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Tag comparative-genomics [47 articles]

Articoli recentemente classificati sotto il tag comparative-genomics.
  • In vivo acquisition of prophage in Streptococcus pyogenes.
    Trends Microbiol (30 May 2007)
    by Vincent A A Fischetti
    posted to comparative-genomics fischetti gas phage prophage by ramykaram on 2007-06-06 22:28:23 as *****
  • Chromosome Evolution in the Thermotogales: Large-Scale Inversions and Strain Diversification of CRISPR Sequences
    J. Bacteriol., Vol. 188, No. 7. (1 April 2006), pp. 2364-2374.
    by Robert T Deboy, Emmanuel F Mongodin, Joanne B Emerson, Karen E Nelson
    posted to comparative-genomics evolution by rabu on 2006-08-03 00:52:11 as ** along with 1 person saru
  • The genomics gamble.
    Nat Genet, Vol. 26, No. 2. (October 2000), pp. 134-135.
    by SG Andersson
    posted to comparative-genomics evolution by rabu on 2006-08-04 19:19:05 as **
  • Genomes to aid in bioremediation of dry cleaning solvents, mothballs and more
    Environmental Microbiology, Vol. 8, No. 6. (2006), pp. 949-955.
    by Michael Y Galperin
    posted to comparative-genomics by rabu on 2006-11-08 18:24:14 as **
  • Genome rearrangement by replication-directed translocation.
    Nat Genet, Vol. 26, No. 2. (October 2000), pp. 195-197.
    by ER Tillier, RA Collins
    posted to comparative-genomics evolution by rabu on 2006-08-04 19:15:14 as ** along with 1 person operon
  • Human-macaque comparisons illuminate variation in neutral substitution rates
    Genome Biology, Vol. 9 (30 April 2008), R76.
    by Svitlana Tyekucheva, Kateryna D Makova, John E Karro, Ross C Hardison, Webb Miller, Francesca Chiaromonte
    posted to comparative-genomics by mailund on 2008-05-23 12:38:58 as read
  • SeqAn - An efficient, generic C++ library for sequence analysis
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Andreas Doring, David Weese, Tobias Rausch, Knut Reinert
    posted to comparative-genomics sequence-analysis software by mailund on 2008-01-10 10:34:18 as read along with 8 people jyuh chad_davis laughcry ryanraaum nklee barriot magusina reyez
  • 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 comparative-genomics statistical-alignment by mailund on 2008-01-09 13:42:39 as read along with 3 people and 1 group aprasad AaronDarling elfar Bioinformatics
  • Genome-Wide Identification of Human Functional DNA Using a Neutral Indel Model.
    PLoS Comput Biol, Vol. 2, No. 1. (13 January 2006)
    by Gerton Lunter, Chris P P Ponting, Jotun Hein
    posted to comparative-genomics by mailund on 2008-01-09 13:42:57 as read along with 9 people and 2 groups aprasad eckart_bindewald eweaver lhonigberg acidwizard juliettecolinas bpcusack Stew cisevol EisenLab cis-regulatory-evolution
  • Mapping Human Genetic Ancestry
    Mol Biol Evol, Vol. 24, No. 10. (1 October 2007), pp. 2266-2276.
    by Ingo Ebersberger, Petra Galgoczy, Stefan Taudien, Simone Taenzer, Matthias Platzer, Arndt von Haeseler
    posted to comparative-genomics genetics phylogenetics by mailund on 2008-01-29 20:06:08 as read along with 2 people dchughes ryanraaum
  • Genomic Relationships and Speciation Times of Human, Chimpanzee, and Gorilla Inferred from a Coalescent Hidden Markov Model
    PLoS Genetics, Vol. 3, No. 2. (1 February 2007), e7.
