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knaseanka's library [95 articles]

最近录入 knaseanka's 文献库.
  • Analyzing Large Data Sets in Reasonable Times: Solutions for Composite Optima
    Cladistics, Vol. 15, No. 4. (1999), pp. 415-428.
    by Pablo A Goloboff
    posted to phylogeny proj-alphamito-2 by knaseanka on 2007-04-24 08:14:54 as **
  • Data exploration in phylogenetic inference: scientific, heuristic, or neither
    Cladistics, Vol. 19, No. 5. (2003), pp. 379-418.
    by Taran Grant, Arnold G Kluge
    posted to phylogeny proj-alphamito-2 by knaseanka on 2007-04-24 08:13:54 as ** along with 1 person Thaverkamp
  • Changing the landscape: a new strategy for estimating large phylogenies.
    Syst Biol, Vol. 50, No. 1. (February 2001), pp. 60-66.
    by DL Quicke, J Taylor, A Purvis
    posted to phylogeny proj-alphamito-2 by knaseanka on 2007-04-24 08:12:09 as **
  • Origin and Evolution of the Mitochondrial Aminoacyl-tRNA Synthetases.
    Mol Biol Evol (20 December 2006)
    by Björn Brindefalk, Johan Viklund, Daniel Larsson, Mikael Thollesson, Siv G E G Andersson
    posted to mine proj-alphamito sub-biology sub-mitocondrie by knaseanka on 2007-01-07 20:54:03 as read
  • The Evolutionary Fate and Consequences of Duplicate Genes
    Science, Vol. 290, No. 5494. (10 November 2000), pp. 1151-1155.
    by Michael Lynch, John S Conery
    posted to birth death duplication sub-bioinformatics by knaseanka on 2006-12-18 12:51:19 as ***** along with 7 people clearbluespring BioNica arve nirfriedman echinotrix treangen timflutre
  • A basic result on the integral for birth-death Markov processes.
    Math Biosci, Vol. 161, No. 1-2. (October 1999), pp. 95-104.
    by CM Hernández-Suárez, C Castillo-Chavez
    posted to birth death mathematics stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:26:03 as *****
  • Extinction times for a birth-death process with two phases.
    Math Biosci, Vol. 202, No. 2. (August 2006), pp. 310-322.
    by JV Ross, PK Pollett
    posted to birth death mathematics stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:24:58 as *****
  • Modeling genome evolution with a diffusion approximation of a birth-and-death process.
    Bioinformatics, Vol. 21 Suppl 3 (1 November 2005)
    by GP Karev, FS Berezovskaya, EV Koonin
    posted to birth death stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:24:30 as **
  • Simple stochastic birth and death models of genome evolution: was there enough time for us to evolve?
    Bioinformatics, Vol. 19, No. 15. (12 October 2003), pp. 1889-1900.
    by GP Karev, YI Wolf, EV Koonin
    posted to birth death stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:24:13 as *** along with 1 person csgillespie
  • Birth and death of protein domains: a simple model of evolution explains power law behavior.
    BMC Evol Biol, Vol. 2, No. 1. (2002)
    by GP Karev, YI Wolf, AY Rzhetsky, FS Berezovskaya, EV Koonin
    posted to birth death stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:23:53 as *** along with 1 person martainn
  • Gene family evolution: an in-depth theoretical and simulation analysis of non-linear birth-death-innovation models.
    BMC Evol Biol, Vol. 4 (9 September 2004)
    by GP Karev, YI Wolf, FS Berezovskaya, EV Koonin
    posted to birth death stochastic sub-bioinformatics by knaseanka on 2006-12-15 10:09:08 as ***** along with 1 person ruvido
  • Genome-scale approaches to resolving incongruence in molecular phylogenies.
    Nature, Vol. 425, No. 6960. (23 October 2003), pp. 798-804.
    by A Rokas, BL Williams, N King, SB Carroll
    posted to sub-phylogenetics by knaseanka on 2006-12-11 15:42:23 as *** along with 3 people aprasad AaronDarling srfairclough
  • From gene trees to organismal phylogeny in prokaryotes: the case of the gamma-Proteobacteria.
    PLoS Biol, Vol. 1, No. 1. (October 2003)
    by E Lerat, V Daubin, NA Moran
    posted to sub-phylogenetics by knaseanka on 2006-12-11 15:40:35 as *** along with 2 people AaronDarling treangen
  • Clann: investigating phylogenetic information through supertree analyses.
    Bioinformatics, Vol. 21, No. 3. (1 February 2005), pp. 390-392.
    by CJ Creevey, JO McInerney
    posted to sub-phylogenetics by knaseanka on 2006-12-11 15:00:24 as *****
  • DPRml: distributed phylogeny reconstruction by maximum likelihood.
