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Tag ortholog [51 articles]

Recent papers classified by the tag ortholog.
  • Differential translation efficiency of orthologous genes is involved in phenotypic divergence of yeast species.
    Nat Genet (4 February 2007)
    by Orna Man, Yitzhak Pilpel
    posted to divergence ortholog phenotype translation by zwang on 2007-03-19 12:46:58 as ** along with 3 people and 2 groups jwestbrook grahamc bpcusack ParkinsonLab_at_MaRS King_Lab
  • A map of human protein interactions derived from co-expression of human mRNAs and their orthologs
    Mol Syst Biol, Vol. 4 (15 April 2008)
    by Arun K Ramani, Zhihua Li, Traver G Hart, Mark W Carlson, Daniel R Boutz, Edward M Marcotte
    posted to interaction ortholog protein rna by zwang on 2008-06-13 12:18:37 as ** along with 11 people and 1 group kgutwin windman83 druvus jeremymiller tmmurali biomcgary phoenixzxl giovanni grahamc ardalby ptrobajo OPIG
  • 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 bacterial gene ortholog regulation transcription by zwang on 2007-11-02 08:03:07 as ** along with 10 people and 3 groups druvus treangen carlk operon dpollard dquest djkt cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • MSOAR: A High-Throughput Ortholog Assignment System Based on Genome Rearrangement
    Journal of Computational Biology, Vol. 14, No. 9. (2007), pp. 1160-1175.
    by Zheng Fu, Xin Chen, Vladimir Vacic, Peng Nan, Yang Zhong, Tao Jiang
    posted to software ortholog genome-rearrangement gene-order by treangen on 2008-11-18 16:43:46 as ** along with 1 person AaronDarling
  • Large-scale assignment of orthology: back to phylogenetics?
    Genome Biology, Vol. 9, No. 10. (2008)
    by Toni Gabaldon
    posted to phylogeny ortholog genome by treangen on 2008-11-20 14:00:35 as ** along with 8 people cgaugain GustavoLacerda maximilianh samgj natstreet druvus APRegier barriot
  • Ancestral paralogs and pseudoparalogs and their role in the emergence of the eukaryotic cell
    Nucleic Acids Research, Vol. 33, No. 14. (2005), pp. 4626-4638.
    by Kira S Makarova, Yuri I Wolf, Sergey L Mekhedov, Boris G Mirkin, Eugene V Koonin
    posted to duplication evolution ortholog by tny on 2006-05-23 10:36:37 as ** along with 2 people bluto bpcusack
  • Differences in evolutionary pressure acting within highly conserved ortholog groups
    BMC Evolutionary Biology, Vol. 8 (17 July 2008), 208.
    by Teresa M Przytycka, Raja Jothi, L Aravind, David J Lipman
    posted to entropy_profile evolutionary_rate ortholog by tny on 2008-07-24 10:17:12 as ** along with 1 person operon
  • Null mutations in human and mouse orthologs frequently result in different phenotypes.
    Proceedings of the National Academy of Sciences of the United States of America (5 May 2008)
    by Ben-Yang Y Liao, Jianzhi Zhang
    posted to evoultion mutation ortholog phenotype by sebastien_vigneau on 2008-05-08 16:59:35 as ** along with 1 person bpcusack
  • Constant relative rate of protein evolution and detection of functional diversification among bacterial, archaeal and eukaryotic proteins.
    Genome Biol, Vol. 2, No. 12. (2001)
    by IK Jordan, FA Kondrashov, IB Rogozin, RL Tatusov, YI Wolf, EV Koonin
    posted to evolution ortholog by Schmidtc on 2005-12-05 15:53:48 as ** along with 1 person youdon
  • Genome duplication led to highly selective expansion of the Arabidopsis thaliana proteome.
    Trends Genet, Vol. 20, No. 10. (October 2004), pp. 461-464.
    by C Seoighe, C Gehring
    posted to evolution gene_family ortholog paralog review by Schmidtc on 2005-10-30 17:32:40 as ***** along with 1 person RamuAnandakrishnan
  • Phylogenetic Reconstruction of Orthology, Paralogy, and Conserved Synteny for Dog and Human
    PLoS Computational Biology, Vol. 2, No. 9. (1 September 2006), e133.
    by Leo Goodstadt, Chris P Ponting
    posted to eukaryotic evolution genomics ortholog paralog phylogenetics synteny by operon on 2007-07-23 21:11:47 as ***** along with 1 person and 1 group indigoviolet EisenLab
  • LineUp: statistical detection of chromosomal homology with application to plant comparative genomics.
