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FlyMine: an integrated database for Drosophila and Anopheles genomics
Rachel Lyne, Richard Smith, Kim Rutherford, Matthew Wakeling, Andrew Varley, Francois Guillier, Hilde Janssens, Wenyan Ji, Peter Mclaren, Philip North, Debashis Rana, Tom Riley, Julie Sullivan, Xavier Watkins, Mark Woodbridge, Kathryn Lilley, Steve Russell, Michael Ashburner, Kenji Mizuguchi, Gos Micklem
Genome Biol. 2007; 8(7): R129. Published online 2007 July 5. doi: 10.1186/gb-2007-8-7-r129
PMCID:
PMC2323218
Abstract Full Text PDF–894K
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 Is Cited by the Following 49 Articles in this Archive:
Transcriptome Profiling of Sexual Maturation and Mating in the Mediterranean Fruit Fly, Ceratitis capitata
Ludvik M. Gomulski, George Dimopoulos, Zhiyong Xi, Francesca Scolari, Paolo Gabrieli, Paolo Siciliano, Anthony R. Clarke, Anna R. Malacrida, Giuliano Gasperi
PLoS One. 2012; 7(1): e30857. Published online 2012 January 27. doi: 10.1371/journal.pone.0030857
PMCID:
PMC3267753
Abstract Full Text PDF–307K Supplementary Material
Tramtrack Is Genetically Upstream of Genes Controlling Tracheal Tube Size in Drosophila
Barbara Rotstein, David Molnar, Boris Adryan, Marta Llimargas
PLoS One. 2011; 6(12): e28985. Published online 2011 December 22. doi: 10.1371/journal.pone.0028985
PMCID:
PMC3245245
Abstract Full Text PDF–901K Supplementary Material
MitoMiner: a data warehouse for mitochondrial proteomics data
Anthony C. Smith, James A. Blackshaw, Alan J. Robinson
Nucleic Acids Res. 2012 January; 40(D1): D1160–D1167. Published online 2011 November 24. doi: 10.1093/nar/gkr1101
PMCID:
PMC3245170
Abstract Full Text PDF–4.5M
Saccharomyces Genome Database: the genomics resource of budding yeast
J. Michael Cherry, Eurie L. Hong, Craig Amundsen, Rama Balakrishnan, Gail Binkley, Esther T. Chan, Karen R. Christie, Maria C. Costanzo, Selina S. Dwight, Stacia R. Engel, Dianna G. Fisk, Jodi E. Hirschman, Benjamin C. Hitz, Kalpana Karra, Cynthia J. Krieger, Stuart R. Miyasato, Rob S. Nash, Julie Park, Marek S. Skrzypek, Matt Simison, Shuai Weng, Edith D. Wong
Nucleic Acids Res. 2012 January; 40(D1): D700–D705. Published online 2011 November 21. doi: 10.1093/nar/gkr1029
PMCID:
PMC3245034
Abstract Full Text PDF–103K
FlyRNAi.org—the database of the Drosophila RNAi screening center: 2012 update
Ian T. Flockhart, Matthew Booker, Yanhui Hu, Benjamin McElvany, Quentin Gilly, Bernard Mathey-Prevot, Norbert Perrimon, Stephanie E. Mohr
Nucleic Acids Res. 2012 January; 40(D1): D715–D719. Published online 2011 November 8. doi: 10.1093/nar/gkr953
PMCID:
PMC3245182
Abstract Full Text PDF–1.4M
Drosophila Duplication Hotspots Are Associated with Late-Replicating Regions of the Genome
Margarida Cardoso-Moreira, J. J. Emerson, Andrew G. Clark, Manyuan Long
PLoS Genet. 2011 November; 7(11): e1002340. Published online 2011 November 3. doi: 10.1371/journal.pgen.1002340
PMCID:
PMC3207856
Abstract Full Text PDF–355K Supplementary Material
pubmed2ensembl: A Resource for Mining the Biological Literature on Genes
Joachim Baran, Martin Gerner, Maximilian Haeussler, Goran Nenadic, Casey M. Bergman
PLoS One. 2011; 6(9): e24716. Published online 2011 September 29. doi: 10.1371/journal.pone.0024716
PMCID:
PMC3183000
Abstract Full Text PDF–857K Supplementary Material
Somatic sex-specific transcriptome differences in Drosophila revealed by whole transcriptome sequencing
Peter L Chang, Joseph P Dunham, Sergey V Nuzhdin, Michelle N Arbeitman
