Searching journal content for articles similar to Lin et al. 17 (12): 000.

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  1. Resource: Discovery of high-confidence human protein-coding genes and exons by whole-genome PhyloCSF helps elucidate 118 GWAS loci
    • Jonathan M. Mudge,
    • Irwin Jungreis,
    • Toby Hunt,
    • Jose Manuel Gonzalez,
    • James C. Wright,
    • Mike Kay,
    • Claire Davidson,
    • Stephen Fitzgerald,
    • Ruth Seal,
    • Susan Tweedie,
    • Liang He,
    • Robert M. Waterhouse,
    • Yue Li,
    • Elspeth Bruford,
    • Jyoti S. Choudhary,
    • Adam Frankish,
    • and Manolis Kellis
    Genome Res. December 2019 29: 2073-2087; Published in Advance September 19, 2019, doi:10.1101/gr.246462.118
    ...et al. 2011, 2016), and also to identify novel human and mouse protein-coding genes based on the alignment of 29 mammalian s (Lindblad-Toh et al. 2011). Meanwhile, Mackowiak et al. (2015) used PhyloCSF to find 2000 candidates for conserved short ORFs (sORFs) in the human, mouse, zebrafish, Drosophila...
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  2. Resource: Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines
    • Wen Huang,
    • Andreas Massouras,
    • Yutaka Inoue,
    • Jason Peiffer,
    • Miquel Ràmia,
    • Aaron M. Tarone,
    • Lavanya Turlapati,
    • Thomas Zichner,
    • Dianhui Zhu,
    • Richard F. Lyman,
    • Michael M. Magwire,
    • Kerstin Blankenburg,
    • Mary Anna Carbone,
    • Kyle Chang,
    • Lisa L. Ellis,
    • Sonia Fernandez,
    • Yi Han,
    • Gareth Highnam,
    • Carl E. Hjelmen,
    • John R. Jack,
    • Mehwish Javaid,
    • Joy Jayaseelan,
    • Divya Kalra,
    • Sandy Lee,
    • Lora Lewis,
    • Mala Munidasa,
    • Fiona Ongeri,
    • Shohba Patel,
    • Lora Perales,
    • Agapito Perez,
    • LingLing Pu,
    • Stephanie M. Rollmann,
    • Robert Ruth,
    • Nehad Saada,
    • Crystal Warner,
    • Aneisa Williams,
    • Yuan-Qing Wu,
    • Akihiko Yamamoto,
    • Yiqing Zhang,
    • Yiming Zhu,
    • Robert R.H. Anholt,
    • Jan O. Korbel,
    • David Mittelman,
    • Donna M. Muzny,
    • Richard A. Gibbs,
    • Antonio Barbadilla,
    • J. Spencer Johnston,
    • Eric A. Stone,
    • Stephen Richards,
    • Bart Deplancke,
    • and Trudy F.C. Mackay
    Genome Res. July 2014 24: 1193-1208; Published in Advance April 8, 2014, doi:10.1101/gr.171546.113
    ...insertions of Wolbachia sequences, but effects of Wolbachia infection on quantitative traits are rarely significant. The DGRP complements ongoing efforts to functionally annotate the Drosophila genome. Indeed, 15% of all D. melanogaster genes segregate for potentially damaged proteins in the DGRP...
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  3. 12 Drosophila Genomes/Letter: Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes
    • Alexander Stark,
    • Pouya Kheradpour,
    • Leopold Parts,
    • Julius Brennecke,
    • Emily Hodges,
    • Gregory J. Hannon,
    • and Manolis Kellis
    Genome Res. December 2007 17: 1865-1879; Published in Advance November 7, 2007, doi:10.1101/gr.6593807
    ...Systematic discovery and characterization of fly microRNAs using 12 Drosophila genomes Alexander Stark 1 , 2 , 4 , 6 , Pouya Kheradpour 2 , 4 , Leopold Parts 2 , 5 , Julius Brennecke 3 , Emily Hodges 3 , Gregory J. Hannon 3...
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  4. Method: CRISPR-based modular assembly of a UAS-cDNA/ORF plasmid library for more than 5500 Drosophila genes conserved in humans
    • Ping Wei,
    • Wen Xue,
    • Yun Zhao,
    • Guang Ning,
    • and Jiwu Wang
    Genome Res. January 2020 30: 95-106; Published in Advance November 13, 2019, doi:10.1101/gr.250811.119
    ...flies mapping to about 2850 Drosophila genes have been generated (FlyORF, http://www.FlyORF.ch). In 2018, the human ORF collection containing 365 UAS-ORF plasmids for Drosophila transgenesis was constructed and deposited to the Drosophila Genomics Resource Center (DGRC, https...
