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Tag phylogenetic [121 articles]

Recent papers classified by the tag phylogenetic.
  • Discovering functional linkages and uncharacterized cellular pathways using phylogenetic profile comparisons: a comprehensive assessment
    BMC Bioinformatics, Vol. 8 (23 May 2007), 173.
    by Raja Jothi, Teresa M Przytycka, L Aravind
    posted to phylogenetic protein-function-prediction by yas on 2007-05-24 18:50:56 as ** along with 1 group T_lab
  • Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers
    Genome, Vol. 48, No. 4. (1 August 2005), pp. 731-737.
    by NA Barkley, ML Newman, ML Wang, MW Hotchkiss, GA Pederson
    posted to a and assessment bamboo by collection diversity est-ssr genetic markers of phylogenetic relationships temperate the transferred using by xixibio on 2006-04-19 13:56:48 as ** along with 1 person yife
  • Sequence Evidence in the Archaeal Genomes that tRNAs Emerged Through the Combination of Ancestral Genes as 5′ and 3′ tRNA Halves
    PLoS ONE, Vol. 3, No. 2. (20 February 2008), e1622.
    by Kosuke Fujishima, Junichi Sugahara, Masaru Tomita, Akio Kanai
    posted to trna phylogenetic introns fragment by vwchan on 2008-10-07 19:44:24 as **
  • 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 phylogenetic analysis by treangen on 2008-11-21 13:06:43 as ** along with 5 people renatomilani barriot behindtherabbit druvus nuin
  • Computational reconstruction of ancestral DNA sequences.
    Methods in molecular biology (Clifton, N.J.), Vol. 422 (2008), pp. 171-184.
    by M Blanchette, AB Diallo, ED Green, W Miller, D Haussler
    posted to tree species sequence phylogenetic multiple ancestral alignmnent accuracy 2008 by treangen on 2008-11-25 09:26:55 as ** along with 1 person druvus
  • A new sequence distance measure for phylogenetic tree construction
    Bioinformatics, Vol. 19, No. 16. (1 November 2003), pp. 2122-2130.
    by Hasan H Otu, Khalid Sayood
    posted to tree sequence phylogenetic distance alignment-free by treangen on 2008-11-25 13:00:33 as ** along with 1 person operon
  • XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
    BMC Bioinformatics, Vol. 9 (07 October 2008), 420.
    by Daniel N Frank
    posted to xplorseq software sequence phylogenetic metagenomics by treangen on 2008-11-29 17:47:45 as ** along with 2 people ojabado nuin
  • An efficient algorithm for statistical multiple alignment on arbitrary phylogenetic trees.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 10, No. 6. (2003), pp. 869-889.
    by GA Lunter, I Miklós, YS Song, J Hein
    posted to trees statistical-alignment phylogenetic multiple algorithm by treangen on 2008-11-21 10:34:10 as **
  • Application of Phylogenetic Networks in Evolutionary Studies
    Molecular Biology and Evolution, Vol. 23, No. 2. (20 February 2006), pp. 254-267.
    by Daniel H Huson, David Bryant
    posted to splitstree software phylogenetic networks evolution by treangen on 2008-11-24 10:02:24 as ** along with 6 people and 1 group druvus cvernesi kinestetika cndewey dandaman ArtemPankin microbiology_nijmegen
  • Phylogenetic signal and functional categories in Proteobacteria genomes.
    BMC evolutionary biology, Vol. 7 Suppl 1 (2007)
    by I Comas, A Moya, F González-Candelas
    posted to phylogenetic genome essential-genes bacteria by treangen on 2008-11-25 12:55:18 as **
  • Phylogeny.fr: robust phylogenetic analysis for the non-specialist.
