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treangen's library [537 articles]

Recent papers added to treangen's library.
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  • The meaning of alignment: lessons from structural diversity
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Walter Pirovano, Anton K Feenstra, Jaap Heringa
    posted to structure protein alignment by treangen on 2009-01-07 10:56:30 as ** along with 9 people markusd j3xucite nuin kshameer druvus chad_davis swtimmer taguchi pansapiens
  • DIALIGN-T: An improved algorithm for segment-based multiple sequence alignment
    BMC Bioinformatics, Vol. 6, No. 1. (2005)
    by Amarendran Subramanian, Jan W Menkhoff, Michael Kaufmann, Burkhard Morgenstern
    posted to software sequence segment multiple local alignment by treangen on 2008-12-12 09:21:24 as ** along with 1 person moborg
  • Improving accuracy of multiple sequence alignment algorithms based on alignment of neighboring residues.
    Nucleic acids research (4 December 2008)
    by Yue Lu, Sing-Hoi H Sze
    posted to software sequence nralign multiple jctalk alignment accuracy by treangen on 2008-12-11 15:49:48 as ** along with 1 person nuin
  • On the origin and evolution of new genes--a genomic and experimental perspective.
    Journal of genetics and genomics = Yi chuan xue bao, Vol. 35, No. 11. (November 2008), pp. 639-648.
    by Q Zhou, W Wang
    posted to origin gene-genesis gene-duplication evolution drosophila by treangen on 2008-12-11 14:24:01 as ** along with 2 people druvus operon
  • MAFFT version 5: improvement in accuracy of multiple sequence alignment.
    Nucleic Acids Res, Vol. 33, No. 2. (2005), pp. 511-518.
    by K Katoh, K Kuma, H Toh, T Miyata
    posted to software sequence multiple msa alignment by treangen on 2008-12-11 14:22:50 as ** along with 6 people and 1 group druvus CharlesM caporaso rabio timflutre urgi biomedical-nlp
  • Recent developments in the MAFFT multiple sequence alignment program.
    Briefings in bioinformatics (27 March 2008)
    by Kazutaka Katoh, Hiroyuki Toh
    posted to software sequence multiple msa alignment by treangen on 2008-12-11 14:22:29 as ** along with 2 people urgi timflutre
  • Using ESTs for phylogenomics: can one accurately infer a phylogenetic tree from a gappy alignment?
    BMC Evolutionary Biology, Vol. 8 (26 March 2008), 95.
    by Stefanie Hartmann, Todd J Vision
    posted to gap alignment accuracy 2008 by treangen on 2008-12-08 13:57:44 as ** along with 6 people and 2 groups skembel natstreet druvus stajich Patola aprasad iSEEM Berkeley Mycology
  • Multiple Sequence Alignment Accuracy and Phylogenetic Inference
    Systematic Biology, Vol. 55, No. 2. (April 2006), pp. 314-328.
    by T Ogdenw, Michael Rosenberg
    posted to jctalk alignment accuracy 2006 by treangen on 2008-12-08 13:30:34 as ** along with 3 people druvus aprasad akifumi
  • Phylogenomics of the archaeal flagellum: rare horizontal gene transfer in a unique motility structure
    BMC Evolutionary Biology, Vol. 7 (02 July 2007), 106.
    by Elie Desmond, Celine Brochier-Armanet, Simonetta Gribaldo
    posted to phylogenomics motility hgt eukaryote archael abitalk by treangen on 2008-12-05 09:35:41 as **
  • Exploring the Relationship between Sequence Similarity and Accurate Phylogenetic Trees
    Molecular Biology and Evolution, Vol. 23, No. 11. (November 2006), pp. 2090-2100.
    by Cantarel, L Brandi, Morrison, G Hilary, Pearson, William
    posted to trees similarity sequence phylogenetic accuracy 2006 by treangen on 2008-12-03 15:48:47 as ** along with 4 people druvus gjuggler mblwhoi ArtemPankin
  • Phylogenetic exploration of bacterial genomic rearrangements
    Bioinformatics, Vol. 23, No. 9. (1 May 2007), pp. 1172-1174.
