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Garamonfok library [170 articles]

最近 Garamonfok さんのライブラリ .
  • The gene regulatory logic of transcription factor evolution.
    Trends in ecology & evolution (Personal edition) (21 May 2008)
    by Günter P P Wagner, Vincent J J Lynch
    posted to promotors evolution by Garamonfok on 2008-07-20 10:59:49 as ** along with 1 person Stew
  • Conservation and topology of protein interaction networks under duplication-divergence evolution.
    Proceedings of the National Academy of Sciences of the United States of America (16 July 2008)
    by Kirill Evlampiev, Hervé Isambert
    posted to interaction function evolution by Garamonfok on 2008-07-20 10:54:33 as ** along with 1 person bpcusack
  • More genes underwent positive selection in chimpanzee evolution than in human evolution.
    Proc Natl Acad Sci U S A, Vol. 104, No. 18. (1 May 2007), pp. 7489-7494.
    by MA Bakewell, P Shi, J Zhang
    posted to method evolution by Garamonfok on 2008-07-17 15:41:23 as ** along with 3 people pradiptaray bpb usagi-kirin
  • Sensitivity of the relative-rate test to taxonomic sampling
    Mol Biol Evol, Vol. 15, No. 9. (1 September 1998), pp. 1091-1098.
    by M Robinson, M Gouy, C Gautier, D Mouchiroud
    posted to tools evolution by Garamonfok on 2008-05-19 15:18:01 as **
  • RRTree: Relative-Rate Tests between groups of sequences on a phylogenetic tree
    Bioinformatics, Vol. 16, No. 3. (1 March 2000), pp. 296-297.
    by Marc Robinson-Rechavi, Dorothee Huchon
    posted to tools evolution by Garamonfok on 2008-05-19 14:57:25 as **
  • Evolvability and hierarchy in rewired bacterial gene networks
    Nature, Vol. 452, No. 7189. (17 April 2008), pp. 840-845.
    by Mark Isalan, Caroline Lemerle, Konstantinos Michalodimitrakis, Carsten Horn, Pedro Beltrao, Emanuele Raineri, Mireia Garriga-Canut, Luis Serrano
    posted to promotors expression evolution bacteria by Garamonfok on 2008-04-25 11:23:09 as ** along with 17 people and 4 groups aheilbut chad_davis michaelbarton austin AbnerCYH hryk margaritis cactus dbikard caseybrown biehl aalibes tmmurali dullhunk neils cmzmasek josedavid BergmanLab SynBioSys Centre de Recherches Interdisciplinaires GEB
  • Evolutionary and Biomedical Insights from the Rhesus Macaque Genome
    Science, Vol. 316, No. 5822. (13 April 2007), pp. 222-234.
    by Rhesus, Richard A Gibbs, Jeffrey Rogers, Michael G Katze, Roger Bumgarner, George M Weinstock, Elaine R Mardis, Karin A Remington, Robert L Strausberg, Craig J Venter, Richard K Wilson, Mark A Batzer, Carlos D Bustamante, Evan E Eichler, Matthew W Hahn, Ross C Hardison, Kateryna D Makova, Webb Miller, Aleksandar Milosavljevic, Robert E Palermo, Adam Siepel, James M Sikela, Tony Attaway, Stephanie Bell, Kelly E Bernard, Christian J Buhay, Mimi N Chandrabose, Marvin Dao, Clay Davis, Kimberly D Delehaunty, Yan Ding, Huyen H Dinh, Shannon Dugan-Rocha, Lucinda A Fulton, Ramatu A Gabisi, Toni T Garner, Jennifer Godfrey, Alicia C Hawes, Judith Hernandez, Sandra Hines, Michael Holder, Jennifer Hume, Shalini N Jhangiani, Vandita Joshi, Ziad M Khan, Ewen F Kirkness, Andrew Cree, Gerald R Fowler, Sandra Lee, Lora R Lewis, Zhangwan Li, Yih-Shin Liu, Stephanie M Moore, Donna Muzny, Lynne V Nazareth, Dinh N Ngo, Geoffrey O Okwuonu, Grace Pai, David Parker, Heidie A Paul, Cynthia Pfannkoch, Craig S Pohl, Yu-Hui Rogers, San J Ruiz, Aniko Sabo, Jireh Santibanez, Brian W Schneider, Scott M Smith, Erica Sodergren, Amanda