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Tag orthology [68 articles]

Recent papers classified by the tag orthology.
  • Evolutionary analysis by whole-genome comparisons.
    J Bacteriol, Vol. 184, No. 8. (April 2002), pp. 2260-2272.
    by AK Bansal, TE Meyer
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:54:43 as ** along with 1 person bayesian
  • Genome alignment, evolution of prokaryotic genome organization, and prediction of gene function using genomic context.
    Genome Res, Vol. 11, No. 3. (March 2001), pp. 356-372.
    by YI Wolf, IB Rogozin, AS Kondrashov, EV Koonin
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:51:56 as ***** along with 2 people and 2 groups barry eweaver structural_bioinformatics Bioinformatics
  • Measuring genome evolution.
    Proc Natl Acad Sci U S A, Vol. 95, No. 11. (26 May 1998), pp. 5849-5856.
    by MA Huynen, P Bork
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:38:11 as ***** along with 4 people greger_halltorp operon kaarsinogen ruvido
  • Rapid genome evolution revealed by comparative sequence analysis of orthologous regions from four triticeae genomes.
    Plant Physiol, Vol. 135, No. 1. (May 2004), pp. 459-470.
    by YQ Gu, D Coleman-Derr, X Kong, OD Anderson
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:54:35 as *****
  • Genome sequence comparison and scenarios for gene rearrangements: a test case.
    Genomics, Vol. 30, No. 2. (20 November 1995), pp. 299-311.
    by S Hannenhalli, C Chappey, EV Koonin, PA Pevzner
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:55:09 as *****
  • The balance of driving forces during genome evolution in prokaryotes.
    Genome Res, Vol. 13, No. 7. (July 2003), pp. 1589-1594.
    by V Kunin, CA Ouzounis
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 21:33:35 as ***** along with 2 people kaarsinogen evodeva
  • Computer analysis of transcription regulatory patterns in completely sequenced bacterial genomes.
    Nucleic Acids Res, Vol. 27, No. 14. (15 July 1999), pp. 2981-2989.
    by AA Mironov, EV Koonin, MA Roytberg, MS Gelfand
    posted to evolution homology orthology paralogy transcription by ziquje on 2005-05-09 21:40:22 as ** along with 1 person kaarsinogen
  • Comprehensive comparison between locations of orthologous genes on archaeal and bacterial genomes.
    Bioinformatics, Vol. 17, No. 9. (September 2001), pp. 791-802.
    by K Horimoto, S Fukuchi, K Mori
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:54:22 as **
  • Beyond complete genomes: from sequence to structure and function.
    Curr Opin Struct Biol, Vol. 8, No. 3. (June 1998), pp. 355-363.
    by EV Koonin, RL Tatusov, MY Galperin
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:54:52 as *****
  • Comparing bacterial genomes through conservation profiles.
    Genome Res, Vol. 13, No. 5. (May 2003), pp. 991-998.
    by MJ Martin, J Herrero, A Mateos, J Dopazo
    posted to evolution homology orthology paralogy by ziquje on 2005-05-09 20:55:00 as *****
  • Assessing performance of orthology detection strategies applied to eukaryotic genomes.
    PLoS ONE, Vol. 2 (2007)
    by F Chen, AJ Mackey, JK Vermunt, DS Roos
    posted to methods orthology by winterschlaefer on 2007-09-07 14:26:43 as ** along with 10 people and 3 groups druvus icases operon rvosa indigoviolet stajich cjeans bpcusack cerca natstreet EisenLab FAB-lab TNT
  • An assessment of the uses of homologous interactions
    Bioinformatics (27 November 2007), btm576.
    by Ramazan Saeed, Charlotte Deane
    posted to ppi orthology by winterschlaefer on 2008-10-06 11:49:35 as ** along with 8 people chad_davis grahamc cjeans laughcry mingzhi cdeane Pao-Yang samesense
  • Choosing BLAST options for better detection of orthologs as reciprocal best hits
    Bioinformatics (26 November 2007), btm585.
    by Gabriel Moreno-Hagelsieb, Kristen Latimer
    posted to orthology by winterschlaefer on 2008-02-01 10:09:50 as *** along with 8 people druvus natstreet cdeane guhjy cjeans renatomilani mclarenv cerca
  • Inparanoid: a comprehensive database of eukaryotic orthologs.
