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PetrovLabs library [162 articles]

Neue Artikel in PetrovLabs library ordered by importance.
  • DupMasker: A tool for annotating primate segmental duplications
    Genome Res. (23 May 2008), gr.078477.108.
    by Zhaoshi Jiang, Robert Hubley, Arian Smit, Evan E Eichler
    posted to bioinformatics duplication human by PetrovLab on 2008-05-28 02:22:10 as ***** along with 2 people Neeperando pradiptaray
  • Recent LTR retrotransposon insertion contrasts with waves of non-LTR insertion since speciation in Drosophila melanogaster.
    Proceedings of the National Academy of Sciences of the United States of America, Vol. 104, No. 27. (3 July 2007), pp. 11340-11345.
    by CM Bergman, D Bensasson
    posted to bioinformatics drosophila evolution genomics by PetrovLab on 2008-05-22 02:52:01 as *****
  • Comparative evolution history of SINEs in Arabidopsis thaliana and Brassica oleracea: evidence for a high rate of SINE loss.
    Cytogenetic and genome research, Vol. 110, No. 1-4. (2005), pp. 441-447.
    by A Lenoir, T Pélissier, C Bousquet-Antonelli, JM Deragon
    posted to comparative_genomic te thaliana by PetrovLab on 2008-05-14 18:56:18 as *****
  • Evolutionary History of Mammalian Transposons Determined by Genome-Wide Defragmentation.
    PLoS Comput Biol, Vol. 3, No. 7. (13 July 2007)
    by Joti Giordano, Yongchao Ge, Yevgeniy Gelfand, György Abrusán, Gary Benson, Peter E E Warburton
    posted to genome phylogeny te by PetrovLab on 2008-05-14 18:34:11 as ***** along with 7 people and 3 groups kiara aprasad dchughes sebastien_vigneau N0131826 paulcartwright yoanjacquemin G4ID Genetics-of-Gambling BergmanLab
  • Evolution of genes and genomes on the Drosophila phylogeny
    Nature, Vol. 450, No. 7167. (November 2007), pp. 203-218.
    posted to comparative_genomic drosophila evolution genome phylogeny by PetrovLab on 2008-05-13 20:22:17 as ***** along with 20 people and 6 groups pengchy operon tmmurali indigoviolet djkt timflutre stajich zwang Garamonfok lp2 CharlesM hpaces caseybrown emptyhb urgi noor isimpson balicea cisevol hdopazo Bioinformatics EisenLab csb_journal_club_public Berkeley Mycology BergmanLab Drosophila-Genetics-Genomics-2008
  • Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
    Nature, Vol. 450, No. 7167., pp. 219-232.
    by Alexander Stark, Michael F Lin, Pouya Kheradpour, Jakob S Pedersen, Leopold Parts, Joseph W Carlson, Madeline A Crosby, Matthew D Rasmussen, Sushmita Roy, Ameya N Deoras, Graham J Ruby, Julius Brennecke, Harvard F Curators, Berkeley, Emily Hodges, Angie S Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V Han, Morgan L Maeder, Benjamin J Polansky, Bryanne E Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G Gilbert, Deborah A Eastman, Michael Rice, Michael Weir, Matthew W Hahn, Yongkyu Park, Colin N Dewey, Lior Pachter, James W Kent, David Haussler, Eric C Lai, David P Bartel, Gregory J Hannon, Thomas C Kaufman, Michael B Eisen, Andrew G Clark, Douglas Smith, Susan E Celniker, William M Gelbart, Manolis Kellis
    posted to comparative_genomic drosophila genome phylogeny by PetrovLab on 2008-05-13 20:21:34 as ***** along with 14 people and 3 groups operon tmmurali djkt timflutre stajich lp2 cabbagezs nklee hpaces roys caseybrown gjuggler shuzhens cisevol csb_journal_club_public Berkeley Mycology Drosophila-Genetics-Genomics-2008
  • Complex evolution of gypsy in Drosophilid species.
