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Group: BioinfoCIPF - with tag evolution [92 articles]

Recent papers posted by members of the BioinfoCIPF group with tag evolution
  • Recent acceleration of human adaptive evolution
    Proceedings of the National Academy of Sciences, Vol. 104, No. 52. (26 December 2007), pp. 20753-20758.
    by John Hawks, Eric T Wang, Gregory M Cochran, Henry C Harpending, Robert K Moyzis
    posted to evolution human positive selection by hdopazo to the group BioinfoCIPF on 2008-02-04 17:33:37 as ** along with 9 people and 2 groups balicea laharrin shoshin cannon qwermish wsjames coyotetraxx candypmcg hpaces Oxford Virology Fasting, food and evolution
  • 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 to the group BioinfoCIPF on 2008-01-25 20:03:47 as ***** along with 8 people xili03 aalibes chad_davis sebastien_vigneau lusk nklee maximilianh emptyhb
  • Evolutionary rates vary among rRNA structural elements
    Nucl. Acids Res., Vol. 35, No. 10. (11 May 2007), pp. 3339-3354.
    by S Smit, J Widmann, R Knight
    posted to rna evolution by marcius to the group BioinfoCIPF on 2007-06-12 12:54:21 as ** along with 5 people and 2 groups eckart_bindewald balicea penka i000 cjeans SGU-CIPF YY1
  • From genes to functional classes in the study of biological systems
    BMC Bioinformatics, Vol. 8 (03 April 2007), 114.
    by Fatima Al-Shahrour, Leonardo Arbiza, Hernan Dopazo, Jaime Huerta-Cepas, Pablo Minguez, David Montaner, Joaquin Dopazo
    posted to microarray interaction gene_set_analysis expression evolution by ealloza to the group BioinfoCIPF on 2007-04-17 18:25:54 as ***** along with 6 people jfr Sharpshoot ajw Garamonfok djkt sgoetz
  • Modeling the Evolution of Protein Domain Architectures Using Maximum Parsimony
    Journal of Molecular Biology, Vol. 366, No. 1. (9 February 2007), pp. 307-315.
    by Jessica H Fong, Lewis Y Geer, Anna R Panchenko, Stephen H Bryant
    posted to protein_domains evolution bioinformatics algorithms by marcius to the group BioinfoCIPF on 2007-01-25 08:31:09 as ** along with 5 people and 2 groups icases tny choonpeng redelings zwang SGU-CIPF TNT
  • Diversity of microRNAs in human and chimpanzee brain.
    Nat Genet (29 October 2006)
    by Eugene Berezikov, Fritz Thuemmler, Linda W W van Laake, Ivanela Kondova, Ronald Bontrop, Edwin Cuppen, Ronald H A H Plasterk
    posted to chimpanzee evolution human microrna by ealloza to the group BioinfoCIPF on 2006-12-01 13:09:46 as read along with 6 people and 1 group andersbj mtagaya erbon heliopais maralena hpaces microRNA
  • Protein–Protein Interactions More Conserved within Species than across Species
    PLoS Computational Biology, Vol. 2, No. 7. (1 July 2006), e79.
    by Sven Mika, Burkhard Rost
    posted to algorithms evolution protein_domains protein_interactions by marcius to the group BioinfoCIPF on 2006-10-22 12:13:05 as ** along with 4 people and 1 group jeremymiller chad_davis skhadar dquest SGU-CIPF
  • RNA world - the dark matter of evolutionary genomics
    Journal of Evolutionary Biology, Vol. 19, No. 6. (2006), pp. 1768-1774.
    by P Michalak
    posted to biology evolution rna views by marcius to the group BioinfoCIPF on 2006-10-20 13:19:24 as ** along with 6 people and 4 groups dayjm dchughes cdawson rabu chenlc03 stajich G4ID SGU-CIPF GIG Genetics-of-Gambling
  • Natural history as a predictor of protein evolvability
    Protein Engineering, Design and Selection, Vol. 19, No. 10. (2006), pp. 439-442.
    by O'Loughlin, L Taryn, Patrick, M Wayne, Matsumura, Ichiro
    posted to biology evolution protein structure by marcius to the group BioinfoCIPF on 2006-09-27 13:52:56 as ** along with 1 group SGU-CIPF
  • Protein families and their evolution-a structural perspective.