    Genome research, Vol. 13, No. 5. (May 2003), pp. 999-1010.
    by S Hampson, A McLysaght, B Gaut, P Baldi
    posted to software ortholog homology bioinformatics by operon on 2008-11-11 16:29:39 as ** along with 2 people and 1 group druvus Neeperando LabDros
  • The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
    PLoS Biol, Vol. 3, No. 10. (October 2005)
    by F Ge, LS Wang, J Kim
    posted to ortholog horizontal_transfer genomics evolution by operon on 2008-10-15 15:19:30 as ** along with 3 people and 2 groups ana jmeppley AaronDarling structural_bioinformatics Bioinformatics
  • The Ka/Ks ratio: diagnosing the form of sequence evolution.
    Trends Genet, Vol. 18, No. 9. (September 2002)
    by LD Hurst
    posted to selection ortholog evolution by operon on 2008-10-15 13:00:29 as ** along with 1 person jmeppley
  • HomologMiner: looking for homologous genomic groups in whole genomes
    Bioinformatics, Vol. 23, No. 8. (15 April 2007), pp. 917-925.
    by Hou, Minmei, Berman, Piotr, Hsu, Chih-Hao, Harris, S Robert
    posted to evolution genomics ortholog software by operon on 2008-02-20 00:31:07 as ** along with 2 people treangen george_g
  • The COG database: new developments in phylogenetic classification of proteins from complete genomes.
    Nucleic Acids Res, Vol. 29, No. 1. (1 January 2001), pp. 22-28.
    by RL Tatusov, DA Natale, IV Garkavtsev, TA Tatusova, UT Shankavaram, BS Rao, B Kiryutin, MY Galperin, ND Fedorova, EV Koonin
    posted to software ortholog genomics database annotation by operon on 2008-10-15 17:22:14 as ** along with 2 people and 1 group tharris treangen C. elegans / WormBase
  • Benchmarking ortholog identification methods using functional genomics data.
    Genome Biol, Vol. 7, No. 4. (13 April 2006)
    by Tim Hulsen, Martijn A Huynen, Jacob de Vlieg, Peter M Groenen
    posted to evolution genomics ortholog phylogenetics by operon on 2007-07-23 20:27:59 as ***** along with 6 people and 1 group indigoviolet bluto bootsy alpae tmmurali cerca EisenLab
  • Improving the specificity of high-throughput ortholog prediction.
    BMC Bioinformatics, Vol. 7, No. 1. (28 May 2006)
    by Debra L Fulton, Yvonne Y Li, Matthew R Laird, Benjamin G Horsman, Fiona M Roche, Fiona S Brinkman
    posted to evolution genomics ortholog phylogenetics by operon on 2007-07-23 20:26:19 as ***** along with 4 people and 2 groups indigoviolet kaspermunch cerca rvosa Bioinformatics EisenLab
  • AL2CO: calculation of positional conservation in a protein sequence alignment.
    Bioinformatics, Vol. 17, No. 8. (August 2001), pp. 700-712.
    by J Pei, NV Grishin
    posted to software protein paralog ortholog evolution bioinformatics by operon on 2008-10-15 12:58:44 as ** along with 2 people natstreet kaarsinogen
  • The quest for orthologs: finding the corresponding gene across genomes
    Trends in Genetics (24 September 2008)
    by A Kuzniar, R Vanham, S Pongor, J Leunissen
    posted to ortholog genomics evolution doctorate by operon on 2008-10-15 14:13:06 as ** along with 7 people guhjy natstreet druvus treangen skembel gjuggler dchughes
  • 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 eukaryotic evolution optimization ortholog phylogenetics by operon on 2007-07-23 20:37:13 as ***** along with 10 people and 3 groups druvus icases rvosa indigoviolet stajich cjeans winterschlaefer bpcusack cerca natstreet EisenLab FAB-lab TNT
  • 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 evolution genomics ortholog phylogenetics by operon on 2007-07-23 20:25:11 as ***** along with 1 person svdate
  • Detecting putative orthologs.
