19:38:07 as along with 2 people qluo barry
	Characterization and prediction of residues determining protein functional specificity [My Copy] Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. 1473-1480. by John A. Capra, Mona Singh posted to families motif_discovery software by jameswasmuth on 2009-03-16 19:37:23 as along with 2 people marck renatomilani
	Functional Specificity Lies within the Properties and Evolutionary Changes of Amino Acids [My Copy] Journal of Molecular Biology, Vol. 373, No. 3. (26 October 2007), pp. 801-810. by Saikat Chakrabarti, Stephen H. Bryant, Anna R. Panchenko posted to families motif_discovery software by jameswasmuth on 2009-03-16 19:37:00 as along with 5 people and 2 groups qluo barry Einat biehl mingzhi structural_bioinformatics Bioinformatics
	Evolution after gene duplication: models, mechanisms, sequences, systems, and organisms. [My Copy] J Exp Zoolog B Mol Dev Evol (12 July 2006) by Christian Roth, Shruti Rastogi, Lars Arvestad, et al.Katharina Dittmar, Sara Light, Diana Ekman, David A A. Liberles posted to families models by jameswasmuth on 2009-03-05 21:46:40 as along with 9 people wangbo azazello zhlei operon bjorns treangen signalduplication LouisKa smbe2008
	The impact of next-generation sequencing technology on genetics [My Copy] Trends in Genetics, Vol. 24, No. 3. (11 February 2008), pp. 133-141. by E MARDIS, posted to resequencing by jameswasmuth on 2009-03-02 22:45:57 as along with 24 people and 2 groups rshe jasontsai n00c kiekyon jessopher daforerog psique idoerg floatingpoint brdwilde neils jmcq jbsaltz guhjy dchughes djkt niallhaslam urgi zerojinx hpaces jlgreen cybaer1 giovenko druvus Green Lab iSEEM
	Scanning the human genome for signals of selection [My Copy] Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 624-629. by G. Mcvean, C. Spencer posted to resequencing by jameswasmuth on 2009-03-02 22:43:13 as
	Fitness effects of beneficial mutations: the mutational landscape model in experimental evolution [My Copy] Current Opinion in Genetics & Development, Vol. In Press, Corrected Proof by Andrea J. Betancourt, Jonathan P. Bollback posted to resequencing by jameswasmuth on 2009-03-02 22:41:31 as along with 4 people druvus stevanspringer jmeppley ramensky
	Recent advances in assessing gene flow between diverging populations and species [My Copy] Current Opinion in Genetics & Development, Vol. 16, No. 6. (December 2006), pp. 592-596. by J. Hey posted to resequencing by jameswasmuth on 2009-03-02 22:40:12 as
	Focusing on comparative ape population genetics in the post-genomic age. [My Copy] Curr Opin Genet Dev, Vol. 16, No. 6. (December 2006), pp. 586-591. by A. C. Stone, B. C. Verrelli posted to resequencing by jameswasmuth on 2009-03-02 22:39:00 as along with 1 person Iden-J_GluR
	Insights into recombination from population genetic variation [My Copy] Current Opinion in Genetics & Development In Genomes and evolution, Vol. 16, No. 6. (December 2006), pp. 565-572. by Garrett Hellenthal, Matthew Stephens posted to resequencing by jameswasmuth on 2009-03-02 22:37:40 as along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
	Functional variation and evolution of non-coding DNA [My Copy] Current Opinion in Genetics & Development In Genomes and evolution, Vol. 16, No. 6. (December 2006), pp. 559-564. by C. Bird, B. Stranger, E. Dermitzakis posted to resequencing by jameswasmuth on 2009-03-02 22:36:36 as along with 9 people and 4 groups jrhill dpollard dchughes adepace lusk sujaikumar candypmcg Stew cisevol EisenLab G4ID Genetics-of-Gambling cis-regulatory-evolution
	Whole-genome re-sequencing. [My Copy] Current opinion in genetics & development In Genomes and evolution, Vol. 16, No. 6. (December 2006), pp. 545-552. by David R. Bentley posted to resequencing by jameswasmuth on 2009-03-02 22:35:58 as along with 14 people and 3 groups pristanna rshe druvus n00c anuskap mmartin usagi-kirin jmeppley frohike indigoviolet dchughes azazello jo_davies kmdaily EisenLab G4ID Genetics-of-Gambling