    Molecular biology and evolution, Vol. 21, No. 10. (October 2004), pp. 1831-1842.
    by F Herédia, EL Loreto, VL Valente
    posted to drosophila by PetrovLab on 2008-05-06 01:43:31 as *****
  • Multiple invasions of Errantivirus in the genus Drosophila
    Insect Molecular Biology, Vol. 17, No. 2. (April 2008), pp. 113-124.
    by Ludwig, , Valente, Da, Loreto,
    posted to drosophila by PetrovLab on 2008-05-06 01:38:31 as *****
  • Improved repeat identification and masking in Dipterans
    Gene, Vol. 389, No. 1. (1 March 2007), pp. 1-9.
    by Christopher D Smith, Robert C Edgar, Mark D Yandell, Douglas R Smith, Susan E Celniker, Eugene W Myers, Gary H Karpen
    posted to bioinformatics by PetrovLab on 2008-05-30 02:16:19 as ****
  • Improved detection and annotation of transposable elements in sequenced genomes using multiple reference sequence sets.
    Genomics (13 March 2008)
    by Nicolas Buisine, Hadi Quesneville, Vincent Colot
    posted to athaliana bioinformatics plants repeats by PetrovLab on 2008-05-27 17:11:45 as **** along with 4 people operon dchughes timflutre urgi
  • Abundant and species-specific DINE-1 transposable elements in 12 Drosophila genomes
    Genome Biology, Vol. 9 (21 February 2008), R39.
    by Hsiao-Pei Yang, Daniel A Barbash
    posted to drosophila genomics te by PetrovLab on 2008-05-14 18:58:12 as ****
  • DNA indels in coding regions reveal selective constraints on protein evolution in the human lineage
    BMC Evolutionary Biology, Vol. 7 (12 October 2007), 191.
    by Nicole, Philipp W Messer, Peter F Arndt
    posted to evolution human by PetrovLab on 2008-05-02 19:46:35 as ****
  • The majority of recent short DNA insertions in the human genome are tandem duplications.
    Mol Biol Evol, Vol. 24, No. 5. (May 2007), pp. 1190-1197.
    by PW Messer, PF Arndt
    posted to genomics human repeats by PetrovLab on 2008-05-02 19:43:57 as **** along with 2 people aprasad dchughes
  • Genomewide Spatial Correspondence Between Nonsynonymous Divergence and Neutral Polymorphism Reveals Extensive Adaptation in Drosophila
    Genetics, Vol. 177, No. 4. (1 December 2007), pp. 2083-2099.
    by Michael J Macpherson, Guy Sella, Jerel C Davis, Dmitri A Petrov
    posted to no-tag by PetrovLab on 2008-05-02 19:27:53 as **** along with 3 people brant caseybrown smbe2008
  • Testing Chromosomal Phylogenies and Inversion Breakpoint Reuse in Drosophila
    Genetics, Vol. 175, No. 1. (1 January 2007), pp. 167-177.
    by Josefa González, Ferran Casals, Alfredo Ruiz
    posted to drosophila te by PetrovLab on 2008-05-02 19:26:53 as **** along with 1 person operon
  • Nonadaptive explanations for signatures of partial selective sweeps in Drosophila.
    Molecular biology and evolution (16 January 2008)
    by J Michael M Macpherson, Josefa González, Daniela M M Witten, Jerel C C Davis, Noah A A Rosenberg, Aaron E E Hirsh, Dmitri A A Petrov
    posted to drosophila by PetrovLab on 2008-05-02 19:25:31 as **** along with 1 person caseybrown
  • Chromosomal elements evolve at different rates in the Drosophila genome.
    Genetics, Vol. 161, No. 3. (July 2002), pp. 1137-1154.
    by J González, JM Ranz, A Ruiz
    posted to drosophila te by PetrovLab on 2008-05-02 19:24:37 as ****
  • Abundance and chromosomal distribution of six Drosophila buzzatii transposons: BuT1, BuT2, BuT3, BuT4, BuT5, and BuT6.