    Nucleic acids research (6 May 2008)
    by A Dereeper, V Guignon, G Blanc, S Audic, S Buffet, F Chevenet, J-F F Dufayard, S Guindon, V Lefort, M Lescot, J-M M Claverie, O Gascuel
    posted to webserver software phylogeny phylogenetic analyses by treangen on 2008-11-25 13:03:57 as ** along with 3 people operon druvus sanchezbuelna
  • Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees
    Molecular Biology and Evolution, Vol. 23, No. 11. (November 2006), pp. 2090-2100.
    by Cantarel, L Brandi, Morrison, G Hilary, Pearson, William
    posted to trees similarity sequence phylogenetic accuracy by treangen on 2008-12-03 15:48:47 as ** along with 3 people gjuggler mblwhoi ArtemPankin
  • Tracing origins with molecular sequences: metazoan and eukaryotic beginnings.
    Trends in biochemical sciences, Vol. 16, No. 2. (February 1991), pp. 46-50.
    by JA Lake
    posted to reconstruction phylogenetic method by treangen on 2008-11-25 18:49:08 as **
  • Stability of Multiple Alignments and Phylogenetic Trees: An Analysis of ABC-Transporter Proteins
    Algorithms for Molecular Biology, Vol. 3 (06 November 2008), 15.
    by Andreas WM Dress, Burkhard Morgenstern, Holger Wagner
    posted to trees testing sequence phylogenetic multiple alignment accuracy 2008 by treangen on 2008-11-25 11:42:17 as ** along with 2 people nuin druvus
  • Phylogenetic and comparative gene expression analysis of barley (Hordeum vulgare) WRKY transcription factor family reveals putatively retained functions between monocots and dicots
    BMC Genomics, Vol. 9 (28 April 2008), 194.
    by Elke Mangelsen, Joachim Kilian, Kenneth W Berendzen, Uener H Kolukisaoglu, Klaus Harter, Christer Jansson, Dierk Wanke
    posted to expression gene phylogenetic by tonia_schwartz on 2008-05-01 15:51:18 as ** along with 1 person moborg
  • A distance metric for a class of tree-sibling phylogenetic networks
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. 1481-1488.
    by Gabriel Cardona, Merce Llabres, Francesc Rossello, Gabriel Valiente
    posted to bioinfpdl distance metric networks phylogenetic by Tingting on 2008-06-27 09:28:49 as ****
  • Phylogenetic comparative methods and the geography of speciation
    Trends in Ecology & Evolution, Vol. 18, No. 5. (May 2003), pp. 220-227.
    by Jonathan B Losos, Richard E Glor
    posted to and comparative geography methods of phylogenetic speciation the by sunye on 2007-12-09 03:26:33 as ** along with 1 person adacier
  • Combining Statistical Alignment and Phylogenetic Footprinting to Detect Regulatory Elements.
    Bioinformatics (18 March 2008)
    by R Satija, L Pachter, J Hein
    posted to alignment cis-regulatory drosophila footprinting phylogenetic prediction regulatory by Stew on 2008-06-06 08:24:29 as **** along with 5 people druvus eckart_bindewald maximilianh gjuggler Ema
  • CSMET: Comparative Genomic Motif Detection via Multi-Resolution Phylogenetic Shadowing
    PLoS Comput Biol, Vol. 4, No. 6. (6 June 2008), e1000090.
    by Pradipta Ray, Suyash Shringarpure, Mladen Kolar, Eric P Xing
    posted to comparative detection footprinting genomics motif phylogenetic by Stew on 2008-06-14 14:43:13 as ***** along with 5 people and 1 group madreach xili03 djkt cisevol Ema cis-regulatory-evolution
  • Evolutionary history and the effect of biodiversity on plant productivity
    Proceedings of the National Academy of Sciences, Vol. 105, No. 44. (4 November 2008), pp. 17012-17017.
    by Marc W Cadotte, Bradley J Cardinale, Todd H Oakley
    posted to phylogenetic ecology community by smkent22 on 2008-11-25 20:06:49 as ***
  • An Automated Phylogenetic Tree-Based Small Subunit rRNA Taxonomy and Alignment Pipeline (STAP)
    PLoS ONE, Vol. 3, No. 7. (2 July 2008), e2566.
    by Dongying Wu, Amber Hartman, Naomi Ward, Jonathan A Eisen
    posted to 16s phylogenetic program rrna by skato_toyaku on 2008-07-07 12:58:34 as ** along with 3 people and 3 groups druvus vaulot djkt Papers recommended by the Roscoff Plankton Group Microbial-Ecology iSEEM
  • ConSurf: identification of functional regions in proteins by surface-mapping of phylogenetic information.