    Bioinformatics, Vol. 21, No. 7. (1 April 2005), pp. 969-974.
    by TM Keane, TJ Naughton, SA Travers, JO McInerney, GP McCormack
    posted to sub-phylogenetics by knaseanka on 2006-12-11 13:57:28 as ***** along with 1 person rdiaz
  • Genome trees and the nature of genome evolution.
    Annu Rev Microbiol, Vol. 59 (2005), pp. 191-209.
    by B Snel, BE Dutilh
    posted to sub-bioinformatics by knaseanka on 2006-12-08 15:18:48 as ***** along with 2 people aprasad dayjm
  • Quality assessment of multiple alignment programs.
    FEBS Lett, Vol. 529, No. 1. (2 October 2002), pp. 126-130.
    by T Lassmann, EL Sonnhammer
    posted to sub-bioinformatics by knaseanka on 2006-11-29 12:05:53 as ** along with 1 person major724
  • Kalign--an accurate and fast multiple sequence alignment algorithm.
    BMC Bioinformatics, Vol. 6 (2005)
    by T Lassmann, EL Sonnhammer
    posted to sub-bioinformatics by knaseanka on 2006-11-29 12:05:11 as ** along with 1 person Haggan
  • MUSCLE: a multiple sequence alignment method with reduced time and space complexity.
    BMC Bioinformatics, Vol. 5, No. 1. (19 August 2004)
    by RC Edgar
    posted to sub-bioinformatics by knaseanka on 2006-11-29 12:04:33 as ** along with 12 people and 3 groups sanchezbuelna wallacei chrn jwm balajis gbart caporaso sriram_s cdallett timflutre gisle urgi Radiation_Damage Stressosome biomedical-nlp
  • Toward Automatic Reconstruction of a Highly Resolved Tree of Life
    Science, Vol. 311, No. 5765. (3 March 2006), pp. 1283-1287.
    by Francesca D Ciccarelli, Tobias Doerks, Christian von Mering, Christopher J Creevey, Berend Snel, Peer Bork
    posted to sub-bioinformatics sub-phylogenetics by knaseanka on 2006-11-28 15:51:50 as **** along with 12 people and 5 groups diamantis Retchless dpollard tny dchughes nirfriedman cmm azazello wenhan maximilianh cmzmasek lonshy EisenLab FAB-lab G4ID Genetics-of-Gambling MBLAB
  • Large punctuational contribution of speciation to evolutionary divergence at the molecular level.
    Science, Vol. 314, No. 5796. (6 October 2006), pp. 119-121.
    by M Pagel, C Venditti, A Meade
    posted to sub-phylogenetics type-journal_club by knaseanka on 2006-11-06 09:59:24 as read along with 2 people and 1 group brant shikin EisenLab
  • Epigenetic gene regulation in the bacterial world.
    Microbiol Mol Biol Rev, Vol. 70, No. 3. (September 2006), pp. 830-856.
    by J Casadesús, D Low
    posted to sub-alphaprot by knaseanka on 2006-09-22 09:41:47 as *** along with 1 person cambray
  • Adaptive evolution of bacterial metabolic networks by horizontal gene transfer
    Nature Genetics, Vol. 37, No. 12. (20 November 2005), pp. 1372-1375.
    by Csaba Pál, Balázs Papp, Martin J Lercher
    posted to sub-orfans by knaseanka on 2006-08-24 10:33:38 as ***** along with 3 people and 1 group michaelbarton icases tny TNT
  • Patterns of bacterial gene movement.
    Mol Biol Evol, Vol. 21, No. 7. (July 2004), pp. 1294-1307.
    by W Hao, GB Golding
    posted to sub-orfans by knaseanka on 2006-08-24 08:58:38 as ***** along with 1 person LeightonP
  • The fate of laterally transferred genes: life in the fast lane to adaptation or death.
    Genome Res, Vol. 16, No. 5. (May 2006), pp. 636-643.
    by W Hao, GB Golding
    posted to sub-orfans by knaseanka on 2006-08-24 08:11:11 as ***** along with 2 people operon treangen
  • Computational inference of scenarios for alpha-proteobacterial genome evolution.
    Proc Natl Acad Sci U S A, Vol. 101, No. 26. (29 June 2004), pp. 9722-9727.
    by B Boussau, EO Karlberg, AC Frank, BA Legault, SG Andersson
    posted to sub-alphaprot by knaseanka on 2006-07-25 10:01:32 as **** along with 2 people bjorns radek
  • The louse-borne human pathogen Bartonella quintana is a genomic derivative of the zoonotic agent Bartonella henselae.