    by Romain Fremez, Thomas Faraut, Gwennaele Fichant, Jerome Gouzy, Yves Quentin
    posted to rearrangements phylogenetics genome bacteria by treangen on 2008-12-02 20:01:58 as ** along with 3 people druvus operon zwang
  • MOSAIC: an online database dedicated to the comparative genomics of bacterial strains at the intra-species level
    BMC Bioinformatics, Vol. 9 (27 November 2008), 498.
    by Helene, Meriem E Karoui
    posted to software genome database comparison bacteria by treangen on 2008-12-02 19:57:06 as ** along with 2 people operon druvus
  • Comparison of methods for estimating the nucleotide substitution matrix
    BMC Bioinformatics, Vol. 9, No. 1. (2008)
    by Maribeth Oscamou, Daniel Mcdonald, Von B Yap, Gavin Huttley, Manuel Lladser, Rob Knight
    posted to subsitution matrix by treangen on 2008-12-02 19:49:53 as ** along with 4 people sconlan nklee nuin druvus
  • Phylogenetic Inference Using Whole Genomes
    Annual Review of Genomics and Human Genetics, Vol. 9, No. 1. (2008), pp. 217-231.
    by Bruce Rannala, Ziheng Yang
    posted to phylgenomics genome by treangen on 2008-12-01 20:08:19 as ** along with 5 people and 1 group operon druvus aprasad gjuggler zwang LabDros
  • XplorSeq: A software environment for integrated management and phylogenetic analysis of metagenomic sequence data
    BMC Bioinformatics, Vol. 9 (07 October 2008), 420.
    by Daniel N Frank
    posted to xplorseq software sequence phylogenetic metagenomics by treangen on 2008-11-29 17:47:45 as ** along with 2 people ojabado nuin
  • Phage response to CRISPR-encoded resistance in Streptococcus thermophilus.
    Journal of bacteriology, Vol. 190, No. 4. (February 2008), pp. 1390-1400.
    by H Deveau, R Barrangou, JE Garneau, J Labonté, C Fremaux, P Boyaval, DA Romero, P Horvath, S Moineau
    posted to repeats phage crispr by treangen on 2008-11-28 16:51:39 as **
  • Rapidly evolving CRISPRs implicated in acquired resistance of microorganisms to viruses
    Environmental Microbiology, Vol. 10, No. 1. (January 2008), pp. 200-207.
    by Tyson, W Gene, Banfield, F Jillian
    posted to repeats crispr by treangen on 2008-11-28 16:50:29 as **
  • Virus Population Dynamics and Acquired Virus Resistance in Natural Microbial Communities
    Science, Vol. 320, No. 5879. (23 May 2008), pp. 1047-1050.
    by Anders F Andersson, Jillian F Banfield
    posted to repeats crispr by treangen on 2008-11-28 16:49:58 as ** along with 2 people and 1 group bluto djkt iSEEM
  • CRISPR — a widespread system that provides acquired resistance against phages in bacteria and archaea
    Nature Reviews Microbiology, Vol. 6, No. 3., pp. 181-186.
    by Rotem Sorek, Victor Kunin, Philip Hugenholtz
    posted to repeats phage crispr bacteria archaea by treangen on 2008-11-28 16:45:55 as ** along with 1 group MuraLab
  • The CRISPRdb database and tools to display CRISPRs and to generate dictionaries of spacers and repeats
    BMC Bioinformatics, Vol. 8 (23 May 2007), 172.
    by Ibtissem Grissa, Gilles Vergnaud, Christine Pourcel
    posted to software repeats database crispr by treangen on 2008-11-28 16:43:34 as ** along with 1 person ibtisss
  • Browsing repeats in genomes: Pygram and an application to non-coding region analysis
    BMC Bioinformatics, Vol. 7 (26 October 2006), 477.