    by Asger Hobolth, Ole F Christensen, Thomas Mailund, Mikkel H Schierup
    posted to coalhmm comparative-genomics by mailund on 2007-12-08 08:48:38 as read along with 6 people and 1 group usagi-kirin nurban nosada17 berthoums kourai lh3 Durbin group
  • Pigs in sequence space: A 0.66X coverage pig genome survey based on shotgun sequencing
    BMC Genomics, Vol. 6, No. 1. (2005)
    by Rasmus Wernersson, Mikkel Schierup, Frank Jorgensen, Jan Gorodkin, Frank Panitz, Hans H Staerfeldt, Ole Christensen, Thomas Mailund, Henrik Hornshoj, Ami Klein, Jun Wang, Bin Liu, Songnian Hu, Wei Dong, Wei Li, Gane Wong, Jun Yu, Jian Wang, Christian Bendixen, Merete Fredholm, Soren Brunak, Huanming Yang, Lars Bolund
    posted to comparative-genomics by mailund on 2007-12-08 08:54:12 as read along with 1 person GustavoLacerda
  • Annotation of selection strengths in viral genomes
    Bioinformatics, Vol. 23, No. 22. (15 November 2007), pp. 2978-2986.
    by Stephen Mccauley, Saskia de Groot, Thomas Mailund, Jotun Hein
    posted to comparative-genomics hmm virus by mailund on 2007-12-08 08:57:53 as read
  • Comparative annotation of viral genomes with non-conserved gene structure
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1080-1089.
    by Saskia de Groot, Thomas Mailund, Jotun Hein
    posted to comparative-genomics hmm virus by mailund on 2007-12-08 08:58:21 as read
  • notes Genomic Analysis Reveals Chromosomal Variation in Natural Populations of the Uncultured Psychrophilic Archaeon Cenarchaeum symbiosum
    J. Bacteriol., Vol. 180, No. 19. (1 October 1998), pp. 5003-5009.
    by Christa Schleper, Edward F Delong, Christina M Preston, Robert A Feldman, Ke-Ying Wu, Ronald V Swanson
    posted to community-genomics comparative-genomics diversity microbial-diversity microbial-genomics variability by jmeppley on 2006-07-05 17:47:36 as read
  • Thermal adaptation analyzed by comparison of protein sequences from mesophilic and extremely thermophilic Methanococcus species
    PNAS, Vol. 96, No. 7. (30 March 1999), pp. 3578-3583.
    by Paul J Haney, Jonathan H Badger, Gerald L Buldak, Claudia I Reich, Carl R Woese, Gary J Olsen
    posted to adaptation comparative-genomics by jmeppley on 2006-08-31 00:16:19 as *** along with 2 people bpb neils
  • Lateral gene transfer and phylogenetic assignment of environmental fosmid clones
    Environmental Microbiology, Vol. 7, No. 12. (December 2005), pp. 2011-2026.
    by Camilla L Nesbø, Yan Boucher, Marlena Dlutek, Ford W Doolittle
    posted to community-genomics comparative-genomics hgt-detection horizontal-gene-transfer z-paper-background by jmeppley on 2006-03-21 21:16:33 as read
  • Human Lineage-Specific Amplification, Selection, and Neuronal Expression of DUF1220 Domains
    Science, Vol. 313, No. 5791. (1 September 2006), pp. 1304-1307.
    by Magdalena C Popesco, Erik J Maclaren, Janet Hopkins, Laura Dumas, Michael Cox, Lynne Meltesen, Loris Mcgavran, Gerald J Wyckoff, James M Sikela
    posted to comparative-genomics by jmeppley on 2006-09-01 19:39:45 as **
  • Scale-invariant structure of strongly conserved sequence in genomic intersections and alignments.
    Proc Natl Acad Sci U S A (21 August 2006)
    by William Salerno, Paul Havlak, Jonathan Miller
    posted to comparative-genomics by jmeppley on 2006-09-01 22:18:00 as *** along with 1 person and 1 group dpollard EisenLab
  • Comparative sequence analyses reveal frequent occurrence of short segments containing an abnormally high number of non-random base variations in bacterial rRNA genes
    Microbiology, Vol. 146, No. 11. (1 November 2000), pp. 2845-2854.
    by Yue Wang, Zhenshui Zhang
    posted to comparative-genomics hgt-mosaic-genome rrna by jmeppley on 2006-03-22 18:23:40 as **
  • notes Studies on codon usage in Thermoplasma acidophilum and its possible implications on the occurrences of lateral gene transfer.