    Bioinformatics, Vol. 19, No. 13. (1 September 2003), pp. 1710-1711.
    by DP Wall, HB Fraser, AE Hirsh
    posted to software ortholog genomics evolution bioinformatics algorithm by operon on 2008-10-15 17:20:51 as ** along with 6 people and 3 groups ana indigoviolet dquest ninch rvosa cerca structural_bioinformatics Bioinformatics EisenLab
  • 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 genome ortholog prokaryotes by kaarsinogen on 2005-05-10 22:49:44 as *** along with 4 people ziquje greger_halltorp operon ruvido
  • 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 2007 bioinformatics comparative_genomics evolution insect ortholog vertebrate by hpaces on 2007-11-20 08:02:22 as ** along with 3 people and 2 groups cjeans hlapp svdate Bioinformatics ParkinsonLab_at_MaRS
  • Using shared genomic synteny and shared protein functions to enhance the identification of orthologous gene pairs
    Bioinformatics, Vol. 21, No. 6. (15 March 2005), pp. 703-710.
    by H Zheng, Lu Fu, Wang Zhen-Yuan, Hoover Jeffrey, Mural Richard
    posted to bioinformatics genomics ortholog synteny by bsmagic to the group Bioinformatics on 2006-07-20 13:30:12 as ** along with 2 people and 2 groups indigoviolet cerca EisenLab bioinplant
  • Combining phylogenetic data with co-regulated genes to identify regulatory motifs.
    Bioinformatics, Vol. 19, No. 18. (12 December 2003), pp. 2369-2380.
    by T Wang, GD Stormo
    posted to alignment discovery motif ortholog phylogenetic by eckart_bindewald on 2008-03-25 20:43:30 as *** along with 4 people maximilianh balajis dquest natstreet
  • The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.
    PLoS ONE, Vol. 2, No. 1. (2007)
    by S Heinicke, MS Livstone, C Lu, R Oughtred, F Kang, SV Angiuoli, O White, D Botstein, K Dolinski
    posted to proteome ortholog gmod chado browser by druvus on 2008-11-12 12:34:36 as ** along with 1 person guhjy
  • PhyloPat: an updated version of the phylogenetic pattern database contains gene neighborhood.
    Nucleic acids research (2 October 2008)
    by Tim Hulsen, Peter M A M Groenen, Jacob de Vlieg, Wynand Alkema
    posted to phylogeny ortholog by druvus on 2008-10-13 07:32:22 as ** along with 2 people and 1 group stajich nuin Berkeley Mycology
  • Algorithm of OMA for large-scale orthology inference
    BMC Bioinformatics, Vol. 9 (04 December 2008), 518.
    by Alexander, Christophe Dessimoz
    posted to ortholog algorithm by druvus on 2008-12-04 16:32:32 as ** along with 1 person barriot
  • OrthologID: automation of genome-scale ortholog identification within a parsimony framework.
    Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 699-707.
    by JC Chiu, EK Lee, MG Egan, IN Sarkar, GM Coruzzi, R DeSalle
    posted to phylogeny ortholog by druvus on 2008-09-30 12:48:33 as ** along with 3 people and 1 group natstreet operon 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 software ortholog by druvus on 2008-10-01 12:30:26 as ** along with 10 people and 2 groups dullhunk natstreet tharris mdimmic operon indigoviolet AaronDarling bluto maximilianh ninch C. elegans / WormBase EisenLab
  • miROrtho: computational survey of microRNA genes
    Nucl. Acids Res. (15 October 2008), gkn707.
    by Daniel Gerlach, Evgenia V Kriventseva, Nazim Rahman, Charles E Vejnar, Evgeny M Zdobnov
    posted to ortholog mirna by druvus on 2008-10-21 07:43:58 as ** along with 5 people and 1 group guhjy moleopard giovenko samgj pengchy microRNA database
  • OmicsViz: Cytoscape plug-in for visualizing Omics data across species.
    Bioinformatics (Oxford, England) (8 September 2008)
    by Tian Xia, Julie A A Dickerson
    posted to ortholog cytoscape by druvus on 2008-10-20 11:07:27 as ** along with 5 people guhjy natstreet cjhall aconesa sjcockell
  • Scipio: Using protein sequences to determine the precise exon/intron structures of genes and their orthologs in closely related species
    BMC Bioinformatics, Vol. 9 (13 June 2008), 278.
    by Oliver Keller, Florian Odronitz, Mario Stanke, Martin Kollmar, Stephan Waack
    posted to software predictions ortholog gene by druvus on 2008-11-04 11:31:28 as ** along with 4 people natstreet guhjy GustavoLacerda tharris
  • 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 software ortholog database by druvus on 2008-10-01 12:33:09 as ** along with 4 people dullhunk operon maximilianh ninch
  • Phylogenomics of plant genomes: a methodology for genome-wide searches for orthologs in plants
    BMC Genomics, Vol. 9 (21 April 2008), 183.