    by Patrick Durand, Frederic Mahe, Anne-Sophie Valin, Jacques Nicolas
    posted to visualization software repeat genome by treangen on 2008-11-28 15:38:57 as ** along with 3 people natstreet druvus dquest
  • New trends in pharmacogenomic strategies against resistance development in microbial infections
    Pharmacogenomics, Vol. 9, No. 11. (November 2008), pp. 1711-1723.
    by Knut Ohlsen, Gudrun Dandekar, Roland Schwarz, Thomas Dandekar
    posted to resistance pharmacogenomic infection bacteria by treangen on 2008-11-27 19:46:15 as ** along with 1 person jmeppley
  • Being pathogenic, plastic, and sexual while living with a nearly minimal bacterial genome.
    PLoS Genet, Vol. 3, No. 5. (18 May 2007)
    by P Sirand-Pugnet, C Lartigue, M Marenda, D Jacob, A Barré, V Barbe, C Schenowitz, S Mangenot, A Couloux, B Segurens, A de Daruvar, A Blanchard, C Citti
    posted to sex plasticity pathogen mycoplasma genome bacteria by treangen on 2008-11-27 19:43:15 as ** along with 4 people JoeBanks operon luschons evodeva
  • Combined evidence annotation of transposable elements in genome sequences.
    PLoS Comput Biol, Vol. 1, No. 2. (July 2005)
    by H Quesneville, CM Bergman, O Andrieu, D Autard, D Nouaud, M Ashburner, D Anxolabehere
    posted to transposable software genome elements annotation by treangen on 2008-11-27 19:40:26 as ** along with 9 people and 2 groups operon briann aprasad dpollard timflutre stajich urgi yoanjacquemin ArtemPankin LabDros EisenLab
  • SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
    BMC Evolutionary Biology, Vol. 7, No. Suppl 1. (2007)
    by Beatrice Roure, Naiara R Ezpeleta, Herve Philippe
    posted to software sequence phylogenomics genome concatenation by treangen on 2008-11-27 19:39:47 as ** along with 6 people natstreet druvus operon aprasad akifumi dmp
  • Orthologous Transcription Factors in Bacteria Have Different Functions and Regulate Different Genes
    PLoS Computational Biology, Vol. 3, No. 9. (1 September 2007), e175.
    by Morgan N Price, Paramvir S Dehal, Adam P Arkin
    posted to phylogeny orthologs gene bbh bacteria by treangen on 2008-11-27 19:38:15 as ** along with 10 people and 3 groups druvus carlk operon dpollard dquest djkt zwang cabbagezs heliopais blobbybirdman EisenLab cis-regulatory-evolution Myxo group
  • Strategies for genome reduction in microbial genomes.
    Genome Inform, Vol. 16, No. 2. (2005), pp. 69-75.
    by KR Sakharkar, VT Chow
    posted to reduction genome bacteria by treangen on 2008-11-27 19:35:59 as ** along with 3 people druvus operon aprasad
  • Pathogens in decay
    Nat Rev Micro, Vol. 2, No. 10. (October 2004), pp. 774-775.
    by Ana Cerdeno-Tarraga, Nicholas Thomson, Julian Parkhill
    posted to pathogens genome decay bacteria by treangen on 2008-11-27 19:34:06 as ** along with 1 person operon
  • The continuing evolution of a bacterial pathogen.
    Proc Natl Acad Sci U S A, Vol. 105, No. 12. (25 March 2008), pp. 4535-4536.
    by JB Kaper, MA Karmali
    posted to pathogen evolution bacteria by treangen on 2008-11-27 15:44:35 as ** along with 1 person operon
  • Selection for gene clustering by tandem duplication.
