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Preferred analysis methods for Affymetrix GeneChips revealed by a wholly defined control dataset
Sung E Choe, Michael Boutros, Alan M Michelson, George M Church, Marc S Halfon
Genome Biol. 2005; 6(2): R16. Published online 2005 January 28. doi: 10.1186/gb-2005-6-2-r16
PMCID:
PMC551536
Abstract Full Text PDF–3.0M Supplementary Material

Is Cited by the Following 124 Articles in this Archive:

HIV Infection and Antiretroviral Therapy Have Divergent Effects on Mitochondria in Adipose Tissue
Caryn G. Morse, Joachim G. Voss, Goran Rakocevic, Mary McLaughlin, Carol L. Vinton, Charles Huber, Xiaojun Hu, Jun Yang, Da Wei Huang, Carolea Logun, Robert L. Danner, Zoila G. Rangel, Peter J. Munson, Jan M. Orenstein, Elisabeth J. Rushing, Richard A. Lempicki, Marinos C. Dalakas, Joseph A. Kovacs
J Infect Dis. 2012 June 15; 205(12): 1778–1787. Published online 2012 April 3. doi: 10.1093/infdis/jis101
PMCID:
PMC3357134
Free in PMC on 2013/06/15
Molecular mechanism underlying the regulatory specificity of a Drosophila homeodomain protein that specifies myoblast identity
Brian W. Busser, Leila Shokri, Savina A. Jaeger, Stephen S. Gisselbrecht, Aditi Singhania, Michael F. Berger, Bo Zhou, Martha L. Bulyk, Alan M. Michelson
Development. 2012 March 15; 139(6): 1164–1174. doi: 10.1242/dev.077362
PMCID:
PMC3283125
Abstract Full Text
The CXCR4/CXCR7/SDF-1 pathway contributes to the pathogenesis of Shiga toxin–associated hemolytic uremic syndrome in humans and mice
Tania N. Petruzziello-Pellegrini, Darren A. Yuen, Andrea V. Page, Sajedabanu Patel, Anna M. Soltyk, Charles C. Matouk, Dennis K. Wong, Paul J. Turgeon, Jason E. Fish, J.J. David Ho, Brent M. Steer, Vahid Khajoee, Jayesh Tigdi, Warren L. Lee, David G. Motto, Andrew Advani, Richard E. Gilbert, S. Ananth Karumanchi, Lisa A. Robinson, Phillip I. Tarr, W. Conrad Liles, James L. Brunton, Philip A. Marsden
J Clin Invest. 2012 February 1; 122(2): 759–776. Published online 2012 January 9. doi: 10.1172/JCI57313
PMCID:
PMC3266777
Abstract Full Text PDF–1.5M Supplementary Material
Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage
Michał J. Okoniewski, Anna Leśniewska, Alicja Szabelska, Joanna Zyprych-Walczak, Martin Ryan, Marco Wachtel, Tadeusz Morzy, Beat Schäfer, Ralph Schlapbach
Nucleic Acids Res. 2012 May; 40(9): e63. Published online 2011 December 29. doi: 10.1093/nar/gkr1249
PMCID:
PMC3351146
Abstract Full Text PDF–11M
Comparison of methods for identifying differentially expressed genes across multiple conditions from microarray data
Yuande Tan, Yin Liu
Bioinformation. 2011; 7(8): 400–404. Published online 2011 December 21.
PMCID:
PMC3280440
Abstract Full Text PDF–242K Supplementary Material
Hematopoietic defects in rps29 mutant zebrafish depend upon p53 activation
Alison M. Taylor, Jessica M. Humphries, Richard M. White, Ryan D. Murphey, Caroline E. Burns, Leonard I. Zon
Exp Hematol. Author manuscript; available in PMC 2012 September 1.