    Nucleic Acids Res, Vol. 33, No. Database issue. (1 January 2005)
    by KP O'Brien, M Remm, EL Sonnhammer
    posted to wormbase orthology nematode elegans celegans caenorhabditis_elegans c_elegans article algorithm by tharris on 2008-09-24 22:52:18 as *** along with 8 people and 2 groups mdimmic tmmurali dragonrez indigoviolet tny bluto incovoma jandot C. elegans / WormBase EisenLab
  • What is a gene, post-ENCODE? History and updated definition.
    Genome Res, Vol. 17, No. 6. (June 2007), pp. 669-681.
    by MB Gerstein, C Bruce, JS Rozowsky, D Zheng, J Du, JO Korbel, O Emanuelsson, ZD Zhang, S Weissman, M Snyder
    posted to bioinformatics encode geneprediction genomeanalysis orthology by tharris on 2008-06-02 20:25:26 as ** along with 26 people and 4 groups guhjy carolh12 eweaver dpollard balicea dchughes dullhunk madhadron cottrell grahamc egonw ghattem sujaikumar Garamonfok PunkRock jasonbobe PredictER cabbagezs Jporci kmdaily krokicki antonkratz Minty hpaces altotor mjoach Bioinformatics EisenLab G4ID Genetics-of-Gambling
  • Quantification of ortholog losses in insects and vertebrates.
    Genome Biology, Vol. 8 (16 November 2007), R242.
    by Stefan Wyder, Evgenia V Kriventseva, Reinhard Schroder, Tatsuhiko Kadowaki, Evgeny M Zdobnov
    posted to bioinformatics comparative orthology phylogenetics by svdate on 2007-12-04 16:37:22 as ** along with 3 people and 2 groups cjeans hpaces hlapp Bioinformatics ParkinsonLab_at_MaRS
  • Orthology prediction at Scalable Resolution by Phylogenetic Tree analysis
    BMC Bioinformatics, Vol. 8 (08 March 2007), 83.
    by Rene TJM van der Heijden, Berend Snel, Vera van Noort, Martijn A Huynen
    posted to orthologs orthology by svdate on 2007-12-04 15:51:27 as *** along with 1 person operon
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference
    Bioinformatics, Vol. 23, No. 7. (1 April 2007), pp. 815-824.
    by Dutilh, , Van Noort, , van der Heijden, , Boekhout, , Snel, , Huynen,
    posted to orthologs orthology phylogenetics by svdate on 2007-12-04 15:52:57 as *** along with 1 person maximilianh
  • Assessing the evolutionary rate of positional orthologous genes in prokaryotes using synteny data
    BMC Evolutionary Biology, Vol. 7 (29 November 2007), 237.
    by Frederic Lemoine, Olivier Lespinet, Bernard Labedan
    posted to orthology phylogenetics prokaryotes by stajich on 2007-12-05 05:01:44 as ** along with 1 group Berkeley Mycology
  • notes BranchClust: A phylogenetic algorithm for selecting gene families
    BMC Bioinformatics, Vol. 8 (10 April 2007), 120.
    by Maria S Poptsova, Peter J Gogarten
    posted to bioinformatics gene_tree methods orthology paralogs phylogenetics phylogenomics by stajich on 2008-08-17 18:17:13 as ** along with 2 people and 2 groups dandaman rvosa FAB-lab Berkeley Mycology
  • Large-scale assignment of orthology: back to phylogenetics?
