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Statistical tests for differential expression in cDNA microarray experiments
Xiangqin Cui, Gary A Churchill
Genome Biol. 2003; 4(4): 210. Published online 2003 March 17. doi: 10.1186/gb-2003-4-4-210
PMCID:
PMC154570
Abstract Full Text PDF–2.7M

Is Cited by the Following 116 Articles in this Archive:

Hnrpab regulates neural development and neuron cell survival after glutamate stimulation
John R. Sinnamon, Catherine B. Waddell, Sara Nik, Emily I. Chen, Kevin Czaplinski
RNA. 2012 April; 18(4): 704–719. doi: 10.1261/rna.030742.111
PMCID:
PMC3312558
Free in PMC on 2013/04/01
Annotator: Post-processing Software for generating function-based signatures from quantitative mass spectrometry
Juliesta E. Sylvester, Tyler S. Bray, Stephen J. Kron
J Proteome Res. Author manuscript; available in PMC 2013 March 2.
Published in final edited form as: J Proteome Res. 2012 March 2; 11(3): 1521–1536. Published online 2012 February 3. doi: 10.1021/pr200460s
PMCID:
PMC3292622
Free in PMC on 2013/03/02
CD34 marks angiogenic tip cells in human vascular endothelial cell cultures
Martin J. Siemerink, Ingeborg Klaassen, Ilse M. C. Vogels, Arjan W. Griffioen, Cornelis J. F. Van Noorden, Reinier O. Schlingemann
Angiogenesis. 2012 March; 15(1): 151–163. Published online 2012 January 17. doi: 10.1007/s10456-011-9251-z
PMCID:
PMC3274677
Abstract Full Text PDF–901K Supplementary Material
A searchable cross-platform gene expression database reveals connections between drug treatments and disease
Gareth Williams
BMC Genomics. 2012; 13: 12. Published online 2012 January 10. doi: 10.1186/1471-2164-13-12
PMCID:
PMC3305579
Abstract Full Text PDF–1.4M Supplementary Material
Analysis of the toxicogenomic effects of exposure to persistent organic pollutants (POPs) in Slovakian girls: correlations between gene expression and disease risk
Partha Sarathi Mitra, Somiranjan Ghosh, Shizhu Zang, Dean Sonneborn, Irva Hertz-Picciotto, Tomas Trnovec, Lubica Palkovicova, Eva Sovcikova, Svetlana Ghimbovschi, Eric Hoffman, Sisir K. Dutta
Environ Int. Author manuscript; available in PMC 2013 February 1.
Published in final edited form as: Environ Int. 2012 February; 39(1): 188–199. Published online 2011 December 8. doi: 10.1016/j.envint.2011.09.003
PMCID:
PMC3259908
Free in PMC on 2013/02/01
Bayesian non-negative factor analysis for reconstructing transcription factor mediated regulatory networks
Jia Meng, Jianqiu (Michelle) Zhang, Yidong Chen, Yufei Huang
Proteome Sci. 2011; 9(Suppl 1): S9. Published online 2011 October 14. doi: 10.1186/1477-5956-9-S1-S9
PMCID:
PMC3289087
Abstract Full Text PDF–2.2M
Protist-Type Lysozymes of the Nematode Caenorhabditis elegans Contribute to Resistance against Pathogenic Bacillus thuringiensis
Claudia Boehnisch, Daniel Wong, Michael Habig, Kerstin Isermann, Nicolaas K. Michiels, Thomas Roeder, Robin C. May, Hinrich Schulenburg
PLoS One. 2011; 6(9): e24619. Published online 2011 September 8. doi: 10.1371/journal.pone.0024619
PMCID:
PMC3169628
Abstract Full Text PDF–892K Supplementary Material
Datgan, a reusable software system for facile interrogation and visualization of complex transcription profiling data
Gareth R Howell, David O Walton, Benjamin L King, Richard T Libby, Simon WM John
BMC Genomics. 2011; 12: 429. Published online 2011 August 24. doi: 10.1186/1471-2164-12-429
PMCID:
PMC3171729
Abstract Full Text PDF–6.9M
Reporting FDR analogous confidence intervals for the log fold change of differentially expressed genes
Klaus Jung, Tim Friede, Tim Beißbarth
BMC Bioinformatics. 2011; 12: 288. Published online 2011 July 15. doi: 10.1186/1471-2105-12-288
PMCID:
PMC3154206
Abstract Full Text PDF–340K Supplementary Material
Microbial laboratory evolution in the era of genome-scale science
Tom M Conrad, Nathan E Lewis, Bernhard Ø Palsson
Mol Syst Biol. 2011; 7: 509. Published online 2011 July 5. doi: 10.1038/msb.2011.42
PMCID:
PMC3159978
Abstract Full Text PDF–731K
Meta-Analysis and Functional Validation of Nutritional Requirements of Solventogenic Clostridia Growing under Butanol Stress Conditions and Coutilization of d-Glucose and d-Xylose
Humberto Heluane, Matthew R. Evans, Sue F. Dagher, José M. Bruno-Bárcena
Appl Environ Microbiol. 2011 July; 77(13): 4473–4485. doi: 10.1128/AEM.00116-11
PMCID:
PMC3127714
Abstract Full Text PDF–1006K
A heuristic method for discovering biomarker candidates based on rough set theory
Yasuo Kudo, Yoshifumi Okada
Bioinformation. 2011; 6(5): 200–203. Published online 2011 May 26.