F Svatek, Teresa R Utterback, Selina Vattathil, Wesley Warren, Courtney S White, Asif T Chinwalla, Yucheng Feng, Aaron L Halpern, Ladeana W Hillier, Xiaoqiu Huang, Pat Minx, Joanne O Nelson, Kymberlie H Pepin, Xiang Qin, Granger G Sutton, Eli Venter, Brian P Walenz, John W Wallis, Kim C Worley, Shiaw-Pyng Yang, Steven M Jones, Marco A Marra, Mariano Rocchi, Jacqueline E Schein, Robert Baertsch, Laura Clarke, Miklos Csuros, Jarret Glasscock, Alan R Harris, Paul Havlak, Andrew R Jackson, Huaiyang Jiang, Yue Liu, David N Messina, Yufeng Shen, Henry X Song, Todd Wylie, Lan Zhang, Ewan Birney, Kyudong Han, Miriam K Konkel, Jungnam Lee, Arian F Smit, Brygg Ullmer, Hui Wang, Jinchuan Xing, Richard Burhans, Ze Cheng, John E Karro, Jian Ma, Brian Raney, Xinwei She, Michael J Cox, Jeffery P Demuth, Laura J Dumas, Sang-Gook Han, Janet Hopkins, Anis Karimpour-Fard, Young H Kim, Jonathan R Pollack, Tomas Vinar, Charles Addo-Quaye, Jeremiah Degenhardt, Alexandra Denby, Melissa J Hubisz, Amit Indap, Carolin Kosiol, Bruce T Lahn, Heather A Lawson, Alison Marklein, Rasmus Nielsen, Eric J Vallender, Andrew G Clark, Betsy Ferguson, Ryan D Hernandez, Kashif Hirani, Hildegard Kehrer-Sawatzki, Jessica Kolb, Shobha Patil, Ling-Ling Pu, Yanru Ren, David G Smith, David A Wheeler, Ian Schenck, Edward V Ball, Rui Chen, David N Cooper, Belinda Giardine, Fan Hsu, James W Kent, Arthur Lesk, David L Nelson, William E O'Brien, Kay Prufer, Peter D Stenson, James C Wallace, Hui Ke, Xiao-Ming Liu, Peng Wang, Andy P Xiang, Fan Yang, Galt P Barber, David Haussler, Donna Karolchik, Andy D Kern, Robert M Kuhn, Kayla E Smith, Ann S Zwieg
    posted to tools genome evolution disease by Garamonfok on 2008-04-24 16:16:50 as *** along with 4 people and 4 groups dchughes djkt stajich hpaces Bioinformatics G4ID Genetics-of-Gambling Berkeley Mycology
  • Mechanisms and Rates of Birth and Death of Dispersed Duplicated Genes during the Evolution of a Multigene Family in Diploid and Tetraploid Wheats
    Molecular Biology and Evolution, Vol. 24, No. 2. (February 2007), pp. 539-550.
    by Akhunov, D Eduard, Akhunova, R Alina, Dvorak, Jan
    posted to evolution hyphy positiveselection by Garamonfok on 2008-03-14 13:15:51 as **
  • Quaternary Structure Constraints on Evolutionary Sequence Divergence
    Molecular Biology and Evolution, Vol. 24, No. 2. (February 2007), pp. 349-351.
    by Fornasari, Maria Silvina, Parisi, Gustavo, Echave, Julian
    posted to evolution hyphy positiveselection tools by Garamonfok on 2008-03-14 13:14:57 as ** along with 1 person zwang
  • Function and evolution of a gene family encoding odorant binding-like proteins in a social insect, the honey bee (Apis mellifera)
    Genome Res., Vol. 16, No. 11. (1 November 2006), pp. 1404-1413.
    by Sylvain Foret, Ryszard Maleszka
    posted to evolution hyphy positiveselection tools by Garamonfok on 2008-03-14 13:09:40 as **
  • Sheep Mitochondrial DNA Variation in European, Caucasian, and Central Asian Areas
    Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1776-1783.
    by Miika Tapio, Nurbiy Marzanov, Mikhail Ozerov, Mirjana Cinkulov, Galina Gonzarenko, Tatyana Kiselyova, Maciej Murawski, Haldja Viinalass, Juha Kantanen
    posted to evolution hyphy positiveselection by Garamonfok on 2008-03-14 13:06:40 as ** along with 1 person Montrachet
  • Robust inference of positive selection from recombining coding sequences
    Bioinformatics, Vol. 22, No. 20. (15 October 2006), pp. 2493-2499.
