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Analysis of Variance for Gene Expression Microarray Data

To cite this article:
M. Kathleen Kerr, Mitchell Martin, and Gary A. Churchill. Journal of Computational Biology. December 2000, 7(6): 819-837. doi:10.1089/10665270050514954.

Published in Volume: 7 Issue 6: July 5, 2004

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Author information

M. Kathleen Kerr

The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609

Mitchell Martin

Genome and Information Sciences, Hoffmann-La Roche, Inc., Nutley, NJ

Gary A. Churchill

The Jackson Laboratory, 600 Main Street, Bar Harbor, ME 04609

ABSTRACT

Spotted cDNA microarrays are emerging as a powerful and cost-effective tool for large-scale analysis of gene expression. Microarrays can be used to measure the relative quantities of specific mRNAs in two or more tissue samples for thousands of genes simultaneously. While the power of this technology has been recognized, many open questions remain about appropriate analysis of microarray data. One question is how to make valid estimates of the relative expression for genes that are not biased by ancillary sources of variation. Recognizing that there is inherent "noise" in microarray data, how does one estimate the error variation associated with an estimated change in expression, i.e., how does one construct the error bars? We demonstrate that ANOVA methods can be used to normalize microarray data and provide estimates of changes in gene expression that are corrected for potential confounding effects. This approach establishes a framework for the general analysis and interpretation of microarray data.

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References

. May 2008: 222-236

Cross-Species Comparison of Human and Mouse Intestinal Polyps Reveals Conserved Mechanisms in Adenomatous Polyposis Coli (APC)-Driven Tumorigenesis

Claudia Gaspar, Joana Cardoso, Patrick Franken, Lia Molenaar, Hans Morreau, Gabriela Möslein, Julian Sampson, Judith M. Boer, Renée X. de Menezes, Riccardo Fodde

The American Journal of Pathology. May 2008, Vol. 172, No. 5: 1363-1380

A Comprehensive Analysis of the Combined Effects of High Light and High Temperature Stresses on Gene Expression in Sunflower

T. Hewezi, M. Leger, L. Gentzbittel

Annals of Botany. Apr 2008, Vol. 102, No. 1: 127-140

The transcriptomics of life-history trade-offs in whitefish species pairs ( Coregonus sp.)

J. ST-CYR, N. DEROME, L. BERNATCHEZ

Molecular Ecology. Apr 2008, Vol. 17, No. 7: 1850-1870

Global monitoring of autumn gene expression within and among phenotypically divergent populations of Sitka spruce (Picea sitchensis)

Jason A. Holliday, Steven G. Ralph, Richard White, Jörg Bohlmann, Sally N. Aitken

New Phytologist. Apr 2008, Vol. 178, No. 1: 103-122

Effect of p53 genotype on gene expression profiles in murine liver

Suzanne M. Morris, Gregory S. Akerman, Varsha G. Desai, Chen-an Tsai, William H. Tolleson, William B. Melchior, Chien-Ju Lin, James C. Fuscoe, Daniel A. Casciano, James J. Chen

Mutation Research/Fundamental and Molecular Mechanisms of Mutagenesis. Apr 2008, Vol. 640, No. 1-2: 54-73

Data Mining in Genomics

Jae K. Lee, Paul D. Williams, Sooyoung Cheon

Clinics in Laboratory Medicine. Mar 2008, Vol. 28, No. 1: 145-166

Gene expression profiling to identify markers associated with deregulated hTERT in HPV-transformed keratinocytes and cervical cancer

Jillian de Wilde, Saskia M. Wilting, Chris J.L.M. Meijer, Mark A. van de Wiel, Bauke Ylstra, Peter J.F. Snijders, Renske D.M. Steenbergen

International Journal of Cancer. Feb 2008, Vol. 122, No. 4: 877-888

Lifelong α-Tocopherol Supplementation Increases the Median Life Span of C57BL/6 Mice in the Cold but Has Only Minor Effects on Oxidative Damage

Colin Selman, Jane S. McLaren, Claus Mayer, Jackie S. Duncan, Andrew R. Collins, Garry G. Duthie, Paula Redman, John R. Speakman