Published in final edited form as: Exp Hematol. 2012 March; 40(3): 228–237.e5. Published online 2011 November 25. doi: 10.1016/j.exphem.2011.11.007
PMCID:
PMC3310385
Free in PMC on 2012/09/01
Fully Moderated T-statistic for Small Sample Size Gene Expression Arrays
Lianbo Yu, Parul Gulati, Soledad Fernandez, Michael Pennell, Lawrence Kirschner, David Jarjoura
Stat Appl Genet Mol Biol. 2011 January 1; 10(1): Article 42. Published online 2011 September 15. doi: 10.2202/1544-6115.1701
PMCID:
PMC3192003
Free in PMC on 2012/09/15
In-Depth Temporal Transcriptome Profiling Reveals a Crucial Developmental Switch with Roles for RNA Processing and Organelle Metabolism That Are Essential for Germination in Arabidopsis
Reena Narsai, Simon R. Law, Chris Carrie, Lin Xu, James Whelan
Plant Physiol. 2011 November; 157(3): 1342–1362. Published online 2011 September 9. doi: 10.1104/pp.111.183129
PMCID:
PMC3252162
Abstract Full Text PDF–2.2M
The Cell-Adhesion Gene PVRL3 is Associated with Congenital Ocular Defects
Salil A. Lachke, Anne W. Higgins, Maiko Inagaki, Irfan Saadi, Qiongchao Xi, Michelle Long, Bradley J. Quade, Michael E. Talkowski, James F. Gusella, Atsuko Fujimoto, Michael L. Robinson, Ying Yang, Quynh T. Duong, Irit Shapira, Benny Motro, Jun Miyoshi, Yoshimi Takai, Cynthia C. Morton, Richard L. Maas
Hum Genet. Author manuscript; available in PMC 2013 February 1.
Published in final edited form as: Hum Genet. 2012 February; 131(2): 235–250. Published online 2011 July 17. doi: 10.1007/s00439-011-1064-z
PMCID:
PMC3279124
Free in PMC on 2013/02/01
A Systems Level, Functional Genomics Analysis of Chronic Epilepsy
Kellen D. Winden, Stanislav L. Karsten, Anatol Bragin, Lili C. Kudo, Lauren Gehman, Josephine Ruidera, Daniel H. Geschwind, Jerome Engel, Jr.
PLoS One. 2011; 6(6): e20763. Published online 2011 June 14. doi: 10.1371/journal.pone.0020763
PMCID:
PMC3114768
Abstract Full Text PDF–4.1M Supplementary Material
Kernel density weighted loess normalization improves the performance of detection within asymmetrical data
Wen-Ping Hsieh, Tzu-Ming Chu, Yu-Min Lin, Russell D Wolfinger
BMC Bioinformatics. 2011; 12: 222. Published online 2011 June 1. doi: 10.1186/1471-2105-12-222
PMCID:
PMC3118355
Abstract Full Text PDF–479K Supplementary Material
Sterile Protective Immunity to Malaria is Associated with a Panel of Novel P. falciparum Antigens
Angela Trieu, Matthew A. Kayala, Chad Burk, Douglas M. Molina, Daniel A. Freilich, Thomas L. Richie, Pierre Baldi, Philip L. Felgner, Denise L. Doolan
Mol Cell Proteomics. 2011 September; 10(9): M111.007948. Published online 2011 May 31. doi: 10.1074/mcp.M111.007948
PMCID:
PMC3186199
Free in PMC on 2012/09/01
Transcriptome response of high- and low-light-adapted Prochlorococcus strains to changing iron availability
Anne W Thompson, Katherine Huang, Mak A Saito, Sallie W Chisholm
ISME J. 2011 October; 5(10): 1580–1594. Published online 2011 May 12. doi: 10.1038/ismej.2011.49
PMCID:
PMC3176520
Free in PMC on 2012/10/01
Principal component analysis-based filtering improves detection for Affymetrix gene expression arrays
