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vwchans library [81 articles]

Neue Artikel in vwchans Bibliothek.
  • ARAGORN, a program to detect tRNA genes and tmRNA genes in nucleotide sequences.
    Nucleic Acids Res, Vol. 32, No. 1. (2004), pp. 11-16.
    by D Laslett, B Canback
    posted to trna-like trna prediction by vwchan on 2008-06-13 20:21:40 as read along with 3 people evaf Cortel dandaman
  • A memory-efficient dynamic programming algorithm for optimal alignment of a sequence to an RNA secondary structure.
    BMC Bioinformatics, Vol. 3, No. 1. (2 July 2002)
    by SR Eddy
    posted to covariance rna by vwchan on 2007-05-29 22:58:37 as ** along with 3 people and 3 groups evaf marcius mtagaya beta BioinfoCIPF SGU-CIPF
  • Query-Dependent Banding (QDB) for Faster RNA Similarity Searches
    PLoS Computational Biology, Vol. 3, No. 3. (1 March 2007), e56.
    by Eric P Nawrocki, Sean R Eddy
    posted to covariance rna by vwchan on 2007-05-23 09:42:12 as ** along with 1 group beta
  • MED: a new non-supervised gene prediction algorithm for bacterial and archaeal genomes
    BMC Bioinformatics, Vol. 8 (16 March 2007), 97.
    by Huaiqiu Zhu, Gang-Qing Hu, Yi-Fan Yang, Jin Wang, Zhen-Su She
    posted to phage-genes by vwchan on 2007-04-18 21:36:35 as ** along with 1 group beta
  • Does common architecture reveal a viral lineage spanning all three domains of life?
    Mol Cell, Vol. 16, No. 5. (3 December 2004), pp. 673-685.
    by SD Benson, JK Bamford, DH Bamford, RM Burnett
    posted to classification phage by vwchan on 2007-04-05 21:03:04 as ** along with 1 group beta
  • Bacteriophage taxonomy in 1987.
    Microbiol Sci, Vol. 4, No. 7. (July 1987), pp. 214-218.
    by HW Ackermann
    posted to classification phage by vwchan on 2007-04-05 20:55:04 as ** along with 1 group beta
  • Guidelines for bacteriophage characterization.
    Adv Virus Res, Vol. 23 (1978), pp. 1-24.
    by HW Ackermann, A Audurier, L Berthiaume, LA Jones, JA Mayo, AK Vidaver
    posted to classification phage by vwchan on 2007-04-05 20:50:01 as ** along with 1 group beta
  • Opinion: Viral metagenomics
    Nature Reviews Microbiology, Vol. 3, No. 6. (01 June 2005), pp. 504-510.
    by Robert A Edwards, Forest Rohwer
    posted to classification phage by vwchan on 2007-04-05 20:42:07 as ** along with 4 people and 1 group mcox dayjm AaronDarling bluto beta
  • Family relationships: should consensus reign?--consensus clustering for protein families.
    Bioinformatics, Vol. 23, No. 2. (15 January 2007)
    by M Nikolski, DJ Sherman
    posted to alignment clustering protein by vwchan on 2007-04-01 21:33:54 as ** along with 1 group beta
  • A method for aligning RNA secondary structures and its application to RNA motif detection.
    BMC Bioinformatics, Vol. 6 (2005)
    by J Liu, JT Wang, J Hu, B Tian
    posted to rna alignment by vwchan on 2007-02-01 12:38:57 as ** along with 2 people and 1 group arcticrasta emidio_capriotti beta
  • Detecting overlapping coding sequences in virus genomes.
    BMC Bioinformatics, Vol. 7, No. 1. (16 February 2006)
    by Andrew E Firth, Chris M Brown
    posted to phage-genes phage by vwchan on 2007-01-26 00:53:17 as ** along with 1 person and 1 group Ayest beta
  • On the origin of microbial ORFans: quantifying the strength of the evidence for viral lateral transfer
    BMC Evolutionary Biology, Vol. 6 (16 August 2006), 63.
    by Yanbin Yin, Daniel Fischer
    posted to phage-genes phage by vwchan on 2007-01-26 00:46:58 as ** along with 1 group beta
  • Genome Annotation Transfer Utility (GATU): rapid annotation of viral genomes using a closely related reference genome
    BMC Genomics, Vol. 7 (13 June 2006), 150.
    by Vasily T Tcherepanov, Angelika Ehlers, Chris Upton
    posted to phage-genes phage by vwchan on 2007-01-26 00:43:59 as ** along with 1 group beta
  • GeneMarkS: a self-training method for prediction of gene starts in microbial genomes. Implications for finding sequence motifs in regulatory regions.
