Searching journal content for articles similar to Birney and Durbin 10 (4): 547.

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  1. ENSEMBL Special: GeneWise and Genomewise
    • Ewan Birney,
    • Michele Clamp,
    • and Richard Durbin
    Genome Res. May 2004 14: 988-995; doi:10.1101/gr.1865504
    .... Science 297 : 1301 -1310. ↵ Birney, E. and Durbin, R. 1997 . Dynamite: A flexible code generating language for dynamic programming methods used in sequence comparison. ISMB 97 : 56 -64. ↵ Birney, E. and Durbin, R. 2000 . Using GeneWise in the Drosophila annotation experiment. Genome Res. 10 : 547 -548...
  2. Research: The evolution of sex-biased gene expression in the Drosophila brain
    • Samuel Khodursky,
    • Nicolas Svetec,
    • Sylvia M. Durkin,
    • and Li Zhao
    Genome Res. June 2020 30: 874-884; Published in Advance June 18, 2020, doi:10.1101/gr.259069.119
    ...in Drosophila.To further understand whether positive selection has influenced the evolution of coding sequences of sex-biased genes, we examined published McDonald–Kreitman (MK) test data of annotated protein-coding genes in D. melanogaster (Langley et al. 2012). The MK test infers the presence of positive...
  3. LETTER: Genome Annotation Assessment in Drosophila melanogaster
    • Martin G. Reese,
    • George Hartzell,
    • Nomi L. Harris,
    • Uwe Ohler,
    • Josep F. Abril,
    • and Suzanna E. Lewis
    Genome Res. April 1, 2000 10: 483-501; doi:10.1101/gr.10.4.483
    ...Genome Annotation Assessment in Drosophila melanogaster Martin G. Reese 1 , 4 , George Hartzell 1 , Nomi L. Harris 1 , Uwe Ohler 1 , 2 , Josep F. Abril 3 , and Suzanna E. Lewis 1 1Berkeley Drosophila Genome...
  4. Research: Evolutionarily new genes in humans with disease phenotypes reveal functional enrichment patterns shaped by adaptive innovation and sexual selection
    • Jian-Hai Chen,
    • Patrick Landback,
    • Deanna Arsala,
    • Alexander Guzzetta,
    • Shengqian Xia,
    • Jared Atlas,
    • Dylan Sosa,
    • Yong E. Zhang,
    • Jingqiu Cheng,
    • Bairong Shen,
    • and Manyuan Long
    Genome Res. March 2025 35: 379-392; Published in Advance February 14, 2025, doi:10.1101/gr.279498.124
    ...disease genes. (C) The fractions of disease genes at four major phylostrata from Euteleostomi to Eutheria. (D) The protein lengths between disease and nondisease genes across four phylostrata. (E) The gene-wise burden based on de novo germline variants from the Gene4Denovo database (Zhao et al. 2020...
    OPEN ACCESS ARTICLE
  5. METHODS: Drosophila Genomic Sequence Annotation Using the BLOCKS+ Database
    • Jorja G. Henikoff and
    • Steven Henikoff
    Genome Res. April 1, 2000 10: 543-546; doi:10.1101/gr.10.4.543
    ...S.R. Finn R.D. Sonnhammer E.L.L. ( 1999 ) Pfam 3.1: 1313 multiple alignments and profile HMMs match the majority of proteins. Nucleic Acids Res. 27 : 260 – 262 . Birney, E. and R. Durbin. 2000. Using in the Drosophila annotation experiment. Genome Res. (this issue). . GeneWise . Corpet F. Gouzy J...
  6. Research: Unexpectedly low recombination rates and presence of hotspots in termite genomes
    • Turid Everitt,
    • Tilman Rönneburg,
    • Daniel Elsner,
    • Anna Olsson,
    • Yuanzhen Liu,
    • Tuuli Larva,
    • Judith Korb,
    • and Matthew T. Webster
    Genome Res. May 2025 35: 1124-1137; Published in Advance March 20, 2025, doi:10.1101/gr.279180.124
    ...order of conserved domains by alignment of the Zootermopsis nevadensis PRDM9 protein sequence to the M. bellicosus using GeneWise (Fig. 4C; Supplemental Table S4; Madeira et al. 2024).View larger version: In this window In a new window Figure 4. PRMD9 structure and predicted zinc-finger motifs in the M...
  7. Methods: Gene and alternative splicing annotation with AIR
    • Liliana Florea,
    • Valentina Di Francesco,
    • Jason Miller,
    • Russell Turner,
    • Alison Yao,
    • Michael Harris,
    • Brian Walenz,
    • Clark Mobarry,
    • Gennady V. Merkulov,
    • Rosane Charlab,
    • Ian Dew,
    • Zuoming Deng,
    • Sorin Istrail,
    • Peter Li,
    • and Granger Sutton
    Genome Res. January 2005 15: 54-66; doi:10.1101/gr.2889405
    ...on alignments of protein and cDNA (EST, mRNA) sequences with genomic sequences (Procrustes, Gelfand et al. 1996 ; EstGenome, Mott 1997 ; sim4, Florea et al. 1998 ; GeneWise, Birney and Durbin 2000 ; Spidey, Wheelan et al. 2001 ) depend critically on the completeness and quality of sequences used. More recently...
  8. METHODS: MAGPIE/EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region
    • Terry Gaasterland,
    • Alexander Sczyrba,
    • Elizabeth Thomas,
    • Gulriz Aytekin-Kurban,
    • Paul Gordon,
    • and Christoph W. Sensen
    Genome Res. April 1, 2000 10: 502-510; doi:10.1101/gr.10.4.502
    ...MAGPIE / EGRET Annotation of the 2.9-Mb Drosophila melanogaster Adh Region Terry Gaasterland 1 , 4 , Alexander Sczyrba 1 , Elizabeth Thomas 1 , 2 , Gulriz Aytekin-Kurban 1 , Paul Gordon 3 , and Christoph W. Sensen 3...
  9. PERSPECTIVE: Genome annotation past, present, and future: How to define an ORF at each locus
    • Michael R. Brent
    Genome Res. December 2005 15: 1777-1786; doi:10.1101/gr.3866105
    ...their true loci from nontranscribed pseudogenes. GeneWise (Birney and Durbin 1997 , 2000 ; Birney et al. 2004b ) is certainly the most important protein-to- alignment program, since it forms a central part of the highly influential Ensembl gene annotation pipeline. The accuracy of GeneWise is determined...
  10. Letter: Population dynamics of PIWI-interacting RNAs (piRNAs) and their targets in Drosophila
    • Jian Lu and
    • Andrew G. Clark
    Genome Res. February 2010 20: 212-227; Published in Advance November 30, 2009, doi:10.1101/gr.095406.109
    ...annotations of TEs are only available for the euchromatic regions, we only focus on piRTs located there. It is challenging todetermine the retrotransposons in theDrosophila that are not repressed by piRNAs, i.e., the piRTs strictly under scenario I in our simulations. Our simulations indicate that relative...
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