    Genome Biology, Vol. 9, No. 10. (2008)
    by Toni Gabaldon
    posted to orthology by samgj on 2008-11-10 11:24:11 as ** along with 8 people cgaugain GustavoLacerda treangen maximilianh natstreet druvus APRegier barriot
  • InParanoid 6: eukaryotic ortholog clusters with inparalogs.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by AC Berglund, E Sjölund, G Ostlund, EL Sonnhammer
    posted to clustering database inparanoid orthology paralogy by ninch on 2008-05-12 12:51:40 as read along with 1 person guhjy
  • A genomic perspective on protein families.
    Science, Vol. 278, No. 5338. (24 October 1997), pp. 631-637.
    by RL Tatusov, EV Koonin, DJ Lipman
    posted to clustering cog orthology rbh by ninch on 2007-10-20 01:18:55 as read along with 6 people bjorns balajis nuke2005 AaronDarling ruvido Ema
  • Automatic clustering of orthologs and inparalogs shared by multiple proteomes.
    Bioinformatics, Vol. 22, No. 14. (15 July 2006)
    by A Alexeyenko, I Tamas, G Liu, EL Sonnhammer
    posted to clustering inparanoid orthology single-linkage by ninch on 2007-10-13 00:41:48 as read along with 3 people and 2 groups operon indigoviolet jhc EisenLab BioinfoCIPF
  • Detecting putative orthologs.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711.
    by DP Wall, HB Fraser, AE Hirsh
    posted to orthology rsd by ninch on 2007-10-13 00:55:52 as read along with 6 people and 3 groups operon ana indigoviolet dquest rvosa cerca structural_bioinformatics Bioinformatics EisenLab
  • The role of lineage-specific gene family expansion in the evolution of eukaryotes.
    Genome Res, Vol. 12, No. 7. (July 2002), pp. 1048-1059.
    by O Lespinet, YI Wolf, EV Koonin, L Aravind
    posted to clustering orthology single-linkage by ninch on 2007-10-13 01:19:59 as read along with 1 person and 1 group tharris C. elegans / WormBase
  • Automatic clustering of orthologs and in-paralogs from pairwise species comparisons.
    J Mol Biol, Vol. 314, No. 5. (14 December 2001), pp. 1041-1052.
    by M Remm, CE Storm, EL Sonnhammer
    posted to bootstrapping clustering inparanoid orthology paralogy rbh by ninch on 2007-10-13 00:38:32 as read along with 10 people and 3 groups tharris tmmurali indigoviolet Sharpshoot jhc gurkanbebek bluto incovoma cerca wiedehopf C. elegans / WormBase EisenLab BioinfoCIPF
  • Automated ortholog inference from phylogenetic trees and calculation of orthology reliability.
    Bioinformatics, Vol. 18, No. 1. (January 2002), pp. 92-99.
    by CE Storm, EL Sonnhammer
    posted to bootstrapping clustering orthology phylogeny by ninch on 2007-10-13 00:32:00 as read along with 5 people and 1 group mdimmic operon rvosa dlr indigoviolet EisenLab
  • OrthoMCL: identification of ortholog groups for eukaryotic genomes.
    Genome Res, Vol. 13, No. 9. (September 2003), pp. 2178-2189.
    by L Li, CJ Stoeckert, DS Roos
    posted to clustering orthology orthomcl by ninch on 2007-10-14 12:25:45 as read along with 10 people and 2 groups dullhunk natstreet druvus tharris mdimmic operon indigoviolet AaronDarling bluto maximilianh C. elegans / WormBase EisenLab
  • Bayesian gene/species tree reconciliation and orthology analysis using MCMC.