    J Basic Microbiol, Vol. 45, No. 5. (2005), pp. 344-354.
    by SK Gupta, T Banerjee, S Basak, K Sahu, S Sau, TC Ghosh
    posted to comparative-genomics hgt-archaea horizontal-gene-transfer x-recomb-evidence by jmeppley on 2006-05-12 20:12:26 as read
  • notes The cobweb of life revealed by genome-scale estimates of horizontal gene transfer.
    PLoS Biol, Vol. 3, No. 10. (October 2005)
    by F Ge, LS Wang, J Kim
    posted to comparative-genomics hgt-detection horizontal-gene-transfer phylogenetics tree-of-life by jmeppley on 2006-03-21 19:39:24 as ** along with 2 people and 2 groups ana AaronDarling structural_bioinformatics Bioinformatics
  • Metagenomics: genomic analysis of microbial communities.
    Annu Rev Genet, Vol. 38 (2004), pp. 525-552.
    by CS Riesenfeld, PD Schloss, J Handelsman
    posted to community-genomics comparative-genomics microbial-genomics by jmeppley on 2006-07-05 17:51:56 as ** along with 4 people and 2 groups knaseanka wenhan mcox djkt Green Lab iSEEM
  • Phytophthora Genome Sequences Uncover Evolutionary Origins and Mechanisms of Pathogenesis
    Science, Vol. 313, No. 5791. (1 September 2006), pp. 1261-1266.
    by Brett M Tyler, Sucheta Tripathy, Xuemin Zhang, Paramvir Dehal, Rays H Jiang, Andrea Aerts, Felipe D Arredondo, Laura Baxter, Douda Bensasson, Jim L Beynon, Jarrod Chapman, Cynthia M Damasceno, Anne E Dorrance, Daolong Dou, Allan W Dickerman, Inna L Dubchak, Matteo Garbelotto, Mark Gijzen, Stuart G Gordon, Francine Govers, Niklaus J Grunwald, Wayne Huang, Kelly L Ivors, Richard W Jones, Sophien Kamoun, Konstantinos Krampis, Kurt H Lamour, Mi-Kyung Lee, Hayes W Mcdonald, Monica Medina, Harold J Meijer, Eric K Nordberg, Donald J Maclean, Manuel D Ospina-Giraldo, Paul F Morris, Vipaporn Phuntumart, Nicholas H Putnam, Sam Rash, Jocelyn K Rose, Yasuko Sakihama, Asaf A Salamov, Alon Savidor, Chantel F Scheuring, Brian M Smith, Bruno W Sobral, Astrid Terry, Trudy A Torto-Alalibo, Joe Win, Zhanyou Xu, Hongbin Zhang, Igor V Grigoriev, Daniel S Rokhsar, Jeffrey L Boore
    posted to comparative-genomics by jmeppley on 2006-09-01 19:39:37 as **
  • Horizontal gene transfer in prokaryotes: quantification and classification.
    Annu Rev Microbiol, Vol. 55 (2001), pp. 709-742.
    by EV Koonin, KS Makarova, L Aravind
    posted to comparative-genomics horizontal-gene-transfer by jmeppley on 2006-03-21 19:36:16 as ** along with 4 people and 4 groups ana madhadron caporaso vwchan structural_bioinformatics Bioinformatics biomedical-nlp beta
  • Integrated data analysis for genome-wide research.
    EXS, Vol. 97 (2007), pp. 309-329.
    by M Steinfath, D Repsilber, M Scholz, D Walther, J Selbig
    posted to comparative-genomics genomics statistics by jmeppley on 2008-05-14 18:15:46 as ***** along with 1 person lh1
  • Evidence of recent lateral gene transfer among hyperthermophilic archaea.
    Mol Microbiol, Vol. 38, No. 4. (November 2000), pp. 684-693.
    by J Diruggiero, D Dunn, DL Maeder, R Holley-Shanks, J Chatard, R Horlacher, FT Robb, W Boos, RB Weiss
    posted to archaea comparative-genomics horizontal-gene-transfer hyperthermophile x-recomb-evidence by jmeppley on 2006-03-21 21:32:38 as **
  • Who's your neighbor? New computational approaches for functional genomics.