    Annu Rev Biochem, Vol. 74 (2005), pp. 867-900.
    by CA Orengo, JM Thornton
    posted to evolution protein review structure by marcius to the group BioinfoCIPF on 2006-09-08 12:28:15 as ** along with 13 people and 5 groups ana barry tjimenez jwm chad_davis Einat Schmidtc sriram_s ezotenko redelings medic0747 nigham sim82 structural_bioinformatics Radiation_Damage Stressosome Bioinformatics SGU-CIPF
  • Exploiting protein structure data to explore the evolution of protein function and biological complexity.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 425-440.
    by RL Marsden, JA Ranea, A Sillero, O Redfern, C Yeats, M Maibaum, D Lee, S Addou, GA Reeves, TJ Dallman, CA Orengo
    posted to evolution function protein structure by marcius to the group BioinfoCIPF on 2006-09-08 12:26:40 as ** along with 1 person and 1 group jsnoddy SGU-CIPF
  • Assigning new GO annotations to protein data bank sequences by combining structure and sequence homology.
    Proteins, Vol. 58, No. 4. (1 March 2005), pp. 855-865.
    by JV Ponomarenko, PE Bourne, IN Shindyalov
    posted to bioinformatics evolution protein_function protein_structure by marcius to the group BioinfoCIPF on 2006-09-07 17:24:49 as ** along with 1 group SGU-CIPF
  • Exploiting sequence and structure homologs to identify protein-protein binding sites.
    Proteins, Vol. 62, No. 3. (15 March 2006), pp. 630-640.
    by JL Chung, W Wang, PE Bourne
    posted to bioinformatics evolution protein_interactions by marcius to the group BioinfoCIPF on 2006-09-07 17:22:13 as ** along with 2 people and 1 group bicko ameetsoni SGU-CIPF
  • Equivalent binding sites reveal convergently evolved interaction motifs
    Bioinformatics, Vol. 22, No. 5. (1 March 2006), pp. 550-555.
    by Andreas Henschel, Wan K Kim, Michael Schroeder
    posted to bioinformatics evolution protein_domains protein_interactions by marcius to the group BioinfoCIPF on 2006-09-07 17:16:11 as ** along with 2 people and 1 group chad_davis nickolay SGU-CIPF
  • The Rna World (Cold Spring Harbor Monograph Series) (Cold Spring Harbor Monograph Series)
    (14 October 2005)
    by Thomas R Cech, John F Atkins
    posted to evolution review rna by marcius to the group BioinfoCIPF on 2006-08-24 15:31:06 as ** along with 1 person and 1 group tardigrade SGU-CIPF
  • The gain and loss of genes during 600 million years of vertebrate evolution
    Genome Biology, Vol. 7 (24 May 2006), R43.
    by Tine Blomme, Klaas Vandepoele, Stefanie De Bodt, Cedric Simillion, Steven Maere, Yves Van de Peer
    posted to evolution genome human by marcius to the group BioinfoCIPF on 2006-08-23 13:16:00 as ** along with 6 people and 3 groups operon balicea dchughes jhc jryanstevens FMoncini G4ID SGU-CIPF Genetics-of-Gambling
  • An RNA gene expressed during cortical development evolved rapidly in humans
    Nature (16 August 2006)
    by Katherine S Pollard, Sofie R Salama, Nelle Lambert, Marie-Alexandra Lambot, Sandra Coppens, Jakob S Pedersen, Sol Katzman, Bryan King, Courtney Onodera, Adam Siepel, Andrew D Kern, Colette Dehay, Haller Igel, Manuel Ares, Pierre Vanderhaeghen, David Haussler
    posted to evolution function rna by marcius to the group BioinfoCIPF on 2006-08-23 09:49:50 as ** along with 13 people and 2 groups Ema carlfulp brian bpb nickluscombe larios joshuashen ealloza ce2benna lusk bpcusack nolodie rrhudson EBI-regulation SGU-CIPF
  • Human Evolutionary Genetics: Origins, People and Disease
    (09 December 2003)
    by M Jobling
    posted to evolution human by marcius to the group BioinfoCIPF on 2006-08-11 09:39:21 as ** along with 2 people and 1 group larios jhc SGU-CIPF
  • Noncoding RNAs and homeodomains get together
    Nature Structural & Molecular Biology, Vol. 13, No. 7., pp. 574-574.
    by Sabbi Lall
    posted to evolution ncrna by marcius to the group BioinfoCIPF on 2006-07-26 15:34:33 as ** along with 1 person and 1 group tardigrade SGU-CIPF
  • Ecological networks and their fragility
    Nature, Vol. 442, No. 7100., pp. 259-264.
    by Josã© M Montoya, Stuart L Pimm, Ricard V Solã©
    posted to bioinformatics evolution by marcius to the group BioinfoCIPF on 2006-07-24 12:49:27 as ** along with 3 people and 4 groups cmm mattjb stefanoallesina FAB-lab ComplexAdaptiveSystems SGU-CIPF DSTO-CAS
  • A model for the interaction of learning and evolution.
