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aprasad's evolution [59 articles]

Recent papers added to aprasad's library classified by the tag evolution. You can also see everyone's evolution.
  • Reduced purifying selection prevails over positive selection in human copy number variant evolution.
    Genome research (7 August 2008)
    by Duc-Quang Q Nguyen, Caleb P P Webber, Jayne Hehir-Kwa, Rolph Pfundt, Joris Veltman, Chris P P Ponting
    posted to selection human genomics genome_evolution genome evolution cnv by aprasad on 2008-08-19 22:52:06 as ** along with 1 person bpcusack
  • Comparative analysis of testis protein evolution in rodents
    Genetics (9 August 2008), genetics.107.085902.
    by Leslie M Turner, Edward B Chuong, Hopi E Hoekstra
    posted to selection rodents protein evolution by aprasad on 2008-08-11 16:22:58 as ** along with 2 people dchughes djkt
  • The Chromosomal Polymorphism Linked to Variation in Social Behavior in the White-Throated Sparrow (Zonotrichia albicollis) Is a Complex Rearrangement and Suppressor of Recombination
    Genetics, Vol. 179, No. 3. (1 July 2008), pp. 1455-1468.
    by James W Thomas, Mario Caceres, Joshua J Lowman, Caroline B Morehouse, Meghan E Short, Erin L Baldwin, Donna L Maney, Christa L Martin
    posted to thomas rearrangement evolution chromosome by aprasad on 2008-07-23 19:11:43 as **
  • Coexpression of Linked Genes in Mammalian Genomes Is Generally Disadvantageous
    Mol Biol Evol, Vol. 25, No. 8. (1 August 2008), pp. 1555-1565.
    by Ben-Yang Liao, Jianzhi Zhang
    posted to selection linkage expression evolution by aprasad on 2008-07-17 00:31:56 as ** along with 3 people zwang bpcusack djkt
  • A Mixed Branch Length Model of Heterotachy Improves Phylogenetic Accuracy
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1054-1066.
    by Bryan Kolaczkowski, Joseph W Thornton
    posted to simulation phylogenetics model evolution by aprasad on 2008-06-26 21:39:09 as **
  • Fast Evolution of Core Promoters in Primate Genomes
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1239-1244.
    by Han Liang, Yeong-Shin Lin, Wen-Hsiung Li
    posted to substitution_rate promoter primate evolution by aprasad on 2008-06-26 21:31:30 as ** along with 2 people and 1 group cisevol Stew cis-regulatory-evolution
  • Life-history traits drive the evolutionary rates of mammalian coding and noncoding genomic elements
    Proceedings of the National Academy of Sciences (11 December 2007), 0705658104.
    by Sergey I Nikolaev, Juan I Montoya-Burgos, Konstantin Popadin, Leila Parand, Elliott H Margulies, National, Stylianos E Antonarakis
    posted to substitution_rate evolution coding cns by aprasad on 2008-05-22 20:05:25 as ** along with 4 people and 1 group djkt cjeans zwang cisevol cis-regulatory-evolution
  • Sequence Context affects the rate of short insertions and deletions in flies and primates
    Genome Biology, Vol. 9 (21 February 2008), R37.
    by Amos Tanay, Eric D Siggia
    posted to mutation_rate indel human_genome evolution drosophila by aprasad on 2008-05-19 15:38:57 as ** along with 5 people brant djkt lusk biomcgary gjuggler
  • 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 **
  • 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 4 people and 1 group echinotrix ArtemPankin timflutre biomcgary Khavkin's lab
  • 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 **
  • 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 16 people and 2 groups skoch3 jyuh chrisamiller maximilianh vplagnol kintoki chad_davis Ema hpaces kaniko psique shikin balicea djkt dchughes bpb Koch_Lab GeneGo
  • 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 12 people and 3 groups cambray joseph_x_zhou ucbcjbm barry aalibes jwm dgront zwang sobolevnrm davidlott msuarezdiez scienbox McCammon structural_bioinformatics baker-group
  • 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 **
  • 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 3 people and 3 groups stevanspringer dchughes Garamonfok FAB-lab G4ID Genetics-of-Gambling
  • 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 ** along with 1 person jyuh
  • 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
  • DNA assembly with gaps (Dawg): simulating sequence evolution.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by RA Cartwright
    posted to evolution phylogenetics sequence simulation tools by aprasad on 2007-09-10 15:50:05 as **
  • Using evolutionary Expectation Maximization to estimate indel rates.