    Bioinformatics, Vol. 19, No. 1. (January 2003), pp. 163-164.
    by F Glaser, T Pupko, I Paz, RE Bell, D Bechor-Shental, E Martz, N Ben-Tal
    posted to consurf detection functional information mapping phylogenetic proteins regions surface by siebertm on 2007-05-22 14:41:58 as * along with 2 people chrn bicko
  • Microbial life at high salt concentrations: phylogenetic and metabolic diversity
    Saline Systems, Vol. 4 (15 April 2008), 2.
    by Aharon Oren
    posted to metabolism oren phylogenetic review by rowenabrennavart on 2008-04-24 16:28:17 as *****
  • An improved method for identifying functionally linked proteins using phylogenetic profiles
    BMC Bioinformatics, Vol. 8, No. Suppl 4. (2007)
    by Shawn Cokus, Sayaka Mizutani, Matteo Pellegrini
    posted to profile phylogenetic by Robinder on 2008-10-23 16:50:30 as ** along with 1 person Pao-Yang
  • Predicting functional gene links from phylogenetic-statistical analyses of whole genomes.
    PLoS Comput Biol, Vol. 1, No. 1. (June 2005)
    by D Barker, M Pagel
    posted to profiles phylogenetic co-evolution by Robinder on 2008-11-14 22:34:50 as ** along with 8 people and 1 group skembel rw294 balajis maryee arunyan bartleby pradiptaray rvosa iSEEM
  • Assigning protein functions by comparative genome analysis: protein phylogenetic profiles.
    Proc Natl Acad Sci U S A, Vol. 96, No. 8. (13 April 1999), pp. 4285-4288.
    by M Pellegrini, EM Marcotte, MJ Thompson, D Eisenberg, TO Yeates
    posted to profiles phylogenetic by Robinder on 2008-10-23 16:56:36 as ** along with 10 people and 1 group dragonrez bicko lfriedl balajis opheliav tny ruvido winterschlaefer shung carlk kdl
  • Computational methods for the prediction of protein interactions.
    Curr Opin Struct Biol, Vol. 12, No. 3. (June 2002), pp. 368-373.
    by A Valencia, F Pazos
    posted to profiles phylogenetic co-evolution by Robinder on 2008-11-14 22:30:32 as ** along with 3 people chad_davis eckart_bindewald marti
  • A bias in ML estimates of branch lengths in the presence of multiple signals.
    Molecular biology and evolution, Vol. 25, No. 2. (February 2008), pp. 239-242.
    by D Penny, WT White, MD Hendy, MJ Phillips
    posted to tree phylogenetic maximum likelihood by renewang on 2008-11-18 04:21:24 as read
  • PAL2NAL: robust conversion of protein sequence alignments into the corresponding codon alignments.
    Nucleic Acids Res, Vol. 34, No. Web Server issue. (1 July 2006)
    by M Suyama, D Torrents, P Bork
    posted to alignments codon pal2nal phylogenetic r1 software by pv on 2007-03-19 12:09:03 as ** along with 1 person bluesky2006
  • Phylogenetic incongruence among oncogenic genital alpha human papillomaviruses.
    J Virol, Vol. 79, No. 24. (December 2005), pp. 15503-15510.
    by A Narechania, Z Chen, R DeSalle, RD Burk
    posted to alpha hpv incongruence phylogenetic by pv on 2006-12-12 17:00:19 as ** along with 2 people bpb chrn
  • r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock.
