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Within the fold: assessing differential expression measures and reproducibility in microarray assays
Ivana V Yang, Emily Chen, Jeremy P Hasseman, Wei Liang, Bryan C Frank, Shuibang Wang, Vasily Sharov, Alexander I Saeed, Joseph White, Jerry Li, Norman H Lee, Timothy J Yeatman, John Quackenbush
Genome Biol. 2002; 3(11): research0062.1–research0062.12. Published online 2002 October 24.
PMCID:
PMC133446
Abstract Full Text PDF–4.1M Supplementary Material
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 Is Cited by the Following 52 Articles in this Archive:
Transcriptome Analysis of Aedes aegypti Transgenic Mosquitoes with Altered Immunity
Zhen Zou, Jayme Souza-Neto, Zhiyong Xi, Vladimir Kokoza, Sang Woon Shin, George Dimopoulos, Alexander Raikhel
PLoS Pathog. 2011 November; 7(11): e1002394. Published online 2011 November 17. doi: 10.1371/journal.ppat.1002394
PMCID:
PMC3219725
Abstract Full Text PDF–844K Supplementary Material
The Campylobacter jejuni Transcriptional Regulator Cj1556 Plays a Role in the Oxidative and Aerobic Stress Response and Is Important for Bacterial Survival In Vivo
Ozan Gundogdu, Dominic C. Mills, Abdi Elmi, Melissa J. Martin, Brendan W. Wren, Nick Dorrell
J Bacteriol. 2011 August; 193(16): 4238–4249. doi: 10.1128/JB.05189-11
PMCID:
PMC3147681
Abstract Full Text PDF–902K
Introducing Knowledge into Differential Expression Analysis
Ewa Szczurek, Przemysław Biecek, Jerzy Tiuryn, Martin Vingron
J Comput Biol. 2010 August; 17(8): 953–967. doi: 10.1089/cmb.2010.0034
PMCID:
PMC3122906
Abstract Full Text PDF–424K
Dengue Virus Inhibits Immune Responses in Aedes aegypti Cells
Shuzhen Sim, George Dimopoulos
PLoS One. 2010; 5(5): e10678. Published online 2010 May 18. doi: 10.1371/journal.pone.0010678
PMCID:
PMC2872661
Abstract Full Text PDF–512K Supplementary Material
Meta-analysis of archived DNA microarrays identifies genes regulated by hypoxia and involved in a metastatic phenotype in cancer cells
Michael Pierre, Benoît DeHertogh, Anthoula Gaigneaux, Bertrand DeMeulder, Fabrice Berger, Eric Bareke, Carine Michiels, Eric Depiereux
BMC Cancer. 2010; 10: 176. Published online 2010 April 30. doi: 10.1186/1471-2407-10-176
PMCID:
PMC2880990
Abstract Full Text PDF–1.0M Supplementary Material
Transcriptional targets of Drosophila JAK/STAT pathway signalling as effectors of haematopoietic tumour formation
Samira Bina, Victoria M Wright, Katherine H Fisher, Marta Milo, Martin P Zeidler
EMBO Rep. 2010 March; 11(3): 201–207. Published online 2010 February 19. doi: 10.1038/embor.2010.1
PMCID:
PMC2838687
Abstract Full Text PDF–766K Supplementary Material
An efficient algorithm for the stochastic simulation of the hybridization of DNA to microarrays
Erdem Arslan, Ian J Laurenzi
BMC Bioinformatics. 2009; 10: 411. Published online 2009 December 10. doi: 10.1186/1471-2105-10-411
PMCID:
PMC2805644
Abstract Full Text PDF–1.5M Supplementary Material
An evolutionary conserved function of the JAK-STAT pathway in anti-dengue defense
Jayme A. Souza-Neto, Shuzhen Sim, George Dimopoulos
Proc Natl Acad Sci U S A. 2009 October 20; 106(42): 17841–17846. Published online 2009 October 1. doi: 10.1073/pnas.0905006106
PMCID:
PMC2764916
Abstract Full Text PDF–1.1M Supplementary Material
Integrative modeling of transcriptional regulation in response to antirheumatic therapy
Michael Hecker, Robert Hermann Goertsches, Robby Engelmann, Hans-Juergen Thiesen, Reinhard Guthke
BMC Bioinformatics. 2009; 10: 262. Published online 2009 August 24. doi: 10.1186/1471-2105-10-262
PMCID:
PMC2757030
Abstract Full Text PDF–1.5M Supplementary Material
Implication of the Mosquito Midgut Microbiota in the Defense against Malaria Parasites