    Bioinformatics, Vol. 21, No. 10. (15 May 2005), pp. 2294-2300.
    by I Holmes
    posted to evolution indel methods mutation_rate by aprasad on 2007-09-02 13:29:54 as ** along with 1 person nirfriedman
  • Evolutionary coupling between the deleteriousness of gene mutations and the amount of non-coding sequences
    Journal of Theoretical Biology, Vol. 244, No. 4. (21 February 2007), pp. 621-630.
    by Carole Knibbe, Olivier Mazet, Fabien Chaudier, Jean-Michel Fayard, Guillaume Beslon
    posted to evolution genome_size indel mutation selection by aprasad on 2007-08-28 13:43:46 as ** along with 1 person timflutre
  • A Long-Term Evolutionary Pressure on the Amount of Non-Coding DNA.
    Mol Biol Evol (19 August 2007)
    by Carole Knibbe, Antoine Coulon, Olivier Mazet, Jean-Michel M Fayard, Guillaume Beslon
    posted to evolution genome_evolution genome_size mutation selection by aprasad on 2007-08-28 13:42:48 as ** along with 5 people and 2 groups pradiptaray operon bpb cisevol coldmeadow cis-regulatory-evolution BergmanLab
  • A Comparative Genomics Analysis of Codon Reassignments Reveals a Link with Mitochondrial Proteome Size and a Mechanism of Genetic Code Change Via Suppressor tRNAs
    Journal of Molecular Evolution, Vol. 64, No. 4. (April 2007), pp. 399-410.
    by Massey, Steven, Garey, James
    posted to evolution genetic_code mitochondria by aprasad on 2007-08-13 16:30:00 as **
  • Probabilistic whole-genome alignments reveal high indel rates in the human and mouse genomes.
    Bioinformatics, Vol. 23, No. 13. (1 July 2007)
    by G Lunter
    posted to evolution human indel mouse mutation_rate whole_genome by aprasad on 2007-08-07 22:22:46 as ** along with 3 people and 1 group AaronDarling mailund elfar Bioinformatics
  • Opposite Evolutionary Effects between Different Alternative Splicing Patterns
    Mol Biol Evol, Vol. 24, No. 7. (1 July 2007), pp. 1443-1446.
    by Feng-Chi Chen, Shu-Miaw Chaw, Yun-Huei Tzeng, Sheng-Shun Wang, Trees-Juen Chuang
    posted to coding evolution genome_evolution splicing whole_genome by aprasad on 2007-07-24 17:22:39 as **
  • Exact and heuristic algorithms for the Indel Maximum Likelihood Problem.
    J Comput Biol, Vol. 14, No. 4. (May 2007), pp. 446-461.
    by AB Diallo, V Makarenkov, M Blanchette
    posted to algorithm evolution indel methods model phylogenetics by aprasad on 2007-07-21 21:34:52 as **
  • Tracking the in vivo evolution of multidrug resistance in Staphylococcus aureus by whole-genome sequencing.
    Proc Natl Acad Sci U S A, Vol. 104, No. 22. (29 May 2007), pp. 9451-9456.
    by MM Mwangi, SW Wu, Y Zhou, K Sieradzki, H de Lencastre, P Richardson, D Bruce, E Rubin, E Myers, ED Siggia, A Tomasz
    posted to bacteria drug_resistance evolution sequencing whole_genome by aprasad on 2007-07-03 12:47:00 as ** along with 1 person Xavier
  • Variation in genome size of argasid and ixodid ticks.
    Insect Biochem Mol Biol, Vol. 37, No. 5. (May 2007), pp. 399-408.
    by NS Geraci, J Spencer Johnston, J Paul Robinson, SK Wikel, CA Hill
    posted to evolution genome_size variation by aprasad on 2007-04-30 13:09:29 as **
  • Time dependency of molecular rate estimates and systematic overestimation of recent divergence times.
    Mol Biol Evol, Vol. 22, No. 7. (July 2005), pp. 1561-1568.
    by SY Ho, MJ Phillips, A Cooper, AJ Drummond
    posted to evolution mutation_rate selection time by aprasad on 2007-03-03 18:11:50 as **
  • Rate of Evolution in Brain-Expressed Genes in Humans and Other Primates.
    PLoS Biol, Vol. 5, No. 2. (26 December 2006)
    by Hurng-Yi Y Wang, Huan-Chieh C Chien, Naoki Osada, Katsuyuki Hashimoto, Sumio Sugano, Takashi Gojobori, Chen-Kung K Chou, Shih-Feng F Tsai, Chung-I I Wu, C-K James K Shen
    posted to mutation_rate human_genome evolution by aprasad on 2007-01-30 18:43:57 as ** along with 1 person Iden-J_GluR
  • Pattern and Rate of Indel Evolution Inferred from Whole Chloroplast Intergenic Regions in Sugarcane, Maize and Rice.