    Nat Biotechnol, Vol. 18, No. 6. (June 2000), pp. 609-613.
    by MY Galperin, EV Koonin
    posted to comparative-genomics function-prediction functional-genomics phylogenetics by jmeppley on 2006-08-18 16:09:28 as **** along with 4 people bicko balajis eweaver bluto
  • Evidence for lateral gene transfer between Archaea and bacteria from genome sequence of Thermotoga maritima.
    Nature, Vol. 399, No. 6734. (27 May 1999), pp. 323-329.
    by KE Nelson, RA Clayton, SR Gill, ML Gwinn, RJ Dodson, DH Haft, EK Hickey, JD Peterson, WC Nelson, KA Ketchum, L McDonald, TR Utterback, JA Malek, KD Linher, MM Garrett, AM Stewart, MD Cotton, MS Pratt, CA Phillips, D Richardson, J Heidelberg, GG Sutton, RD Fleischmann, JA Eisen, O White, SL Salzberg, HO Smith, JC Venter, CM Fraser
    posted to archaea bacteria comparative-genomics horizontal-gene-transfer by jmeppley on 2006-03-21 17:24:15 as ** along with 2 people and 2 groups ana karfunkel structural_bioinformatics Bioinformatics
  • Patterns and Implications of Gene Gain and Loss in the Evolution of Prochlorococcus.
    PLoS Genet, Vol. 3, No. 12. (21 December 2007)
    by Gregory C C Kettler, Adam C C Martiny, Katherine Huang, Jeremy Zucker, Maureen L L Coleman, Sebastien Rodrigue, Feng Chen, Alla Lapidus, Steven Ferriera, Justin Johnson, Claudia Steglich, George M M Church, Paul Richardson, Sallie W W Chisholm
    posted to comparative-genomics prochlorococccus by jmeppley on 2008-04-09 13:36:34 as ** along with 2 people operon JeremyZucker
  • notes Detecting horizontal gene transfer with T-REX and RHOM programs
    Briefings in Bioinformatics, Vol. 6, No. 4. (December 2005), pp. 394-401.
    by Li, Zuofeng, Wang, Li, Zhong, Yang
    posted to comparative-genomics hgt-detection hgt-detection-software horizontal-gene-transfer phylogenetics software by jmeppley on 2006-03-21 19:15:30 as **
  • notes Comparative Genomic Analysis of Archaeal Genotypic Variants in a Single Population and in Two Different Oceanic Provinces
    Appl. Environ. Microbiol., Vol. 68, No. 1. (1 January 2002), pp. 335-345.
    by Oded Beja, Eugene V Koonin, L Aravind, Lance T Taylor, Heidi Seitz, Jefferey L Stein, Daniel C Bensen, Robert A Feldman, Ronald V Swanson, Edward F Delong
    posted to community-genomics comparative-genomics diversity genomics microbial-genomics variability by jmeppley on 2006-07-05 17:50:08 as read
  • ESTIMATING RECOMBINATION RATES FROM POPULATION-GENETIC DATA
    Nat Rev Genet, Vol. 4, No. 12. (December 2003), pp. 959-968.
    by Michael P Stumpf, Gilean A Mcvean
    posted to comparative-genomics recombination x-recomb-frequency by jmeppley on 2006-06-17 00:06:40 as **
  • Design and testing of ‘genome-proxy’ microarrays to profile marine microbial communities
    Environmental Microbiology, Vol. 0, No. 0. (0), pp. ???-???.
    by Virginia I Rich, Konstantinos Konstantinidis, Edward F Delong
    posted to comparative-genomics delong-lab metagenomics microarray oceanic-microbiology by jmeppley on 2007-12-12 20:51:00 as **
  • MBGD: a platform for microbial comparative genomics based on the automated construction of orthologous groups.