    Nucleic Acids Res, Vol. 29, No. 12. (15 June 2001), pp. 2607-2618.
    by J Besemer, A Lomsadze, M Borodovsky
    posted to phage-genes phage by vwchan on 2007-01-26 00:38:11 as ** along with 2 people and 1 group azazello wenhan beta
  • ZCURVE_V: a new self-training system for recognizing protein-coding genes in viral and phage genomes.
    BMC Bioinformatics, Vol. 7 (2006)
    by FB Guo, CT Zhang
    posted to phage-genes phage by vwchan on 2007-01-26 00:30:57 as ** along with 1 group beta
  • Recoding in bacteriophages and bacterial IS elements.
    Trends Genet, Vol. 22, No. 3. (March 2006), pp. 174-181.
    by PV Baranov, O Fayet, RW Hendrix, JF Atkins
    posted to phage-genes phage by vwchan on 2007-01-26 00:24:06 as ** along with 1 group beta
  • Bacteriophages and pathogenicity: more than just providing a toxin?
    Microbes Infect, Vol. 8, No. 5. (April 2006), pp. 1365-1371.
    by CR Tinsley, E Bille, X Nassif
    posted to review phage by vwchan on 2007-01-21 19:09:28 as **** along with 1 group beta
  • Distribution of prophages and SGI-1 antibiotic-resistance genes among different Salmonella enterica serovar Typhimurium isolates.
    Microbiology, Vol. 152, No. Pt 7. (July 2006), pp. 2137-2147.
    by AP Hermans, AM Beuling, AH van Hoek, HJ Aarts, T Abee, MH Zwietering
    posted to prophage phage antibiotic_resistance by vwchan on 2007-01-21 18:51:59 as ** along with 1 group beta
  • Prophage Finder: a prophage loci prediction tool for prokaryotic genome sequences.
    In Silico Biol, Vol. 6, No. 3. (15 April 2006)
    by Michael Bose, Robert D Barber
    posted to prediction prophage by vwchan on 2006-11-15 00:11:27 as ** along with 1 group beta
  • Information resources at the National Center for Biotechnology Information.
    Bull Med Libr Assoc, Vol. 81, No. 3. (July 1993), pp. 282-284.
    by RM Woodsmall, DA Benson
    posted to database by vwchan on 2006-11-14 16:46:41 as ** along with 1 group beta
  • Phage_Finder: Automated identification and classification of prophage regions in complete bacterial genome sequences.
    Nucleic Acids Res (24 October 2006)
    by Derrick E Fouts
    posted to lateral_gene_transfer phage prediction prophage trna by vwchan on 2006-11-03 22:13:11 as ***** along with 1 group beta
  • Distribution of minigenes in the bacteriophage lambda chromosome.
    Gene, Vol. 329 (31 March 2004), pp. 115-124.
    by NA Oviedo, H Salgado, J Collado-Vides, G Guarneros
    posted to phage phage-genes by vwchan on 2006-11-03 01:15:37 as ** along with 1 person and 1 group discreteonyxorb beta
  • Unusual structure of the attB site of the site-specific recombination system of Lactobacillus delbrueckii bacteriophage mv4.
    J Bacteriol, Vol. 181, No. 23. (December 1999), pp. 7385-7389.
    by F Auvray, M Coddeville, RC Ordonez, P Ritzenthaler
    posted to insertion-site trna by vwchan on 2006-11-03 01:12:14 as ** along with 1 group beta
  • A proline tRNA(CGG) gene encompassing the attachment site of temperate phage 16-3 is functional and convertible to suppressor tRNA.
    Mol Microbiol, Vol. 54, No. 3. (November 2004), pp. 742-754.
    by B Blaha, S Semsey, S Ferenczi, Z Csiszovszki, PP Papp, L Orosz
    posted to insertion-site phage trna by vwchan on 2006-11-03 01:08:24 as ** along with 1 group beta
  • Impact of forced selection of tRNAs on HIV-1 replication and genome stability highlight preferences for selection of certain tRNAs.
    Virus Res (27 October 2006)
    by Na Ni, Casey D Morrow
    posted to trna by vwchan on 2006-11-03 01:05:55 as ** along with 1 group beta
  • Prophage-like elements in bifidobacteria: insights from genomics, transcription, integration, distribution, and phylogenetic analysis.
    Appl Environ Microbiol, Vol. 71, No. 12. (December 2005), pp. 8692-8705.
    by M Ventura, JH Lee, C Canchaya, R Zink, S Leahy, JA Moreno-Munoz, M O'Connell-Motherway, D Higgins, GF Fitzgerald, DJ O'Sullivan, D van Sinderen
    posted to integration lateral_gene_transfer prophage by vwchan on 2006-11-03 00:54:57 as *** along with 1 group beta
  • A class of eukaryotic GTPase with a punctate distribution suggesting multiple functional replacements of translation elongation factor 1alpha.