    DNA Res (16 November 2006)
    by Kyoko Yamane, Kentaro Yano, Taihachi Kawahara
    posted to evolution indel plants by aprasad on 2006-11-21 14:00:52 as **
  • Comparative genomic analysis of human and chimpanzee indicates a key role for indels in primate evolution.
    J Mol Evol, Vol. 63, No. 5. (November 2006), pp. 682-690.
    by A Wetterbom, M Sevov, L Cavelier, TF Bergström
    posted to chimp evolution human_genome indel primate by aprasad on 2006-11-15 15:34:16 as **
  • Bats, clocks, and rocks: diversification patterns in Chiroptera.
    Evolution Int J Org Evolution, Vol. 59, No. 10. (October 2005), pp. 2243-2255.
    by KE Jones, OR Bininda-Emonds, JL Gittleman
    posted to bat evolution mutation_rate by aprasad on 2006-10-18 23:04:06 as **
  • Frequent appearance of novel protein-coding sequences by frameshift translation.
    Genomics (3 August 2006)
    by Kohji Okamura, Lars Feuk, Tomàs Marquès-Bonet, Arcadi Navarro, Stephen W W Scherer
    posted to evolution exon by aprasad on 2006-09-26 13:59:03 as **
  • Comparison of multiple vertebrate genomes reveals the birth and evolution of human exons
    PNAS, Vol. 103, No. 36. (5 September 2006), pp. 13427-13432.
    by Xiang H Zhang, Lawrence A Chasin
    posted to evolution exon by aprasad on 2006-09-26 13:58:25 as ** along with 4 people and 3 groups eoghanharr dayjm dchughes paulcartwright G4ID Genetics-of-Gambling BergmanLab
  • Genetic and environmental influences on the relation between parental social class and mortality.
    Int J Epidemiol (21 March 2006)
    by Merete Osler, Liselotte Petersen, Eva Prescott, Thomas W W Teasdale, Thorkild I A I Sørensen
    posted to evolution social_class by aprasad on 2006-09-26 13:55:53 as **
  • Heterotachy in mammalian promoter evolution.
    PLoS Genet, Vol. 2, No. 4. (April 2006)
    by MS Taylor, C Kai, J Kawai, P Carninci, Y Hayashizaki, CA Semple
    posted to evolution indel mammal mutation_rate promoter regulatory whole_genome by aprasad on 2006-06-27 13:35:17 as ** along with 4 people and 1 group kentsis olympos cisevol gjuggler cis-regulatory-evolution
  • notes Duplication events and the evolution of segmental identity
    Evolution & Development, Vol. 7, No. 6. (November 2005), pp. 556-567.
    by I Hurley, ME Hale, VE Prince
    posted to duplication evolution genome_evolution selection speciation by aprasad on 2006-04-28 15:14:24 as ** along with 1 person and 2 groups dchughes G4ID Genetics-of-Gambling
  • Multiple sequence alignment accuracy and evolutionary distance estimation.
    BMC Bioinformatics, Vol. 6 (2005)
    by MS Rosenberg
    posted to alignment comparative_genomics evolution by aprasad on 2006-04-10 19:16:26 as ** along with 2 people and 2 groups dpollard cisevol EisenLab cis-regulatory-evolution
  • The Fundamental Theorem of Neutral Evolution: Rates of Substitution and Mutation Should Factor in Premeiotic Clusters
    Genetica, Vol. 125, No. 2-3. (November 2005), pp. 333-339.
    by RC Woodruff, JN Thomson
    posted to evolution neutral theory by aprasad on 2006-04-10 19:01:09 as **
  • Loss of dispensable genes is not adaptive in yeast.
    Proc Natl Acad Sci U S A, Vol. 102, No. 49. (6 December 2005), pp. 17670-17674.
    by P Sliwa, R Korona
    posted to coding evolution selection yeast by aprasad on 2006-04-05 16:43:07 as ** along with 2 people and 1 group dpollard i41m EisenLab
  • Low Rates of Expression-Profile Divergence in Highly-Expressed Genes and Tissue-Specific Genes During Mammalian Evolution.
    Mol Biol Evol (6 March 2006)
    by Ben-Yang Y Liao, Jianzhi Zhang
    posted to evolution genome_evolution human_genome jc selection whole_genome by aprasad on 2006-03-31 00:39:36 as ** along with 5 people and 1 group dragonrez dpollard djkt cjeans emarker EisenLab
  • Why highly expressed proteins evolve slowly.