PMCID:
PMC3124797
Abstract Full Text PDF–162K Supplementary Material
Systems-Scale Analysis Reveals Pathways Involved in Cellular Response to Methamphetamine
Lijie Sun, Hong-Mei Li, Manfredo J. Seufferheld, Kent R. Walters, Jr., Venu M. Margam, Amber Jannasch, Naomi Diaz, Catherine P. Riley, Weilin Sun, Yueh-Feng Li, William M. Muir, Jun Xie, Jing Wu, Fan Zhang, Jake Y. Chen, Eric L. Barker, Jiri Adamec, Barry R. Pittendrigh
PLoS One. 2011; 6(4): e18215. Published online 2011 April 20. doi: 10.1371/journal.pone.0018215
PMCID:
PMC3080363
Abstract Full Text PDF–515K Supplementary Material
Effects of Streptolysin O On Extracellular Matrix Gene Expression in Normal Human Epidermal Keratinocytes
Stephen W. Mamber, Volkan Gurel, Ryan G. Rhodes, John McMichael
Dose Response. 2011; 9(4): 554–578. Published online 2011 March 14. doi: 10.2203/dose-response.10-050.Mamber
PMCID:
PMC3315172
Abstract Full Text PDF–1.1M
Assessing the Biological Significance of Gene Expression Signatures and Co-Expression Modules by Studying Their Network Properties
Pablo Minguez, Joaquin Dopazo
PLoS One. 2011; 6(3): e17474. Published online 2011 March 7. doi: 10.1371/journal.pone.0017474
PMCID:
PMC3049771
Abstract Full Text PDF–625K Supplementary Material
MMP1 bimodal expression and differential response to inflammatory mediators is linked to promoter polymorphisms
Muna Affara, Benjamin J Dunmore, Deborah A Sanders, Nicola Johnson, Cristin G Print, D Stephen Charnock-Jones
BMC Genomics. 2011; 12: 43. Published online 2011 January 19. doi: 10.1186/1471-2164-12-43
PMCID:
PMC3040839
Abstract Full Text PDF–1.5M Supplementary Material
Early response mechanisms of perennial ryegrass (Lolium perenne) to phosphorus deficiency
Stephen L. Byrne, Alexandre Foito, Pete E. Hedley, Jenny A. Morris, Derek Stewart, Susanne Barth
Ann Bot. 2011 February; 107(2): 243–254. Published online 2010 December 9. doi: 10.1093/aob/mcq234
PMCID:
PMC3025732
Abstract Full Text PDF–263K Supplementary Material
Suppression of statin effectiveness by copper and zinc in yeast and human cells
Douglas M. Fowler, Sara J. Cooper, Jason J. Stephany, Natalie Hendon, Sven Nelson, Stanley Fields
Mol Biosyst. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: Mol Biosyst. 2011 February; 7(2): 533–544. Published online 2010 November 17. doi: 10.1039/c0mb00166j
PMCID:
PMC3138400
Abstract Full Text PDF–1.8M Supplementary Material
Systematical Detection of Significant Genes in Microarray Data by Incorporating Gene Interaction Relationship in Biological Systems
Junwei Wang, Meiwen Jia, Liping Zhu, Zengjin Yuan, Peng Li, Chang Chang, Jian Luo, Mingyao Liu, Tieliu Shi
PLoS One. 2010; 5(10): e13721. Published online 2010 October 29. doi: 10.1371/journal.pone.0013721
PMCID:
PMC2966410
Abstract Full Text PDF–851K Supplementary Material
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
Alexander A Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M Sarwal, Atul J Butte
BMC Bioinformatics. 2010; 11(Suppl 9): S6. Published online 2010 October 28. doi: 10.1186/1471-2105-11-S9-S6
PMCID:
PMC2967747
Abstract Full Text PDF–471K
