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aprasads library [463 articles]

Neue Artikel in aprasads Bibliothek.
  • Widespread Discordance of Gene Trees with Species Tree in Drosophila: Evidence for Incomplete Lineage Sorting
    PLoS Genetics, Vol. 2, No. 10. (1 October 2006), e173.
    by Daniel A Pollard, Venky N Iyer, Alan M Moses, Michael B Eisen
    posted to phylogenetics lineage_sorting drosophila by aprasad on 2008-05-16 21:17:53 as ** along with 1 person mailund
  • Darwin's dilemma: the realities of the Cambrian ‘explosion’
    Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 361, No. 1470. (29 June 2006), pp. 1069-1083.
    by Simon C Morris
    posted to molecular_clock evolution cambrian by aprasad on 2008-05-16 21:02:17 as **
  • The impact of recombination on nucleotide substitutions in the human genome.
    PLoS genetics, Vol. 4, No. 5. (May 2008)
    by L Duret, PF Arndt
    posted to recombination mutation_rate isochore human_genome gc by aprasad on 2008-05-15 15:46:09 as **
  • Physical mapping in large genomes: accelerating anchoring of BAC contigs to genetic maps through in silico analysis.
    Funct Integr Genomics, Vol. 8, No. 1. (February 2008), pp. 29-32.
    by E Paux, F Legeai, N Guilhot, AF Adam-Blondon, M Alaux, J Salse, P Sourdille, P Leroy, C Feuillet
    posted to fpc bac_mapping bac by aprasad on 2008-05-13 15:45:28 as ** along with 1 person urgi
  • Analysis of Sequence Conservation at Nucleotide Resolution
    PLoS Computational Biology, Vol. 3, No. 12. (1 December 2007), e254.
    by Saurabh Asthana, Mikhail Roytberg, John Stamatoyannopoulos, Shamil Sunyaev
    posted to methods mcs conservation comparative_genomics by aprasad on 2008-05-13 15:42:29 as ** along with 4 people djkt GustavoLacerda nklee maximilianh
  • Genomic clocks and evolutionary timescales.
    Trends Genet, Vol. 19, No. 4. (April 2003), pp. 200-206.
    by S Blair Hedges, S Kumar
    posted to review molecular_clock methods by aprasad on 2008-05-13 01:20:45 as ** along with 1 person bandrewfox
  • Selection on Major Components of Angiosperm Genomes
    Science, Vol. 320, No. 5875. (25 April 2008), pp. 484-486.
    by Brandon S Gaut, Jeffrey Ross-Ibarra
    posted to selection plant genome_size evolution by aprasad on 2008-05-12 20:01:54 as ** along with 3 people and 1 group ArtemPankin timflutre biomcgary Khavkin's lab
  • Population size and genome size in fishes: a closer look.
    Genome / National Research Council Canada = Génome / Conseil national de recherches Canada, Vol. 51, No. 4. (April 2008), pp. 309-313.
    by TR Gregory, JD Witt
    posted to population_genetics genome_size fish by aprasad on 2008-05-12 19:04:02 as **
  • High-Resolution Mapping and Characterization of Open Chromatin across the Genome.
    Cell, Vol. 132, No. 2. (25 January 2008), pp. 311-322.
    by AP Boyle, S Davis, HP Shulha, P Meltzer, EH Margulies, Z Weng, TS Furey, GE Crawford
    posted to human_genome epigenetics chromatin by aprasad on 2008-05-10 14:23:20 as ** along with 3 people djkt bootsy epigenetics
  • Genome size, cell size, and the evolution of enucleated erythrocytes in attenuate salamanders.
    Zoology (Jena, Germany), Vol. 111, No. 3. (1 May 2008), pp. 218-230.
    by Rachel Lockridge L Mueller, T Ryan Gregory, Sean M M Gregory, Alice Hsieh, Jeffrey L L Boore
    posted to nucleotypic_effect genome_size by aprasad on 2008-05-09 18:02:15 as **
  • The evolution of genome size in ants
    BMC Evolutionary Biology, Vol. 8 (26 February 2008), 64.
    by Neil D Tsutsui, Andrew V Suarez, Joseph C Spagna, Spencer J Johnston
    posted to nucleotypic_effect genome_size evolution by aprasad on 2008-05-09 17:59:11 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 phylogenomics phylogenetics indel est alignment by aprasad on 2008-05-09 17:56:28 as ** along with 2 people and 1 group stajich Patola Berkeley Mycology
  • Mapping and sequencing of structural variation from eight human genomes
    Nature, Vol. 453, No. 7191., pp. 56-64.
