My NCBISign In
Assessing the impact of comparative genomic sequence data on the functional annotation of the Drosophila genome
Casey M Bergman, Barret D Pfeiffer, Diego E Rincón-Limas, Roger A Hoskins, Andreas Gnirke, Chris J Mungall, Adrienne M Wang, Brent Kronmiller, Joanne Pacleb, Soo Park, Mark Stapleton, Kenneth Wan, Reed A George, Pieter J de Jong, Juan Botas, Gerald M Rubin, Susan E Celniker
Genome Biol. 2002; 3(12): research0086.1–86.2. Published online 2002 December 30. doi: 10.1186/gb-2002-3-12-research0086
PMCID:
PMC151188
Abstract Full Text PDF–505K Supplementary Material

Is Cited by the Following 39 Articles in this Archive:

Rate of Amino Acid Substitution Is Influenced by the Degree and Conservation of Male-Biased Transcription Over 50 Myr of Drosophila Evolution
Sonja Grath, John Parsch
Genome Biol Evol. 2012; 4(3): 346–359. Published online 2012 February 8. doi: 10.1093/gbe/evs012
PMCID:
PMC3318448
Abstract Full Text PDF–654K
Formation of Regulatory Modules by Local Sequence Duplication
Armita Nourmohammad, Michael Lässig
PLoS Comput Biol. 2011 October; 7(10): e1002167. Published online 2011 October 6. doi: 10.1371/journal.pcbi.1002167
PMCID:
PMC3188502
Abstract Full Text PDF–412K Supplementary Material
High resolution mapping of Twist to DNA in Drosophila embryos: Efficient functional analysis and evolutionary conservation
Anil Ozdemir, Katherine I. Fisher-Aylor, Shirley Pepke, Manoj Samanta, Leslie Dunipace, Kenneth McCue, Lucy Zeng, Nobuo Ogawa, Barbara J. Wold, Angelike Stathopoulos
Genome Res. 2011 April; 21(4): 566–577. doi: 10.1101/gr.104018.109
PMCID:
PMC3065704
Abstract Full Text PDF–1.7M
The Evolution of tRNA Genes in Drosophila
Hubert H. Rogers, Casey M. Bergman, Sam Griffiths-Jones
Genome Biol Evol. 2010; 2: 467–477. Published online 2010 June 23. doi: 10.1093/gbe/evq034
PMCID:
PMC2997554
Abstract Full Text PDF–535K
The Transposon Galileo Generates Natural Chromosomal Inversions in Drosophila by Ectopic Recombination
Alejandra Delprat, Bàrbara Negre, Marta Puig, Alfredo Ruiz
PLoS One. 2009; 4(11): e7883. Published online 2009 November 18. doi: 10.1371/journal.pone.0007883
PMCID:
PMC2775673
Abstract Full Text PDF–714K Supplementary Material
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, Peter F. Stadler
Genome Res. 2009 July; 19(7): 1289–1300. doi: 10.1101/gr.090050.108
PMCID:
PMC2704441
Abstract Full Text PDF–1.2M
Big Genomes Facilitate the Comparative Identification of Regulatory Elements
Brant K. Peterson, Emily E. Hare, Venky N. Iyer, Steven Storage, Laura Conner, Daniel R. Papaj, Rick Kurashima, Eric Jang, Michael B. Eisen
PLoS ONE. 2009; 4(3): e4688. Published online 2009 March 4. doi: 10.1371/journal.pone.0004688
PMCID:
PMC2650094
Abstract Full Text PDF–1.4M Supplementary Material
Complex organizational structure of the genome revealed by genome-wide analysis of single and alternative promoters in Drosophila melanogaster
Qianqian Zhu, Marc S Halfon
BMC Genomics. 2009; 10: 9. Published online 2009 January 7. doi: 10.1186/1471-2164-10-9
PMCID:
PMC2631479
Abstract Full Text PDF–1.7M Supplementary Material
A Regulatory Code for Neuron-Specific Odor Receptor Expression
Anandasankar Ray, Wynand van der Goes van Naters, John R Carlson
PLoS Biol. 2008 May; 6(5): e125. Published online 2008 May 27. doi: 10.1371/journal.pbio.0060125
PMCID:
PMC2430909
Abstract Full Text PDF–969K Supplementary Material
Performance and Scalability of Discriminative Metrics for Comparative Gene Identification in 12 Drosophila Genomes
Michael F. Lin, Ameya N. Deoras, Matthew D. Rasmussen, Manolis Kellis
PLoS Comput Biol. 2008 April; 4(4): e1000067. Published online 2008 April 18. doi: 10.1371/journal.pcbi.1000067
PMCID:
PMC2291194
Abstract Full Text PDF–523K Supplementary Material
Evolutionary rate analyses of orthologs and paralogs from 12 Drosophila genomes
Andreas Heger, Chris P. Ponting
Genome Res. 2007 December; 17(12): 1837–1849. doi: 10.1101/gr.6249707
PMCID:
PMC2099592