    Proc Natl Acad Sci U S A, Vol. 101, No. 26. (29 June 2004), pp. 9716-9721.
    by CM Alsmark, AC Frank, EO Karlberg, BA Legault, DH Ardell, B Canbäck, AS Eriksson, AK Näslund, SA Handley, M Huvet, B La Scola, M Holmberg, SG Andersson
    posted to sub-alphaprot by knaseanka on 2006-07-25 10:00:41 as **** along with 3 people shandley operon bjorns
  • Complete genome sequencing of Anaplasma marginale reveals that the surface is skewed to two superfamilies of outer membrane proteins.
    Proc Natl Acad Sci U S A, Vol. 102, No. 3. (18 January 2005), pp. 844-849.
    by KA Brayton, LS Kappmeyer, DR Herndon, MJ Dark, DL Tibbals, GH Palmer, TC McGuire, DP Knowles
    posted to sub-alphaprot by knaseanka on 2006-07-25 09:59:54 as **** along with 1 person bjorns
  • The genome of the heartwater agent Ehrlichia ruminantium contains multiple tandem repeats of actively variable copy number.
    Proc Natl Acad Sci U S A, Vol. 102, No. 3. (18 January 2005), pp. 838-843.
    by NE Collins, J Liebenberg, EP de Villiers, KA Brayton, E Louw, A Pretorius, FE Faber, H van Heerden, A Josemans, M van Kleef, HC Steyn, MF van Strijp, E Zweygarth, F Jongejan, JC Maillard, D Berthier, M Botha, F Joubert, CH Corton, NR Thomson, MT Allsopp, BA Allsopp
    posted to sub-alphaprot by knaseanka on 2006-07-25 09:59:21 as ****
  • The Wolbachia genome of Brugia malayi: endosymbiont evolution within a human pathogenic nematode.
    PLoS Biol, Vol. 3, No. 4. (April 2005)
    by J Foster, M Ganatra, I Kamal, J Ware, K Makarova, N Ivanova, A Bhattacharyya, V Kapatral, S Kumar, J Posfai, T Vincze, J Ingram, L Moran, A Lapidus, M Omelchenko, N Kyrpides, E Ghedin, S Wang, E Goltsman, V Joukov, O Ostrovskaya, K Tsukerman, M Mazur, D Comb, E Koonin, B Slatko
    posted to sub-alphaprot by knaseanka on 2006-07-25 09:58:33 as **** along with 1 person operon
  • Phylogenomics of the reproductive parasite Wolbachia pipientis wMel: a streamlined genome overrun by mobile genetic elements.
    PLoS Biol, Vol. 2, No. 3. (March 2004)
    by M Wu, LV Sun, J Vamathevan, M Riegler, R Deboy, JC Brownlie, EA McGraw, W Martin, C Esser, N Ahmadinejad, C Wiegand, R Madupu, MJ Beanan, LM Brinkac, SC Daugherty, AS Durkin, JF Kolonay, WC Nelson, Y Mohamoud, P Lee, K Berry, MB Young, T Utterback, J Weidman, WC Nierman, IT Paulsen, KE Nelson, H Tettelin, SL O'Neill, JA Eisen
    posted to sub-alphaprot by knaseanka on 2006-07-25 09:57:51 as **** along with 3 people and 1 group operon radek wrowell Cline_lab
  • Spectral clustering of protein sequences.
    Nucleic Acids Res, Vol. 34, No. 5. (2006), pp. 1571-1580.
    by A Paccanaro, JA Casbon, MA Saqi
    posted to sub-bioinformatics subsub-clustering subsub-method by knaseanka on 2006-06-22 13:02:46 as read along with 1 person bobychan
  • An efficient algorithm for large-scale detection of protein families.
    Nucleic Acids Res, Vol. 30, No. 7. (1 April 2002), pp. 1575-1584.
    by AJ Enright, S Van Dongen, CA Ouzounis
    posted to proj-alphaspec sub-bioinformatics subsub-clustering subsub-method by knaseanka on 2006-06-22 12:07:36 as read along with 12 people and 2 groups Borelli camster operon indigoviolet skhadar nirfriedman dgront entropy gcalda GustavoLacerda hpaces RebeccaHamer dbk-lab EisenLab
  • Degenerative evolution and functional diversification of type-III secretion systems in the insect endosymbiont Sodalis glossinidius.
    Mol Biol Evol, Vol. 22, No. 3. (March 2005), pp. 758-766.
    by C Dale, T Jones, M Pontes
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 14:05:38 as ***
  • Type III secretion systems and the evolution of mutualistic endosymbiosis.
    Proc Natl Acad Sci U S A, Vol. 99, No. 19. (17 September 2002), pp. 12397-12402.
    by C Dale, GR Plague, B Wang, H Ochman, NA Moran
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 14:03:05 as *** along with 2 people gelack manzanita
  • Bacterial flagella and type III secretion systems.
    FEMS Microbiol Lett, Vol. 202, No. 2. (21 August 2001), pp. 157-164.
    by SI Aizawa
    posted to flagella sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 13:49:59 as **** along with 1 person cam-flagella
  • Type III protein secretion systems in bacterial pathogens of animals and plants.
