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Tag molecular_evolution [45 articles]

Recent papers classified by the tag molecular_evolution.
  • Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages.
    Mol Biol Evol, Vol. 19, No. 6. (June 2002), pp. 908-917.
    by Z Yang, R Nielsen
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:31:03 as ** along with 3 people and 2 groups stevanspringer operon Garamonfok FAB-lab Berkeley Mycology
  • Bayes Empirical Bayes Inference of Amino Acid Sites Under Positive Selection
    Molecular Biology and Evolution, Vol. 22, No. 4. (April 2005), pp. 1107-1118.
    by Ziheng Yang, Wendy S Wong, Rasmus Nielsen
    posted to coccipaper codon_model molecular_evolution paml positive_selecion selection selection_test by stajich on 2008-04-19 21:29:42 as ** along with 5 people and 1 group skumagai rabu BioNica Natasha Garamonfok Berkeley Mycology
  • PAML 4: Phylogenetic Analysis by Maximum Likelihood
    Mol Biol Evol (4 May 2007), msm088.
    by Ziheng Yang
    posted to coccipaper codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:29:02 as ** along with 7 people and 1 group CharlesM RamuAnandakrishnan operon akifumi hdopazo BioNica ryanraaum Berkeley Mycology
  • Mutation-Selection Models of Codon Substitution and Their Use to Estimate Selective Strengths on Codon Usage.
    Mol Biol Evol (3 January 2008)
    by Ziheng Yang, Rasmus Nielsen
    posted to codon_model molecular_evolution paml selection selection_test by stajich on 2008-04-19 21:28:47 as ** along with 2 people and 1 group cjeans gjuggler Berkeley Mycology
  • A Model of Directional Selection Applied to the Evolution of Drug Resistance in HIV-1
    Molecular Biology and Evolution, Vol. 24, No. 4. (April 2007), pp. 1025-1031.
    by Seoighe, Cathal, Ketwaroo, Farahnaz, Pillay, Visva, Scheffler, Konrad, Wood, Natasha, Duffet, Rodger, Zvelebil, Marketa, Martinson, Neil, Mcintyre, James, Morris, Lynn, Hide, Winston
    posted to drug_resistance hiv molecular_evolution positive_selection by stajich on 2007-11-26 18:48:57 as **
  • Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level
    Heredity, Vol. aop, No. current.
    by AL Hughes
    posted to adaptive evolution molecular_evolution by stajich on 2007-09-26 14:41:41 as ** along with 1 person stevanspringer
  • Natural selection of protein structural and functional properties: a SNP perspective
    Genome Biology, Vol. 9, No. 4. (2008)
    by Jinfeng Liu, Yan Zhang, Xingye Lei, Zemin Zhang
    posted to molecular_evolution natural_selection polymorphism snp by stajich on 2008-04-09 00:01:16 as ** along with 4 people and 1 group operon fernan ramensky dandaman Berkeley Mycology
  • Positive selection on an acrosomal sperm protein, M7 lysin, in three species of the mussel genus Mytilus.
    Mol Biol Evol, Vol. 20, No. 2. (February 2003), pp. 200-207.
    by C Riginos, JH McDonald
    posted to molecular_evolution mytilus population_genetics positive_selection sexual_selection by stajich on 2007-08-27 04:01:14 as read along with 1 group FAB-lab
  • A Maximum Likelihood Method for Detecting Directional Evolution in Protein Sequences and its Application to Influenza A Virus.
    Molecular biology and evolution (29 May 2008)
    by Sergei L L Kosakovsky Pond, Art F Y F Poon, Andrew J J Leigh Brown, Simon D W D Frost
    posted to positive_selection molecular_evolution by stajich on 2008-06-01 13:47:44 as ** along with 1 person and 1 group zwang Berkeley Mycology
  • Evidence against the energetic cost hypothesis for the short introns in highly expressed genes
    BMC Evolutionary Biology, Vol. 8 (20 May 2008), 154.
    by Yi-Fei Huang, Deng-Ke Niu
    posted to molecular_evolution intron_evolution intron by stajich on 2008-05-27 16:19:13 as ** along with 1 person and 2 groups cisevol Berkeley Mycology BergmanLab
  • An Improved General Amino Acid Replacement Matrix
    Mol Biol Evol, Vol. 25, No. 7. (1 July 2008), pp. 1307-1320.