Yuemei Dong, Fabio Manfredini, George Dimopoulos
PLoS Pathog. 2009 May; 5(5): e1000423. Published online 2009 May 8. doi: 10.1371/journal.ppat.1000423
PMCID:
PMC2673032
Abstract Full Text PDF–546K Supplementary Material
Caspar Controls Resistance to Plasmodium falciparum in Diverse Anopheline Species
Lindsey S. Garver, Yuemei Dong, George Dimopoulos
PLoS Pathog. 2009 March; 5(3): e1000335. Published online 2009 March 13. doi: 10.1371/journal.ppat.1000335
PMCID:
PMC2647737
Abstract Full Text PDF–481K Supplementary Material
Ca2+/calmodulin-dependent kinase II triggers cell membrane injury by inducing complement factor B gene expression in the mouse heart
Madhu V. Singh, Ann Kapoun, Linda Higgins, William Kutschke, Joshua M. Thurman, Rong Zhang, Minati Singh, Jinying Yang, Xiaoqun Guan, John S. Lowe, Robert M. Weiss, Kathy Zimmermann, Fiona E. Yull, Timothy S. Blackwell, Peter J. Mohler, Mark E. Anderson
J Clin Invest. 2009 April 1; 119(4): 986–996. Published online 2009 March 9. doi: 10.1172/JCI35814
PMCID:
PMC2662543
Abstract Full Text PDF–1.5M Supplementary Material
Experimental identification of microRNA-140 targets by silencing and overexpressing miR-140
Francisco Esteban Nicolas, Helio Pais, Frank Schwach, Morten Lindow, Sakari Kauppinen, Vincent Moulton, Tamas Dalmay
RNA. 2008 December; 14(12): 2513–2520. doi: 10.1261/rna.1221108
PMCID:
PMC2590970
Abstract Full Text PDF–313K
Statistical issues in the analysis of DNA Copy Number Variations
Nathan E. Wineinger, Richard E. Kennedy, Stephen W. Erickson, Mary K. Wojczynski, Carl E. Bruder, Hemant K. Tiwari
Int J Comput Biol Drug Des. Author manuscript; available in PMC 2009 September 21.
Published in final edited form as: Int J Comput Biol Drug Des. 2008 January 1; 1(4): 368–395. doi: 10.1504/IJCBDD.2008.022208
PMCID:
PMC2747762
Abstract Full Text PDF–436K
Transcriptome Analysis of Sorbic Acid-Stressed Bacillus subtilis Reveals a Nutrient Limitation Response and Indicates Plasma Membrane Remodeling
Alex Ter Beek, Bart J. F. Keijser, Andre Boorsma, Anna Zakrzewska, Rick Orij, Gertien J. Smits, Stanley Brul
J Bacteriol. 2008 March; 190(5): 1751–1761. Published online 2007 December 21. doi: 10.1128/JB.01516-07
PMCID:
PMC2258692
Abstract Full Text PDF–361K Supplementary Material
Continuous exposure to Plasmodium results in decreased susceptibility and transcriptomic divergence of the Anopheles gambiae immune system
Ruth Aguilar, Suchismita Das, Yuemei Dong, George Dimopoulos
BMC Genomics. 2007; 8: 451. Published online 2007 December 5. doi: 10.1186/1471-2164-8-451
PMCID:
PMC2234432
Abstract Full Text PDF–411K Supplementary Material
Application of a correlation correction factor in a microarray cross-platform reproducibility study
Kellie J Archer, Catherine I Dumur, G Scott Taylor, Michael D Chaplin, Anthony Guiseppi-Elie, Geraldine Grant, Andrea Ferreira-Gonzalez, Carleton T Garrett
BMC Bioinformatics. 2007; 8: 447. Published online 2007 November 15. doi: 10.1186/1471-2105-8-447
PMCID:
PMC2211756
Abstract Full Text PDF–443K
Genes involved in TGFβ1-driven epithelial-mesenchymal transition of renal epithelial cells are topologically related in the human interactome map
Stefano Campanaro, Simone Picelli, Rossella Torregrossa, Laura Colluto, Monica Ceol, Dorella Del Prete, Angela D'Angelo, Giorgio Valle, Franca Anglani
BMC Genomics. 2007; 8: 383. Published online 2007 October 22. doi: 10.1186/1471-2164-8-383
PMCID:
PMC2174485
Abstract Full Text PDF–2.5M Supplementary Material
Experimental Approach for Assessing the Outcome Accuracy of Antibody Microarray Experiments
Qiang Gu, Thamil Mani Sivanandam, Jessica Haymore
J Proteome Res. Author manuscript; available in PMC 2008 April 10.