    Bull Math Biol, Vol. 63, No. 1. (January 2001), pp. 117-134.
    by H Dopazo, MB Gordon, R Perazzo, S Risau-Gusman
    posted to baldwin development effect evolution learning plasticity by hdopazo to the group BioinfoCIPF on 2006-07-20 14:20:19 as *****
  • A Model for the Emergence of Adaptive Subsystems
    Bulletin of Mathematical Biology, Vol. 65, No. 1. (January 2003), pp. 27-56.
    by H Dopazo, MB Gordon, R Perazzo, S Risau-Gusman
    posted to baldwin development effect evolution learning plasticity by hdopazo to the group BioinfoCIPF on 2006-07-20 14:16:25 as ***** along with 1 person RobMills
  • Functional classification using phylogenomic inference.
    PLoS Comput Biol, Vol. 2, No. 6. (30 June 2006)
    by D Brown, K Sjölander
    posted to bioinformatics classification evolution phylogeny by marcius to the group BioinfoCIPF on 2006-07-19 10:36:11 as ** along with 1 person and 1 group jhc SGU-CIPF
  • Prebiotic chemistry and the origin of the RNA world.
    Crit Rev Biochem Mol Biol, Vol. 39, No. 2. (r 2004), pp. 99-123.
    by LE Orgel
    posted to biology evolution rna by marcius to the group BioinfoCIPF on 2006-07-18 12:32:52 as ** along with 1 person and 1 group dayjm SGU-CIPF
  • RNA Sequence Evolution With Secondary Structure Constraints: Comparison of Substitution Rate Models Using Maximum-Likelihood Methods
    Genetics, Vol. 157, No. 1. (1 January 2001), pp. 399-411.
    by Nicholas J Savill, David C Hoyle, Paul G Higgs
    posted to alignment bioinformatics evolution phylogeny rna by marcius to the group BioinfoCIPF on 2006-07-18 12:24:57 as ** along with 3 people and 3 groups penka condon i000 beta SGU-CIPF YY1
  • Molecular evolution of a microRNA cluster.
    J Mol Biol, Vol. 339, No. 2. (28 May 2004), pp. 327-335.
    by A Tanzer, PF Stadler
    posted to evolution microrna phylogeny by marcius to the group BioinfoCIPF on 2006-07-18 10:36:12 as ** along with 4 people and 1 group tardigrade mtagaya mtw maralena SGU-CIPF
  • The Expansion of the Metazoan MicroRNA Repertoire.
    BMC Genomics, Vol. 7, No. 1. (15 February 2006)
    by Jana Hertel, Manuela Lindemeyer, Kristin Missal, Claudia Fried, Andrea Tanzer, Christoph Flamm, Ivo L Hofacker, Peter F Stadler
    posted to bioinformatics evolution microrna phylogeny by marcius to the group BioinfoCIPF on 2006-07-18 10:30:10 as ** along with 10 people and 5 groups imouthesmp balicea andersbj dchughes mtagaya ilh brettc mtw akiezun heliopais microRNA G4ID evo-devo SGU-CIPF Genetics-of-Gambling
  • 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 bioinformatics evolution by marcius to the group BioinfoCIPF on 2006-07-13 14:55:30 as ** along with 5 people and 2 groups operon jordibc hdopazo Garamonfok rvosa SGU-CIPF FAB-lab
  • Conservation and divergence of plant microRNA genes
    The Plant Journal, Vol. 46, No. 2. (April 2006), pp. 243-259.
    by Baohong Zhang, Xiaoping Pan, Charles H Cannon, George P Cobb, Todd A Anderson
    posted to classification evolution microrna plant by marcius to the group BioinfoCIPF on 2006-07-13 14:04:46 as ** along with 4 people and 3 groups natstreet mortenlindow andersbj cdawson microRNA SGU-CIPF GIG
  • Family specific rates of protein evolution
    Bioinformatics, Vol. 22, No. 10. (15 May 2006), pp. 1166-1171.
    by Hannes Luz, Martin Vingron
    posted to alignment bioinformatics evolution by marcius to the group BioinfoCIPF on 2006-05-18 00:18:01 as ** along with 1 group SGU-CIPF
  • Directed evolution of nucleic acid enzymes.
    Annu Rev Biochem, Vol. 73 (2004), pp. 791-836.
    by GF Joyce
    posted to bioengineering evolution function review rna by marcius to the group BioinfoCIPF on 2006-05-15 22:38:36 as ** along with 3 people and 2 groups rklancer condon Hosna beta SGU-CIPF
  • Did DNA Come From Viruses?
