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Tag prokaryote [106 articles]

Recent papers classified by the tag prokaryote.
  • Small CRISPR RNAs Guide Antiviral Defense in Prokaryotes
    Science, Vol. 321, No. 5891. (15 August 2008), pp. 960-964.
    by Stan J Brouns, Matthijs M Jore, Magnus Lundgren, Edze R Westra, Rik J Slijkhuis, Ambrosius P Snijders, Mark J Dickman, Kira S Makarova, Eugene V Koonin, John van der Oost
    posted to prokaryote rna by zwang on 2008-08-16 07:30:42 as ** along with 1 person neils
  • An Immunological Determinant of RNase P Protein is Conserved between Escherichia coli and Humans
    Proceedings of the National Academy of Sciences, Vol. 86, No. 22. (15 November 1989), pp. 8717-8721.
    by Mark J Mamula, Madeline Baer, Joe Craft, Sidney Altman
    posted to ecoli human immunity prokaryote protein rnasep by zwang on 2008-03-17 06:07:54 as ***
  • The prokaryotic tree of life: past, present...and future?
    Trends in Ecology & Evolution, Vol. 23, No. 5. (May 2008), pp. 276-281.
    by James O Mcinerney, James A Cotton, Davide Pisani
    posted to evolution phylogeny prokaryote by zwang on 2008-06-16 01:48:25 as ** along with 2 people and 2 groups balicea jlgreen Green Lab iSEEM
  • Genome-wide survey of prokaryotic serine proteases: Analysis of distribution and domain architectures of five serine protease families in prokaryotes
    BMC Genomics, Vol. 9, No. 1. (2008)
    by Lokesh Tripathi, Ramanathan Sowdhamini
    posted to prokaryote genome-wide domain by zwang on 2008-11-24 09:00:54 as ** along with 1 person neils
  • Coevolution of gene families in prokaryotes
    Genome Res., Vol. 18, No. 3. (1 March 2008), pp. 462-468.
    by Otto X Cordero, Berend Snel, Paulien Hogeweg
    posted to co-evolution genefamily prokaryote by zwang on 2008-03-03 04:30:21 as *** along with 2 people operon neils
  • Causes of Insertion Sequences Abundance in Prokaryotic Genomes
    Molecular Biology and Evolution, Vol. 24, No. 4. (April 2007), pp. 969-981.
    by Touchon, Marie, Rocha, PC Eduardo
    posted to prokaryote insertion-sequences genome-rearrangement genome by treangen on 2008-11-21 09:35:36 as ** along with 1 person operon
  • Evolution of prokaryotic gene order: genome rearrangements in closely related species.
    Trends Genet, Vol. 17, No. 1. (January 2001), pp. 10-13.
    by M Suyama, P Bork
    posted to species prokaryote genome-rearrangement genome-evolution gene-order evolution closely-related by treangen on 2008-11-19 13:25:20 as *** along with 1 person AaronDarling
  • Origin of replication in circular prokaryotic chromosomes
    Environmental Microbiology, Vol. 8, No. 2. (February 2006), pp. 353-361.
    by Peder Worning, Lars J Jensen, Peter F Hallin, Hans-Henrik Staerfeldt, David W Ussery
    posted to prokaryote origin genome dna-replication chromsome by treangen on 2008-11-19 13:23:36 as *** along with 4 people operon AaronDarling larsjuhljensen shana
  • 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
  • Evidence of a Large Novel Gene Pool Associated with Prokaryotic Genomic Islands
    PLoS Genetics, Vol. 1, No. 5. (1 November 2005), e62.
    by William W Hsiao, Korine Ung, Dana Aeschliman, Jenny Bryan, Brett B Finlay, Fiona S Brinkman
    posted to prokaryote novel-genes genomic-islands bacteria by treangen on 2008-11-21 13:12:51 as ** along with 2 people and 1 group AaronDarling vwchan beta
  • Hierarchical classification of functionally equivalent genes in prokaryotes
    Nucleic Acids Research, Vol. 35, No. 7. (April 2007), pp. 2125-2140.