Rejuvenation Research. Feb 2008, Vol. 11, No. 1: 83-96

Abstract | Full Text PDF | Reprints | Permissions

Plant simple sequence repeats: distribution, variation, and effects on gene expression

Michael Francki, Natalya Sharopova

Genome. Feb 2008, Vol. 51, No. 2: 79-90

A new class of mixture models for differential gene expression in DNA microarray data

Ming-Hui Chen, Joseph G. Ibrahim, Yueh-Yun Chi

Journal of Statistical Planning and Inference. Feb 2008, Vol. 138, No. 2: 387-404

Performance of Gene Selection and Classification Methods in a Microarray Setting: A Simulation Study

Suzy Van Sanden, Dan Lin, Tomasz Burzykowski

Communications in Statistics - Simulation and Computation. Feb 2008, Vol. 37, No. 2: 409-424

Differential response of the plant Medicago truncatula to its symbiont Sinorhizobium meliloti or an exopolysaccharide-deficient mutant

K. M. Jones, N. Sharopova, D. P. Lohar, J. Q. Zhang, K. A. VandenBosch, G. C. Walker

Proceedings of the National Academy of Sciences. Jan 2008, Vol. 105, No. 2: 704-709

Correlation network analysis for data integration and biomarker selection

Aram Adourian, Ezra Jennings, Raji Balasubramanian, Wade M. Hines, Doris Damian, Thomas N. Plasterer, Clary B. Clish, Paul Stroobant, Robert McBurney, Elwin R. Verheij, Ivana Bobeldijk, Jan van der Greef, Johan Lindberg, Kerstin Kenne, Ulf Andersson, Heike Hellmold, Kerstin Nilsson, Hugh Salter, Ina Schuppe-Koistinen

Molecular BioSystems. Jan 2008, Vol. 4, No. 3: 249

GlobalANCOVA: exploration and assessment of gene group effects

M. Hummel, R. Meister, U. Mansmann

Bioinformatics. Jan 2008, Vol. 24, No. 1: 78-85

Bayesian Mixture Model Analysis for Detecting Differentially Expressed Genes

Zhenyu Jia, Shizhong Xu

International Journal of Plant Genomics. Jan 2008, Vol. 2008: 1-12

Genetic consequences of interbreeding between farmed and wild Atlantic salmon: insights from the transcriptome

CHRISTIAN ROBERGE, ÉRIC NORMANDEAU, SIGURD EINUM, HELGA GUDERLEY, LOUIS BERNATCHEZ

Molecular Ecology. Jan 2008, Vol. 17, No. 1: 314-324

Bioinformatic Tools for Inferring Functional Information from Plant Microarray Data: Tools for the First Steps

Grier P. Page, Issa Coulibaly

International Journal of Plant Genomics. Jan 2008, Vol. 2008: 1-9

Challenges in DNA Microarray Studies from the Regulatory Perspective

Samir Lababidi

Journal of Biopharmaceutical Statistics. Jan 2008, Vol. 18, No. 1: 183-202

Overlapping gene expression profiles of model compounds provide opportunities for immunotoxicity screening

Kirsten A. Baken, Jeroen L.A. Pennings, Martijs J. Jonker, Mirjam M. Schaap, Annemieke de Vries, Harry van Steeg, Timo M. Breit, Henk van Loveren

Toxicology and Applied Pharmacology. Jan 2008, Vol. 226, No. 1: 46-59

Gene expression in endometrial cancer cells (Ishikawa) after short time high dose exposure to progesterone

Ruth H. Paulssen, Bjørn Moe, Halvor Grønaas, Anne Ørbo

Steroids. Jan 2008, Vol. 73, No. 1: 116-128

Validation of peptide epitope microarray experiments and extraction of quality data

T NAHTMAN, A JERNBERG, S MAHDAVIFAR, J ZERWECK, M SCHUTKOWSKI, M MAEURER, M REILLY

Journal of Immunological Methods. Dec 2007, Vol. 328, No. 1-2: 1-13

In pursuit of a super producer—alternative paths to high producing recombinant mammalian cells

G SETH, S CHARANIYA, K WLASCHIN, W HU

Current Opinion in Biotechnology. Dec 2007, Vol. 18, No. 6: 557-564

Biotechnology. Gene expression and microchips: Problems of the quantitative analysis