BMC Genomics. 2011; 12: 364. Published online 2011 July 14. doi: 10.1186/1471-2164-12-364
PMCID:
PMC3152543
Abstract Full Text PDF–4.5M Supplementary Material
The strategies WDK: a graphical search interface and web development kit for functional genomics databases
Steve Fischer, Cristina Aurrecoechea, Brian P. Brunk, Xin Gao, Omar S. Harb, Eileen T. Kraemer, Cary Pennington, Charles Treatman, Jessica C. Kissinger, David S. Roos, Christian J. Stoeckert
Database (Oxford) 2011; 2011: bar027. Published online 2011 June 24. doi: 10.1093/database/bar027
PMCID:
PMC3122067
Abstract Full Text PDF–1.2M
Genome-wide dFOXO targets and topology of the transcriptomic response to stress and insulin signalling
Nazif Alic, T Daniel Andrews, Maria E Giannakou, Irene Papatheodorou, Cathy Slack, Matthew P Hoddinott, Helena M Cochemé, Eugene F Schuster, Janet M Thornton, Linda Partridge
Mol Syst Biol. 2011; 7: 502. Published online 2011 June 21. doi: 10.1038/msb.2011.36
PMCID:
PMC3159968
Abstract Full Text PDF–830K Supplementary Material
A comprehensive gene expression atlas of sex- and tissue-specificity in the malaria vector, Anopheles gambiae
Dean A Baker, Tony Nolan, Bettina Fischer, Alex Pinder, Andrea Crisanti, Steven Russell
BMC Genomics. 2011; 12: 296. Published online 2011 June 7. doi: 10.1186/1471-2164-12-296
PMCID:
PMC3129592
Abstract Full Text PDF–732K Supplementary Material
An analysis of single amino acid repeats as use case for application specific background models
Paweł P Łabaj, Peter Sykacek, David P Kreil
BMC Bioinformatics. 2011; 12: 173. Published online 2011 May 19. doi: 10.1186/1471-2105-12-173
PMCID:
PMC3124433
Abstract Full Text PDF–318K Supplementary Material
Integrating diverse databases into an unified analysis framework: a Galaxy approach
Daniel Blankenberg, Nathan Coraor, Gregory Von Kuster, James Taylor, Anton Nekrutenko
Database (Oxford) 2011; 2011: bar011. Published online 2011 April 29. doi: 10.1093/database/bar011
PMCID:
PMC3092608
Abstract Full Text PDF–1.0M
In Vivo Analysis of Proteomes and Interactomes Using Parallel Affinity Capture (iPAC) Coupled to Mass Spectrometry
Johanna S. Rees, Nick Lowe, Irina M. Armean, John Roote, Glynnis Johnson, Emma Drummond, Helen Spriggs, Edward Ryder, Steven Russell, Daniel St Johnston, Kathryn S. Lilley
Mol Cell Proteomics. 2011 June; 10(6): M110.002386. Published online 2011 March 29. doi: 10.1074/mcp.M110.002386
PMCID:
PMC3108830
Abstract Full Text
LabKey Server: An open source platform for scientific data integration, analysis and collaboration
Elizabeth K Nelson, Britt Piehler, Josh Eckels, Adam Rauch, Matthew Bellew, Peter Hussey, Sarah Ramsay, Cory Nathe, Karl Lum, Kevin Krouse, David Stearns, Brian Connolly, Tom Skillman, Mark Igra
BMC Bioinformatics. 2011; 12: 71. Published online 2011 March 9. doi: 10.1186/1471-2105-12-71
PMCID:
PMC3062597
Abstract Full Text PDF–3.0M
TargetMine, an Integrated Data Warehouse for Candidate Gene Prioritisation and Target Discovery
Yi-An Chen, Lokesh P. Tripathi, Kenji Mizuguchi
PLoS One. 2011; 6(3): e17844. Published online 2011 March 8. doi: 10.1371/journal.pone.0017844
PMCID:
PMC3050930
Abstract Full Text PDF–1.1M Supplementary Material
RGD: A comparative genomics platform
Mary Shimoyama, Jennifer R. Smith, Tom Hayman, Stan Laulederkind, Tim Lowry, Rajni Nigam, Victoria Petri, Shur-Jen Wang, Melinda Dwinell, Howard Jacob, RGD Team
Hum Genomics. Author manuscript; available in PMC 2011 November 22.
Published in final edited form as: Hum Genomics. 2011 January; 5(2): 124–129.