    by Wu, Hongwei, Mao, Fenglou, Olman, Victor, Xu, Ying
    posted to prokaryote genes classification by treangen on 2008-11-20 14:26:43 as ** along with 1 person druvus
  • Comparative genomics and the evolution of prokaryotes
    Trends in Microbiology, Vol. 15, No. 3. (March 2007), pp. 135-141.
    by S Abby, V Daubin
    posted to review prokaryote genome evolution bacteria by treangen on 2008-11-20 14:03:48 as ** along with 1 person druvus
  • 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
  • Towards a genome-based taxonomy for prokaryotes.
    J Bacteriol, Vol. 187, No. 18. (September 2005), pp. 6258-6264.
    by KT Konstantinidis, JM Tiedje
    posted to prokaryote genome-taxonomy bacteria by treangen on 2008-11-21 10:05:43 as ** along with 2 people and 1 group balajis gelack iSEEM
  • Evolutionary patterns in prokaryotic genomes.
    Current opinion in microbiology, Vol. 11, No. 5. (October 2008), pp. 454-460.
    by EP Rocha
    posted to prokaryote genome evolution bacteria by treangen on 2008-11-18 16:44:52 as ** along with 1 person druvus
  • Predataxis behavior in Myxococcus xanthus
    Proceedings of the National Academy of Sciences, Vol. 105, No. 44. (4 November 2008), pp. 17127-17132.
    by James E Berleman, Jodie Scott, Tatiana Chumley, John R Kirby
    posted to taxis prokaryote predation by smit2jam on 2008-11-06 05:43:53 as **
  • Analysis of complete genomes suggests that many prokaryotes do not rely on hairpin formation in transcription termination.
    Nucleic acids research, Vol. 26, No. 23. (1 December 1998), pp. 5456-5463.
    by T Washio, J Sasayama, M Tomita
    posted to mycoplasma prokaryote transcription_termination by shana on 2008-06-24 03:37:31 as *
  • Phylogenetic footprinting of transcription factor binding sites in proteobacterial genomes.
    Nucleic Acids Res, Vol. 29, No. 3. (1 February 2001), pp. 774-782.
    by L McCue, W Thompson, C Carmack, MP Ryan, JS Liu, V Derbyshire, CE Lawrence
    posted to bacteria footprinting motif phylogeny prokaryote regulation tfbs by pradiptaray on 2008-08-07 16:23:07 as ** along with 3 people and 1 group dquest adepace nklee EisenLab
  • Comparative Genomics of Bordetella pertussis Reveals Progressive Gene Loss in Finnish Strains.
    PLoS ONE, Vol. 2, No. 9. (2007)
    by E Heikkinen, T Kallonen, L Saarinen, R Sara, AJ King, FR Mooi, JT Soini, J Mertsola, Q He
    posted to genomics prokaryote reduction by operon on 2007-09-21 14:13:22 as ****
  • Modeling DNA-binding of Escherichia coli sigma70 exhibits a characteristic energy landscape around strong promoters
    Nucl. Acids Res. (16 October 2007), gkm720.
    by Johanna Weindl, Pavol Hanus, Zaher Dawy, Juergen Zech, Joachim Hagenauer, Jakob C Mueller
    posted to promoter structure bioinformatics genomics prokaryote protein by operon on 2007-10-21 17:46:07 as ***** along with 2 people and 1 group dpollard maximilianh EisenLab
  • Bacterial endophytes: recent developments and applications
    FEMS Microbiology Letters, Vol. 0, No. 0. (0), pp. ???-???.
    by Robert P Ryan, Kieran Germaine, Ashley Franks, David J Ryan, David N Dowling
    posted to prokaryote biotechnology endophytes by operon on 2007-11-27 16:01:51 as ** along with 1 person maren
  • Global transcriptional analysis of Mycoplasma hyopneumoniae following exposure to hydrogen peroxide.