    Microbiol Mol Biol Rev, Vol. 62, No. 2. (June 1998), pp. 379-433.
    by CJ Hueck
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 13:33:03 as *** along with 3 people manzanita bjorns robert
  • Acquisition and Evolution of the exoU Locus in Pseudomonas aeruginosa.
    J Bacteriol, Vol. 188, No. 11. (June 2006), pp. 4037-4050.
    by BR Kulasekara, HD Kulasekara, MC Wolfgang, L Stevens, DW Frank, S Lory
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 13:29:45 as **
  • Secretory compartments as instances of dynamic self-evolving structures.
    Acta Biotheor, Vol. 50, No. 4. (2002), pp. 209-221.
    by F Képès
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 13:18:13 as **
  • A directed evolution strategy for optimized export of recombinant proteins reveals critical determinants for preprotein discharge.
    Protein Sci, Vol. 13, No. 9. (September 2004), pp. 2458-2469.
    by MA Kaderbhai, HM Davey, NN Kaderbhai
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 13:13:02 as **
  • Bacterial type III secretion systems are ancient and evolved by multiple horizontal-transfer events.
    Gene, Vol. 312 (17 July 2003), pp. 151-163.
    by U Gophna, EZ Ron, D Graur
    posted to sub-biology subsub-evolution ttss by knaseanka on 2006-05-23 12:55:38 as ****
  • Characterization of the ysa pathogenicity locus in the chromosome of Yersinia enterocolitica and phylogeny analysis of type III secretion systems.
    J Mol Evol, Vol. 55, No. 1. (July 2002), pp. 37-51.
    by B Foultier, P Troisfontaines, S Müller, FR Opperdoes, GR Cornelis
    posted to sub-biology subsub-evolution subsub-phylogeny ttss by knaseanka on 2006-05-23 12:42:54 as ****
  • Signature proteins that are distinctive of alpha proteobacteria.
    BMC Genomics, Vol. 6 (2005)
    by P Kainth, RS Gupta
    posted to proj-alphaspec sub-alphaprot by knaseanka on 2006-05-04 09:41:37 as read
  • Enrichment for microbes living in association with plant tissues
    Journal of Applied Microbiology, Vol. 100, No. 4. (April 2006), pp. 830-837.
    by JY Jiao, HX Wang, Y Zeng, YM Shen
    posted to sub-metagenomics subsub-method by knaseanka on 2006-03-27 07:52:25 as *
  • The Genome Sequence of Rickettsia felis Identifies the First Putative Conjugative Plasmid in an Obligate Intracellular Parasite.
    PLoS Biol, Vol. 3, No. 8. (August 2005)
    by H Ogata, P Renesto, S Audic, C Robert, G Blanc, PE Fournier, H Parinello, JM Claverie, D Raoult
    posted to sub-alphaprot by knaseanka on 2006-03-27 07:50:18 as **** along with 1 person bjorns
  • An application of statistics to comparative metagenomics.
    BMC Bioinformatics, Vol. 7, No. 1. (20 March 2006)
    by Beltran Rodriguez-Brito, Forest Rohwer, Robert Edwards
    posted to sub-bioinformatics sub-metagenomics by knaseanka on 2006-03-24 12:11:55 as *** along with 3 people carpi jmeppley bluto
  • A molecular revolution in the study of intestinal microflora.
    Gut, Vol. 55, No. 2. (February 2006), pp. 141-143.
    by E Furrie
    posted to sub-metagenomics by knaseanka on 2006-03-24 07:13:10 as read
  • Bioinformatic Insights from Metagenomics through Visualization.
    Proc IEEE Comput Syst Bioinform Conf, Vol. 4 (2005), pp. 341-350.
    by Susan L Havre, Bobbie-Jo J Webb-Robertson, Anuj Shah, Christian Posse, Banu Gopalan, Fred J Brockman
    posted to sub-bioinformatics subsub-visualization by knaseanka on 2006-03-24 07:12:02 as *** along with 3 people jmeppley Schmidtc eweaver
  • Metaproteomics: studying functional gene expression in microbial ecosystems.
    Trends Microbiol, Vol. 14, No. 2. (February 2006), pp. 92-97.
    by P Wilmes, PL Bond
    posted to sub-metagenomics sub-metaproteomics by knaseanka on 2006-03-24 07:11:07 as ** along with 6 people mcox Yanno jmeppley bluto nitiniitk barberan
  • Comparative analysis of environmental sequences: potential and challenges.
    Philos Trans R Soc Lond B Biol Sci, Vol. 361, No. 1467. (29 March 2006), pp. 519-523.
    by KU Foerstner, C von Mering, P Bork
    posted to sub-metagenomics type-review by knaseanka on 2006-03-24 07:04:55 as ****
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