    Annu Rev Microbiol, Vol. 58 (2004), pp. 119-142.
    by AB Reams, EL Neidle
    posted to tandem-duplication prokaryote hgt gene clustering by treangen on 2008-11-27 09:38:42 as ** along with 3 people druvus rabu fhsantanna
  • Building communities one bacterium at a time
    Proceedings of the National Academy of Sciences, Vol. 105, No. 47. (25 November 2008), pp. 18075-18076.
    by Douglas B Weibel
    posted to communities bacteria by treangen on 2008-11-27 09:25:18 as ** along with 1 person druvus
  • Uncovering rate variation of lateral gene transfer during bacterial genome evolution
    BMC Genomics, Vol. 9 (20 May 2008), 235.
    by Weilong Hao, Brian Golding
    posted to hgt genome evolution bacteria by treangen on 2008-11-26 20:47:14 as **
  • Differential replication dynamics for large and small Vibrio chromosomes affect gene dosage, expression and location
    BMC Genomics, Vol. 9 (26 November 2008), 559.
    by Rikard, Tetsuya Iida
    posted to vibrio replication genome gene-dosage chromosome by treangen on 2008-11-26 20:45:28 as **
  • Investigations of Oligonucleotide Usage Variance Within and Between Prokaryotes
    PLoS Comput Biol, Vol. 4, No. 4. (18 April 2008), e1000057.
    by Jon Bohlin, Eystein Skjerve, David W Ussery
    posted to prokaryote oligonucleotide gc compoosition by treangen on 2008-11-26 13:16:27 as ** along with 2 people and 2 groups djkt jlgreen iSEEM Green Lab
  • The Effect of Chromosome Geometry on Genetic Diversity
    Genetics, Vol. 179, No. 1. (1 May 2008), pp. 511-516.
    by Pradeep R Marri, Leigh K Harris, Kathryn Houmiel, Steven C Slater, Howard Ochman
    posted to linear geometry genetic diversity circular chromosome bacteria by treangen on 2008-11-26 11:17:30 as ** along with 1 person and 1 group stajich Berkeley Mycology
  • Intracellular pathogens go extreme: genome evolution in the Rickettsiales.
    Trends Genet, Vol. 23, No. 10. (October 2007), pp. 511-520.
    by AC Darby, NH Cho, HH Fuxelius, J Westberg, SG Andersson
    posted to rickettsia pathogens genome evolution by treangen on 2008-11-26 11:06:38 as ** along with 2 people johanviklund operon
  • The Whole-genome sequencing of the obligate intracellular bacterium Orientia tsutsugamushi revealed massive gene amplification during reductive genome evolution.
    DNA research : an international journal for rapid publication of reports on genes and genomes, Vol. 15, No. 4. (August 2008), pp. 185-199.
    by K Nakayama, A Yamashita, K Kurokawa, T Morimoto, M Ogawa, M Fukuhara, H Urakami, M Ohnishi, I Uchiyama, Y Ogura, T Ooka, K Oshima, A Tamura, M Hattori, T Hayashi
    posted to sequence orientia genome gene duplication amplification by treangen on 2008-11-26 11:04:57 as **
  • Similar compositional biases are caused by very different mutational effects.
    Genome Res, Vol. 16, No. 12. (December 2006), pp. 1537-1547.
    by EP Rocha, M Touchon, EJ Feil
    posted to mutations composition bias bacteria by treangen on 2008-11-26 11:02:59 as ** along with 2 people operon gjuggler
  • Bacterial networking
    Genome Biology, Vol. 9 (12 November 2008), 327.
    by Kathleen Marchal, Sigrid CJ De Keersmaecker
    posted to networking bacterial by treangen on 2008-11-26 10:47:41 as **
  • Direct Visualization of Horizontal Gene Transfer
    Science, Vol. 319, No. 5869. (14 March 2008), pp. 1533-1536.
    by Ana Babic, Ariel B Lindner, Marin Vulic, Eric J Stewart, Miroslav Radman
    posted to visualization hgt ecoli bacteria by treangen on 2008-11-26 09:29:35 as ** along with 5 people madhadron zwang niallhaslam melting dbikard
  • Evolution of Mammals and Their Gut Microbes
    Science, Vol. 320, No. 5883. (20 June 2008), pp. 1647-1651.