    Chromosoma, Vol. 115, No. 5. (October 2006), pp. 403-412.
    by F Casals, J González, A Ruiz
    posted to drosophila te by PetrovLab on 2008-05-02 19:23:30 as ****
  • Co-evolution of transcription factors and their targets depends on mode of regulation
    Genome Biology, Vol. 7 (19 July 2006), R62.
    by Ruth Hershberg, Hanah Margalit
    posted to no-tag by PetrovLab on 2008-05-02 19:20:49 as **** along with 4 people and 2 groups indigoviolet dpollard cjeans cisevol EisenLab cis-regulatory-evolution
  • Reduced selection leads to accelerated gene loss in Shigella
    Genome Biology, Vol. 8 (08 August 2007), R164.
    by Ruth Hershberg, Hua Tang, Dmitri A Petrov
    posted to no-tag by PetrovLab on 2008-05-02 19:19:53 as **** along with 2 people operon AaronDarling
  • Accelerated evolutionary rate may be responsible for the emergence of lineage-specific genes in ascomycota.
    Journal of molecular evolution, Vol. 63, No. 1. (July 2006), pp. 1-11.
    by JJ Cai, PC Woo, SK Lau, DK Smith, KY Yuen
    posted to no-tag by PetrovLab on 2008-05-02 19:18:50 as ****
  • MBEToolbox: a MATLAB toolbox for sequence data analysis in molecular biology and evolution.
    BMC bioinformatics, Vol. 6 (2005)
    by JJ Cai, DK Smith, X Xia, KY Yuen
    posted to no-tag by PetrovLab on 2008-05-02 19:18:07 as ****
  • PGEToolbox: A Matlab Toolbox for Population Genetics and Evolution.
    The Journal of heredity (29 February 2008)
    by James J J Cai
    posted to bioinformatics pop_genetics population_genetics by PetrovLab on 2008-05-02 19:13:33 as ****
  • The impact of recombination on nucleotide substitutions in the human genome.
    PLoS genetics, Vol. 4, No. 5. (May 2008)
    by L Duret, PF Arndt
    posted to recombination population_genetics evolution by PetrovLab on 2008-10-06 21:09:01 as ** along with 3 people aprasad gjuggler balicea
  • LTR retrotransposons in rice (Oryza sativa, L.): recent burst amplifications followed by rapid DNA loss
    BMC Genomics, Vol. 8 (06 July 2007), 218.
    by Clementine Vitte, Olivier Panaud, Hadi Quesneville
    posted to bioinformatics plants te by PetrovLab on 2008-05-29 02:27:14 as ** along with 2 people timflutre urgi
  • Genomic heterogeneity of background substitutional patterns in Drosophila melanogaster.
    Genetics, Vol. 169, No. 2. (February 2005), pp. 709-722.
    by ND Singh, PF Arndt, DA Petrov
    posted to drosophila by PetrovLab on 2008-05-02 20:00:03 as ** along with 1 person operon
  • The large genome constraint hypothesis: evolution, ecology and phenotype.
    Ann Bot (Lond), Vol. 95, No. 1. (January 2005), pp. 177-190.
    by CA Knight, NA Molinari, DA Petrov
    posted to ecology evolution by PetrovLab on 2008-05-02 19:59:27 as ** along with 4 people echinotrix timflutre TaqSys qwermish
  • Protein evolution in the context of Drosophila development.
    Journal of molecular evolution, Vol. 60, No. 6. (June 2005), pp. 774-785.
    by JC Davis, O Brandman, DA Petrov
    posted to drosophila evolution by PetrovLab on 2008-05-02 19:58:39 as **
  • Substantial regional variation in substitution rates in the human genome: importance of GC content, gene density, and telomere-specific effects.
    Journal of molecular evolution, Vol. 60, No. 6. (June 2005), pp. 748-763.
    by PF Arndt, T Hwa, DA Petrov
    posted to human by PetrovLab on 2008-05-02 19:58:06 as **
  • X-linked genes evolve higher codon bias in Drosophila and Caenorhabditis.
    Genetics, Vol. 171, No. 1. (September 2005), pp. 145-155.
    by ND Singh, JC Davis, DA Petrov
    posted to drosophila by PetrovLab on 2008-05-02 19:57:32 as **
  • Codon bias and noncoding GC content correlate negatively with recombination rate on the Drosophila X chromosome.