    Proc Natl Acad Sci U S A, Vol. 101, No. 43. (26 October 2004), pp. 15380-15385.
    by PJ Keeling, Y Inagaki
    posted to lateral_gene_transfer by vwchan on 2006-11-03 00:51:04 as * along with 1 person and 3 groups ana structural_bioinformatics Bioinformatics beta
  • Repetitive elements in genomes of parasitic protozoa.
    Microbiol Mol Biol Rev, Vol. 67, No. 3. (September 2003)
    by B Wickstead, K Ersfeld, K Gull
    posted to boundary review by vwchan on 2006-11-03 00:43:15 as ** along with 1 group beta
  • Gene transfer: gene swapping craze reaches eukaryotes.
    Curr Biol, Vol. 13, No. 2. (21 January 2003)
    by JP Gogarten
    posted to lateral_gene_transfer by vwchan on 2006-11-02 23:53:46 as ** along with 1 person and 1 group karfunkel beta
  • Horizontally transferred genes in plant-parasitic nematodes: a high-throughput genomic approach.
    Genome Biol, Vol. 4, No. 6. (2003)
    by EH Scholl, JL Thorne, JP Mccarter, DM Bird
    posted to lateral_gene_transfer prediction by vwchan on 2006-11-02 23:44:22 as ** along with 1 group beta
  • A novel strategy for the identification of genomic islands by comparative analysis of the contents and contexts of tRNA sites in closely related bacteria.
    Nucleic Acids Res, Vol. 34, No. 1. (2006)
    by HY Ou, LL Chen, J Lonnen, RR Chaudhuri, AB Thani, R Smith, NJ Garton, J Hinton, M Pallen, MR Barer, K Rajakumar
    posted to island prediction trna by vwchan on 2006-07-24 18:05:30 as ** along with 1 group beta
  • Complete genome sequence of enterohemorrhagic Escherichia coli O157:H7 and genomic comparison with a laboratory strain K-12.
    DNA Res, Vol. 8, No. 1. (28 February 2001), pp. 11-22.
    by T Hayashi, K Makino, M Ohnishi, K Kurokawa, K Ishii, K Yokoyama, CG Han, E Ohtsubo, K Nakayama, T Murata, M Tanaka, T Tobe, T Iida, H Takami, T Honda, C Sasakawa, N Ogasawara, T Yasunaga, S Kuhara, T Shiba, M Hattori, H Shinagawa
    posted to prediction prophage by vwchan on 2006-07-18 19:54:48 as ** along with 1 person and 1 group Xavier beta
  • Use of Artificial Genomes in Assessing Methods for Atypical Gene Detection.
    PLoS Comput Biol, Vol. 1, No. 6. (11 November 2005)
    by Rajeev K Azad, Jeffrey G Lawrence
    posted to lateral_gene_transfer prediction by vwchan on 2006-07-18 19:34:11 as ** along with 3 people and 5 groups kaspermunch neveaire karfunkel Biostatistics Computational-Genomics Bioinformatics Neuroscience beta
  • Score-based prediction of genomic islands in prokaryotic genomes using hidden Markov models.
    BMC Bioinformatics, Vol. 7 (2006)
    by S Waack, O Keller, R Asper, T Brodag, C Damm, WF Fricke, K Surovcik, P Meinicke, R Merkl
    posted to island prediction by vwchan on 2006-07-18 19:31:23 as ** along with 1 group beta
  • A computational approach for identifying pathogenicity islands in prokaryotic genomes.
    BMC Bioinformatics, Vol. 6 (2005)
    by SH Yoon, CG Hur, HY Kang, YH Kim, TK Oh, JF Kim
    posted to island prediction by vwchan on 2006-07-18 19:29:18 as ** along with 1 group beta
  • Complete nucleotide sequence of the prophage VT1-Sakai carrying the Shiga toxin 1 genes of the enterohemorrhagic Escherichia coli O157:H7 strain derived from the Sakai outbreak.
    Gene, Vol. 258, No. 1-2. (27 November 2000), pp. 127-139.
    by K Yokoyama, K Makino, Y Kubota, M Watanabe, S Kimura, CH Yutsudo, K Kurokawa, K Ishii, M Hattori, I Tatsuno, H Abe, M Yoh, T Iida, M Ohnishi, T Hayashi, T Yasunaga, T Honda, C Sasakawa, H Shinagawa
    posted to prediction prophage by vwchan on 2006-07-18 19:26:26 as ** along with 1 group beta
  • ACLAME: a CLAssification of Mobile genetic Elements.