Jun Lu, Robnet T. Kerns, Shyamal D. Peddada, Pierre R. Bushel
Nucleic Acids Res. 2011 July; 39(13): e86. Published online 2011 April 27. doi: 10.1093/nar/gkr241
PMCID:
PMC3141272
Abstract Full Text PDF–4.0M Supplementary Material
A wholly defined Agilent microarray spike-in dataset
Qianqian Zhu, Jeffrey C. Miecznikowski, Marc S. Halfon
Bioinformatics. 2011 May 1; 27(9): 1284–1289. Published online 2011 March 16. doi: 10.1093/bioinformatics/btr135
PMCID:
PMC3109518
Abstract Full Text PDF–643K Supplementary Material
The impact of quantitative optimization of hybridization conditions on gene expression analysis
Peter Sykacek, David P Kreil, Lisa A Meadows, Richard P Auburn, Bettina Fischer, Steven Russell, Gos Micklem
BMC Bioinformatics. 2011; 12: 73. Published online 2011 March 14. doi: 10.1186/1471-2105-12-73
PMCID:
PMC3065421
Abstract Full Text PDF–544K
Integration of pre-normalized microarray data using quantile correction
Takashi Yoneya, Tatsuya Miyazawa
Bioinformation. 2011; 5(9): 382–385. Published online 2011 February 7.
PMCID:
PMC3044426
Abstract Full Text PDF–108K Supplementary Material
Biological assessment of robust noise models in microarray data analysis
A. Posekany, K. Felsenstein, P. Sykacek
Bioinformatics. 2011 March 15; 27(6): 807–814. Published online 2011 January 19. doi: 10.1093/bioinformatics/btr018
PMCID:
PMC3051324
Abstract Full Text PDF–377K
Exploring the use of internal and externalcontrols for assessing microarray technical performance
Katrice A Lippa, David L Duewer, Marc L Salit, Laurence Game, Helen C Causton
BMC Res Notes. 2010; 3: 349. Published online 2010 December 28. doi: 10.1186/1756-0500-3-349
PMCID:
PMC3020182
Abstract Full Text PDF–3.1M Supplementary Material
OPTIMIZING THE ANALYSIS OF HUMAN INTESTINAL MICROBIOTA WITH PHYLOGENETIC MICROARRAY
Laura Rigsbee, Richard Agans, Brent Foy, Oleg Paliy
FEMS Microbiol Ecol. Author manuscript; available in PMC 2012 February 1.
Published in final edited form as: FEMS Microbiol Ecol. 2011 February; 75(2): 332–342. Published online 2010 December 13. doi: 10.1111/j.1574-6941.2010.01009.x
PMCID:
PMC3077101
Abstract Full Text PDF–442K
A transcriptional map of the impact of endurance exercise training on skeletal muscle phenotype
Pernille Keller, Niels B. J. Vollaard, Thomas Gustafsson, Iain J. Gallagher, Carl Johan Sundberg, Tuomo Rankinen, Steven L. Britton, Claude Bouchard, Lauren G. Koch, James A. Timmons
J Appl Physiol. 2011 January; 110(1): 46–59. Published online 2010 October 7. doi: 10.1152/japplphysiol.00634.2010
PMCID:
PMC3253010
Abstract Full Text Supplementary Material
Modeling Oncogenic Signaling in Colon Tumors by Multidirectional Analyses of Microarray Data Directed for Maximization of Analytical Reliability
Magdalena Skrzypczak, Krzysztof Goryca, Tymon Rubel, Agnieszka Paziewska, Michal Mikula, Dorota Jarosz, Jacek Pachlewski, Janusz Oledzki, Jerzy Ostrowsk
PLoS One. 2010; 5(10): e13091. Published online 2010 October 1. doi: 10.1371/journal.pone.0013091
Correction in:
PLoS One. 2010; 5(12): 10.1371/annotation/8c585739-a354-4fc9-a7d0-d5ae26fa06ca.