    Bioinformatics, Vol. 19, No. 2. (22 January 2003), pp. 301-302.
    by MJ Sanderson
    posted to absolute clock divergence evolution molecular phylogenetic r1 r8s rates software times by pv on 2007-03-19 11:57:26 as ** along with 1 person operon
  • PAML: a program package for phylogenetic analysis by maximum likelihood.
    Comput Appl Biosci, Vol. 13, No. 5. (October 1997), pp. 555-556.
    by Z Yang
    posted to likelihood maximum paml phylogenetic r1 software by pv on 2007-03-19 12:15:45 as ** along with 13 people and 3 groups alexeid druvus jmjimenez bjorns chrn chad_davis indigoviolet penka BioNica stajich usagi-kirin tharris skumagai EisenLab Nie Berkeley Mycology
  • Comparative genomics of small RNA regulatory pathway components in vector mosquitoes.
    BMC genomics, Vol. 9, No. 1. (18 September 2008)
    by Corey L Campbell, William C Black, Ann M Hess, Brian D Foy
    posted to small_rna phylogenetic pathway mosquito microrna by pengchy on 2008-09-21 01:36:41 as read along with 1 person imina
  • Genomes, phylogeny, and evolutionary systems biology.
    Proc Natl Acad Sci U S A, Vol. 102 Suppl 1 (3 May 2005), pp. 6630-6635.
    by M Medina
    posted to systems_biology phylogenetic genome evolution by pengchy on 2008-10-09 06:56:56 as ** along with 2 people and 1 group karthikram mangtronix Neoscientists
  • Prediction of evolutionarily conserved interologs in Mus musculus
    BMC Genomics, Vol. 9 (08 October 2008), 465.
    by Sailu Yellaboina, Dawood B Dudekula, Minoru SH Ko
    posted to predict ppi phylogenetic mouse evolution conservation by pengchy on 2008-10-19 13:38:07 as **
  • TBMap: A taxonomic perspective on the phylogenetic database TreeBASE
    BMC Bioinformatics, Vol. 8 (18 May 2007), 158.
    by Roderic DM Page
    posted to taxonomy phylogenetic database by orovellotti on 2008-09-04 17:04:24 as ** along with 1 group Eco informatics
  • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782.
    by L McCue, W Thompson, C Carmack, MP Ryan, JS Liu, V Derbyshire, CE Lawrence
    posted to gibbs phylogenetic sampling by nklee on 2008-01-22 00:36:18 as ** along with 3 people and 1 group dquest adepace pradiptaray EisenLab
  • Tick-borne Disease Systems: Mapping Geographic and Phylogenetic Space.
    Adv Parasitol, Vol. 62 (2006), pp. 263-291.
    by SE Randolph, DJ Rogers
    posted to ehrlichiosis phylogenetic tick-borne ticks by neteler on 2007-05-07 14:26:24 as ** along with 1 person carpi
  • Comparative Phylogenetic Analysis of the Evolution of Semelparity and Life History in Salmonid Fishes
    Evolution, Vol. 56, No. 5. (2002), pp. 1008-1020.
    by Bernard J Crespi, Roy Teo
    posted to phylogenetic semelparity by MartinBrummell on 2006-05-16 21:58:03 as ***
  • Phylogenetic Signal in the Eukaryotic Tree of Life
    Science, Vol. 321, No. 5885. (4 July 2008), pp. 121-123.
    by Michael J Sanderson
    posted to phylogenetic by marck on 2008-07-04 03:52:27 as ** along with 7 people and 3 groups caseybrown dchughes stajich gulsacan jlgreen aprasad djkt Berkeley Mycology Green Lab iSEEM
  • Estimating true evolutionary distances under the DCJ model
    Bioinformatics, Vol. 24, No. 13. (1 July 2008), pp. i114-122.