    Nucleic Acids Res, Vol. 32, No. Database issue. (1 January 2004)
    by R Leplae, A Hebrant, SJ Wodak, A Toussaint
    posted to prediction prophage by vwchan on 2006-07-18 18:25:13 as ** along with 1 group beta
  • Prophages and bacterial genomics: what have we learned so far?
    Molecular Microbiology, Vol. 49, No. 2. (2003), pp. 277-300.
    by Sherwood Casjens
    posted to prophage review by vwchan on 2006-07-11 21:20:13 as ***** along with 1 group beta
  • Construction, characterization, and use of two Listeria monocytogenes site-specific phage integration vectors.
    J Bacteriol, Vol. 184, No. 15. (August 2002), pp. 4177-4186.
    by P Lauer, MY Chow, MJ Loessner, DA Portnoy, R Calendar
    posted to integration phage by vwchan on 2006-06-28 21:00:14 as ** along with 1 group beta
  • Medical Microbiology
    (1996)
    edited by Samuel Baron
    posted to review by vwchan on 2006-06-21 00:16:49 as ** along with 1 group beta
  • The origin of viruses and their possible roles in major evolutionary transitions
    Virus Research, Vol. 117, No. 1. (April 2006), pp. 5-16.
    by Patrick Forterre
    posted to phage by vwchan on 2006-06-21 00:00:03 as ** along with 1 person and 1 group philosof beta
  • Transfer RNA genes frequently serve as integration sites for prokaryotic genetic elements.
    Nucleic Acids Res, Vol. 17, No. 5. (11 March 1989), pp. 1907-1914.
    by WD Reiter, P Palm, S Yeats
    posted to insertion-site integration trna by vwchan on 2006-06-20 23:21:08 as ** along with 1 group beta
  • Virus Taxonomy: Classification and Nomenclature of Viruses: Seventh Report of the International Committee on Taxonomy of Viruses
    (15 October 2000)
    by MH Van Regenmortel, International, CM Fauquet
    posted to phage review by vwchan on 2006-06-20 22:45:43 as ** along with 1 group beta
  • Integration sites for genetic elements in prokaryotic tRNA and tmRNA genes: sublocation preference of integrase subfamilies.
    Nucleic Acids Res, Vol. 30, No. 4. (15 February 2002), pp. 866-875.
    by KP Williams
    posted to integrase trna by vwchan on 2006-06-20 22:23:33 as ** along with 1 group beta
  • Pathogenicity islands: the tip of the iceberg.
    Microbes Infect, Vol. 3, No. 7. (June 2001), pp. 545-548.
    by U Hentschel, J Hacker
    posted to island by vwchan on 2006-06-20 22:19:44 as ** along with 1 group beta
  • 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 lateral_gene_transfer review by vwchan on 2006-06-20 22:17:19 as ** along with 4 people and 4 groups ana jmeppley madhadron caporaso structural_bioinformatics Bioinformatics biomedical-nlp beta
  • GENOMIC ISLANDS IN PATHOGENIC AND ENVIRONMENTAL MICROORGANISMS
    Nat Rev Micro, Vol. 2, No. 5. (May 2004), pp. 414-424.
    by Ulrich Dobrindt, Bianca Hochhut, Ute Hentschel, Jorg Hacker
    posted to island lateral_gene_transfer review by vwchan on 2006-06-20 22:14:37 as ** along with 1 group beta
  • STUDYING PLASMID HORIZONTAL TRANSFER IN SITU: A CRITICAL REVIEW
    Nat Rev Micro, Vol. 3, No. 9. (2005), pp. 700-710.
    by Soren J Sorensen, Mark Bailey, Lars H Hansen, Niels Kroer, Stefan Wuertz
    posted to lateral_gene_transfer review by vwchan on 2006-06-20 22:10:30 as ** along with 1 person and 1 group karfunkel beta
  • The Ins and Outs of DNA Transfer in Bacteria
    Science, Vol. 310, No. 5753. (2 December 2005), pp. 1456-1460.
    by Ines Chen, Peter J Christie, David Dubnau
    posted to lateral_gene_transfer by vwchan on 2006-06-20 21:47:28 as ** along with 4 people and 1 group dayjm jmeppley Ayest treangen beta
  • Mechanisms of, and Barriers to, Horizontal Gene Transfer between Bacteria
    Nature Reviews Microbiology, Vol. 3, No. 9. (01 September 2005), pp. 711-721.
    by Christopher M Thomas, Kaare M Nielsen
    posted to lateral_gene_transfer review by vwchan on 2006-06-20 21:45:39 as ** along with 1 group beta
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