    by Ruth E Ley, Micah Hamady, Catherine Lozupone, Peter J Turnbaugh, Rob R Ramey, Stephen J Bircher, Michael L Schlegel, Tammy A Tucker, Mark D Schrenzel, Rob Knight, Jeffrey I Gordon
    posted to phylogeny mammals gene-content diet bacteria by treangen on 2008-11-26 09:27:56 as ** along with 9 people and 2 groups skembel krausedo Zephyrus dinnes djkt dchughes lp2 jlgreen qwermish Green Lab iSEEM
  • The evolutionary relationships between the two bacteria Escherichia coli and Haemophilus influenzae and their putative last common ancestor.
    Mol Biol Evol, Vol. 15, No. 1. (January 1998), pp. 17-27.
    by R de Rosa, B Labedan
    posted to lca influenzae genome evolution ecoli comparison by treangen on 2008-11-25 23:34:22 as ** along with 1 person operon
  • A minimal gene set for cellular life derived by comparison of complete bacterial genomes.
    Proc Natl Acad Sci U S A, Vol. 93, No. 19. (17 September 1996), pp. 10268-10273.
    by AR Mushegian, EV Koonin
    posted to set minimum gene bacteria by treangen on 2008-11-25 23:31:04 as ** along with 7 people and 2 groups balicea operon ana bjorns jwm gbart westoll structural_bioinformatics Bioinformatics
  • Prokaryotic genomes: the emerging paradigm of genome-based microbiology.
    Current opinion in genetics & development, Vol. 7, No. 6. (December 1997), pp. 757-763.
    by EV Koonin, MY Galperin
    posted to prokaryotic genome fw comparison by treangen on 2008-11-25 23:27:38 as **
  • Reconstructing evolution of sequences subject to recombination using parsimony.
    Mathematical biosciences, Vol. 98, No. 2. (March 1990), pp. 185-200.
    by J Hein
    posted to reconstruction recombination phylogeny parsimony hgt by treangen on 2008-11-25 18:50:02 as **
  • Tracing origins with molecular sequences: metazoan and eukaryotic beginnings.
    Trends in biochemical sciences, Vol. 16, No. 2. (February 1991), pp. 46-50.
    by JA Lake
    posted to reconstruction phylogenetic method by treangen on 2008-11-25 18:49:08 as **
  • Phylogenetic reconstruction from transpositions.
    BMC genomics, Vol. 9 Suppl 2 (2008)
    by F Yue, M Zhang, J Tang
    posted to transpositions rearrangements phlogenetic genome by treangen on 2008-11-25 18:47:33 as ** along with 1 person druvus
  • The tree of genomes: An empirical comparison of genome phylogeny reconstruction methods.
    BMC Evolutionary Biology, Vol. 8 (12 November 2008), 312.
    by Angela Mccann, James A Cotton, James O Mcinerney
    posted to testing phylogeny phylogenomics genome-phylogeny by treangen on 2008-11-25 18:46:27 as ** along with 2 people operon druvus
  • Automatic extraction of reliable regions from multiple sequence alignments
    BMC Bioinformatics, Vol. 8, No. Suppl 5. (2007)
    by Timo Lassmann, Erik Sonnhammer
    posted to sequence reliability multiple alignment accuracy 2007 by treangen on 2008-11-25 15:49:47 as ** along with 1 person druvus
  • How Well Does the HoT Score Reflect Sequence Alignment Accuracy?
    Mol Biol Evol, Vol. 25, No. 8. (1 August 2008), pp. 1576-1580.
    by Barry G Hall
    posted to testing sequence multiple jctalk hot alignment accuracy 2008 by treangen on 2008-11-25 15:47:13 as ** along with 6 people and 1 group druvus nuin gjuggler bpcusack stajich cabbagesofdoom Berkeley Mycology
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