    by Scheffler, Konrad, Martin, P Darren, Seoighe, Cathal
    posted to evolution hyphy positiveselection tools by Garamonfok on 2008-03-14 13:02:26 as ** along with 2 people operon Natasha
  • Automated Phylogenetic Detection of Recombination Using a Genetic Algorithm
    Molecular Biology and Evolution, Vol. 23, No. 10. (15 October 2006), pp. 1891-1901.
    by Kosakovsky Pond, L Sergei, Posada, David, Gravenor, B Michael, Woelk, H Christopher, Frost, DW Simon
    posted to evolution hyphy tools by Garamonfok on 2008-03-14 13:00:47 as ** along with 3 people larbiza operon Natasha
  • Not So Different After All: A Comparison of Methods for Detecting Amino Acid Sites Under Selection
    Molecular Biology and Evolution, Vol. 22, No. 5. (15 May 2005), pp. 1208-1222.
    by SL Kosakovsky, Simon D Frost
    posted to evolution hyphy positiveselection by Garamonfok on 2008-03-14 13:00:08 as ** along with 3 people marck operon BioNica
  • HyPhy: hypothesis testing using phylogenies
    Bioinformatics, Vol. 21, No. 5. (01 March 2005), pp. 676-679.
    by SLK Sergei, Simon DW Frost, Spencer V Muse
    posted to evolution hyphy statistics tools by Garamonfok on 2008-03-14 12:56:43 as ** along with 3 people operon radek Natasha
  • Mammalian Nonsynonymous Sites are not Overdispersed: Comparative Genomic Analysis of Index of Dispersion of Mammalian Proteins.
    Mol Biol Evol (19 December 2007)
    by Seong-Ho H Kim, Soojin V V Yi
    posted to evolution project_ratemutanalysismamals by Garamonfok on 2008-03-12 13:46:50 as **
  • A Phylogenomic Study of Human, Dog, and Mouse.
    PLoS Comput Biol, Vol. 3, No. 1. (5 January 2007)
    by Gina Cannarozzi, Adrian Schneider, Gaston Gonnet
    posted to evolution phylome project_funcanalysis by Garamonfok on 2008-03-11 10:44:29 as ** along with 2 people and 1 group aprasad dpollard EisenLab
  • Enhancer sequence conservation between vertebrates is favoured in developmental regulator genes
    Trends in Genetics, Vol. 21, No. 4. (April 2005), pp. 207-210.
    by Charles Plessy, Thomas Dickmeis, Frederic Chalmel, Uwe Strahle
    posted to evolution promotors by Garamonfok on 2008-03-11 10:42:27 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 encode evolution by Garamonfok on 2008-03-11 10:40:10 as ** along with 2 people aprasad maximilianh
  • Evidencia molecular de la seleccion natural
    (1995)
    by Martin Kreitman, Horoshi Akasi
    posted to evolution generalknowledge naturalselection by Garamonfok on 2008-03-11 10:27:39 as **
  • Natural selection
    (2002)
    by Gil Mcvean
    posted to evolution generalknowledge naturalselection by Garamonfok on 2008-03-11 10:25:53 as **
  • Evidence for positive selection on the E2 gene of bovine viral diarrhoea virus type 1
    Virus Genes, Vol. 35, No. 3. (24 December 2007), pp. 629-634.
    by Fangqiang Tang, Chuyu Zhang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-11 10:17:25 as **
  • Mutation rate variation in the mammalian genome.
    Curr Opin Genet Dev, Vol. 13, No. 6. (December 2003), pp. 562-568.
    by H Ellegren, NG Smith, MT Webster
    posted to evolution project_ratemutanalysismamals by Garamonfok on 2008-03-11 10:02:55 as **
  • Local Similarity in Evolutionary Rates Extends over Whole Chromosomes in Human-Rodent and Mouse-Rat Comparisons: Implications for Understanding the Mechanistic Basis of the Male Mutation Bias
    Mol Biol Evol, Vol. 18, No. 11. (1 November 2001), pp. 2032-2039.
    by Martin J Lercher, Elizabeth J Williams, Laurence D Hurst
    posted to evolution project_ratemutanalysismamals by Garamonfok on 2008-03-11 10:00:13 as **
  • The origin of genomes -- not by natural selection?
    Current Biology, Vol. 18, No. 4. (26 February 2008), pp. R140-R141.
    by Brian Charlesworth
    posted to adaptiveevolution evolution project_funcanalysis by Garamonfok on 2008-03-11 09:55:33 as **
  • 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 adaptiveevolution project_funcanalysis by Garamonfok on 2008-03-11 09:50:34 as ** along with 5 people pradiptaray bpb RMGraze brant Stew
  • Adaptive evolution of metabolic pathways in Drosophila.