    Microbiology, Vol. 153, No. Pt 11. (November 2007), pp. 3785-3790.
    by ER Schafer, MJ Oneal, ML Madsen, FC Minion
    posted to prokaryote genomics microarray mycoplasma stress transcription transcriptome by operon on 2007-12-16 21:34:33 as **** along with 1 person shana
  • Positive selection acting on a surface membrane protein of the plant-pathogenic phytoplasmas.
    J Bacteriol, Vol. 188, No. 9. (May 2006), pp. 3424-3428.
    by S Kakizawa, K Oshima, HY Jung, S Suzuki, H Nishigawa, R Arashida, S Miyata, M Ugaki, H Kishino, S Namba
    posted to evolution firmicute genomics master membrane phylogenetics phytoplasma prokaryote by operon on 2007-07-04 23:01:53 as ***** along with 2 people ejeffery BioNica
  • DarkHorse: a method for genome-wide prediction of horizontal gene transfer
    Genome Biology, Vol. 8 (02 February 2007), R16.
    by Sheila Podell, Terry Gaasterland
    posted to genomics prokaryote bioinformatics evolution horizontal_transfer phylogenetics by operon on 2007-07-26 16:59:58 as ***** along with 2 people eweaver karfunkel
  • Evolutionary conservation of sequence and secondary structures in CRISPR repeats
    Genome Biology, Vol. 8 (18 April 2007), R61.
    by Victor Kunin, Rotem Sorek, Philip Hugenholtz
    posted to evolution genomics master repeats prokaryote by operon on 2008-01-23 15:28:14 as *** along with 1 person and 1 group saru MuraLab
  • Comprehensive analysis of pseudogenes in prokaryotes: widespread gene decay and failure of putative horizontally transferred genes.
    Genome Biol, Vol. 5, No. 9. (2004)
    by Y Liu, PM Harrison, V Kunin, M Gerstein
    posted to evolution master prokaryote pseudogene by operon on 2008-01-24 17:52:28 as ** along with 2 people and 1 group azazello alexl MBLAB
  • Adaptive Mutations in Bacteria: High Rate and Small Effects
    Science, Vol. 317, No. 5839. (10 August 2007), pp. 813-815.
    by Lilia Perfeito, Lisete Fernandes, Catarina Mota, Isabel Gordo
    posted to prokaryote adaptation bioinformatics evolution genomics mutation phylogenetics by operon on 2007-08-20 02:57:59 as ***** along with 3 people and 1 group alexeid stevanspringer zwang FAB-lab
  • Extensive horizontal transfer of core genome genes between two Lactobacillus species found in the gastrointestinal tract.
    BMC Evolutionary Biology, Vol. 7 (20 August 2007), 141.
    by Pierre Nicolas, Philippe Bessieres, Dusko S Ehrlich, Emmanuelle Maguin, Maarten van de Guchte
    posted to horizontal_transfer master prokaryote by operon on 2008-02-19 11:44:48 as **
  • PseudoPipe: an automated pseudogene identification pipeline.
    Bioinformatics, Vol. 22, No. 12. (15 June 2006), pp. 1437-1439.
    by Z Zhang, N Carriero, D Zheng, J Karro, PM Harrison, M Gerstein
    posted to genomics prokaryote pseudogene master by operon on 2008-01-24 17:52:17 as ** along with 3 people alexl Jporci xingxu
  • Amino Acid Cost and Codon-Usage Biases in 6 Prokaryotic Genomes: A Whole-Genome Analysis
    Mol Biol Evol, Vol. 23, No. 9. (1 September 2006), pp. 1670-1680.
    by Esley M Heizer, Douglas W Raiford, Michael L Raymer, Travis E Doom, Robert V Miller, Dan E Krane
    posted to prokaryote codon_bias evolution genomics by operon on 2007-07-23 19:59:21 as **** along with 2 people dylan77 bpcusack
  • Statistical tests for detecting gene conversion.
