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Research: Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster genome
- Harsh G. Shukla,
- Mahul Chakraborty,
- and J.J. Emerson
Genome Res. September 2025 35: 2023-2040; Published in Advance July 16, 2025, doi:10.1101/gr.280728.125
...Genetic variation in recalcitrant repetitive regions of the Drosophila melanogaster Harsh G. Shukla1,2, Mahul Chakraborty3 and J.J. Emerson1,4 1Department of Ecology and Evolutionary Biology, University of California Irvine, Irvine, California 92697, USA; 2Graduate Program in Mathematical...
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Resource: The Release 6 reference sequence of the Drosophila melanogaster genome
- Roger A. Hoskins,
- Joseph W. Carlson,
- Kenneth H. Wan,
- Soo Park,
- Ivonne Mendez,
- Samuel E. Galle,
- Benjamin W. Booth,
- Barret D. Pfeiffer,
- Reed A. George,
- Robert Svirskas,
- Martin Krzywinski,
- Jacqueline Schein,
- Maria Carmela Accardo,
- Elisabetta Damia,
- Giovanni Messina,
- María Méndez-Lago,
- Beatriz de Pablos,
- Olga V. Demakova,
- Evgeniya N. Andreyeva,
- Lidiya V. Boldyreva,
- Marco Marra,
- A. Bernardo Carvalho,
- Patrizio Dimitri,
- Alfredo Villasante,
- Igor F. Zhimulev,
- Gerald M. Rubin,
- Gary H. Karpen,
- and Susan E. Celniker
Genome Res. March 2015 25: 445-458; Published in Advance January 14, 2015, doi:10.1101/gr.185579.114
...Resource The Release 6 reference sequence of the Drosophila melanogaster Roger A. Hoskins,1 Joseph W. Carlson,1,10 Kenneth H. Wan,1 Soo Park,1 Ivonne Mendez,1 Samuel E. Galle,1 Benjamin W. Booth,1 Barret D. Pfeiffer,2 Reed A. George,2 Robert Svirskas,2 Martin Krzywinski,3 Jacqueline Schein,3 Maria...
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Research: Deep sequencing of natural and experimental populations of Drosophila melanogaster reveals biases in the spectrum of new mutations
- Zoe June Assaf,
- Susanne Tilk,
- Jane Park,
- Mark L. Siegal,
- and Dmitri A. Petrov
Genome Res. December 2017 27: 1988-2000; Published in Advance October 27, 2017, doi:10.1101/gr.219956.116
...and allowing new mutations to accrue in the . The second, rare genetic variation from natural populations allows the study of mutation because extremely rare polymorphisms are relatively unaffected by the filter of natural selection. We use both methods in Drosophila melanogaster, first generating our own...
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Research: Systems genetics of the Drosophila metabolome
- Shanshan Zhou,
- Fabio Morgante,
- Matthew S. Geisz,
- Junwu Ma,
- Robert R.H. Anholt,
- and Trudy F.C. Mackay
Genome Res. March 2020 30: 392-405; Published in Advance November 6, 2019, doi:10.1101/gr.243030.118
..., metabolites, and complex phenotypes can be evaluated on the same genotypes. Here, we focused on the metabolome, which represents the most proximal link between genetic variation and organismal phenotype, and quantified metabolite levels in 40 lines of the Drosophila melanogaster Genetic Reference Panel. We...
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Method: Large-scale identification of chemically induced mutations in Drosophila melanogaster
- Nele A. Haelterman,
- Lichun Jiang,
- Yumei Li,
- Vafa Bayat,
- Hector Sandoval,
- Berrak Ugur,
- Kai Li Tan,
- Ke Zhang,
- Danqing Bei,
- Bo Xiong,
- Wu-Lin Charng,
- Theodore Busby,
- Adeel Jawaid,
- Gabriela David,
- Manish Jaiswal,
- Koen J.T. Venken,
- Shinya Yamamoto,
- Rui Chen,
- and Hugo J. Bellen
Genome Res. October 2014 24: 1707-1718; Published in Advance September 25, 2014, doi:10.1101/gr.174615.114
...Large-scale identification of chemically induced mutations in Drosophila melanogaster Nele A. Haelterman 1 , Lichun Jiang 2 , 3 , Yumei Li 2 , 3 , Vafa Bayat 1 , 4 , Hector Sandoval 2 , Berrak Ugur 1...
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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
...Natural variation in genome architecture among 205 Drosophila melanogaster Genetic Reference Panel lines Wen Huang 1 , 10 , Andreas Massouras 2 , 3 , 10 , Yutaka Inoue 4 , Jason Peiffer 1 , Miquel Ràmia 5 , Aaron M. Tarone 6...
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Research: Transposon expression in the Drosophila brain is driven by neighboring genes and diversifies the neural transcriptome
- Christoph D. Treiber and
- Scott Waddell
Genome Res. November 2020 30: 1559-1569; Published in Advance September 24, 2020, doi:10.1101/gr.259200.119
....Single-cell read alignmentsThe Drosophila melanogaster reference release 6.25 was used for all sequence alignments (Hoskins et al. 2015). Transposon reference sequences were from Repbase (Jurka 2000; Kaminker et al. 2002). Repetitive sequences in the Drosophila reference were masked using RepeatMasker (Smit et al...
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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
...on DNA variability in the tomato genus. Genetics 158: 1725–1735. Begun DJ, Aquadro CF. 1992. Levels of naturally-occurring DNA polymorphism correlate with recombination rates in Drosophila melanogaster. Nature 356: 519–520. Begun DJ, Holloway AK, Stevens K, Hillier LW, Poh YP, HahnMW, Nista PM, Jones CD...
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Research: Critical roles of long noncoding RNAs in Drosophila spermatogenesis
- Kejia Wen,
- Lijuan Yang,
- Tuanlin Xiong,
- Chao Di,
- Danhui Ma,
- Menghua Wu,
- Zhaoyu Xue,
- Xuedi Zhang,
- Li Long,
- Weimin Zhang,
- Jiaying Zhang,
- Xiaolin Bi,
- Junbiao Dai,
- Qiangfeng Zhang,
- Zhi John Lu,
- and Guanjun Gao
Genome Res. September 2016 26: 1233-1244; Published in Advance August 11, 2016, doi:10.1101/gr.199547.115
...Critical roles of long noncoding RNAs in Drosophila spermatogenesis Kejia Wen 1 , 6 , Lijuan Yang 1 , 2 , 6 , Tuanlin Xiong 1 , 6 , Chao Di 1 , Danhui Ma 1 , Menghua Wu 1 , Zhaoyu Xue 1 , Xuedi Zhang 1...
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Method: Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans
- Wei-Jen Chung,
- Phaedra Agius,
- Jakub O. Westholm,
- Michael Chen,
- Katsutomo Okamura,
- Nicolas Robine,
- Christina S. Leslie,
- and Eric C. Lai
Genome Res. February 2011 21: 286-300; Published in Advance December 22, 2010, doi:10.1101/gr.113050.110
...Computational and experimental identification of mirtrons in Drosophila melanogaster and Caenorhabditis elegans Wei-Jen Chung 1 , 3 , 4 , Phaedra Agius 2 , 3 , Jakub O. Westholm 1 , Michael Chen 1 , Katsutomo Okamura 1...
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