    Mol Biol Evol, Vol. 24, No. 6. (June 2007), pp. 1347-1354.
    by JM Flowers, E Sezgin, S Kumagai, DD Duvernell, LM Matzkin, PS Schmidt, WF Eanes
    posted to adaptiveevolution annotation evolution project_funcanalysis by Garamonfok on 2008-03-11 09:49:03 as **
  • Positive selection, relaxation, and acceleration in the evolution of the human and chimp genome.
    PLoS Comput Biol, Vol. 2, No. 4. (April 2006)
    by L Arbiza, J Dopazo, H Dopazo
    posted to evolution positiveselection by Garamonfok on 2008-03-06 11:05:32 as read along with 4 people and 2 groups operon marcius jordibc hdopazo BioinfoCIPF SGU-CIPF
  • 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 evolution paml positiveselection by Garamonfok on 2008-03-05 18:01:13 as ** along with 5 people and 1 group skumagai rabu BioNica Natasha stajich Berkeley Mycology
  • Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models.
    Mol Biol Evol, Vol. 17, No. 1. (January 2000), pp. 32-43.
    by Z Yang, R Nielsen
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:57:19 as ** along with 8 people and 1 group bjorns fernan hdopazo BioNica timflutre ankur_iitg RamuAnandakrishnan Ema BioinfoCIPF
  • 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 evolution paml positiveselection by Garamonfok on 2008-03-05 17:56:01 as ** along with 3 people and 2 groups stevanspringer operon stajich FAB-lab Berkeley Mycology
  • Frequent False Detection of Positive Selection by the Likelihood Method with Branch-Site Models
    Mol Biol Evol, Vol. 21, No. 7. (1 July 2004), pp. 1332-1339.
    by Jianzhi Zhang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:53:04 as **
  • Evaluation of an Improved Branch-Site Likelihood Method for Detecting Positive Selection at the Molecular Level
    Mol Biol Evol, Vol. 22, No. 12. (1 December 2005), pp. 2472-2479.
    by Jianzhi Zhang, Rasmus Nielsen, Ziheng Yang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:51:05 as ** along with 4 people and 1 group stevanspringer AaronDarling usagi-kirin mingzhi FAB-lab
  • Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution.
    Mol Biol Evol, Vol. 15, No. 5. (May 1998), pp. 568-573.
    by Z Yang
    posted to evolution paml positiveselection by Garamonfok on 2008-03-05 17:46:09 as read along with 2 people AaronDarling usagi-kirin
  • 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 evolution paml positiveselection by Garamonfok on 2008-03-05 17:43:51 as read along with 7 people fernan BioNica Natasha dylan77 tale gjuggler emptyhb
  • Recombination in AIDS viruses.
    J Mol Evol, Vol. 40, No. 3. (March 1995), pp. 249-259.
    by DL Robertson, BH Hahn, PM Sharp
    posted to adaptiveevolution evolution paml positiveselection by Garamonfok on 2008-03-05 17:42:25 as read
  • 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 adaptiveevolution evolution positiveselection by Garamonfok on 2008-02-19 13:06:16 as ***** along with 3 people and 3 groups stevanspringer aprasad dchughes FAB-lab G4ID Genetics-of-Gambling
  • The functional landscape of mouse gene expression.
    J Biol, Vol. 3, No. 5. (2004)
    by W Zhang, QD Morris, R Chang, O Shai, MA Bakowski, N Mitsakakis, N Mohammad, MD Robinson, R Zirngibl, E Somogyi, N Laurin, E Eftekharpour, E Sat, J Grigull, Q Pan, WT Peng, N Krogan, J Greenblatt, M Fehlings, D van der Kooy, J Aubin, BG Bruneau, J Rossant, BJ Blencowe, BJ Frey, TR Hughes
    posted to expression go by Garamonfok on 2008-02-14 12:25:49 as ** along with 5 people jyuh miguel j3xucite gjuggler vidhya
  • Comparing Patterns of Natural Selection across Species Using Selective Signatures
    PLoS Genetics, Vol. 4, No. 2. (1 February 2008), e23.
    by Jesse B Shapiro, Eric J Alm
    posted to evolution go by Garamonfok on 2008-02-12 21:07:32 as ***** along with 3 people operon djkt qwermish
  • Natural selection on protein-coding genes in the human genome
    Nature, Vol. 437, No. 7062. (October 2005), 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 evolution mendelian positiveselection snp by Garamonfok on 2008-02-09 15:59:43 as ***** along with 15 people and 5 groups shoshin stevanspringer operon jwortman aprasad dayjm balajis marcius dpollard hdopazo djkt JBEgwa01 ramensky iris42 dmc EisenLab FAB-lab BioinfoCIPF SGU-CIPF Durbin group
  • Recent and ongoing selection in the human genome
    Nat Rev Genet, Vol. 8, No. 11. (November 2007), pp. 857-868.