PMCID:
PMC3222152
Abstract Full Text PDF–116K
The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of a button
Morris A Swertz, Martijn Dijkstra, Tomasz Adamusiak, Joeri K van der Velde, Alexandros Kanterakis, Erik T Roos, Joris Lops, Gudmundur A Thorisson, Danny Arends, George Byelas, Juha Muilu, Anthony J Brookes, Engbert O de Brock, Ritsert C Jansen, Helen Parkinson
BMC Bioinformatics. 2010; 11(Suppl 12): S12. Published online 2010 December 21. doi: 10.1186/1471-2105-11-S12-S12
PMCID:
PMC3040526
Abstract Full Text PDF–1.8M
Neighbourhood Continuity Is Not Required for Correct Testis Gene Expression in Drosophila
Lisa A. Meadows, Yuk Sang Chan, John Roote, Steven Russell
PLoS Biol. 2010 November; 8(11): e1000552. Published online 2010 November 30. doi: 10.1371/journal.pbio.1000552
PMCID:
PMC2994658
Abstract Full Text PDF–990K Supplementary Material
FlyFactorSurvey: a database of Drosophila transcription factor binding specificities determined using the bacterial one-hybrid system
Lihua Julie Zhu, Ryan G. Christensen, Majid Kazemian, Christopher J. Hull, Metewo Selase Enuameh, Matthew D. Basciotta, Jessie A. Brasefield, Cong Zhu, Yuna Asriyan, David S. Lapointe, Saurabh Sinha, Scot A. Wolfe, Michael H. Brodsky
Nucleic Acids Res. 2011 January; 39(Database issue): D111–D117. Published online 2010 November 19. doi: 10.1093/nar/gkq858
PMCID:
PMC3013762
Abstract Full Text PDF–5.1M
Analyses of Nuclearly Encoded Mitochondrial Genes Suggest Gene Duplication as a Mechanism for Resolving Intralocus Sexually Antagonistic Conflict in Drosophila
Miguel Gallach, Chitra Chandrasekaran, Esther Betrán
Genome Biol Evol. 2010; 2: 835–850. Published online 2010 October 29. doi: 10.1093/gbe/evq069
PMCID:
PMC2995371
Abstract Full Text PDF–328K
The GMOD Drupal Bioinformatic Server Framework
Alexie Papanicolaou, David G. Heckel
Bioinformatics. 2010 December 15; 26(24): 3119–3124. Published online 2010 October 22. doi: 10.1093/bioinformatics/btq599
PMCID:
PMC2995126
Abstract Full Text PDF–197K
Dynamic, mating-induced gene expression changes in female head and brain tissues of Drosophila melanogaster
Justin E Dalton, Tanvi S Kacheria, Simon RV Knott, Matthew S Lebo, Allison Nishitani, Laura E Sanders, Emma J Stirling, Ari Winbush, Michelle N Arbeitman
BMC Genomics. 2010; 11: 541. Published online 2010 October 6. doi: 10.1186/1471-2164-11-541
PMCID:
PMC3091690
Abstract Full Text PDF–395K Supplementary Material
Dynamic isomiR regulation in Drosophila development
Selene L. Fernandez-Valverde, Ryan J. Taft, John S. Mattick
RNA. 2010 October; 16(10): 1881–1888. doi: 10.1261/rna.2379610
PMCID:
PMC2941097
Abstract Full Text PDF–1016K
Genomic repertoires of DNA-binding transcription factors across the tree of life
Varodom Charoensawan, Derek Wilson, Sarah A. Teichmann
Nucleic Acids Res. 2010 November; 38(21): 7364–7377. Published online 2010 July 30. doi: 10.1093/nar/gkq617
PMCID:
PMC2995046
Abstract Full Text PDF–2.4M Supplementary Material
BSQA: integrated text mining using entity relation semantics extracted from biological literature of insects
Xin He, Yanen Li, Radhika Khetani, Barry Sanders, Yue Lu, Xu Ling, ChengXiang Zhai, Bruce Schatz
Nucleic Acids Res. 2010 July 1; 38(Web Server issue): W175–W181. Published online 2010 June 21. doi: 10.1093/nar/gkq544
PMCID:
PMC2896161
Abstract Full Text PDF–6.1M
Germline-dependent gene expression in distant non-gonadal somatic tissues of Drosophila
Michael J Parisi, Vaijayanti Gupta, David Sturgill, James T Warren, Jean-Marc Jallon, John H Malone, Yu Zhang, Lawrence I Gilbert, Brian Oliver
BMC Genomics. 2010; 11: 346. Published online 2010 June 1. doi: 10.1186/1471-2164-11-346
PMCID:
PMC2887422
Abstract Full Text PDF–1.0M Supplementary Material
The developmental expression dynamics of Drosophila melanogaster transcription factors
Boris Adryan, Sarah A Teichmann
Genome Biol. 2010; 11(4): R40. Published online 2010 April 12. doi: 10.1186/gb-2010-11-4-r40
PMCID:
PMC2884543
Abstract Full Text PDF–1.3M Supplementary Material
A doublecortin containing microtubule-associated protein is implicated in mechanotransduction in Drosophila sensory cilia
S. Bechstedt, J.T. Albert, D.P. Kreil, T. Müller-Reichert, M.C. Göpfert, J. Howard
Nat Commun. 2010 April 12; 1(1): 1–11. doi: 10.1038/ncomms1007
PMCID:
PMC2892299
Abstract Full Text PDF–995K Supplementary Material
Evolution of the Sequence Ontology terms and relationships
Christopher J. Mungall, Colin Batchelor, Karen Eilbeck
J Biomed Inform. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: J Biomed Inform. 2011 February; 44(1): 87–93. Published online 2010 March 10. doi: 10.1016/j.jbi.2010.03.002
PMCID:
PMC3052763
Abstract Full Text PDF–259K
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