  5. Methods: Conserved introns reveal novel transcripts in Drosophila melanogaster
    • Michael Hiller,
    • Sven Findeiß,
    • Sandro Lein,
    • Manja Marz,
    • Claudia Nickel,
    • Dominic Rose,
    • Christine Schulz,
    • Rolf Backofen,
    • Sonja J. Prohaska,
    • Gunter Reuter,
    • and Peter F. Stadler
    Genome Res. July 2009 19: 1289-1300; Published in Advance May 20, 2009, doi:10.1101/gr.090050.108
    ..., which allows comparative genomics methods to annotate features such as protein-coding genes, structured RNAs, and regulatory motifs with high accuracy (Drosophila 12 Genomes Consortium 2007; Kheradpour et al. 2007; Stark et al. 2007a,b). (2) The majority (54%) of introns in Drosophila melanogaster...
  6. RESOURCE: Cross-Referencing Eukaryotic Genomes: TIGR Orthologous Gene Alignments (TOGA)
    • Yuandan Lee,
    • Razvan Sultana,
    • Geo Pertea,
    • Jennifer Cho,
    • Svetlana Karamycheva,
    • Jennifer Tsai,
    • Babak Parvizi,
    • Foo Cheung,
    • Valentin Antonescu,
    • Joseph White,
    • Ingeborg Holt,
    • Feng Liang,
    • and John Quackenbush
    Genome Res. March 1, 2002 12: 493-502; doi:10.1101/gr.212002
    ...genes. With the available complete sequences or comprehensive drafts of several eukaryotic s including Saccharomyces cerevisiae ( Goffeau et al. 1996 ), Caenorhabditis elegans ( The C. elegans sequencing consortium 1998 ), Drosophila melanogaster ( Adams et al. 2000 ), Arabidopsis thaliana...
  7. Research: Evidence of abundant stop codon readthrough in Drosophila and other metazoa
    • Irwin Jungreis,
    • Michael F. Lin,
    • Rebecca Spokony,
    • Clara S. Chan,
    • Nicolas Negre,
    • Alec Victorsen,
    • Kevin P. White,
    • and Manolis Kellis
    Genome Res. December 2011 21: 2096-2113; Published in Advance October 12, 2011, doi:10.1101/gr.119974.110
    ...observed for only a handful of eukaryotic genes. We previously used comparative genomics evidence to recognize protein-coding regions in 12 species of Drosophila and showed that for 149 genes, the open reading frame following the stop codon has a protein-coding conservation signature, hinting that stop...
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  8. Research: Global analysis of Drosophila Cys2-His2 zinc finger proteins reveals a multitude of novel recognition motifs and binding determinants
    • Metewo Selase Enuameh,
    • Yuna Asriyan,
    • Adam Richards,
    • Ryan G. Christensen,
    • Victoria L. Hall,
    • Majid Kazemian,
    • Cong Zhu,
    • Hannah Pham,
    • Qiong Cheng,
    • Charles Blatti,
    • Jessie A. Brasefield,
    • Matthew D. Basciotta,
    • Jianhong Ou,
    • Joseph C. McNulty,
    • Lihua J. Zhu,
    • Susan E. Celniker,
    • Saurabh Sinha,
    • Gary D. Stormo,
    • Michael H. Brodsky,
    • and Scot A. Wolfe
    Genome Res. June 2013 23: 928-940; Published in Advance March 7, 2013, doi:10.1101/gr.151472.112
    ...and their resulting DNA-binding specificity, highlighting how different isoforms can increase the complexity of available trans-acting factors for gene regulationwithout expanding gene number. These data can be used to predict genomic targets for these TFs within the Drosophila . In addition, we have defined...
  9. Research: A second-generation assembly of the Drosophila simulans genome provides new insights into patterns of lineage-specific divergence
    • Tina T. Hu,
    • Michael B. Eisen,
    • Kevin R. Thornton,
    • and Peter Andolfatto
    Genome Res. January 2013 23: 89-98; Published in Advance August 30, 2012, doi:10.1101/gr.141689.112
    ...rearrangement (LR) events in our assembly (Supplemental Table 4). When incorporating Drosophila yakuba, the number of orthologs found in all three species reduces to 12,747 genes (92.9% of D. melanogaster genes). From this subset, rates of evolution along the D. melanogaster and D. simulans lineages...
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