    Bioinformatics, Vol. 19 Suppl 1 (2003), pp. i7-i15.
    by L Arvestad, AC Berglund, J Lagergren, B Sennblad
    posted to bayesian orthology reconciliation by ninch on 2007-10-13 00:50:32 as *** along with 2 people arve bioinfo
  • Roundup: a multi-genome repository of orthologs and evolutionary distances
    Bioinformatics, Vol. 22, No. 16. (15 August 2006), pp. 2044-2046.
    by Todd F Deluca, I-Hsien Wu, Jian Pu, Thomas Monaghan, Leonid Peshkin, Saurav Singh, Dennis P Wall
    posted to clustering orthology rsd by ninch on 2007-10-20 01:13:56 as read along with 3 people and 1 group operon indigoviolet cjeans EisenLab
  • Ortholog Clustering on a Multipartite Graph
    IEEE/ACM Trans. Comput. Biol. Bioinformatics, Vol. 4, No. 1. (January 2007), pp. 17-27.
    by Akshay Vashist, Casimir A Kulikowski, Ilya Muchnik
    posted to clustering orthology by ninch on 2007-10-13 01:03:37 as *** along with 2 people bigbossman SimonStrel
  • OrthoMCL-DB: querying a comprehensive multi-species collection of ortholog groups.
    Nucleic Acids Res, Vol. 34, No. Database issue. (1 January 2006)
    by F Chen, AJ Mackey, CJ Stoeckert, DS Roos
    posted to database orthology orthomcl by ninch on 2008-05-12 13:02:16 as * along with 4 people dullhunk druvus operon maximilianh
  • COCO-CL: hierarchical clustering of homology relations based on evolutionary correlations.
    Bioinformatics, Vol. 22, No. 7. (1 April 2006), pp. 779-788.
    by R Jothi, E Zotenko, A Tasneem, TM Przytycka
    posted to bootstrapping clustering correlation orthology single-linkage by ninch on 2007-10-13 01:37:04 as read along with 1 person tny
  • Hierarchical clustering algorithm for comprehensive orthologous-domain classification in multiple genomes.
    Nucleic Acids Res, Vol. 34, No. 2. (2006), pp. 647-658.
    by I Uchiyama
    posted to clustering orthology by ninch on 2007-10-13 01:39:53 as *****
  • Enhancing the prediction of protein pairings between interacting families using orthology information
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Jose Izarzugaza, David Juan, Carles Pons, Florencio Pazos, Alfonso Valencia
    posted to bioinformatics interaction orthology phylogeny prediction protein-protein by neils on 2008-01-24 02:01:55 as ** along with 1 person chad_davis
  • eggNOG: automated construction and annotation of orthologous groups of genes
    Nucl. Acids Res. (16 October 2007), gkm796.
    by Lars J Jensen, Philippe Julien, Michael Kuhn, Christian von Mering, Jean Muller, Tobias Doerks, Peer Bork
    posted to orthology by maximilianh on 2008-01-14 11:27:51 as ** along with 5 people guhjy jmeppley Thaverkamp hplatero larsjuhljensen
  • Circular reasoning rather than cyclic expression
    Genome Biology, Vol. 9 (23 June 2008), 403.
    by Lars J Jensen, Ulrik de Lichtenberg, Thomas S Jensen, Søren Brunak, Peer Bork
    posted to cell-cycle evolution expression function orthology periodicity regulation by larsjuhljensen on 2008-06-29 08:00:35 as read along with 2 people bpcusack marck
  • Functionality of system components: conservation of protein function in protein feature space.
    Genome Res, Vol. 13, No. 11. (November 2003), pp. 2444-2449.
    by LJ Jensen, DW Ussery, S Brunak
    posted to evolution function machine-learning orthology protein-features by larsjuhljensen on 2008-03-24 15:05:15 as read
  • Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary.
    Bioinformatics (7 April 2005)
    by Xizeng Mao, Tao Cai, John G G Olyarchuk, Liping Wei
    posted to go kegg orthology pathways by incovoma on 2007-07-14 19:18:24 as ** along with 2 people aalibes duartemolha
  • Human and orthologous gene nomenclature
    Gene, Vol. 369 (15 March 2006), pp. 1-6.
    by Mathew W Wright, Elspeth A Bruford
    posted to gene-nomenclature orthology by dchughes to the group G4ID on 2006-03-10 09:58:57 as ** along with 1 person and 1 group guhjy Genetics-of-Gambling
  • A phylogenomic approach to microbial evolution.