    by Matthieu G Conte, Sylvain Gaillard, Gaetan Droc, Christophe Perin
    posted to phylogeny ortholog genome by druvus on 2008-09-17 07:47:54 as ** along with 3 people natstreet kengg dandaman
  • 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 ortholog phd phylogeny by dlr on 2005-11-04 18:41:59 as *** along with 5 people and 1 group mdimmic operon rvosa indigoviolet ninch EisenLab
  • 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 database ortholog by cjeans on 2007-12-08 06:38:13 as ** along with 3 people and 1 group operon indigoviolet ninch EisenLab
  • POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome
    Bioinformatics, Vol. 20, No. 17. (22 November 2004), pp. 3273-3276.
    by Tao-Wei Huang, An-Chi Tien, Wen-Shien Huang, Yuan-Chii G Lee, Chin-Lin Peng, Huei-Hun Tseng, Cheng-Yan Kao, Chi-Ying F Huang
    posted to evolution ortholog ppi by cjeans on 2007-11-30 06:47:59 as ** along with 1 person cerca
  • Orthology, paralogy and proposed classification for paralog subtypes
    Trends in Genetics, Vol. 18, No. 12. (1 December 2002), pp. 619-620.
    by Erik L Sonnhammer, Eugene V Koonin
    posted to ortholog paralog by cjeans on 2007-11-25 09:43:37 as ** along with 1 person treangen
  • Comprehensive Analysis of Orthologous Protein Domains Using the HOPS Database
    Genome Res., Vol. 13, No. 10. (1 October 2003), pp. 2353-2362.
    by Christian E Storm, Erik L Sonnhammer
    posted to detect ortholog by cjeans on 2007-06-09 04:53:45 as ****
  • RIO: analyzing proteomes by automated phylogenomics using resampled inference of orthologs.
    BMC Bioinformatics, Vol. 3 (16 May 2002)
    by CM Zmasek, SR Eddy
    posted to detect ortholog by cjeans on 2007-06-09 04:52:33 as **** along with 2 people and 1 group indigoviolet biehl EisenLab
  • 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 detect ortholog by cjeans on 2007-11-29 08:37:28 as ** along with 8 people druvus natstreet cdeane guhjy winterschlaefer renatomilani mclarenv cerca
  • Independent sorting-out of thousands of duplicated gene pairs in two yeast species descended from a whole-genome duplication
    PNAS, Vol. 104, No. 20. (15 May 2007), pp. 8397-8402.
    by Devin R Scannell, Carolin A Frank, Gavin C Conant, Kevin P Byrne, Megan Woolfit, Kenneth H Wolfe
    posted to evolution ortholog paralog by cjeans on 2007-06-10 13:20:00 as **** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • PhyloPat: phylogenetic pattern analysis of eukaryotic genes
    BMC Bioinformatics, Vol. 7 (01 September 2006), 398.
    by Tim Hulsen, Jacob de Vlieg, Peter MA Groenen
    posted to evolution ortholog phylogenetic by cjeans on 2007-06-12 10:47:53 as *** along with 1 person asddd
  • BLASTO: a tool for searching orthologous groups.
    Nucleic Acids Res, Vol. 35, No. Web Server issue. (1 July 2007)
    by Y Zhou, LF Landweber
    posted to blast ortholog search server by bpb on 2007-11-08 16:36:21 as ** along with 2 people guhjy cerca
  • POPE - a tool to aid high-throughput phylogenetic analysis.
    Bioinformatics (Oxford, England) (10 October 2008)
    by Thorhildur Juliusdottir, Fredrik Pettersson, Richard R R Copley
    posted to software phylogeny perl paralog ortholog java genomics bioinformatics by behindtherabbit on 2008-11-21 17:40:41 as ** along with 5 people renatomilani barriot treangen druvus nuin
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference.
    Bioinformatics (19 January 2007)
    by BEE Dutilh, V van Noort, van der Heijden, T Boekhout, B Snel, MAA Huynen
    posted to whole_genome phylogenomics phylogenetics ortholog alignment by aprasad on 2007-01-29 14:41:46 as **
  • Combining Bioinformatics and Phylogenetics to Identify Large Sets of Single-Copy Orthologous Genes (COSII) for Comparative, Evolutionary and Systematic Studies: A Test Case in the Euasterid Plant Clade
    Genetics, Vol. 174, No. 3. (1 November 2006), pp. 1407-1420.
    by Feinan Wu, Lukas A Mueller, Dominique Crouzillat, Vincent Petiard, Steven D Tanksley
    posted to ortholog algorithm by aprasad on 2007-01-17 21:01:35 as ** along with 1 person rsandie
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