Abstract Full Text PDF–935K
Discovery of functional elements in 12 Drosophila genomes using evolutionary signatures
Alexander Stark, Michael F. Lin, Pouya Kheradpour, Jakob S. Pedersen, Leopold Parts, Joseph W. Carlson, Madeline A. Crosby, Matthew D. Rasmussen, Sushmita Roy, Ameya N. Deoras, J. Graham Ruby, Julius Brennecke, Harvard FlyBase curators, Berkeley Drosophila Genome Project, Emily Hodges, Angie S. Hinrichs, Anat Caspi, Benedict Paten, Seung-Won Park, Mira V. Han, Morgan L. Maeder, Benjamin J. Polansky, Bryanne E. Robson, Stein Aerts, Jacques van Helden, Bassem Hassan, Donald G. Gilbert, Deborah A. Eastman, Michael Rice, Michael Weir, Matthew W. Hahn, Yongkyu Park, Colin N. Dewey, Lior Pachter, W. James Kent, David Haussler, Eric C. Lai, David P. Bartel, Gregory J. Hannon, Thomas C. Kaufman, Michael B. Eisen, Andrew G. Clark, Douglas Smith, Susan E. Celniker, William M. Gelbart, Manolis Kellis
Nature. Author manuscript; available in PMC 2008 November 8.
Published in final edited form as: Nature. 2007 November 8; 450(7167): 219–232. doi: 10.1038/nature06340
PMCID:
PMC2474711
Abstract Full Text PDF–3.7M Supplementary Material
Phylogenetic Footprinting Analysis in the Upstream Regulatory Regions of the Drosophila Enhancer of split Genes
Morgan L. Maeder, Benjamin J. Polansky, Bryanne E. Robson, Deborah A. Eastman
Genetics. 2007 November; 177(3): 1377–1394. doi: 10.1534/genetics.107.070425
PMCID:
PMC2147979
Abstract Full Text PDF–2.0M
Identification of novel regulatory factor X (RFX) target genes by comparative genomics in Drosophila species
Anne Laurençon, Raphaëlle Dubruille, Evgeni Efimenko, Guillaume Grenier, Ryan Bissett, Elisabeth Cortier, Vivien Rolland, Peter Swoboda, Bénédicte Durand
Genome Biol. 2007; 8(9): R195. Published online 2007 September 17. doi: 10.1186/gb-2007-8-9-r195
PMCID:
PMC2375033
Abstract Full Text PDF–2.0M Supplementary Material
Extensive parallelism in protein evolution
Georgii A Bazykin, Fyodor A Kondrashov, Michael Brudno, Alexander Poliakov, Inna Dubchak, Alexey S Kondrashov
Biol Direct. 2007; 2: 20. Published online 2007 August 16. doi: 10.1186/1745-6150-2-20
PMCID:
PMC2020468
Abstract Full Text PDF–422K
Large-scale analysis of transcriptional cis-regulatory modules reveals both common features and distinct subclasses
Long Li, Qianqian Zhu, Xin He, Saurabh Sinha, Marc S Halfon
Genome Biol. 2007; 8(6): R101. Published online 2007 June 5. doi: 10.1186/gb-2007-8-6-r101
PMCID:
PMC2394749
Abstract Full Text PDF–1.1M Supplementary Material
Mechanisms of odor receptor gene choice in Drosophila
Anandasankar Ray, Wynand van der Goes van Naters, Takashi Shiraiwa, John R. Carlson
Neuron. Author manuscript; available in PMC 2008 February 1.
Published in final edited form as: Neuron. 2007 February 1; 53(3): 353–369. doi: 10.1016/j.neuron.2006.12.010
PMCID:
PMC1986798
Abstract Full Text PDF–5.0M Supplementary Material
Fine scale structural variants distinguish the genomes of Drosophila melanogaster and D. pseudoobscura
Stuart J Macdonald, Anthony D Long
Genome Biol. 2006; 7(7): R67. Published online 2006 July 27. doi: 10.1186/gb-2006-7-7-r67
PMCID:
PMC1779558
Abstract Full Text PDF–376K Supplementary Material
Evolution of two alanine glyoxylate aminotransferases in mosquito
Qian Han, Seong Ryul Kim, Haizhen Ding, Jianyong Li
Biochem J. 2006 August 1; 397(Pt 3): 473–481. Prepublished online 2006 May 9. Published online 2006 July 13. doi: 10.1042/BJ20060469
PMCID:
PMC1533304
Abstract Full Text PDF–831K
Ubiquitous selective constraints in the Drosophila genome revealed by a genome-wide interspecies comparison
Daniel L. Halligan, Peter D. Keightley
Genome Res. 2006 July; 16(7): 875–884. doi: 10.1101/gr.5022906
PMCID:
PMC1484454
Abstract Full Text PDF–514K
Interaction of Heterochromatin Protein 2 with HP1 defines a novel HP1 binding domain
Gena E. Stephens, Elizabeth E. Slawson, Carolyn A. Craig, Sarah C. R. Elgin
Biochemistry. Author manuscript; available in PMC 2008 September 12.