    Science, Vol. 312, No. 5775. (12 May 2006), pp. 870-872.
    by Carl Zimmer
    posted to evolution views virus by marcius to the group BioinfoCIPF on 2006-05-13 02:52:53 as ** along with 7 people and 7 groups dayjm dchughes kmcolo echinotrix balvarez cursonivel1 candypmcg G4ID cliamte_change instaar_graduate_students climate_change SGU-CIPF Genetics-of-Gambling cursonivel1
  • A distal enhancer and an ultraconserved exon are derived from a novel retroposon
    Nature (16 April 2006)
    by Gill Bejerano, Craig B Lowe, Nadav Ahituv, Bryan King, Adam Siepel, Sofie R Salama, Edward M Rubin, James W Kent, David Haussler
    posted to bioinformatics evolution gene_expression genome by marcius to the group BioinfoCIPF on 2006-05-09 00:21:57 as ** along with 6 people and 5 groups dchughes nickluscombe djkt cisevol gjuggler carlfulp G4ID EBI-regulation SGU-CIPF Genetics-of-Gambling cis-regulatory-evolution
  • How different amino acid sequences determine similar protein structures: The structure and evolutionary dynamics of the globins
    Journal of Molecular Biology, Vol. 136, No. 3. (25 January 1980), pp. 225-230.
    by Arthur M Lesk, Cyrus Chothia
    posted to biophysics comparative_modeling evolution protein_structure by marcius to the group BioinfoCIPF on 2006-04-30 01:12:36 as ** along with 2 people and 3 groups ana barry structural_bioinformatics Bioinformatics SGU-CIPF
  • Physical Origins of Protein Superfamilies.
    J Mol Biol (6 February 2006)
    by Konstantin B B Zeldovich, Igor N N Berezovsky, Eugene I I Shakhnovich
    posted to biophysics computational_biology evolution protein structure by marcius to the group BioinfoCIPF on 2006-04-27 20:29:04 as ** along with 3 people and 2 groups Einat laurabailey happy_manatee structural_bioinformatics SGU-CIPF
  • Three RNA cells for ribosomal lineages and three DNA viruses to replicate their genomes: a hypothesis for the origin of cellular domain.
    Proc Natl Acad Sci U S A, Vol. 103, No. 10. (7 March 2006), pp. 3669-3674.
    by P Forterre
    posted to biology dna evolution hypotesis rna virus by marcius to the group BioinfoCIPF on 2006-04-27 18:01:25 as ** along with 3 people and 3 groups Retchless jwm brixtonmc Radiation_Damage Stressosome SGU-CIPF
  • Darwinian Evolution Can Follow Only Very Few Mutational Paths to Fitter Proteins
    Science, Vol. 312, No. 5770. (7 April 2006), pp. 111-114.
    by Daniel M Weinreich, Nigel F Delaney, Mark A Depristo, Daniel L Hartl
    posted to evolution protein by marcius to the group BioinfoCIPF on 2006-04-21 17:29:24 as ** along with 14 people and 4 groups stevanspringer barry pansapiens imouthesmp dayjm Einat i41m nirfriedman cmm RowanBarrett ramensky Vaquero Ema bpcusack structural_bioinformatics Bioinformatics FAB-lab SGU-CIPF
  • Designed divergent evolution of enzyme function
    Nature (22 February 2006)
    by Yasuo Yoshikuni, Thomas E Ferrin, Jay D Keasling
    posted to bioinformatics evolution protein_function by marcius to the group BioinfoCIPF on 2006-04-20 21:51:55 as ** along with 3 people and 1 group lingchong tny dbikard SGU-CIPF
  • The evolving role of microRNAs in animal gene expression.
    Bioessays, Vol. 28, No. 5. (13 April 2006), pp. 449-452.
    by Katlin B B Massirer, Amy E E Pasquinelli
    posted to evolution microrna by marcius to the group BioinfoCIPF on 2006-04-18 19:14:49 as ** along with 4 people and 3 groups eckart_bindewald tardigrade balicea dchughes G4ID SGU-CIPF Genetics-of-Gambling
  • In silico sequence evolution with site-specific interactions along phylogenetic trees
    Bioinformatics, Vol. 22, No. 6. (15 March 2006), pp. 716-722.
    by Tanja Gesell, Arndt von Haeseler
    posted to bioinformatics evolution by marcius to the group BioinfoCIPF on 2006-04-03 23:42:33 as ** along with 2 people and 1 group chad_davis tale SGU-CIPF
  • Evolving strategies for enzyme engineering
    Current Opinion in Structural Biology, Vol. 15, No. 4. (August 2005), pp. 447-452.