    by Jeffrey M Kidd, Gregory M Cooper, William F Donahue, Hillary S Hayden, Nick Sampas, Tina Graves, Nancy Hansen, Brian Teague, Can Alkan, Francesca Antonacci, Eric Haugen, Troy Zerr, Alice N Yamada, Peter Tsang, Tera L Newman, Eray Tüzün, Ze Cheng, Heather M Ebling, Nadeem Tusneem, Robert David, Will Gillett, Karen A Phelps, Molly Weaver, David Saranga, Adrianne Brand, Wei Tao, Erik Gustafson, Kevin Mckernan, Lin Chen, Maika Malig, Joshua D Smith, Joshua M Korn, Steven A Mccarroll, David A Altshuler, Daniel A Peiffer, Michael Dorschner, John Stamatoyannopoulos, David Schwartz, Deborah A Nickerson, James C Mullikin, Richard K Wilson, Laurakay Bruhn, Maynard V Olson, Rajinder Kaul, Douglas R Smith, Evan E Eichler
    posted to structural_variation human_genome genomics evolution by aprasad on 2008-05-08 23:27:36 as ** along with 9 people and 1 group Ema hpaces kaniko psique shikin balicea djkt dchughes bpb GeneGo
  • Incorporating gaps as phylogenetic characters across eight DNA regions: ramifications for North American Psoraleeae (Leguminosae).
    Molecular phylogenetics and evolution, Vol. 46, No. 2. (February 2008), pp. 532-546.
    by AN Egan, KA Crandall
    posted to review phylogenetics methods indel by aprasad on 2008-05-07 19:35:44 as **
  • 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 tree placental phylogenomics phylogenetics nisc mammal atlantogenata by aprasad on 2008-05-07 13:34:54 as **
  • Computation and Analysis of Genomis Multi-Sequence Alignments.
    Annu Rev Genomics Hum Genet (9 May 2007)
    by Mathieu Blanchette
    posted to review methods alignment by aprasad on 2008-05-06 19:35:12 as ** along with 4 people and 1 group dpollard lilou nklee maximilianh EisenLab
  • Large-scale genomic 2D visualization reveals extensive CG-AT skew correlation in bird genomes
    BMC Evolutionary Biology, Vol. 7 (23 November 2007), 234.
    by Xuegong Deng, Ilkka Havukkala, Xuemei Deng
    posted to gc bird by aprasad on 2008-05-06 19:31:30 as **
  • Phylogenetic Mixture Models Can Reduce Node-Density Artifacts
    Systematic Biology, Vol. 57, No. 2. (2008), pp. 286-293.
    by Chris Venditti, Andrew Meade, Mark Pagel
    posted to simulation phylogenetics mixture_models methods long_branch_attraction likelihood by aprasad on 2008-04-30 17:17:03 as **
  • A simulation study of the reliability of recombination detection methods.
    Molecular biology and evolution, Vol. 18, No. 10. (October 2001), pp. 1929-1939.
    by C Wiuf, T Christensen, J Hein
    posted to simulation recombination methods incongruence bacteria by aprasad on 2008-04-28 16:35:34 as **
  • Gene conversion and the evolution of euryarchaeal chaperonins: a maximum likelihood-based method for detecting conflicting phylogenetic signals.
    Journal of molecular evolution, Vol. 55, No. 2. (August 2002), pp. 232-245.
    by JM Archibald, AJ Roger
    posted to phylogenetics lrt likelihood congruence by aprasad on 2008-04-26 14:18:59 as **
  • Influence Function for Robust Phylogenetic Reconstructions
    Mol Biol Evol, Vol. 25, No. 5. (1 May 2008), pp. 869-873.
    by Avner Bar-Hen, Mahendra Mariadassou, Marie-Anne Poursat, Philippe Vandenkoornhuyse
    posted to phylogenetics methods likelihood congruence by aprasad on 2008-04-26 13:55:27 as **
  • Analysis of chimpanzee history based on genome sequence alignments.
    PLoS genetics, Vol. 4, No. 4. (April 2008)
    by JL Caswell, S Mallick, DJ Richter, J Neubauer, C Schirmer, S Gnerre, D Reich
    posted to tree lineage_sorting human chimp alignment by aprasad on 2008-04-25 20:24:29 as **
  • Delimiting Species in Recent Radiations
    Systematic Biology, Vol. 56, No. 6. (2007), pp. 896-906.
    by Bradley H Shaffer, Robert C Thomson
    posted to bac population_genetics speciation by aprasad on 2008-04-21 16:47:07 as **
  • Molecular dating of phylogenetic trees: A brief review of current methods that estimate divergence times
    Diversity & Distributions, Vol. 12, No. 1. (January 2006), pp. 35-48.