	Domain deletions and substitutions in the modular protein evolution [My Copy] FEBS Journal, Vol. 273, No. 9. (May 2006), pp. 2037-2047. by January W. 3rd, Francois Beaussart, Erich Bornberg-Bauer posted to domains by jameswasmuth on 2009-01-21 16:28:50 as along with 4 people clearbluespring wiedenhoeft choonpeng kluck
	Arrangements in the modular evolution of proteins [My Copy] Trends in Biochemical Sciences, Vol. 33, No. 9. (September 2008), pp. 444-451. by A. Moore posted to domains by jameswasmuth on 2009-01-21 16:27:26 as along with 2 people druvus cmzmasek
	Domain tree-based analysis of protein architecture evolution. [My Copy] Molecular biology and evolution, Vol. 25, No. 2. (1 February 2008), pp. 254-264. by Kristoffer Forslund, Anna Henricson, Volker Hollich, Erik L. Sonnhammer posted to domains by jameswasmuth on 2009-01-21 16:26:09 as along with 5 people martainn calderonv cjeans vinithepooh gulkur
	Metabolic pathway alignment between species using a comprehensive and flexible similarity measure. [My Copy] BMC systems biology, Vol. 2, No. 1. (2008) by Yunlei Li, Dick de Ridder, Marco J. de Groot, Marcel J. Reinders posted to comparative metabolism by jameswasmuth on 2008-12-30 16:01:35 as along with 2 people irenas TRHvidsten
	Duplication and Gene Conversion in the Drosophila melanogaster Genome [My Copy] PLoS Genet, Vol. 4, No. 12. (12 December 2008), e1000305. by Naoki Osada, Hideki Innan posted to comparative genomics by jameswasmuth on 2008-12-30 15:57:43 as along with 3 people proulx renewang djkt
	Predicting Pathway Membership via Domain Signatures [My Copy] Bioinformatics (1 August 2008), btn403. by Holger Frohlich, Mark Fellmann, Holger Sultmann, Annemarie Poustka, Tim Beissbarth posted to comparative domains metabolism by jameswasmuth on 2008-12-30 15:00:19 as along with 9 people le-gal druvus kshameer jfr barriot ptrobajo mdstobbe phoenixzxl guhjy
	Host-cell invasion by malaria parasites: insights from Plasmodium and Toxoplasma. [My Copy] Trends in parasitology (1 October 2008) by Jake Baum, Tim-Wolf W. Gilberger, Freddy Frischknecht, Markus Meissner posted to apicomplexa by jameswasmuth on 2008-12-30 14:59:33 as
	Annotation transfer for genomics: measuring functional divergence in multi-domain proteins. [My Copy] Genome Res, Vol. 11, No. 10. (October 2001), pp. 1632-1640. by H. Hegyi, M. Gerstein posted to domains by jameswasmuth on 2008-10-24 19:03:29 as along with 2 people and 2 groups ana tny structural_bioinformatics Bioinformatics
	The geometry of domain combination in proteins. [My Copy] J Mol Biol, Vol. 315, No. 4. (25 January 2002), pp. 927-939. by M. Bashton, C. Chothia posted to domains by jameswasmuth on 2008-10-24 19:02:57 as along with 4 people martainn Schmidtc tny choonpeng
	Just how versatile are domains? [My Copy] BMC Evolutionary Biology, Vol. 8, No. 1. (2008) by January W. 3rd, Andrew Moore, Erich B. Bauer posted to domains by jameswasmuth on 2008-10-22 16:23:49 as along with 3 people druvus cmzmasek phoenixzxl
	Modules, multidomain proteins and organismic complexity. [My Copy] FEBS J, Vol. 272, No. 19. (October 2005), pp. 5064-5078. by H. Tordai, A. Nagy, K. Farkas, L. Bányai, L. Patthy posted to domains protein by jameswasmuth on 2008-09-26 18:57:40 as along with 3 people wiedenhoeft choonpeng cckan
	Quantification of the Elevated Rate of Domain Rearrangements in Metazoa [My Copy] Journal of Molecular Biology, Vol. 372, No. 5. (05 October 2007), pp. 1337-1348. by Diana Ekman, Åsa K. Björklund, Arne Elofsson posted to domains by jameswasmuth on 2009-10-07 20:25:32 as along with 3 people cjeans kluck gulkur