Comparison of multiplex meta analysis techniques for understanding the acute rejection of solid organ transplants
Alexander A Morgan, Purvesh Khatri, Richard Hayden Jones, Minnie M Sarwal, Atul J Butte
BMC Bioinformatics. 2010; 11(Suppl 9): S6. Published online 2010 October 28. doi: 10.1186/1471-2105-11-S9-S6
PMCID:
PMC2967747
Abstract Full Text PDF–471K
Optimising experimental design for high-throughput phenotyping in mice: a case study
Natasha A. Karp, Lauren A. Baker, Anna-Karin B. Gerdin, Niels C. Adams, Ramiro Ramírez-Solis, Jacqueline K. White
Mamm Genome. 2010 October; 21(9-10): 467–476. Published online 2010 August 27. doi: 10.1007/s00335-010-9279-1
PMCID:
PMC2974211
Abstract Full Text PDF–345K Supplementary Material
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
Computing gene expression data with a knowledge-based gene clustering approach
Bruce A. Rosa, Sookyung Oh, Beronda L. Montgomery, Jin Chen, Wensheng Qin
Int J Biochem Mol Biol. 2010; 1(1): 51–68. Published online 2010 June 15.
PMCID:
PMC3180043
Abstract Full Text PDF–2.0M
Comparison of normalization methods for Illumina BeadChip HumanHT-12 v3
Ramona Schmid, Patrick Baum, Carina Ittrich, Katrin Fundel-Clemens, Wolfgang Huber, Benedikt Brors, Roland Eils, Andreas Weith, Detlev Mennerich, Karsten Quast
BMC Genomics. 2010; 11: 349. Published online 2010 June 2. doi: 10.1186/1471-2164-11-349
PMCID:
PMC3091625
Abstract Full Text PDF–3.1M Supplementary Material
Making Informed Choices about Microarray Data Analysis
Mark Reimers
PLoS Comput Biol. 2010 May; 6(5): e1000786. Published online 2010 May 27. doi: 10.1371/journal.pcbi.1000786
PMCID:
PMC2877726
Full Text PDF–428K Supplementary Material
PepC: proteomics software for identifying differentially expressed proteins based on spectral counting
N.L. Heinecke, B.S. Pratt, T. Vaisar, L. Becker
Bioinformatics. 2010 June 15; 26(12): 1574–1575. Published online 2010 April 22. doi: 10.1093/bioinformatics/btq171
PMCID:
PMC2881356
Abstract Full Text PDF–161K
Gene Profiling in Experimental Models of Eye Growth: Clues to Myopia Pathogenesis
Richard A. Stone, Tejvir S. Khurana
Vision Res. Author manuscript; available in PMC 2011 November 23.
Published in final edited form as: Vision Res. 2010 November 23; 50(23): 2322–2333. Published online 2010 April 2. doi: 10.1016/j.visres.2010.03.021
PMCID:
PMC2933412
Abstract Full Text PDF–566K
ProbFAST: Probabilistic Functional Analysis System Tool
Israel T Silva, Ricardo ZN Vêncio, Thiago YK Oliveira, Greice A Molfetta, Wilson A Silva, Jr
BMC Bioinformatics. 2010; 11: 161. Published online 2010 March 30. doi: 10.1186/1471-2105-11-161
PMCID:
PMC2868004
Abstract Full Text PDF–7.0M Supplementary Material
Differences in adherence and virulence gene expression between two outbreak strains of enterohaemorrhagic Escherichia coli O157 : H7
Galeb S. Abu-Ali, Lindsey M. Ouellette, Scott T. Henderson, Thomas S. Whittam, Shannon D. Manning
Microbiology. 2010 February; 156(Pt 2): 408–419. doi: 10.1099/mic.0.033126-0
PMCID:
PMC2890088
Abstract Full Text PDF–524K Supplementary Material
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