    by Si Q Le, Olivier Gascuel
    posted to protein_evolution phylogenetics molecular_evolution methods evolution bioinformatics by stajich on 2008-06-14 07:08:00 as ** along with 1 group Berkeley Mycology
  • The McDonald-Kreitman Test and Slightly Deleterious Mutations
    Mol Biol Evol, Vol. 25, No. 6. (1 June 2008), pp. 1007-1015.
    by Jane Charlesworth, Adam Eyre-Walker
    posted to population_genomics population_genetics molecular_evolution methods adaptation by stajich on 2008-05-10 01:44:49 as ** along with 4 people and 1 group gjuggler Stew cabbagesofdoom stevanspringer Berkeley Mycology
  • Revisiting the Saccharomyces cerevisiae predicted ORFeome
    Genome Res. (23 May 2008), gr.076661.108.
    by Qian-Ru Li, Anne-Ruxandra Carvunis, Haiyuan Yu, Jing-Dong J Han, Quan Zhong, Nicolas Simonis, Stanley Tam, Tong Hao, Niels J Klitgord, Denis Dupuy, Danny Mou, Ilan Wapinski, Aviv Regev, David E Hill, Michael E Cusick, Marc Vidal
    posted to yeast saccharomyces molecular_evolution genome_annotation fungi by stajich on 2008-05-28 05:57:18 as ** along with 2 people and 1 group nklee dbensasson Berkeley Mycology
  • On the Varied Pattern of Evolution of 2 Fungal Genomes: A Critique of Hughes and Friedman
    Molecular Biology and Evolution, Vol. 23, No. 12. (15 December 2006), pp. 2279-2282.
    by Yang, Ziheng
    posted to positive_selection molecular_evolution by stajich on 2007-01-18 01:09:37 as ****
  • THE MODERN MOLECULAR CLOCK
    Nat Rev Genet, Vol. 4, No. 3. (March 2003), pp. 216-224.
    by Lindell Bromham, David Penny
    posted to molecular_evolution by stajich on 2007-12-14 22:09:41 as ** along with 1 person and 1 group tmmurali Berkeley Mycology
  • Overdispersion of the molecular clock varies between yeast, Drosophila and mammals
    Genetics (27 May 2008), genetics.108.089185.
    by Trevor Bedford, Ilan Wapinski, Daniel L Hartl
    posted to molecular_evolution by stajich on 2008-05-28 05:55:05 as ** along with 1 person and 1 group djkt Berkeley Mycology
  • 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 coccipaper codon_model methods molecular_evolution paml phylogenetics by stajich on 2008-04-19 21:34:23 as ** along with 11 people and 3 groups skumagai tharris bjorns chrn chad_davis indigoviolet penka BioNica pv usagi-kirin jmjimenez EisenLab Nie Berkeley Mycology
  • The modern molecular clock.
    Nat Rev Genet, Vol. 4, No. 3. (March 2003), pp. 216-224.
    by L Bromham, D Penny
    posted to a_exam evolution molecular_clock molecular_evolution by ryang on 2006-01-12 23:47:20 as ** along with 1 person and 1 group kinestetika microbiology_nijmegen
  • Adaptive protein evolution at the Adh locus in Drosophila
    Nature, Vol. 351, No. 6328. (20 June 1991), pp. 652-654.
    by John H Mcdonald, Martin Kreitman
    posted to molecular_evolution by RMGraze on 2006-06-15 21:31:45 as ** along with 5 people pradiptaray bpb brant Garamonfok Stew
  • Cuticle protein genes of Drosophila: Structure, organization and evolution of four clustered genes
    Cell, Vol. 29, No. 3. (July 1982), pp. 1027-1040.
    by Michael Snyder, Michael Hunkapiller, David Yuen, Donald Silvert, James Fristrom, Norman Davidson
    posted to drosophila molecular_evolution by RMGraze on 2006-10-05 20:27:59 as **
  • Observations of Amino Acid Gain and Loss During Protein Evolution are Explained by Statistical Bias.