	Domain Rearrangements in Protein Evolution [My Copy] Journal of Molecular Biology, Vol. 353, No. 4. (04 November 2005), pp. 911-923. by Åsa K. Björklund, Diana Ekman, Sara Light, Johannes Frey-Skött, Arne Elofsson posted to domains by jameswasmuth on 2009-10-07 20:20:59 as along with 3 people wiedenhoeft swp09 tny
	Birth and death of protein domains: A simple model of evolution explains power law behavior [My Copy] BMC Evolutionary Biology, Vol. 2, No. 1. (2002), 18. by Georgy Karev, Yuri Wolf, Andrey Rzhetsky, Faina Berezovskaya, Eugene Koonin posted to domains by jameswasmuth on 2009-10-07 20:13:18 as along with 2 people knaseanka martainn
	Lophotrochozoa internal phylogeny: new insights from an up-to-date analysis of nuclear ribosomal genes [My Copy] Proceedings of the Royal Society B: Biological Sciences by Jordi Paps, Jaume Baguñà, Marta Riutort posted to comparative nematode phylogenetics platyhelminths by jameswasmuth on 2009-04-01 16:33:06 as
	Utility of complete large and small subunit rRNA genes in resolving the phylogeny of the Neodermata (Platyhelminthes): implications and a review of the cercomer theory [My Copy] Biological Journal of the Linnean Society, Vol. 78, No. 2. (2003), pp. 155-171. by A. E. Lockyer, P. D. Olson, D. T. J. Littlewood posted to phylogenetics platyhelminths by jameswasmuth on 2009-03-26 23:21:52 as
	Sorting by reversals, block interchanges, tandem duplications, and deletions. [My Copy] BMC bioinformatics, Vol. 10 Suppl 1 (2009) by M. Bader posted to comparative phylogenetics by jameswasmuth on 2009-03-06 15:07:54 as
	The SRS superfamily of Toxoplasma surface proteins [My Copy] International Journal for Parasitology, Vol. 34, No. 3. (09 March 2004), pp. 285-296. by C. Jung, C. Lee, M. Grigg posted to srs toxoplasma by jameswasmuth on 2009-03-03 20:12:14 as
	Highly Polymorphic Family of Glycosylphosphatidylinositol-Anchored Surface Antigens with Evidence of Developmental Regulation in Toxoplasma gondii [My Copy] Infect. Immun., Vol. 76, No. 1. (1 January 2008), pp. 103-110. by Angela M. Pollard, Krystal N. Onatolu, Luisa Hiller, Kasturi Haldar, Laura J. Knoll posted to srs toxoplasma by jameswasmuth on 2009-03-03 20:11:12 as
	Strains of Sarcocystis neurona exhibit differences in their surface antigens, including the absence of the major surface antigen SnSAG1 [My Copy] International Journal for Parasitology, Vol. 38, No. 6. (May 2008), pp. 623-631. by D. Howe, R. Gaji, A. Marsh, et al.B. Patil, W. Saville, D. Lindsay, J. Dubey, D. Granstrom posted to sarcocystis srs by jameswasmuth on 2009-03-03 20:10:02 as
	Pulling together: an integrated model of Toxoplasma cell invasion [My Copy] Current Opinion in Microbiology In Host-microbe interactions: bacteria, Vol. 10, No. 1. (February 2007), pp. 83-89. by Vern Carruthers, John C. Boothroyd posted to srs toxoplasma by jameswasmuth on 2009-03-03 20:09:06 as
	Sarcocystis neurona Merozoites Express a Family of Immunogenic Surface Antigens That Are Orthologues of the Toxoplasma gondii Surface Antigens (SAGs) and SAG-Related Sequences [My Copy] Infect. Immun., Vol. 73, No. 2. (1 February 2005), pp. 1023-1033. by Daniel K. Howe, Rajshekhar Y. Gaji, Meaghan Mroz-Barrett, Marc-Jan Gubbels, Boris Striepen, Shelby Stamper posted to srs by jameswasmuth on 2009-03-03 20:08:14 as
	Investigation of SnSPR1, a novel and abundant surface protein of Sarcocystis neurona merozoites☆ [My Copy] Veterinary Parasitology, Vol. 152, No. 3-4. (15 April 2008), pp. 210-219. by D. Zhang posted to srs by jameswasmuth on 2009-03-03 20:07:10 as
	Structural characterization of the bradyzoite surface antigen (BSR4) from Toxoplasma gondii: A unique addition to the SAG1 related superfamily. [My Copy] The Journal of biological chemistry (20 January 2009) by Joanna Crawford, Ognjen Grujic, Ekaterina Bruic, Mirjam Czjek, Michael E E. Grigg, Martin J J. Boulanger posted to srs by jameswasmuth on 2009-03-03 20:06:23 as