    Journal of molecular evolution, Vol. 61, No. 3. (September 2005), pp. 315-324.
    by ND Singh, JC Davis, DA Petrov
    posted to drosophila recombination by PetrovLab on 2008-05-02 19:56:55 as **
  • Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila.
    Science (New York, N.Y.), Vol. 309, No. 5735. (29 July 2005), pp. 764-767.
    by YT Aminetzach, JM Macpherson, DA Petrov
    posted to drosophila te by PetrovLab on 2008-05-02 19:56:16 as **
  • Do disparate mechanisms of duplication add similar genes to the genome?
    Trends in Genetics, Vol. In Press, Corrected Proof
    by Jerel C Davis, Dmitri A Petrov
    posted to duplication by PetrovLab on 2008-05-02 19:55:20 as ** along with 5 people and 2 groups Retchless dchughes mikemacpherson nirfriedman bpcusack G4ID Genetics-of-Gambling
  • Minor shift in background substitutional patterns in the Drosophila saltans and willistoni lineages is insufficient to explain GC content of coding sequences
    BMC Biology, Vol. 4 (18 October 2006), 37.
    by Nadia D Singh, Peter F Arndt, Dmitri A Petrov
    posted to drosophila evolution by PetrovLab on 2008-05-02 19:54:35 as **
  • Similar Levels of X-linked and Autosomal Nucleotide Variation in African and non-African populations of Drosophila melanogaster
    BMC Evolutionary Biology, Vol. 7 (25 October 2007), 202.
    by Nadia D Singh, Michael J Macpherson, Jeffrey D Jensen, Dmitri A Petrov
    posted to drosophila by PetrovLab on 2008-05-02 19:53:31 as ** along with 1 person and 1 group dpollard EisenLab
  • Effects of long-range correlations in DNA on sequence alignment score statistics.
    Journal of computational biology : a journal of computational molecular cell biology, Vol. 14, No. 5. (June 2007), pp. 655-668.
    by PW Messer, R Bundschuh, M Vingron, PF Arndt
    posted to genomics by PetrovLab on 2008-05-02 19:44:53 as **
  • CorGen--measuring and generating long-range correlations for DNA sequence analysis.
    Nucleic acids research, Vol. 34, No. Web Server issue. (1 July 2006)
    by PW Messer, PF Arndt
    posted to bioinformatics genomics by PetrovLab on 2008-05-02 19:42:39 as **
  • Paucity of chimeric gene-transposable element transcripts in the Drosophila melanogaster genome.
    BMC biology, Vol. 3 (2005)
    by M Lipatov, K Lenkov, DA Petrov, CM Bergman
    posted to no-tag by PetrovLab on 2008-05-02 19:29:15 as **
  • A novel method distinguishes between mutation rates and fixation biases in patterns of single-nucleotide substitution.
    Journal of molecular evolution, Vol. 62, No. 2. (February 2006), pp. 168-175.
    by M Lipatov, PF Arndt, T Hwa, DA Petrov
    posted to no-tag by PetrovLab on 2008-05-02 19:28:49 as ** along with 1 person smbe2008
  • Chromosomal organization is shaped by the transcription regulatory network.
    Trends in genetics : TIG, Vol. 21, No. 3. (March 2005), pp. 138-142.
    by R Hershberg, E Yeger-Lotem, H Margalit
    posted to no-tag by PetrovLab on 2008-05-02 19:21:51 as **
  • Exploring the Penicillium marneffei genome.
    Archives of microbiology, Vol. 179, No. 5. (May 2003), pp. 339-353.
    by KY Yuen, G Pascal, SS Wong, P Glaser, PC Woo, F Kunst, JJ Cai, EY Cheung, C Médigue, A Danchin
    posted to no-tag by PetrovLab on 2008-05-02 19:17:24 as **
  • Metabolic diversification--independent assembly of operon-like gene clusters in different plants.
    Science (New York, N.Y.), Vol. 320, No. 5875. (25 April 2008), pp. 543-547.
    by B Field, AE Osbourn
    posted to gene_cluster plants thaliana by PetrovLab on 2008-05-02 18:34:02 as ** along with 2 people and 1 group jmjimenez jlgreen Green Lab
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