    Mol Biol Evol (11 May 2006)
    by Richard A A Goldstein, David D D Pollock
    posted to genetics molecular_evolution by RMGraze on 2006-06-15 17:34:47 as ** along with 1 person and 1 group dpollard EisenLab
  • Molecular Evolution of Sex-Biased Genes in Drosophila
    Mol Biol Evol, Vol. 21, No. 11. (1 November 2004), pp. 2130-2139.
    by Zhi Zhang, Tina M Hambuch, John Parsch
    posted to microarray molecular_evolution sex_comb_ref sexual_selection by RMGraze on 2006-09-28 20:28:45 as ** along with 1 person and 1 group penka Nie
  • Effects of Selective Neutrality on the Evolution of Molecular Species
    Proceedings: Biological Sciences, Vol. 265, No. 1403. (1998), pp. 1333-1338.
    by MEJ Newman, Robin Engelhardt
    posted to molecular_evolution by mrm on 2005-01-21 15:41:28 as **
  • Regulatory change in YABBY-like transcription factor led to evolution of extreme fruit size during tomato domestication.
    Nature genetics (11 May 2008)
    by Bin Cong, Luz S S Barrero, Steven D D Tanksley
    posted to transcription plants molecular_evolution by mariakmejia on 2008-05-15 02:05:10 as ** along with 1 person imtechnology
  • Structural evolution of multisubunit RNA polymerases.
    Trends in microbiology (9 May 2008)
    by Finn Werner
    posted to transcription molecular_evolution by mariakmejia on 2008-05-15 02:01:54 as **
  • Molecular evolution of the RNA polymerase II CTD.
    Trends in genetics : TIG (8 May 2008)
    by Rob D D Chapman, Martin Heidemann, Corinna Hintermair, Dirk Eick
    posted to transcription molecular_evolution by mariakmejia on 2008-05-15 02:01:20 as **
  • U12 intron positions are more strongly conserved between animals and plants than U2 intron positions
    Biology Direct, Vol. 3, No. 1. (2008)
    by Malay Basu, Wojciech Makalowski, Igor Rogozin, Eugene Koonin
    posted to transcription molecular_evolution by mariakmejia on 2008-05-15 02:17:11 as ** along with 1 person Ema
  • Which evolutionary processes influence natural genetic variation for phenotypic traits?
    Nat Rev Genet, Vol. 8, No. 11. (November 2007), pp. 845-856.
    by Thomas Mitchell-Olds, John H Willis, David B Goldstein
    posted to molecular_evolution phenotypic_evolution population_genetics review by cwbrown to the group EisenLab on 2007-11-08 00:35:36 as ** along with 2 people zwang ryanraaum
  • Population Genomics: Whole-Genome Analysis of Polymorphism and Divergence in Drosophila simulans
    PLoS Biology, Vol. 5, No. 11. (1 November 2007), e310.
    by David J Begun, Alisha K Holloway, Kristian Stevens, Ladeana W Hillier, Yu-Ping Poh, Matthew W Hahn, Phillip M Nista, Corbin D Jones, Andrew D Kern, Colin N Dewey, Lior Pachter, Eugene Myers, Charles H Langley
    posted to drosophila molecular_evolution species_divergence by emptyhb on 2008-01-20 16:53:21 as ** along with 3 people pradiptaray bpb dmc
  • Evolutionary dynamics of the enhancer region of even-skipped in Drosophila.
    Mol Biol Evol, Vol. 12, No. 6. (November 1995), pp. 1002-1011.
    by MZ Ludwig, M Kreitman
    posted to cis_regulatory_evolution detecting_selection drosophila even-skipped_enhancer molecular_evolution by emptyhb on 2008-03-25 23:40:33 as ** along with 1 person and 1 group cisevol cis-regulatory-evolution
  • Purifying Selection Maintains Highly Conserved Noncoding Sequences in Drosophila.
    Mol Biol Evol (23 July 2007)
    by Sònia Casillas, Antonio Barbadilla, Casey M M Bergman
    posted to drosophila molecular_evolution by emptyhb on 2008-02-15 22:45:28 as ** along with 7 people and 2 groups brant operon dpollard emilyhare Garamonfok Stew cisevol EisenLab cis-regulatory-evolution
  • Evolution of genes and genomes on the Drosophila phylogeny
    Nature, Vol. 450, No. 7167. (November 2007), pp. 203-218.
    posted to cis_regulatory_evolution drosophila molecular_evolution by emptyhb on 2008-02-24 23:13:30 as ** along with 15 people and 4 groups CharlesM PetrovLab operon tmmurali indigoviolet djkt timflutre stajich zwang Garamonfok lp2 hpaces caseybrown urgi noor Bioinformatics EisenLab csb_journal_club_public Berkeley Mycology
  • Molecular drive: a cohesive mode of species evolution
    Nature, Vol. 299, No. 5879. (1982), pp. 111-117.
    by Gabriel Dover
    posted to natural_selection molecular_evolution by emptyhb on 2008-05-02 15:40:55 as **
  • Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin.