Published in final edited form as: J Proteome Res. 2007 November; 6(11): 4210–4217. Published online 2007 October 2. doi: 10.1021/pr0703932
PMCID:
PMC2291551
Abstract Full Text PDF–1.5M Supplementary Material
Normalization of two-channel microarrays accounting for experimental design and intensity-dependent relationships
Alan R Dabney, John D Storey
Genome Biol. 2007; 8(3): R44. Published online 2007 March 28. doi: 10.1186/gb-2007-8-3-r44
PMCID:
PMC1868928
Abstract Full Text PDF–1.3M Supplementary Material
"NeuroStem Chip": a novel highly specialized tool to study neural differentiation pathways in human stem cells
Sergey V Anisimov, Nicolaj S Christophersen, Ana S Correia, Jia-Yi Li, Patrik Brundin
BMC Genomics. 2007; 8: 46. Published online 2007 February 8. doi: 10.1186/1471-2164-8-46
PMCID:
PMC1802744
Abstract Full Text PDF–1.0M Supplementary Material
Evaluating different methods of microarray data normalization
André Fujita, João Ricardo Sato, Leonardo de Oliveira Rodrigues, Carlos Eduardo Ferreira, Mari Cleide Sogayar
BMC Bioinformatics. 2006; 7: 469. Published online 2006 October 23. doi: 10.1186/1471-2105-7-469
PMCID:
PMC1636075
Abstract Full Text PDF–497K
Novel design and controls for focused DNA microarrays: applications in quality assurance/control and normalization for the Health Canada ToxArray™
Carole L Yauk, Andrew Williams, Sherri Boucher, Lynn M Berndt, Gu Zhou, Jenny L Zheng, Andrea Rowan-Carroll, Hongyan Dong, Iain B Lambert, George R Douglas, Craig L Parfett
BMC Genomics. 2006; 7: 266. Published online 2006 October 19. doi: 10.1186/1471-2164-7-266
PMCID:
PMC1635050
Abstract Full Text PDF–567K
Gene expression profiling of Spodoptera frugiperda hemocytes and fat body using cDNA microarray reveals polydnavirus-associated variations in lepidopteran host genes transcript levels
M Barat-Houari, F Hilliou, F-X Jousset, L Sofer, E Deleury, J Rocher, M Ravallec, L Galibert, P Delobel, R Feyereisen, P Fournier, A-N Volkoff
BMC Genomics. 2006; 7: 160. Published online 2006 June 21. doi: 10.1186/1471-2164-7-160
PMCID:
PMC1559612
Abstract Full Text PDF–1.3M Supplementary Material
Persisters: a distinct physiological state of E. coli
Devang Shah, Zhigang Zhang, Arkady Khodursky, Niilo Kaldalu, Kristi Kurg, Kim Lewis
BMC Microbiol. 2006; 6: 53. Published online 2006 June 12. doi: 10.1186/1471-2180-6-53
PMCID:
PMC1557402
Abstract Full Text PDF–612K Supplementary Material
Anopheles gambiae Immune Responses to Human and Rodent Plasmodium Parasite Species
Yuemei Dong, Ruth Aguilar, Zhiyong Xi, Emma Warr, Emmanuel Mongin, George Dimopoulos
PLoS Pathog. 2006 June; 2(6): e52. Published online 2006 June 9. doi: 10.1371/journal.ppat.0020052
PMCID:
PMC1475661
Abstract Full Text PDF–500K Supplementary Material
Empirical array quality weights in the analysis of microarray data
Matthew E Ritchie, Dileepa Diyagama, Jody Neilson, Ryan van Laar, Alexander Dobrovic, Andrew Holloway, Gordon K Smyth
BMC Bioinformatics. 2006; 7: 261. Published online 2006 May 19. doi: 10.1186/1471-2105-7-261
PMCID:
PMC1564422
Abstract Full Text PDF–518K
Gene expression profiling of lymphoblastoid cell lines from monozygotic twins discordant in severity of autism reveals differential regulation of neurologically relevant genes
Valerie W Hu, Bryan C Frank, Shannon Heine, Norman H Lee, John Quackenbush
BMC Genomics. 2006; 7: 118. Published online 2006 May 18. doi: 10.1186/1471-2164-7-118
PMCID:
PMC1525191
Abstract Full Text PDF–1.3M Supplementary Material
A universal reference sample derived from clone vector for improved detection of differential gene expression
Rishi L Khan, Gregory E Gonye, Guang Gao, James S Schwaber
BMC Genomics. 2006; 7: 109. Published online 2006 May 5. doi: 10.1186/1471-2164-7-109
PMCID:
PMC1475850
Abstract Full Text PDF–719K
CARMA: A platform for analyzing microarray datasets that incorporate replicate measures
Kevin A Greer, Matthew R McReynolds, Heddwen L Brooks, James B Hoying
BMC Bioinformatics. 2006; 7: 149. Published online 2006 March 17. doi: 10.1186/1471-2105-7-149
PMCID:
PMC1450302
Abstract Full Text PDF–609K Supplementary Material
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