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Items: 19

1.
Paralog transcriptional differentiation in the D. melanogaster-specific gene family Sdic across populations and spermatogenesis stages
Bryan D. Clifton, Imtiyaz Hariyani, Ashlyn Kimura, Fangning Luo, Alvin Nguyen, José M. Ranz
Commun Biol. 2023; 6: 1069. Published online 2023 Oct 20. doi: 10.1038/s42003-023-05427-4
PMCID:
PMC10589255
AbstractArticlePDF–1.0M
2.
Understanding the Early Evolutionary Stages of a Tandem Drosophilamelanogaster-Specific Gene Family: A Structural and Functional Population Study
Bryan D Clifton, Jamie Jimenez, Ashlyn Kimura, Zeinab Chahine, Pablo Librado, Alejandro Sánchez-Gracia, Mashya Abbassi, Francisco Carranza, Carolus Chan, Marcella Marchetti, Wanting Zhang, Mijuan Shi, Christine Vu, Shudan Yeh, Laura Fanti, Xiao-Qin Xia, Julio Rozas, José M Ranz
Mol Biol Evol. 2020 Sep; 37(9): 2584–2600. Published online 2020 May 2. doi: 10.1093/molbev/msaa109
PMCID:
PMC7475035
AbstractArticlePDF–798K
3.
Rapid Functional and Sequence Differentiation of a Tandemly Repeated Species-Specific Multigene Family in Drosophila
Bryan D. Clifton, Pablo Librado, Shu-Dan Yeh, Edwin S. Solares, Daphne A. Real, Suvini U. Jayasekera, Wanting Zhang, Mijuan Shi, Ronni V. Park, Robert D. Magie, Hsiu-Ching Ma, Xiao-Qin Xia, Antonio Marco, Julio Rozas, José M. Ranz
Mol Biol Evol. 2017 Jan; 34(1): 51–65. Published online 2016 Oct 3. doi: 10.1093/molbev/msw212
PMCID:
PMC6404660
AbstractArticlePDF–1023K
4.
Transcription elongation rate has a tissue-specific impact on alternative cleavage and polyadenylation in Drosophila melanogaster
Xiaochuan Liu, Jaime Freitas, Dinghai Zheng, Marta S. Oliveira, Mainul Hoque, Torcato Martins, Telmo Henriques, Bin Tian, Alexandra Moreira
RNA. 2017 Dec; 23(12): 1807–1816. doi: 10.1261/rna.062661.117
PMCID:
PMC5689002
AbstractArticlePDF–4.0M
5.
Diverse Roles of Axonemal Dyneins in Drosophila Auditory Neuron Function and Mechanical Amplification in Hearing
Somdatta Karak, Julie S. Jacobs, Maike Kittelmann, Christian Spalthoff, Radoslaw Katana, Elena Sivan-Loukianova, Michael A. Schon, Maurice J. Kernan, Daniel F. Eberl, Martin C. Göpfert
Sci Rep. 2015; 5: 17085. Published online 2015 Nov 26. doi: 10.1038/srep17085
PMCID:
PMC4660584
AbstractArticlePDF–1.0M
6.
Gene Model Annotations for Drosophila melanogaster: The Rule-Benders
Madeline A. Crosby, L. Sian Gramates, Gilberto dos Santos, Beverley B. Matthews, Susan E. St. Pierre, Pinglei Zhou, Andrew J. Schroeder, Kathleen Falls, David B. Emmert, Susan M. Russo, William M. Gelbart, the FlyBase Consortium
G3 (Bethesda) 2015 Aug; 5(8): 1737–1749. Published online 2015 Jun 24. doi: 10.1534/g3.115.018937
PMCID:
PMC4528330
AbstractArticlePDF–2.2M
7.
Gene Model Annotations for Drosophila melanogaster: Impact of High-Throughput Data
Beverley B. Matthews, Gilberto dos Santos, Madeline A. Crosby, David B. Emmert, Susan E. St. Pierre, L. Sian Gramates, Pinglei Zhou, Andrew J. Schroeder, Kathleen Falls, Victor Strelets, Susan M. Russo, William M. Gelbart, the FlyBase Consortium
G3 (Bethesda) 2015 Aug; 5(8): 1721–1736. Published online 2015 Jun 24. doi: 10.1534/g3.115.018929
PMCID:
PMC4528329
AbstractArticlePDF–4.9M
8.
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, Susan E. Celniker
Genome Res. 2015 Mar; 25(3): 445–458. doi: 10.1101/gr.185579.114
PMCID:
PMC4352887
AbstractArticlePDF–1022K
9.
Phenotypic rescue of a Drosophila model of mitochondrial ANT1 disease
Suvi Vartiainen, Shanjun Chen, Jack George, Tea Tuomela, Kaisa R. Luoto, Kevin M. C. O’Dell, Howard T. Jacobs
Dis Model Mech. 2014 Jun; 7(6): 635–648. Published online 2014 May 8. doi: 10.1242/dmm.016527
PMCID:
PMC4036471
AbstractArticle
10.
Functional relevance of the newly evolved sperm dynein intermediate chain multigene family in Drosophila melanogaster males
Shu-Dan Yeh, Tiffanie Do, Mashya Abbassi, José M. Ranz
Commun Integr Biol. 2012 Sep 1; 5(5): 462–465. doi: 10.4161/cib.21136
PMCID:
PMC3502208
AbstractArticlePDF–505K
11.
The Many Landscapes of Recombination in Drosophila melanogaster
Josep M. Comeron, Ramesh Ratnappan, Samuel Bailin
PLoS Genet. 2012 Oct; 8(10): e1002905. Published online 2012 Oct 11. doi: 10.1371/journal.pgen.1002905
PMCID:
PMC3469467
AbstractArticlePDF–1.6M
12.