    by Jesse D Bloom, Michelle M Meyer, Peter Meinhold, Christopher R Otey, Derek Macmillan, Frances H Arnold
    posted to evolution experimental review by marcius to the group BioinfoCIPF on 2006-03-28 23:39:46 as ** along with 1 person and 2 groups okarsligil Bioinformatics SGU-CIPF
  • Evolution in Four Dimensions : Genetic, Epigenetic, Behavioral, and Symbolic Variation in the History of Life (Life and Mind: Philosophical Issues in Biology and Psychology)
    (01 May 2005)
    by Eva Jablonka, Marion J Lamb
    posted to biology evolution by marcius to the group BioinfoCIPF on 2006-03-27 05:10:32 as ** along with 1 person and 1 group tautai SGU-CIPF
  • Comprehensive genome analysis of 203 genomes provides structural genomics with new insights into protein family space
    Nucleic Acids Research, Vol. 34, No. 3. (2006), pp. 1066-1080.
    by Russell L Marsden, David Lee, Michael Maibaum, Corin Yeats, Christine A Orengo
    posted to bioinformatics evolution genome protein_domains structural_genomics by marcius to the group BioinfoCIPF on 2006-03-15 23:00:52 as ** along with 1 person and 1 group eweaver SGU-CIPF
  • Universally conserved positions in protein folds: reading evolutionary signals about stability, folding kinetics and function.
    J Mol Biol, Vol. 291, No. 1. (6 August 1999), pp. 177-196.
    by LA Mirny, EI Shakhnovich
    posted to biophysics evolution folding by marcius to the group BioinfoCIPF on 2006-03-14 17:21:55 as ** along with 3 people and 3 groups ana barry Einat structural_bioinformatics Bioinformatics SGU-CIPF
  • Uncovering evolutionary patterns of gene expression using microarrays
    Trends in Ecology & Evolution, Vol. 21, No. 1. (January 2006), pp. 29-37.
    by Jose M Ranz, Carlos A Machado
    posted to evolution gene_expression microarray by marcius to the group BioinfoCIPF on 2006-03-14 03:00:32 as ** along with 8 people and 4 groups jmeppley balicea tabu cmm sameetmehta natstreet sunye klo Bioinformatics ProkaryoteInterestGroup FAB-lab SGU-CIPF
  • Identification of hundreds of conserved and nonconserved human microRNAs
    Nature Genetics, Vol. 37, No. 7. (19 June 2005), pp. 766-770.
    by Isaac Bentwich, Amir Avniel, Yael Karov, Ranit Aharonov, Shlomit Gilad, Omer Barad, Adi Barzilai, Paz Einat, Uri Einav, Eti Meiri, Eilon Sharon, Yael Spector, Zvi Bentwich
    posted to evolution microrna ncrna rna by marcius to the group BioinfoCIPF on 2006-03-13 07:22:07 as ** along with 2 people and 1 group jfr mtagaya SGU-CIPF
  • Evolution of exon-intron structure and alternative splicing in fruit flies and malarial mosquito genomes.
    Genome Res (6 March 2006)
    by Dmitry B B Malko, Vsevolod J J Makeev, Andrey A A Mironov, Mikhail S S Gelfand
    posted to evolution genome by marcius to the group BioinfoCIPF on 2006-03-09 22:56:10 as ** along with 4 people and 3 groups eoghanharr indigoviolet penka stajich EisenLab Nie SGU-CIPF
  • The path from the RNA world.
    J Mol Evol, Vol. 46, No. 1. (January 1998), pp. 1-17.
    by AM Poole, DC Jeffares, D Penny
    posted to evolution ncrna rna by marcius to the group BioinfoCIPF on 2006-03-08 17:28:19 as ** along with 1 person and 1 group arcticrasta SGU-CIPF
  • The involvement of RNA in ribosome function.
    Nature, Vol. 418, No. 6894. (11 July 2002), pp. 229-235.
    by PB Moore, TA Steitz
    posted to biology evolution ribosome rna by marcius to the group BioinfoCIPF on 2006-03-06 23:02:59 as ** along with 1 person and 1 group mercaptan SGU-CIPF
  • How RNA folds.
    J Mol Biol, Vol. 293, No. 2. (22 October 1999), pp. 271-281.
    by I Tinoco, C Bustamante
    posted to biophysics evolution folding rna by marcius to the group BioinfoCIPF on 2006-03-06 23:02:38 as ** along with 9 people and 2 groups eskay dayjm eckart_bindewald perrywoo arcticrasta condon Hosna apop physics beta SGU-CIPF
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