    Mol Biol Evol, Vol. 6, No. 5. (September 1989), pp. 526-538.
    by S Sawyer
    posted to prokaryote evolution gene genomics phylogenetics by operon on 2007-07-23 20:04:51 as ***** along with 3 people jmeppley AaronDarling treangen
  • The net of life: reconstructing the microbial phylogenetic network.
    Genome research, Vol. 15, No. 7. (July 2005), pp. 954-959.
    by V Kunin, L Goldovsky, N Darzentas, CA Ouzounis
    posted to visualization prokaryote phylogenetics horizontal_transfer genomics evolution bioinformatics bacteria by operon on 2008-11-14 21:23:00 as ** along with 1 person and 1 group druvus LabDros
  • Control of Mycoplasma hyopneumoniae infections in pigs
    Veterinary Microbiology, Vol. In Press, Corrected Proof
    by D Maes, J Segales, T Meyns, M Sibila, M Pieters, F Haesebrouck
    posted to immunology master mycoplasma prokaryote by operon on 2007-11-10 21:19:53 as ****
  • Some bacteria degrade explosives, others prefer boiling methanol
    Environmental Microbiology, Vol. 9, No. 12. (December 2007), pp. 2905-2910.
    by Galperin, Y Michael
    posted to biodiversity biofuels biotechnology prokaryote by operon on 2008-01-27 16:40:38 as *****
  • Statistical properties of open reading frames in complete genome sequences
    Computers & Chemistry, Vol. 23, No. 3-4. (15 June 1999), pp. 283-301.
    by Wentian Li
    posted to bioinformatics gene genometrics genomics prokaryote statistics strand by operon on 2007-06-27 03:10:16 as *****
  • Mutational equilibrium model of genome size evolution.
    Theor Popul Biol, Vol. 61, No. 4. (June 2002), pp. 531-544.
    by DA Petrov
    posted to evolution genomics master mutation prokaryote reduction by operon on 2008-01-25 21:20:03 as ** along with 3 people and 1 group aprasad dpollard timflutre EisenLab
  • Replication-associated purine asymmetry may contribute to strand-biased gene distribution
    Genomics, Vol. In Press, Corrected Proof
    by Jianfei Hu, Xiaoqian Zhao, Jun Yu
    posted to prokaryote phylogenetics bioinformatics dna evolution gene genomics strand by operon on 2007-06-27 01:19:59 as *****
  • Decreasing the effects of horizontal gene transfer on bacterial phylogeny: the Escherichia coli case study
    Molecular Phylogenetics and Evolution, Vol. 30, No. 1. (January 2004), pp. 243-250.
    by P Escobar-Paramo, A Sabbagh, P Darlu, O Pradillon, C Vaury, E Denamur, G Lecointre
    posted to horizontal_transfer phylogenetics prokaryote by operon on 2007-04-29 03:34:18 as ***
  • Augura computational pipeline for whole genome microbial surface protein prediction and classification
    Bioinformatics, Vol. 22, No. 22. (15 November 2006), pp. 2819-2820.
    by Billion, , Ghai, , Chakraborty, , Hain,
    posted to bioinformatics genomics pathogenics prokaryote protein by operon on 2007-11-11 03:44:11 as **
  • Distinctive Repertoire of Contingency Genes Conferring Mutation- Based Phase Variation and Combinatorial Expression of Surface Lipoproteins in Mycoplasma capricolum subsp. capricolum of the Mycoplasma mycoides Phylogenetic Cluster
    J. Bacteriol., Vol. 188, No. 13. (1 July 2006), pp. 4926-4941.
    by Kim S Wise, Mark F Foecking, Kerstin Roske, Young J Lee, Young M Lee, Anup Madan, Michael J Calcutt
    posted to evolution expression lipoprotein master membrane mycoplasma phylogenetics prokaryote protein reduction by operon on 2007-07-05 14:28:10 as *****
  • Neutral microepidemic evolution of bacterial pathogens.