    by Frank Rutschmann
    posted to methods molecular_clock review time by aprasad on 2008-04-18 15:04:56 as ** along with 1 person akifumi
  • Sources of Incongruence among Mammalian Mitochondrial Sequences: COII, COIII, and ND6 Genes Are Main Contributors
    Molecular Phylogenetics and Evolution, Vol. 21, No. 1. (October 2001), pp. 43-54.
    by Nikolai A Shevchuk, Marc W Allard
    posted to congruence ild mitochondria phylogenetics by aprasad on 2008-04-16 20:59:23 as **
  • De Novo Computational Design of Retro-Aldol Enzymes
    Science, Vol. 319, No. 5868. (7 March 2008), pp. 1387-1391.
    by Lin Jiang, Eric A Althoff, Fernando R Clemente, Lindsey Doyle, Daniela Rothlisberger, Alexandre Zanghellini, Jasmine L Gallaher, Jamie L Betker, Fujie Tanaka, Carlos F Barbas, Donald Hilvert, Kendall N Houk, Barry L Stoddard, David Baker
    posted to design enzyme evolution by aprasad on 2008-04-15 23:30:01 as ** along with 10 people and 2 groups ucbcjbm barry aalibes jwm dgront zwang sobolevnrm davidlott msuarezdiez scienbox structural_bioinformatics baker-group
  • Local conservation scores without a priori assumptions on neutral substitution rates
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Janis Dingel, Pavol Hanus, Niccolo Leonardi, Joachim Hagenauer, Juergen Zech, Jakob Mueller
    posted to conservation likelihood mcs by aprasad on 2008-04-15 23:28:07 as ** along with 3 people and 2 groups maximilianh RamuAnandakrishnan cisevol cis-regulatory-evolution BergmanLab
  • Understanding Neutral Genomic Molecular Clocks
    Evolutionary Biology, Vol. 34, No. 3. (22 December 2007), pp. 144-151.
    by Soojin Yi
    posted to molecular_clock mutation_rate neutral by aprasad on 2008-04-15 15:10:43 as **
  • Nutritional Control of Reproductive Status in Honeybees via DNA Methylation.
    Science (13 March 2008)
    by R Kucharski, J Maleszka, S Foret, R Maleszka
    posted to epigenetics honeybee methylation by aprasad on 2008-04-14 19:56:59 as ** along with 8 people and 1 group stevanspringer kengg djkt epigenetics aubinhon faion kjglennie sunhwan Integrative_biology_behavior
  • A phylogenetic analysis of indel dynamics in the cotton genus.
    Molecular biology and evolution (9 April 2008)
    by Corrinne E E Grover, Yeisoo Yu, Rod A A Wing, Andrew H H Paterson, Jonathan F F Wendel
    posted to evolution genome_size genomics indel plant by aprasad on 2008-04-13 03:44:11 as **
  • Coyotes demonstrate how habitat specialization by individuals of a generalist species can diversify populations in a heterogeneous ecoregion
    Mol Biol Evol (7 April 2008), msn082.
    by Benjamin N Sacks, Danika L Bannasch, Bruno B Chomel, Holly B Ernest
    posted to coyote gene_flow population_genetics by aprasad on 2008-04-11 21:52:16 as **
  • A phylogenetic approach to the problem of differential lineage sorting
    MOL. BIOL. EVOL., Vol. 14, No. 9. (1997), pp. 968-975.
    by J Lyons-Weiler, MC Milinkovitch
    posted to congruence lineage_sorting by aprasad on 2008-04-10 01:12:40 as **
  • mILD: a tool for constructing and analyzing matrices of pairwise phylogenetic character incongruence tests
    Bioinformatics, Vol. 21, No. 24. (15 December 2005), pp. 4423-4424.
    by Paul J Planet, Indra N Sarkar
    posted to congruence ild by aprasad on 2008-03-31 17:08:11 as **
  • Strong Variations of Mitochondrial Mutation Rate across Mammals--the Longevity Hypothesis
    Mol Biol Evol, Vol. 25, No. 1. (1 January 2008), pp. 120-130.
    by Benoit Nabholz, Sylvain Glemin, Nicolas Galtier
    posted to mitochondria mutation_rate by aprasad on 2008-03-31 16:52:04 as ** along with 1 person renatomilani
  • Increasing the Efficiency of Searches for the Maximum Likelihood Tree in a Phylogenetic Analysis of up to 150 Nucleotide Sequences.
    Syst Biol, Vol. 56, No. 6. (December 2007), pp. 988-1010.
    by DA Morrison
    posted to likelihood methods phylogenetics tools by aprasad on 2008-03-29 08:24:22 as ** along with 1 person akifumi
  • The genomic rate of adaptive evolution
    Trends in Ecology & Evolution, Vol. 21, No. 10. (October 2006), pp. 569-575.
    by Adam Eyre-Walker
    posted to evolution genomics mutation population_genetics selection by aprasad on 2008-03-26 17:33:45 as ** along with 4 people and 3 groups stevanspringer dchughes Garamonfok hevol FAB-lab G4ID Genetics-of-Gambling
  • Is There a Star Tree Paradox?
