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aprasad phylogenomics [36 articles]

Recent papers added to aprasad library classified by the tag phylogenomics. You can also see everyone's phylogenomics.
  • Resolution among major placental mammal interordinal relationships with genome data imply that speciation influenced their earliest radiations.
    BMC Evolutionary Biology, Vol. 8 (27 May 2008), 162.
    by Bjorn M Hallstrom, Axel Janke
    posted to tree phylogenomics phylogenetics mammal coding by aprasad on 2008-09-30 01:09:32 as **
  • Phylogenetic Inference Using Whole Genomes
    Annual Review of Genomics and Human Genetics, Vol. 9, No. 1. (2008), pp. 217-231.
    by Bruce Rannala, Ziheng Yang
    posted to review phylogenomics phylogenetics methods incongruence genomics by aprasad on 2008-09-04 17:04:51 as ** along with 3 people druvus gjuggler zwang
  • 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 phylogenetics phylogenetic_signal phylogenomics by aprasad on 2008-07-07 20:05:55 as ** along with 7 people and 3 groups dchughes stajich gulsacan jlgreen caseybrown djkt marck Berkeley Mycology Green Lab iSEEM
  • EVOLUTION: Building the Tree of Life, Genome by Genome
    Science, Vol. 320, No. 5884. (27 June 2008), pp. 1716-1717.
    by Elizabeth Pennisi
    posted to phylogenomics review by aprasad on 2008-06-27 23:43:07 as ** along with 3 people and 2 groups renatomilani gulsacan jlgreen Green Lab iSEEM
  • More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy.
    Molecular biology and evolution, Vol. 22, No. 5. (May 2005), pp. 1337-1344.
    by A Rokas, SB Carroll
    posted to phylogenetic_accuracy phylogenetics phylogenomics taxon_sampling by aprasad on 2008-06-19 21:49:06 as **
  • Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
    BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95.
    by Stefanie Hartmann, Todd J Vision
    posted to alignment est indel phylogenetics phylogenomics by aprasad on 2008-05-09 17:56:28 as ** along with 4 people and 1 group natstreet druvus stajich Patola Berkeley Mycology
  • Confirming the Phylogeny of Mammals by Use of Large Comparative Sequence Datasets.
    Molecular biology and evolution (2 May 2008)
    by Arjun B Prasad, Marc W Allard, Eric D Green
    posted to atlantogenata mammal nisc phylogenetics phylogenomics placental tree by aprasad on 2008-05-07 13:34:54 as ** along with 2 people dchughes Stew
  • Species trees from gene trees: reconstructing Bayesian posterior distributions of a species phylogeny using estimated gene tree distributions.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 504-514.
    by L Liu, DK Pearl
    posted to bayesian congruence consensus phylogenetics phylogenomics by aprasad on 2008-03-24 14:48:00 as ** along with 1 person akifumi
  • From phylogenetics to phylogenomics: the evolutionary relationships of insect endosymbiotic gamma-Proteobacteria as a test case.
    Syst Biol, Vol. 56, No. 1. (February 2007), pp. 1-16.
    by I Comas, A Moya, F González-Candelas
    posted to bacteria congruence phylogenetics phylogenomics by aprasad on 2008-03-21 15:24:52 as ** along with 1 person operon
  • The effect of branch lengths on phylogeny: An empirical study using highly conserved orthologs from mammalian genomes
    Molecular Phylogenetics and Evolution, Vol. 45, No. 1. (October 2007), pp. 81-88.
    by Austin L Hughes, Robert Friedman
    posted to mammal phylogenetics phylogenomics tree by aprasad on 2008-02-28 23:07:38 as **
  • Molecular and Genomic Data Identify the Closest Living Relative of Primates
    Science, Vol. 318, No. 5851. (2 November 2007), pp. 792-794.
    by Jan E Janecka, Webb Miller, Thomas H Pringle, Frank Wiens, Annette Zitzmann, Kristofer M Helgen, Mark S Springer, William J Murphy
    posted to phylogenetics phylogenomics primate tree by aprasad on 2007-11-09 21:43:44 as ** along with 4 people dchughes djkt zwang hpaces
  • Detecting and overcoming systematic errors in genome-scale phylogenies.
    Syst Biol, Vol. 56, No. 3. (June 2007), pp. 389-399.
    by N Rodríguez-Ezpeleta, H Brinkmann, B Roure, N Lartillot, BF Lang, H Philippe
    posted to methods non-phylogenetic_signal phylogenetics phylogenomics by aprasad on 2007-09-27 21:07:39 as ** along with 3 people and 2 groups rvosa stajich dandaman FAB-lab Berkeley Mycology
  • Phylogenomics of species from four genera of New World monkeys by flow sorting and reciprocal chromosome painting.
