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Research: Genome-wide profiles of H3K9me3, H3K27me3 modifications, and DNA methylation during diapause of Asian corn borer (Ostrinia furnacalis)
- Pengfei Lv,
- Xingzhuo Yang,
- Xianguo Zhao,
- Zhangwu Zhao,
- and Juan Du
Genome Res. May 2024 34: 725-739; Published in Advance June 12, 2024, doi:10.1101/gr.278661.123
...on SU(VAR)3-9 and E(Z) activities in Drosophila melanogaster, respectively (Greiner et al. 2005; Bhat et al. 2021). Through protein sequence comparison, we found that SUV39H2-like and E(Z) in the Asian corn borer share 35.92% and 62.17% homology with SU(VAR)3-9 and E(Z) in D. melanogaster, respectively...
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Research: Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster
- Daniel R. Schrider,
- Kristian Stevens,
- Charis M. Cardeño,
- Charles H. Langley,
- and Matthew W. Hahn
Genome Res. December 2011 21: 2087-2095; doi:10.1101/gr.116434.110
...Genome-wide analysis of retrogene polymorphisms in Drosophila melanogaster Daniel R. Schrider 1 , 2 , 5 , Kristian Stevens 3 , 4 , Charis M. Cardeño 3 , 4 , Charles H. Langley 3 , 4 and Matthew W. Hahn 1 , 2 1...
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LETTER: Genome-Wide Analysis of the Odorant-Binding Protein Gene Family in Drosophila melanogaster
- Daria S. Hekmat-Scafe,
- Charles R. Scafe,
- Aimee J. McKinney,
- and Mark A. Tanouye
Genome Res. September 1, 2002 12: 1357-1369; doi:10.1101/gr.239402
...Genome-Wide Analysis of the Odorant-Binding Protein Gene Family in Drosophila melanogaster Daria S. Hekmat-Scafe 1 , 6 , Charles R. Scafe 3 , 5 , Aimee J. McKinney 4 , and Mark A. Tanouye 1 , 2 1Department of Environmental...
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LETTER: A Genome-Wide Survey of Human Pseudogenes
- David Torrents,
- Mikita Suyama,
- Evgeny Zdobnov,
- and Peer Bork
Genome Res. December 2003 13: 2559-2567; doi:10.1101/gr.1455503
....M., von Mering, C., Letunic, I., Torrents, D., Suyama, M., Copley, R.R., Christophides, G.K., Thomasova, D., Holt, R.A., Subramanian, G.M., et al. 2002 . Comparative and proteome analysis of Anopheles gambiae and Drosophila melanogaster. Science 298 : 149 -159. ↵ Zhang, Z., Harrison, P., and Gerstein, M...
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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...
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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
...the full sequence, which is necessary when considering individual exons.We previously showed the ability of PhyloCSF and its predecessor, CSF, to add CDS annotation to s within the Schizosaccharomyces (Lin et al. 2011) and Drosophila lineages (Lin et al. 2007; The modENCODE Consortium et al. 2010; Jungreis...
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12 Drosophila Genomes/Letter: Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes
- Michael F. Lin,
- Joseph W. Carlson,
- Madeline A. Crosby,
- Beverley B. Matthews,
- Charles Yu,
- Soo Park,
- Kenneth H. Wan,
- Andrew J. Schroeder,
- L. Sian Gramates,
- Susan E. St. Pierre,
- Margaret Roark,
- Kenneth L. Wiley, Jr.,
- Rob J. Kulathinal,
- Peili Zhang,
- Kyl V. Myrick,
- Jerry V. Antone,
- Susan E. Celniker,
- William M. Gelbart,
- and Manolis Kellis
Genome Res. December 2007 17: 1823-1836; Published in Advance November 7, 2007, doi:10.1101/gr.6679507
...Revisiting the protein-coding gene catalog of Drosophila melanogaster using 12 fly genomes Michael F. Lin 1 , Joseph W. Carlson 2 , Madeline A. Crosby 3 , Beverley B. Matthews 3 , Charles Yu 2 , Soo Park 2 , Kenneth H. Wan 2...
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Methods: Whole Genome Sequence Comparisons and “Full-Length” cDNA Sequences: A Combined Approach to Evaluate and Improve Arabidopsis Genome Annotation
- Vanina Castelli,
- Jean-Marc Aury,
- Olivier Jaillon,
- Patrick Wincker,
- Christian Clepet,
- Manuella Menard,
- Corinne Cruaud,
- Francis Quétier,
- Claude Scarpelli,
- Vincent Schächter,
- Gary Temple,
- Michel Caboche,
- Jean Weissenbach,
- and Marcel Salanoubat
Genome Res. March 2004 14: 406-413; doi:10.1101/gr.1515604
...local and global sequence information. Nucleic Acids Res. 24 : 3439 –3452. ↵ Jaillon, O., Dossat, C., Eckenberg, R., Eiglmeier, K., Segurens, B., Aury, J.M., Roth, C.W., Scarpelli, C., Brey, P.T., Weissenbach, J., et al. 2003 . Assessing the Drosophila melanogaster and Anopheles gambiae annotations...
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ARTICLE: Comparative genome sequencing of Drosophila pseudoobscura: Chromosomal, gene, and cis-element evolution
- Stephen Richards,
- Yue Liu,
- Brian R. Bettencourt,
- Pavel Hradecky,
- Stan Letovsky,
- Rasmus Nielsen,
- Kevin Thornton,
- Melissa J. Hubisz,
- Rui Chen,
- Richard P. Meisel,
- Olivier Couronne,
- Sujun Hua,
- Mark A. Smith,
- Peili Zhang,
- Jing Liu,
- Harmen J. Bussemaker,
- Marinus F. van Batenburg,
- Sally L. Howells,
- Steven E. Scherer,
- Erica Sodergren,
- Beverly B. Matthews,
- Madeline A. Crosby,
- Andrew J. Schroeder,
- Daniel Ortiz-Barrientos,
- Catharine M. Rives,
- Michael L. Metzker,
- Donna M. Muzny,
- Graham Scott,
- David Steffen,
- David A. Wheeler,
- Kim C. Worley,
- Paul Havlak,
- K. James Durbin,
- Amy Egan,
- Rachel Gill,
- Jennifer Hume,
- Margaret B. Morgan,
- George Miner,
- Cerissa Hamilton,
- Yanmei Huang,
- Lenée Waldron,
- Daniel Verduzco,
- Kerstin P. Clerc-Blankenburg,
- Inna Dubchak,
- Mohamed A.F. Noor,
- Wyatt Anderson,
- Kevin P. White,
- Andrew G. Clark,
- Stephen W. Schaeffer,
- William Gelbart,
- George M. Weinstock,
- and Richard A. Gibbs
Genome Res. January 2005 15: 1-18; doi:10.1101/gr.3059305
...these species of Drosophila . Comparative sequencing is an important tool in the ongoing effort to annotate and analyze genes, cis -regulatory elements, and architectural features of s. A single genomic sequence provides a wealth of information about the number and location of genes, but the experimental...
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Research: Natural selection shapes nucleotide polymorphism across the genome of the nematode Caenorhabditis briggsae
- Asher D. Cutter and
- Jae Young Choi
Genome Res. August 2010 20: 1103-1111; Published in Advance May 27, 2010, doi:10.1101/gr.104331.109
...a signature of more effective purifying selection in high-recombination regions of the genome. Finally, we identify an emerging contrast between widespread adaptive hitchhiking effects in species with large outcrossing populations (e.g., Drosophila ) versus pervasive background selection effects...
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