    Proc Natl Acad Sci U S A (21 September 2005)
    by D Allan A Drummond, Jesse D D Bloom, Christoph Adami, Claus O O Wilke, Frances H H Arnold
    posted to evolution genome_evolution jc selection by aprasad on 2006-03-31 00:25:58 as ** along with 14 people and 5 groups wilbur balicea RamuAnandakrishnan rklancer stevanspringer bjorns imouthesmp dayjm Einat marcius xwbcn penka balabu malcook structural_bioinformatics Nie FAB-lab BioinfoCIPF SGU-CIPF
  • Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes.
    Genome Res, Vol. 15, No. 8. (August 2005), pp. 1034-1050.
    by A Siepel, G Bejerano, JS Pedersen, AS Hinrichs, M Hou, K Rosenbloom, H Clawson, J Spieth, LW Hillier, S Richards, GM Weinstock, RK Wilson, RA Gibbs, WJ Kent, W Miller, D Haussler
    posted to cns comparative_genomics conservation evolution genome_evolution mutation_rate phastcons by aprasad on 2005-12-02 22:15:13 as ** along with 15 people and 3 groups AlexanderPico pradiptaray bpb balajis eckart_bindewald indigoviolet brant adepace djkt olympos sujaikumar Stew cisevol dmc elfar ConklinLab EisenLab cis-regulatory-evolution
  • Darwin In the Genome: Molecular Strategies in Biological Evolution
    (09 October 2002)
    by Lynn Caporale
    posted to evolution mutation mutation_rate by aprasad on 2005-12-02 22:13:54 as ** along with 1 person HugoMarcelo
  • Correlation between sequence conservation and the genomic context after gene duplication
    Nucl. Acids Res., Vol. 33, No. 19. (27 October 2005), pp. 6164-6171.
    by Richard A Notebaart, Martijn A Huynen, Bas Teusink, Roland J Siezen, Berend Snel
    posted to coding evolution paralog by aprasad on 2005-12-02 22:06:51 as ** along with 2 people BarrosH xwbcn
  • Natural selection on protein-coding genes in the human genome
    Nature, Vol. 437, No. 7062., pp. 1153-1157.
    by Carlos D Bustamante, Adi Fledel-Alon, Scott Williamson, Rasmus Nielsen, Melissa T Hubisz, Stephen Glanowski, David M Tanenbaum, Thomas J White, John J Sninsky, Ryan D Hernandez, Daniel Civello, Mark D Adams, Michele Cargill, Andrew G Clark
    posted to coding evolution genome_evolution mutation_rate selection by aprasad on 2005-10-31 21:12:42 as ***** along with 15 people and 5 groups shoshin stevanspringer operon jwortman dayjm balajis marcius dpollard hdopazo djkt JBEgwa01 ramensky Garamonfok iris42 dmc EisenLab FAB-lab BioinfoCIPF SGU-CIPF Durbin group
  • Why do human diversity levels vary at a megabase scale?
    Genome Res, Vol. 15, No. 9. (September 2005), pp. 1222-1231.
    by I Hellmann, K Prüfer, H Ji, MC Zody, S Pääbo, SE Ptak
    posted to analysis chimp evolution human_genome jc mutation mutation_rate recombination by aprasad on 2005-10-25 16:43:19 as ***
  • Evidence of functional selection pressure for alternative splicing events that accelerate evolution of protein subsequences.
    Proc Natl Acad Sci U S A, Vol. 102, No. 38. (20 September 2005), pp. 13526-13531.
    by Y Xing, C Lee
    posted to coding evolution mutation mutation_rate splicing by aprasad on 2005-10-25 16:26:12 as **** along with 3 people and 3 groups radek penka bsmagic Bioinformatics Nie bioinplant
  • Distribution and intensity of constraint in mammalian genomic sequence.
    Genome Res, Vol. 15, No. 7. (July 2005), pp. 901-913.
    by GM Cooper, EA Stone, G Asimenos, ED Green, S Batzoglou, A Sidow
    posted to comparative_genomics evolution genome_evolution sequence by aprasad on 2005-09-20 19:42:46 as **** along with 5 people operon nirfriedman JeffR100 Garamonfok tale
  • Patterns of nucleotide substitution, insertion and deletion in the human genome inferred from pseudogenes.
    Nucleic Acids Res, Vol. 31, No. 18. (15 September 2003), pp. 5338-5348.
    by Z Zhang, M Gerstein
    posted to evolution genome_evolution genomics indel mutation_rate by aprasad on 2005-09-15 21:42:56 as **
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