    Nucleic acids research, Vol. 35, No. Database issue. (January 2007)
    by I Uchiyama
    posted to software microbial-genomics comparative-genomics bioinformatics by jmeppley on 2008-09-02 02:47:15 as ***
  • notes Horizontal gene transfer among microbial genomes: new insights from complete genome analysis
    Current Opinion in Genetics & Development, Vol. 10, No. 6. (1 December 2000), pp. 606-611.
    by Jonathan A Eisen
    posted to comparative-genomics hgt-detection horizontal-gene-transfer by jmeppley on 2006-03-21 19:44:26 as **
  • Horizontal gene transfer and phylogenetics
    Current Opinion in Microbiology, Vol. 6, No. 5. (October 2003), pp. 498-505.
    by Herve Philippe, Christophe J Douady
    posted to archaea classification comparative-genomics evolution genomics horizontal-gene-transfer microbial-genomics phylogenetics proteins sequence-alignment tree-of-life by jmeppley on 2005-10-04 23:44:45 as **
  • notes Insights on biology and evolution from microbial genome sequencing
    Genome Res., Vol. 15, No. 12. (1 December 2005), pp. 1603-1610.
    by Claire M Fraser-Liggett
    posted to community-genomics comparative-genomics evolution genomics horizontal-gene-transfer microbial-diversity microbial-genomics by jmeppley on 2005-12-16 06:19:43 as read along with 2 people Retchless operon
  • notes 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 comparative-genomics comparative-metagenomics statistics by jmeppley on 2008-01-09 17:12:04 as **** along with 4 people and 1 group knaseanka bluto carpi djkt iSEEM
  • notes Detection of lateral gene transfer among microbial genomes
    Current Opinion in Genetics & Development, Vol. 11, No. 6. (1 December 2001), pp. 620-626.
    by Mark A Ragan
    posted to comparative-genomics hgt-detection horizontal-gene-transfer by jmeppley on 2006-03-21 19:53:47 as **
  • Comparative genomics of major histocompatibility complexes.
    Immunogenetics, Vol. 56, No. 10. (January 2005), pp. 683-695.
    by J Kelley, L Walter, J Trowsdale
    posted to comparative-genomics mhc by jermth on 2006-09-13 09:13:08 as ** along with 1 person and 1 group nknii TCR_Signaling
  • Constraint and turnover in sex-biased gene expression in the genus Drosophila
    Nature, Vol. 450, No. 7167., pp. 233-237.
    by Yu Zhang, David Sturgill, Michael Parisi, Sudhir Kumar, Brian Oliver
    posted to comparative-genomics expression fly by indigoviolet on 2007-12-03 00:22:02 as ** along with 1 person and 2 groups dpollard EisenLab cis-regulatory-evolution
  • GeneSyn: a tool for detecting conserved gene order across genomes
    Bioinformatics, Vol. 20, No. 9. (12 June 2004), pp. 1472-1474.
    by G Pavesi, G Mauri, F Iannelli, C Gissi, G Pesole
    posted to algorithm comparative-genomics synteny by indigoviolet on 2007-11-27 11:34:33 as ** along with 1 person and 1 group operon EisenLab
  • Gene Family Evolution across 12 Drosophila Genomes
    PLoS Genetics, Vol. 3, No. 11. (1 November 2007), e197.
    by Matthew W Hahn, Mira V Han, Sang-Gook Han
    posted to comparative-genomics gene-family by indigoviolet on 2007-12-03 06:53:13 as ** along with 2 people and 1 group proulx djkt EisenLab
  • The Global Landscape of Sequence Diversity
    Genome Biology, Vol. 8 (08 November 2007), R238.
    by Jose M Peregrin-Alvarez, John Parkinson
    posted to comparative-genomics by ale on 2007-11-09 09:27:43 as *** along with 4 people skhadar gpalidwor cjeans hpaces
  • Characterization and Identification of MicroRNA Core Promoters in Four Model Species.
    PLoS Comput Biol, Vol. 3, No. 3. (9 March 2007)
    by Xuefeng Zhou, Jianhua Ruan, Guandong Wang, Weixiong Zhang
    posted to bioinformatics comparative-genomics expression-regulation mirna promoter by ale on 2007-11-18 00:15:18 as *** along with 7 people and 2 groups jfr tardigrade andersbj cdawson maralena bootsy xili03 microRNA GIG
  • A Computational Approach to the Functional Screening of Genomes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e174.
    by Davide Chiarugi, Pierpaolo Degano, Roberto Marangoni
    posted to algorithm bioinformatics comparative-genomics by ale on 2007-11-12 09:16:16 as *** along with 3 people and 1 group cjeans zwang hpaces Bioinformatics
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