PMCID:
PMC2948500
Abstract Full Text PDF–662K Supplementary Material Correction
Candidate gene prioritization by network analysis of differential expression using machine learning approaches
Daniela Nitsch, Joana P Gonçalves, Fabian Ojeda, Bart de Moor, Yves Moreau
BMC Bioinformatics. 2010; 11: 460. Published online 2010 September 14. doi: 10.1186/1471-2105-11-460
PMCID:
PMC2945940
Abstract Full Text PDF–551K Supplementary Material
Gene Expression Profiles in a Rabbit Model of Systemic Lupus Erythematosus Autoantibody Production
Geeta Rai, Satyajit Ray, Jacqueline Milton, Jun Yang, Ping Ren, Richard Lempicki, Rose G. Mage
J Immunol. Author manuscript; available in PMC 2011 October 1.
Published in final edited form as: J Immunol. 2010 October 1; 185(7): 4446–4456. Published online 2010 September 3. doi: 10.4049/jimmunol.1001254
PMCID:
PMC2949067
Abstract Full Text PDF–2.2M Supplementary Material
LTR: Linear Cross-Platform Integration of Microarray Data
Paul C. Boutros
Cancer Inform. 2010; 9: 197–208. Published online 2010 August 27.
PMCID:
PMC2935818
Abstract Full Text PDF–4.5M
Issues in bioinformatics benchmarking: the case study of multiple sequence alignment
Mohamed Radhouene Aniba, Olivier Poch, Julie D. Thompson
Nucleic Acids Res. 2010 November; 38(21): 7353–7363. Published online 2010 July 17. doi: 10.1093/nar/gkq625
PMCID:
PMC2995051
Abstract Full Text PDF–3.7M
TIF1γ controls erythroid cell fate by regulating transcription elongation
Xiaoying Bai, Jonghwan Kim, Zhongan Yang, Michael J. Jurynec, Thomas E. Akie, Joseph Lee, Jocelyn LeBlanc, Anna Sessa, Hong Jiang, Anthony DiBiase, Yi Zhou, David J. Grunwald, Shuo Lin, Alan B. Cantor, Stuart H. Orkin, Leonard I. Zon
Cell. Author manuscript; available in PMC 2011 April 8.
Published in final edited form as: Cell. 2010 July 9; 142(1): 133–143. doi: 10.1016/j.cell.2010.05.028
PMCID:
PMC3072682
Abstract Full Text PDF–2.7M Supplementary Material
Preferred analysis methods for Affymetrix GeneChips. II. An expanded, balanced, wholly-defined spike-in dataset
Qianqian Zhu, Jeffrey C Miecznikowski, Marc S Halfon
BMC Bioinformatics. 2010; 11: 285. Published online 2010 May 27. doi: 10.1186/1471-2105-11-285
PMCID:
PMC2897828
Abstract Full Text PDF–5.1M Supplementary Material
A comparison of probe-level and probeset models for small-sample gene expression data
John R Stevens, Jason L Bell, Kenneth I Aston, Kenneth L White
BMC Bioinformatics. 2010; 11: 281. Published online 2010 May 26. doi: 10.1186/1471-2105-11-281
PMCID:
PMC2901368
Abstract Full Text PDF–4.2M
Large Scale Immune Profiling of Infected Humans and Goats Reveals Differential Recognition of Brucella melitensis Antigens
Li Liang, Diana Leng, Chad Burk, Rie Nakajima-Sasaki, Matthew A. Kayala, Vidya L. Atluri, Jozelyn Pablo, Berkay Unal, Thomas A. Ficht, Eduardo Gotuzzo, Mayuko Saito, W. John W. Morrow, Xiaowu Liang, Pierre Baldi, Robert H. Gilman, Joseph M. Vinetz, Renée M. Tsolis, Philip L. Felgner
PLoS Negl Trop Dis. 2010 May; 4(5): e673. Published online 2010 May 4. doi: 10.1371/journal.pntd.0000673
PMCID:
PMC2864264
Abstract Full Text PDF–1.1M
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