    by Rasmus Nielsen, Ines Hellmann, Melissa Hubisz, Carlos Bustamante, Andrew G Clark
    posted to evolution positiveselection by Garamonfok on 2008-02-09 15:56:21 as ***** along with 5 people and 1 group dchughes ramensky candypmcg ryanraaum lh3 Durbin group
  • Initial sequence of the chimpanzee genome and comparison with the human genome
    Nature, Vol. 437, No. 7055., pp. 69-87.
    by The
    posted to evolution positiveselection by Garamonfok on 2008-02-09 15:51:41 as ***** along with 9 people and 2 groups cannin chrn aprasad great_apes indigoviolet dullhunk djkt JeffR100 iris42 biodiversity_conservation EisenLab
  • Human PAML browser: a database of positive selection on human genes using phylogenetic methods.
    Nucleic Acids Res, Vol. 36, No. Database issue. (January 2008)
    by GC Nickel, D Tefft, MD Adams
    posted to evolution paml positiveselection tools by Garamonfok on 2008-02-09 15:43:26 as ***** along with 1 person operon
  • Evolution and Selection in Yeast Promoters: Analyzing the Combined Effect of Diverse Transcription Factor Binding Sites
    PLoS Computational Biology, Vol. 4, No. 1. (1 January 2008), e7.
    by Daniela Raijman, Ron Shamir, Amos Tanay
    posted to evolution promotors by Garamonfok on 2008-01-25 20:03:47 as ***** along with 7 people and 1 group aalibes chad_davis sebastien_vigneau lusk nklee maximilianh emptyhb BioinfoCIPF
  • Assessing the Determinants of Evolutionary Rates in the Presence of Noise.
    Mol Biol Evol (7 March 2007)
    by Joshua B B Plotkin, Hunter B B Fraser
    posted to coevolution evolution statistics tools by Garamonfok on 2007-12-11 10:50:40 as **** along with 1 person and 1 group dpollard EisenLab
  • Rates of divergence in gene expression profiles of primates, mice, and flies: stabilizing selection and variability among functional categories.
    Evolution Int J Org Evolution, Vol. 59, No. 1. (January 2005), pp. 126-137.
    by B Lemos, CD Meiklejohn, M Cáceres, DL Hartl
    posted to coevolution coexpression evolution expression go by Garamonfok on 2007-12-11 10:48:34 as ****
  • Specificity in protein interactions and its relationship with sequence diversity and coevolution.
    Proc Natl Acad Sci U S A (27 April 2007)
    by Luke Hakes, Simon C C Lovell, Stephen G G Oliver, David L L Robertson
    posted to coevolution evolution interaction by Garamonfok on 2007-12-11 10:46:26 as **** along with 9 people and 2 groups stevanspringer bjorns cjeans zwang cursonivel1 tale winterschlaefer phoenixzxl chrys FAB-lab cursonivel1
  • Adaptive Gene Expression Divergence Inferred from Population Genomics
    PLoS Genetics, Vol. 3, No. 10. (1 October 2007), e187.
    by Alisha K Holloway, Mara K Lawniczak, Jason G Mezey, David J Begun, Corbin D Jones
    posted to coevolution evolution expression by Garamonfok on 2007-12-11 10:43:20 as ***** along with 5 people brant xingxu caseybrown sb_journal_club emptyhb
  • Evolution of Proteins and Gene Expression Levels are Coupled in Drosophila and are Independently Associated with mRNA Abundance, Protein Length, and Number of Protein-Protein Interactions
    Molecular Biology and Evolution, Vol. 22, No. 5. (15 May 2005), pp. 1345-1354.
    by Bernardo Lemos, Brian R Bettencourt, Colin D Meiklejohn, Daniel L Hartl
    posted to coevolution coexpression evolution genome interaction proteinlength by Garamonfok on 2007-12-11 10:38:41 as read along with 2 people and 1 group skumagai penka Nie
  • The codon Adaptation Index--a measure of directional synonymous codon usage bias, and its potential applications.
    Nucleic Acids Research, Vol. 15, No. 3. (11 February 1987), pp. 1281-1295.
    by PM Sharp, Li Wen-Hsiung
    posted to no-tag by Garamonfok on 2007-12-10 18:19:57 as read
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