    PLoS Genet, Vol. 3, No. 11. (30 November 2007)
    by P Fontanillas, DL Hartl, M Reuter
    posted to drosophila molecular_evolution by emptyhb on 2008-03-07 03:45:56 as ** along with 1 person maximilianh
  • Gametophytic self-incompatibility in Lycium parishii (Solanaceae): allelic diversity, genealogical structure, and patterns of molecular evolution at the S-RNase locus
    Heredity, Vol. aop, No. current.
    by AE Savage, JS Miller,
    posted to molecular_evolution self-incompatibility by ejeffery on 2006-05-04 02:00:56 as **
  • Gene losses during human origins.
    PLoS Biol, Vol. 4, No. 3. (March 2006)
    by X Wang, WE Grus, J Zhang
    posted to h_sapiens molecular_evolution by ejeffery on 2006-05-04 18:39:44 as ** along with 1 person djkt
  • Role of positive selection in the retention of duplicate genes in mammalian genomes
    PNAS, Vol. 103, No. 7. (14 February 2006), pp. 2232-2236.
    by Shin-Han Shiu, Jake K Byrnes, Runsun Pan, Peng Zhang, Wen-Hsiung Li
    posted to gene_duplication molecular_evolution positive_selection by ejeffery on 2006-05-04 18:38:04 as ** along with 2 people and 1 group stevanspringer cmm FAB-lab
  • Many genes in fish have species-specific asymmetric rates of molecular evolution.
    BMC Genomics, Vol. 7 (2006)
    by D Steinke, W Salzburger, I Braasch, A Meyer
    posted to detecting_positive_selection genetic_diversity molecular_evolution by ejeffery on 2006-05-04 18:41:57 as **
  • The signature of positive selection on standing genetic variation.
    Evolution Int J Org Evolution, Vol. 59, No. 11. (November 2005), pp. 2312-2323.
    by M Przeworski, G Coop, JD Wall
    posted to detecting_positive_selection molecular_evolution positive_selection by ejeffery on 2006-05-05 22:54:30 as *** along with 1 person and 1 group dmc Durbin group
  • Adaptive Protein Evolution and Regulatory Divergence in Drosophila.
    Mol Biol Evol (14 March 2006)
    by Jeffrey M M Good, Celine A A Hayden, Travis J J Wheeler
    posted to molecular_evolution by ejeffery on 2006-05-04 02:19:52 as ** along with 1 person and 1 group indigoviolet EisenLab
  • Genomic and Evolutionary Insights into Genes Encoding Proteins with Single Amino Acid Repeats.
    Mol Biol Evol (17 April 2006)
    by Pratibha Siwach, Saurabh Dilip D Pophaly, Subramaniam Ganesh
    posted to molecular_evolution by ejeffery on 2006-05-04 02:10:11 as ** along with 1 person fisherp
  • Codon-Substitution Models for Heterogeneous Selection Pressure at Amino Acid Sites
    Genetics, Vol. 155, No. 1. (1 May 2000), pp. 431-449.
    by Ziheng Yang, Rasmus Nielsen, Nick Goldman, Anne-Mette K Pedersen
    posted to codon molecular_evolution selection by dylan77 on 2007-04-23 07:53:54 as **** along with 7 people fernan BioNica Natasha Garamonfok tale gjuggler emptyhb
  • On the Origins of a Crowded Cytoplasm
    Journal of Molecular Evolution, Vol. 63, No. 5. (14 November 2006), pp. 583-590.
    by Luis Acerenza, Martin Graña
    posted to crowding diffusion molecular_evolution by dylan77 on 2007-04-19 08:36:32 as **
  • Timing the Ancestor of the HIV-1 Pandemic Strains
    Science, Vol. 288, No. 5472. (9 June 2000), pp. 1789-1796.
    by B Korber, M Muldoon, J Theiler, F Gao, R Gupta, A Lapedes, BH Hahn, S Wolinsky, T Bhattacharya
    posted to hiv molecular_evolution by dylan77 on 2007-03-27 02:22:12 as ** along with 1 person Ema
  • The appearance of new structures and functions in proteins during evolution.
    J Mol Evol, Vol. 7, No. 1. (31 December 1975), pp. 1-57.
    by E Zuckerkandl
    posted to molecular_evolution by anatiferous on 2006-12-02 01:35:36 as **
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