    BMC Evol Biol, Vol. 7 Suppl 2 (2007)
    by F Dumas, R Stanyon, L Sineo, G Stone, F Bigoni
    posted to karyotype phylogenetics phylogenomics primate tree by aprasad on 2007-09-17 14:05:47 as **
  • The human phylome
    Genome Biology, Vol. 8 (13 June 2007), R109.
    by Jaime Huerta-Cepas, Hernán Dopazo, Joaquín Dopazo, Toni Gabaldón
    posted to coding phylogenetics phylogenomics by aprasad on 2007-07-31 14:39:43 as ** along with 4 people and 2 groups dpollard grahamc cjeans sgoetz EisenLab ParkinsonLab_at_MaRS
  • A phylogenetic foundation for comparative mammalian genomics.
    Genome Inform, Vol. 12 (2001), pp. 141-154.
    by PJ Waddell, H Kishino, R Ota
    posted to mammal phylogenetics phylogenomics tree by aprasad on 2007-07-25 21:13:07 as **
  • Berkeley Phylogenomics Group web servers: resources for structural phylogenomic analysis.
    Nucleic Acids Res (8 May 2007)
    by Jake Gunn G Glanville, Dan Kirshner, Nandini Krishnamurthy, Kimmen Sjölander
    posted to alignment phylogenetics phylogenomics tools by aprasad on 2007-05-14 01:43:21 as **
  • Using genomic data to unravel the root of the placental mammal phylogeny.
    Genome Res, Vol. 17, No. 4. (April 2007), pp. 413-421.
    by WJ Murphy, TH Pringle, TA Crider, MS Springer, W Miller
    posted to indel mammal phylogenomics rare_genomic_characters root_eutheria transposon tree by aprasad on 2007-05-02 14:40:43 as read along with 1 person maximilianh
  • High-resolution species trees without concatenation
    PNAS, Vol. 104, No. 14. (3 April 2007), pp. 5936-5941.
    by Scott V Edwards, Liang Liu, Dennis K Pearl
    posted to bayesian congruence phylogenetics phylogenomics by aprasad on 2007-04-17 22:42:30 as ** along with 3 people and 1 group stevanspringer operon zwang FAB-lab
  • Overview of the First Phylogenomics Conference
    BMC Evolutionary Biology, Vol. 7, No. Suppl 1. (2007)
    by Herve Philippe, Mathieu Blanchette
    posted to phylogenomics review conference by aprasad on 2007-03-19 15:15:04 as **
  • Phylogenomics of nonavian reptiles and the structure of the ancestral amniote genome.
    Proc Natl Acad Sci U S A (16 February 2007)
    by Andrew M M Shedlock, Christopher W W Botka, Shaying Zhao, Jyoti Shetty, Tingting Zhang, Jun S S Liu, Patrick J J Deschavanne, Scott V V Edwards
    posted to genome_evolution genomics intrinsic_features phylogenomics reptile by aprasad on 2007-02-27 20:40:36 as ***
  • Genome-scale phylogeny and the detection of systematic biases.
    Mol Biol Evol, Vol. 21, No. 7. (July 2004), pp. 1455-1458.
    by MJ Phillips, F Delsuc, D Penny
    posted to error gc methods phylogenetics phylogenomics ry_coding by aprasad on 2007-02-13 17:08:55 as **
  • SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
    BMC Evolutionary Biology, Vol. 7, No. Suppl 1. (2007)
    by Beatrice Roure, Naiara R Ezpeleta, Herve Philippe
    posted to alignment ortholog phylogenetics phylogenomics tools by aprasad on 2007-02-12 19:30:28 as ** along with 2 people akifumi dmp
  • Assessment of phylogenomic and orthology approaches for phylogenetic inference.
    Bioinformatics (19 January 2007)
    by B E E Dutilh, V van Noort, R T J M T van der Heijden, T Boekhout, B Snel, M A A Huynen
    posted to whole_genome phylogenomics phylogenetics ortholog alignment by aprasad on 2007-01-29 14:41:46 as **
  • Early History of Mammals Is Elucidated with the ENCODE Multiple Species Sequencing Data
    PLoS Genetics, Vol. 3, No. 1. (1 January 2007), e2.
    by Sergey Nikolaev, Juan I Montoya-Burgos, Elliott H Margulies, Nisc C Program, Jacques Rougemont, Bruno Nyffeler, Stylianos E Antonarakis
    posted to mammal phylogenetics phylogenomics root_eutheria tree zooseq by aprasad on 2007-01-09 17:20:39 as read along with 2 people Garamonfok maximilianh
  • Insertion Events of CR1 Retrotransposable Elements Elucidate the Phylogenetic Branching Order in Galliform Birds
    Mol Biol Evol, Vol. 24, No. 1. (1 January 2007), pp. 338-347.