	Radie: visualizing taxon properties and parsimonious mappings using a radial phylogenetic tree [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 672-673. by Jacqueline Whalley, Stephen Brooks, Robert G. Beiko posted to phylogenetics software by jameswasmuth on 2009-02-25 16:34:25 as along with 1 person pauldobson
	Global Phylogeny Determined by the Combination of Protein Domains in Proteomes [My Copy] Molecular Biology and Evolution, Vol. 23, No. 12. (15 December 2006), pp. 2444-2454. by Wang, Minglei, Caetano-Anolles, Gustavo posted to domains phylogenetics by jameswasmuth on 2009-01-21 16:25:23 as
	A hierarchical model for incomplete alignments in phylogenetic inference [My Copy] Bioinformatics, Vol. 25, No. 5. (1 March 2009), pp. 592-598. by Fuxia Cheng, Stefanie Hartmann, Mayetri Gupta, Joseph G. Ibrahim, Todd J. Vision posted to ests phylogenetics by jameswasmuth on 2009-01-16 14:33:57 as along with 7 people and 1 group nuin druvus skembel djkt mhamada jmeppley sriesenfeld iSEEM
	Masking residues using context-specific evolutionary conservation significantly improves short linear motif discovery [My Copy] Bioinformatics (9 January 2009), btn664. by Norman E. Davey, Denis C. Shields, Richard J. Edwards posted to motif_discovery by jameswasmuth on 2009-01-16 14:33:17 as along with 2 people nuin neils
	Identification of structurally conserved residues of proteins in absence of structural homologs using neural network ensemble [My Copy] Bioinformatics (27 November 2008), btn618. by Ganesan Pugalenthi, Ke Tang, Pn Suganthan, Saikat Chakrabarti posted to structure by jameswasmuth on 2009-01-15 16:08:57 as along with 2 people robfsouza gulkur
	Fusion and Fission of Genes Define a Metric between Fungal Genomes [My Copy] PLoS Comput Biol, Vol. 4, No. 10. (24 October 2008), e1000200. by Pascal Durrens, Macha Nikolski, David Sherman posted to comparative genomics by jameswasmuth on 2008-12-30 14:57:59 as along with 5 people and 2 groups skembel cthachuk taguchi stajich djkt Mycology iSEEM
	Genetic and Computational Identification of a Conserved Bacterial Metabolic Module [My Copy] PLoS Genet, Vol. 4, No. 12. (19 December 2008), e1000310. by Cara C. Boutte, Balaji S. Srinivasan, Jason A. Flannick, et al.Antal F. Novak, Andrew T. Martens, Serafim Batzoglou, Patrick H. Viollier, Sean Crosson posted to comparative metabolism by jameswasmuth on 2008-12-30 14:56:47 as along with 5 people druvus michaelbarton slumpy42 ptrobajo barriot
	The evolution of connectivity in metabolic networks. [My Copy] PLoS Biol, Vol. 3, No. 7. (July 2005) by T. Pfeiffer, O. S. Soyer, S. Bonhoeffer posted to metabolism by jameswasmuth on 2008-10-29 04:34:10 as along with 10 people and 1 group sergiun wangbo wilbur westoll bjorns alexg balicea tny livingthingdan Ema livingthing
	Alignment of metabolic pathways [My Copy] Bioinformatics, Vol. 21, No. 16. (15 August 2005), pp. 3401-3408. by Ron Y. Pinter, Oleg Rokhlenko, Esti Yeger-Lotem, Michal Ziv-Ukelson posted to comparative genomics metabolism by jameswasmuth on 2008-10-29 04:32:04 as along with 3 people cmzmasek mirzazadeh carlk
	BioVenn - a web application for the comparison and visualization of biological lists using area-proportional Venn diagrams [My Copy] BMC Genomics, Vol. 9, No. 1. (2008) by Tim Hulsen, Jacob de Vlieg, Wynand Alkema posted to no-tag by jameswasmuth on 2008-10-22 16:24:01 as along with 22 people and 2 groups daveGerrard n00c jfr lscarafia jmeppley hessec GustavoLacerda stajich dswan polivares egonw ptrobajo guhjy lptolik msampson pengchy natstreet druvus barriot Zephyrus cisevol thulsen Mycology BergmanLab

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