    Nucleic Acids Res, Vol. 29, No. 2. (15 January 2001), pp. 545-552.
    by T Sicheritz-Pontén, SG Andersson
    posted to comparative_genomics genome_evolution hgt orthology phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-16 19:33:02 as * along with 2 people and 1 group LeightonP greger_halltorp structural_bioinformatics
  • Protein Molecular Function Prediction by Bayesian Phylogenomics.
    PLoS Comput Biol, Vol. 1, No. 5. (7 October 2005)
    by Barbara E E Engelhardt, Michael I I Jordan, Kathryn E E Muratore, Steven E E Brenner
    posted to function_prediction gene_duplication hgt orthology phylogenomics protein_evolution protein_function protein_sequence by ana to the group Bioinformatics on 2005-11-22 19:15:19 as ** along with 7 people and 3 groups kentsis eoghanharr Einat dlr marcius sriram_s bootsy structural_bioinformatics BioinfoCIPF SGU-CIPF
  • Identification of functional links between genes using phylogenetic profiles.
    Bioinformatics, Vol. 19, No. 12. (12 August 2003), pp. 1524-1530.
    by J Wu, S Kasif, C DeLisi
    posted to comparative_genomics function_prediction orthology phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-15 19:46:02 as *** along with 3 people and 1 group bioinfo winterschlaefer shung structural_bioinformatics
  • PhyloGenie: automated phylome generation and analysis.
    Nucleic Acids Res, Vol. 32, No. 17. (2004), pp. 5231-5238.
    by T Frickey, AN Lupas
    posted to comparative_genomics genome_evolution hgt orthology phylogeny protein_sequence sequence_comparison by ana to the group Bioinformatics on 2005-06-15 19:38:44 as *** along with 2 people and 1 group Garamonfok Patola structural_bioinformatics
  • Tree pattern matching in phylogenetic trees: automatic search for orthologs or paralogs in homologous gene sequence databases
    Bioinformatics, Vol. 21, No. 11. (1 June 2005), pp. 2596-2603.
    by Jean-Francois Dufayard, Laurent Duret, Simon Penel, Manolo Gouy, Francois Rechenmann, Guy Perriere
    posted to comparative_genomics orthology phylogeny by ana to the group Bioinformatics on 2005-06-15 20:14:03 as **** along with 2 people and 1 group stajich rvosa structural_bioinformatics
  • An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res, Vol. 30, No. 7. (1 April 2002), pp. 1575-1584.
    by AJ Enright, S Van Dongen, CA Ouzounis
    posted to algorithm orthology by indigoviolet to the group EisenLab on 2007-11-29 02:08:35 as ** along with 13 people and 1 group chad_davis camster operon knaseanka skhadar nirfriedman dgront entropy gcalda GustavoLacerda hpaces RebeccaHamer Borelli dbk-lab
  • Cross-referencing eukaryotic genomes: TIGR Orthologous Gene Alignments (TOGA).
    Genome Res, Vol. 12, No. 3. (March 2002), pp. 493-502.
    by Y Lee, R Sultana, G Pertea, J Cho, S Karamycheva, J Tsai, B Parvizi, F Cheung, V Antonescu, J White, I Holt, F Liang, J Quackenbush
    posted to algorithm orthology by indigoviolet to the group EisenLab on 2007-11-29 02:12:26 as ** along with 1 person mdimmic
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to bacteria gene-regulation orthology transcription-factors by blobbybirdman to the group Myxo group on 2008-01-26 15:29:11 as ***** along with 10 people and 2 groups druvus treangen carlk operon dpollard dquest djkt zwang cabbagezs heliopais EisenLab cis-regulatory-evolution
  • Gene family evolution and homology: genomics meets phylogenetics.
    Annu Rev Genomics Hum Genet, Vol. 1 (2000), pp. 41-73.
    by JW Thornton, R DeSalle
    posted to transfer parsimony orthology lateral homology hgt gene evolution duplication by fhsantanna on 2008-05-26 00:47:45 as ** along with 1 person Schmidtc
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