    Proc Natl Acad Sci U S A, Vol. 102, No. 6. (8 February 2005), pp. 1968-1973.
    by C Fraser, WP Hanage, BG Spratt
    posted to prokaryote evolution genomics pathogenics phylogenetics selection by operon on 2007-07-23 20:36:21 as ** along with 5 people and 1 group Retchless marimo jmeppley Xavier gwenknight MathBio
  • Trends in prokaryotic evolution revealed by comparison of closely related bacterial and archaeal genomes.
    Journal of bacteriology (31 October 2008)
    by Pavel S S Novichkov, Yuri I I Wolf, Inna Dubchak, Eugene V V Koonin
    posted to reduction prokaryote phylogenetics genomics genometrics evolution bacteria by operon on 2008-12-03 16:48:10 as **** along with 1 person neils
  • Codon bias and base composition are poor indicators of horizontally transferred genes.
    Mol Biol Evol, Vol. 18, No. 3. (March 2001), pp. 404-412.
    by LB Koski, RA Morton, GB Golding
    posted to genomics codon_bias evolution genometrics horizontal_transfer phylogenetics prokaryote by operon on 2007-07-23 20:01:36 as ** along with 3 people and 2 groups ana jmeppley karfunkel structural_bioinformatics Bioinformatics
  • Quantitative determination of gene strand bias in prokaryotic genomes.
    Genomics (5 October 2007)
    by Marcos Oliveira O de Carvalho, Henrique B B Ferreira
    posted to genomics comparative genometrics prokaryote by operon on 2007-11-05 11:43:42 as read
  • The power of phylogenetic approaches to detect horizontally transferred genes
    BMC Evolutionary Biology, Vol. 7, No. 1. (2007)
    by Maria Poptsova, Peter J Gogarten
    posted to evolution horizontal_transfer phylogenetics prokaryote transposon genomics by operon on 2007-03-24 00:19:31 as ***** along with 1 person karfunkel
  • Genomic plasticity in prokaryotes: the case of the square haloarchaeon.
    ISME J, Vol. 1, No. 3. (July 2007), pp. 235-245.
    by S Cuadros-Orellana, AB Martin-Cuadrado, B Legault, G D'Auria, O Zhaxybayeva, RT Papke, F Rodriguez-Valera
    posted to genomics plasticity prokaryote by operon on 2007-12-02 15:49:44 as ** along with 3 people jmeppley balicea hpaces
  • Metaproteomics: A New Approach for Studying Functional Microbial Ecology
    Microbial Ecology
    by Pierre-Alain Maron, Lionel Ranjard, Christophe Mougel, Philippe Lemanceau
    posted to metaproteomics prokaryote proteome proteomics by operon on 2007-07-23 20:03:16 as ** along with 3 people jmeppley rabu bluto
  • Genome plasticity of Vibrio parahaemolyticus: microevolution of the 'pandemic group'
    BMC Genomics, Vol. 9 (28 November 2008), 570.
    by Haihong, Ruifu Yang
    posted to prokaryote genomics evolution bacteria by operon on 2008-12-03 19:27:35 as **
  • IdentiCS--identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence.
    BMC Bioinformatics, Vol. 5 (16 August 2004)
    by J Sun, AP Zeng
    posted to prokaryote genomics bioinformatics software by operon on 2007-07-23 16:06:58 as ** along with 1 person eweaver
  • Analysis of circular genome rearrangement by fusions, fissions and block-interchanges
    BMC Bioinformatics, Vol. 7 (12 June 2006), 295.
    by Chin L Lu, Yen L Huang, Tsui C Wang, Hsien-Tai Chiu
    posted to master prokaryote rearrangements by operon on 2008-02-19 13:59:33 as **
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