    by Yu Lin, Bernard M Moret
    posted to phylogenetic by marck on 2008-06-30 03:33:48 as **
  • Population Genetics of the Oriental Fruit Fly, Bactrocera dorsalis (Diptera: Tephritidae), in Yunnan (China) Based on Mitochondrial DNA Sequences
    Environmental Entomology, Vol. 34, No. 4. (August 2005), pp. 977-983.
    by Wei Shi, Carole Kerdelhue, Hui Ye
    posted to bactrocera phylogenetic tephritidae by lucamazzon on 2005-11-22 13:40:55 as ***
  • Phylogenetic relationships among Bactrocera species (Diptera: Tephritidae) inferred from mitochondrial DNA sequences
    Molecular Phylogenetics and Evolution, Vol. 26, No. 1. (January 2003), pp. 8-17.
    by PT Smith, S Kambhampati, KA Armstrong
    posted to bactrocera phylogenetic tephritidae by lucamazzon on 2005-11-22 13:39:16 as **
  • Ab initio genotype-phenotype association reveals intrinsic modularity in genetic networks
    Mol Syst Biol, Vol. 2, No. 1. (31 January 2006), pp. msb4100047-E1-msb4100047-E14.
    by Noam Slonim, Olivier Elemento, Saeed Tavazoie
    posted to bacteria evolution modules phenotype phylogenetic by koller on 2006-08-25 01:31:43 as *** along with 5 people and 2 groups okarsligil ccots balajis cmm dylan77 Bioinformatics FAB-lab
  • Fine-scale phylogenetic architecture of a complex bacterial community.
    Nature, Vol. 430, No. 6999. (29 July 2004), pp. 551-554.
    by SG Acinas, V Klepac-Ceraj, DE Hunt, C Pharino, I Ceraj, DL Distel, MF Polz
    posted to phylogenetic by kerekesj on 2008-04-08 05:30:58 as ** along with 4 people jmeppley bluto Thaverkamp mcox
  • Phylogenetic Analysis and the Study of Community Structure
    Oikos, Vol. 82, No. 2. (1998), pp. 397-400.
    by Philippe Grandcolas
    posted to analysis community phylogenetic strucutre by kerekesj on 2008-03-13 17:23:46 as **
  • FootPrinter: A program designed for phylogenetic footprinting.
    Nucleic Acids Res, Vol. 31, No. 13. (1 July 2003), pp. 3840-3842.
    by M Blanchette, M Tompa
    posted to factor footprinting phylogenetic transcription by kaur on 2005-10-09 17:10:05 as read along with 2 people chad_davis balajis
  • notes Multiple losses of sex within a single genus of Microsporidia
    BMC Evolutionary Biology, Vol. 7 (29 March 2007), 48.
    by Joseph E Ironside
    posted to analysis microsporidia nosema phylogenetic rpb1gene rrna sequences sex vairimorpha by jwelby on 2007-07-31 10:13:02 as ***
  • A Three-Stemmed mRNA Pseudoknot in the SARS Coronavirus Frameshift Signal
    PLoS Biology, Vol. 3, No. 6. (1 June 2005), e172.
    by Ewan P Plant, Gabriela C Pérez-Alvarado, Jonathan L Jacobs, Bani Mukhopadhyay, Mirko Hennig, Jonathan D Dinman
    posted to genetics coronavirus genomics computational database frameshift genbank motif mrna mutagenesis mutation phylogenetic predicted protein pseudoknot ribosome rna structure viral by jonathanjacobs on 2008-03-28 04:27:36 as ** along with 1 person physics
  • A bona fide La protein is required for embryogenesis in Arabidopsis thaliana
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3306-3321.
    by Sophie Fleurdepine, Jean-Marc Deragon, Martine Devic, Jocelyne Guilleminot, Cecile Bousquet-Antonelli
    posted to arabidopsis biogenesis cerevisiae development embryogenesis embryonic genome la lethal motif mutant nuclear nucleolar nucleoplasm phenotype phylogenetic plant protein ribosome rna saccharomyces thaliana by jonathanjacobs on 2008-04-08 19:44:53 as read along with 1 group The La Autoantigen.
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