Functional evidence that a recently evolved Drosophila sperm-specific gene boosts sperm competition
Shu-Dan Yeh, Tiffanie Do, Carolus Chan, Adriana Cordova, Francisco Carranza, Eugene A. Yamamoto, Mashya Abbassi, Kania A. Gandasetiawan, Pablo Librado, Elisabetta Damia, Patrizio Dimitri, Julio Rozas, Daniel L. Hartl, John Roote, José M. Ranz
Proc Natl Acad Sci U S A. 2012 Feb 7; 109(6): 2043–2048. Published online 2012 Jan 23. doi: 10.1073/pnas.1121327109
PMCID:
PMC3277543
AbstractArticlePDF–458K
13.
Sequence Finishing and Mapping of Drosophila melanogaster Heterochromatin
Roger A. Hoskins, Joseph W. Carlson, Cameron Kennedy, David Acevedo, Martha Evans-Holm, Erwin Frise, Kenneth H. Wan, Soo Park, Maria Mendez-Lago, Fabrizio Rossi, Alfredo Villasante, Patrizio Dimitri, Gary H. Karpen, Susan E. Celniker
Science. Author manuscript; available in PMC 2010 Feb 19.
Published in final edited form as: Science. 2007 Jun 15; 316(5831): 1625–1628. doi: 10.1126/science.1139816
PMCID:
PMC2825053
AbstractArticlePDF–858K
14.
The Release 5.1 Annotation of Drosophila melanogaster Heterochromatin
Christopher D. Smith, ShengQiang Shu, Christopher J. Mungall, Gary H. Karpen
Science. Author manuscript; available in PMC 2010 Feb 10.
Published in final edited form as: Science. 2007 Jun 15; 316(5831): 1586. doi: 10.1126/science.1139815
Correction in:
volume 317 on page 1325
PMCID:
PMC2819280
AbstractArticlePDF–1.3M
15.
Combined Evidence Annotation of Transposable Elements in Genome Sequences
Hadi Quesneville, Casey M Bergman, Olivier Andrieu, Delphine Autard, Danielle Nouaud, Michael Ashburner, Dominique Anxolabehere
PLoS Comput Biol. 2005 Jul; 1(2): e22. Published online 2005 Jul 29. doi: 10.1371/journal.pcbi.0010022
PMCID:
PMC1185648
AbstractArticlePDF–273K
16.
Heterochromatic sequences in a Drosophila whole-genome shotgun assembly
Roger A Hoskins, Christopher D Smith, Joseph W Carlson, A Bernardo Carvalho, Aaron Halpern, Joshua S Kaminker, Cameron Kennedy, Chris J Mungall, Beth A Sullivan, Granger G Sutton, Jiro C Yasuhara, Barbara T Wakimoto, Eugene W Myers, Susan E Celniker, Gerald M Rubin, Gary H Karpen
Genome Biol. 2002; 3(12): research0085.1–85.16. Published online 2002 Dec 31. doi: 10.1186/gb-2002-3-12-research0085
PMCID:
PMC151187
AbstractArticlePDF–280K
17.
The transposable elements of the Drosophila melanogaster euchromatin: a genomics perspective
Joshua S Kaminker, Casey M Bergman, Brent Kronmiller, Joseph Carlson, Robert Svirskas, Sandeep Patel, Erwin Frise, David A Wheeler, Suzanna E Lewis, Gerald M Rubin, Michael Ashburner, Susan E Celniker
Genome Biol. 2002; 3(12): research0084.1–84.2. Published online 2002 Dec 23. doi: 10.1186/gb-2002-3-12-research0084
PMCID:
PMC151186
AbstractArticlePDF–330K
18.
Annotation of the Drosophila melanogaster euchromatic genome: a systematic review
Sima Misra, Madeline A Crosby, Christopher J Mungall, Beverley B Matthews, Kathryn S Campbell, Pavel Hradecky, Yanmei Huang, Joshua S Kaminker, Gillian H Millburn, Simon E Prochnik, Christopher D Smith, Jonathan L Tupy, Eleanor J Whitfield, Leyla Bayraktaroglu, Benjamin P Berman, Brian R Bettencourt, Susan E Celniker, Aubrey DNJ de Grey, Rachel A Drysdale, Nomi L Harris, John Richter, Susan Russo, Andrew J Schroeder, ShengQiang Shu, Mark Stapleton, Chihiro Yamada, Michael Ashburner, William M Gelbart, Gerald M Rubin, Suzanna E Lewis
Genome Biol. 2002; 3(12): research0083.1–83.22. Published online 2002 Dec 31. doi: 10.1186/gb-2002-3-12-research0083
PMCID:
PMC151185
AbstractArticlePDF–1.1M
19.
Finishing a whole-genome shotgun: Release 3 of the Drosophila melanogaster euchromatic genome sequence
Susan E Celniker, David A Wheeler, Brent Kronmiller, Joseph W Carlson, Aaron Halpern, Sandeep Patel, Mark Adams, Mark Champe, Shannon P Dugan, Erwin Frise, Ann Hodgson, Reed A George, Roger A Hoskins, Todd Laverty, Donna M Muzny, Catherine R Nelson, Joanne M Pacleb, Soo Park, Barret D Pfeiffer, Stephen Richards, Erica J Sodergren, Robert Svirskas, Paul E Tabor, Kenneth Wan, Mark Stapleton, Granger G Sutton, Craig Venter, George Weinstock, Steven E Scherer, Eugene W Myers, Richard A Gibbs, Gerald M Rubin
Genome Biol. 2002; 3(12): research0079.1–79.14. Published online 2002 Dec 23. doi: 10.1186/gb-2002-3-12-research0079
PMCID:
PMC151181
AbstractArticlePDF–171K

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