Published in final edited form as: Biochemistry. 2005 October 11; 44(40): 13394–13403. doi: 10.1021/bi051006+
PMCID:
PMC2534139
Abstract Full Text PDF–585K
Evolutionarily conserved elements in vertebrate, insect, worm, and yeast genomes
Adam Siepel, Gill Bejerano, Jakob S. Pedersen, Angie S. Hinrichs, Minmei Hou, Kate Rosenbloom, Hiram Clawson, John Spieth, LaDeana W. Hillier, Stephen Richards, George M. Weinstock, Richard K. Wilson, Richard A. Gibbs, W. James Kent, Webb Miller, David Haussler
Genome Res. 2005 August; 15(8): 1034–1050. doi: 10.1101/gr.3715005
PMCID:
PMC1182216
Abstract Full Text PDF–1.0M
Conserved genomic organisation of Group B Sox genes in insects.
Carol McKimmie, Gertrud Woerfel, Steven Russell
BMC Genet. 2005; 6: 26. Published online 2005 May 19. doi: 10.1186/1471-2156-6-26
PMCID:
PMC1166547
Abstract Full Text PDF–3.2M
Whole-Genome Analysis Reveals a Strong Positional Bias of Conserved dMyc-Dependent E-Boxes
Toby Hulf, Paola Bellosta, Michael Furrer, Dominik Steiger, David Svensson, Andrew Barbour, Peter Gallant
Mol Cell Biol. 2005 May; 25(9): 3401–3410. doi: 10.1128/MCB.25.9.3401-3410.2005
PMCID:
PMC1084277
Abstract Full Text PDF–362K Supplementary Material
Conservation of regulatory sequences and gene expression patterns in the disintegrating Drosophila Hox gene complex
Bárbara Negre, Sònia Casillas, Magali Suzanne, Ernesto Sánchez-Herrero, Michael Akam, Michael Nefedov, Antonio Barbadilla, Pieter de Jong, Alfredo Ruiz
Genome Res. 2005 May; 15(5): 692–700. doi: 10.1101/gr.3468605
PMCID:
PMC1088297
Abstract Full Text PDF–920K
Whole genome shotgun sequencing of Brassica oleracea and its application to gene discovery and annotation in Arabidopsis
Mulu Ayele, Brian J. Haas, Nikhil Kumar, Hank Wu, Yongli Xiao, Susan Van Aken, Teresa R. Utterback, Jennifer R. Wortman, Owen R. White, Christopher D. Town
Genome Res. 2005 April; 15(4): 487–495. doi: 10.1101/gr.3176505
PMCID:
PMC1074363
Abstract Full Text PDF–588K
Comparison of the oxidative phosphorylation (OXPHOS) nuclear genes in the genomes of Drosophila melanogaster, Drosophila pseudoobscura and Anopheles gambiae
Gaetano Tripoli, Domenica D'Elia, Paolo Barsanti, Corrado Caggese
Genome Biol. 2005; 6(2): R11. Published online 2005 January 31. doi: 10.1186/gb-2005-6-2-r11
PMCID:
PMC551531
Abstract Full Text PDF–334K Supplementary Material
A Model of the Statistical Power of Comparative Genome Sequence Analysis
Sean R Eddy
PLoS Biol. 2005 January; 3(1): e10. Published online 2005 January 4. doi: 10.1371/journal.pbio.0030010
PMCID:
PMC539325
Abstract Full Text PDF–264K
The latest buzz in comparative genomics
Rob J Kulathinal, Daniel L Hartl
Genome Biol. 2005; 6(1): 201. Published online 2005 January 4. doi: 10.1186/gb-2005-6-1-201
PMCID:
PMC549071
Abstract Full Text PDF–160K
Computational identification of developmental enhancers: conservation and function of transcription factor binding-site clusters in Drosophila melanogaster and Drosophila pseudoobscura
Benjamin P Berman, Barret D Pfeiffer, Todd R Laverty, Steven L Salzberg, Gerald M Rubin, Michael B Eisen, Susan E Celniker
Genome Biol. 2004; 5(9): R61. Published online 2004 August 20. doi: 10.1186/gb-2004-5-9-r61
PMCID:
PMC522868
Abstract Full Text PDF–1.2M Supplementary Material
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