    by Vera B Kaiser, Marcel van Tuinen, Hans Ellegren
    posted to tree rare_genomic_characters phylogenomics phylogenetics microinversions by aprasad on 2007-01-08 14:51:00 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Microinversions in mammalian evolution
    PNAS, Vol. 103, No. 52. (26 December 2006), pp. 19824-19829.
    by MJ Chaisson, BJ Raphael, PA Pevzner
    posted to zooseq tree rare_genomic_characters phylogenomics phylogenetics microinversions by aprasad on 2007-01-08 14:49:39 as ** along with 1 person AaronDarling
  • Pegasoferae, an unexpected mammalian clade revealed by tracking ancient retroposon insertions
    PNAS, Vol. 103, No. 26. (27 June 2006), pp. 9929-9934.
    by Hidenori Nishihara, Masami Hasegawa, Norihiro Okada
    posted to laurasiatheria mammal phylogenomics rare_genomic_characters transposon tree by aprasad on 2006-08-17 22:51:05 as ** along with 2 people and 1 group cmm maximilianh FAB-lab
  • Orthologous repeats and mammalian phylogenetic inference.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 998-1006.
    by A Bashir, C Ye, AL Price, V Bafna
    posted to mammal phylogenetics phylogenomics repeats tree by aprasad on 2006-03-31 22:18:40 as ** along with 1 person bpb
  • Mammalian phylogenomics comes of age.
    Trends Genet, Vol. 20, No. 12. (December 2004), pp. 631-639.
    by WJ Murphy, PA Pevzner, SJ O'Brien
    posted to mammal murphy phylogenomics review tree by aprasad on 2006-03-24 18:00:54 as ** along with 1 person balajis
  • Phylogenomics: the beginning of incongruence?
    Trends Genet (18 February 2006)
    by Olivier Jeffroy, Henner Brinkmann, Frédéric Delsuc, Hervé Philippe
    posted to phylogenomics congruence phylogenetics by aprasad on 2006-03-07 15:52:06 as ** along with 4 people and 4 groups indigoviolet dchughes taka kinestetika EisenLab G4ID microbiology_nijmegen Genetics-of-Gambling
  • Legume comparative genomics: progress in phylogenetics and phylogenomics.
    Curr Opin Plant Biol (7 February 2006)
    by Quentin Cronk, Isidro Ojeda, R Toby T Pennington
    posted to phylogenomics by aprasad on 2006-02-23 21:19:59 as **
  • Genome-scale approaches to resolving incongruence in molecular phylogenies.
    Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804.
    by A Rokas, BL Williams, N King, SB Carroll
    posted to congruence missing_data phylogenetics phylogenomics by aprasad on 2005-10-26 23:33:31 as **** along with 3 people knaseanka AaronDarling srfairclough
  • Functional genome annotation through phylogenomic mapping
    Nature Biotechnology, Vol. 23, No. 6. (06 June 2005), pp. 691-698.
    by Balaji S Srinivasan, Nora B Caberoy, Garret Suen, Rion G Taylor, Radhika Shah, Farah Tengra, Barry S Goldman, Anthony G Garza, Roy D Welch
    posted to bacteria functional genomics horizontal_gene_transfer phylogenomics by aprasad on 2005-09-23 18:12:53 as ** along with 11 people and 1 group operon setar tmmurali pggm balajis nuke2005 lyongu nedwards shoshin blobbybirdman kroos Myxo group
  • Genome trees and the nature of genome evolution.
    Annu Rev Microbiol, Vol. 59 (2005), pp. 191-209.
    by B Snel, BE Dutilh
    posted to evolution genome_evolution horizontal_gene_transfer phylogenomics supertree by aprasad on 2005-09-14 16:11:37 as ** along with 2 people knaseanka dayjm
  • Genome phylogeny based on short-range correlations in DNA sequences.
    J Comput Biol, Vol. 12, No. 5. (June 2005), pp. 545-553.
    by M Dehnert, R Plaumann, WE Helm, MT Hütt
    posted to genome_evolution phylogenomics signature by aprasad on 2005-08-29 15:51:31 as **
  • Phylogenomics of eukaryotes: impact of missing data on large alignments.
    Mol Biol Evol, Vol. 21, No. 9. (September 2004), pp. 1740-1752.
    by H Philippe, EA Snell, E Bapteste, P Lopez, PW Holland, D Casane
    posted to missing_data phylogenetics phylogenomics by aprasad on 2005-08-08 22:23:52 as read along with 1 person and 1 group jdelcampo Microbial-Ecology
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