    Molecular Biology and Evolution, Vol. 23, No. 10. (15 October 2006), pp. 1819-1823.
    by Kolaczkowski, Bryan, Thornton, W Joseph
    posted to bayesian phylogenetics star_paradox by aprasad on 2008-03-24 18:42:33 as **
  • 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
  • Phylogenetic relationships of Cyprinidae (Teleostei: Cypriniformes) inferred from the partial S6K1 gene sequences and implication of indel sites in intron 1.
    Sci China C Life Sci, Vol. 50, No. 6. (December 2007), pp. 780-788.
    by X Kong, X Wang, X Gan, J Li, S He
    posted to fish indel phylogenetics tree by aprasad on 2008-03-23 16:07:45 as **
  • 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
  • Epigenetics for ecologists
    Ecology Letters, Vol. 11, No. 2. (February 2008), pp. 106-115.
    by Bossdorf, Oliver, Richards, L Christina, Pigliucci, Massimo
    posted to ecology epigenetics evolution methylation by aprasad on 2008-03-17 01:17:32 as **
  • Simulating DNA coding sequence evolution with EvolveAGene 3
    Mol Biol Evol (12 January 2008), msn008.
    by Barry G Hall
    posted to coding evolution selection sequence simulation by aprasad on 2008-03-12 23:27:54 as ** along with 4 people adacier operon zwang friendpine
  • Mammalian evolution and biomedicine: new views from phylogeny.
    Biol Rev Camb Philos Soc, Vol. 82, No. 3. (August 2007), pp. 375-392.
    by MS Springer, WJ Murphy
    posted to mammal phylogenetics review by aprasad on 2008-03-08 12:11:14 as **
  • Qualifying the relationship between sequence conservation and molecular function
    Genome Res., Vol. 18, No. 2. (1 February 2008), pp. 201-205.
    by Gregory M Cooper, Christopher D Brown
    posted to cns conservation functional_genomics non-coding regulatory by aprasad on 2008-03-07 16:29:07 as ** along with 4 people nklee brant djkt xingxu
  • Molecular phylogenetics: state-of-the-art methods for looking into the past.
    Trends Genet, Vol. 17, No. 5. (May 2001), pp. 262-272.
    by S Whelan, P Liò, N Goldman
    posted to methods model_selection phylogenetics review by aprasad on 2008-03-05 23:05:19 as ** along with 2 people timflutre gjuggler
  • Review of the monotreme fossil record and comparison of palaeontological and molecular data
    Comparative Biochemistry and Physiology - Part A: Molecular & Integrative Physiology, Vol. 136, No. 4. (December 2003), pp. 927-942.
    by AM Musser
    posted to fossil monotreme phylogenetics by aprasad on 2008-02-29 14:28:25 as **
  • The oldest platypus and its bearing on divergence timing of the platypus and echidna clades.
    Proc Natl Acad Sci U S A (23 January 2008)
    by Timothy Rowe, Thomas H H Rich, Patricia Vickers-Rich, Mark Springer, Michael O O Woodburne
    posted to monotreme platypus theria time_tree by aprasad on 2008-02-29 14:24:24 as ** along with 2 people stevanspringer sebastien_vigneau
  • Visualizing differences in phylogenetic information content of alignments and distinction of three classes of long-branch effects
    BMC Evolutionary Biology, Vol. 7 (28 August 2007), 147.
    by Johann W Waegele, Christoph Mayer
    posted to long_branch_attraction methods phylogenetics signal by aprasad on 2008-02-29 14:03:01 as **
  • Phylogenetic analysis of 1.5 Mbp and platypus EST data refute the Marsupionta hypothesis and unequivocally support Monotremata as sister group to Marsupialia/Placentalia
    Zoologica Scripta, Vol. 37, No. 2. (March 2008), pp. 115-127.
    by Kullberg, Morgan, Hallstrom, M Bjorn, Arnason, Ulfur, Janke, Axel
    posted to mammal marsupionta phylogenetics root theria by aprasad on 2008-02-29 13:50:05 as **
  • Visualizing Conflicting Evolutionary Hypotheses in Large Collections of Trees: Using Consensus Networks to Study the Origins of Placentals and Hexapods
    Systematic Biology, Vol. 54, No. 1. (February 2005), pp. 66-76.
    by Barbara Holland, Frederic Delsuc, Vincent Moulton
    posted to consensus mammal methods phylogenetics root tree by aprasad on 2008-02-29 04:45:59 as **
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