A. N. Sveshnikova, P. S. Ivanov

Russian Journal of General Chemistry. Nov 2007, Vol. 77, No. 11: 2071-2081

Regulation of Gene Expression in Rats With Heart Failure Treated With the Thyroid Hormone Analog 3,5-Diiodothyropropionic Acid (DITPA) and the Combination of DITPA and Captopril

Niranjan Maitra, Cynthia Adamson, Kevin Greer, Scott Klewer, James Hoying, Joseph J Bahl, Steven Goldman, Eugene Morkin

Journal of Cardiovascular Pharmacology. Nov 2007, Vol. 50, No. 5: 526-534

An investigation of two multivariate permutation methods for controlling the false discovery proportion

Edward L. Korn, Ming-Chung Li, Lisa M. McShane, Richard Simon

Statistics in Medicine. Oct 2007, Vol. 26, No. 24: 4428-4440

An Oligonucleotide Microarray Resource for Transcriptional Profiling of Bradyrhizobium japonicum

Woo-Suk Chang, William L. Franck, Eddie Cytryn, Sooyoung Jeong, Trupti Joshi, David W. Emerich, Michael J. Sadowsky, Dong Xu, Gary Stacey

Molecular Plant-Microbe Interactions. Oct 2007, Vol. 20, No. 10: 1298-1307

Integration of statistical inference methods and a novel control measure to improve sensitivity and specificity of data analysis in expression profiling studies

Shizhu Zang, Ruifang Guo, Liang Zhang, Youyong Lu

Journal of Biomedical Informatics. Oct 2007, Vol. 40, No. 5: 552-560

Sharp Simultaneous Confidence Intervals for the Means of Selected Populations with Application to Microarray Data Analysis

Jing Qiu, J. T. Gene Hwang

Biometrics. Sep 2007, Vol. 63, No. 3: 767-776

Estimating the False Discovery Rate Using Nonparametric Deconvolution

Mark A. van de Wiel, Kyung In Kim

Biometrics. Sep 2007, Vol. 63, No. 3: 806-815

Transcript abundance profiles reveal larger and more complex responses of grapevine to chilling compared to osmotic and salinity stress

Elizabeth A. R. Tattersall, Jérôme Grimplet, Laurent DeLuc, Matthew D. Wheatley, Delphine Vincent, Craig Osborne, Ali Ergül, Evan Lomen, Robert R. Blank, Karen A. Schlauch, John C. Cushman, Grant R. Cramer

Functional & Integrative Genomics. Aug 2007, Vol. 7, No. 4: 317-333

A global approach to identify differentially expressed genes in cDNA (two-color) microarray experiments

Y. Zhou, C. Cras-Meneur, M. Ohsugi, G. D. Stormo, M. Alan. Permutt

Bioinformatics. Aug 2007, Vol. 23, No. 16: 2073-2079

Systems level analysis of osteoclastogenesis reveals intrinsic and extrinsic regulatory interactions

Jennifer Kiesel, Cheryl Miller, Yousef Abu-Amer, Rajeev Aurora

Developmental Dynamics. Aug 2007, Vol. 236, No. 8: 2181-2197

Designs for two-colour microarray experiments

R. A. Bailey

Journal of the Royal Statistical Society: Series C (Applied Statistics). Aug 2007, Vol. 56, No. 4: 365-394

Transcriptional profiles of primary metabolism and signal transduction-related genes in response to water stress in field-grown sunflower genotypes using a thematic cDNA microarray

Jane Roche, Tarek Hewezi, Andrée Bouniols, Laurent Gentzbittel

Planta. Jul 2007, Vol. 226, No. 3: 601-617

CALIB: a Bioconductor package for estimating absolute expression levels from two-color microarray data

H. Zhao, K. Engelen, B. De Moor, K. Marchal

Bioinformatics. Jul 2007, Vol. 23, No. 13: 1700-1701

Analysis of Expression Data: An Overview

Anoop Grewal, Peter Lambert, Jordan Stockton

. Jul 2007

Molecular portrait of high productivity in recombinant NS0 cells

Gargi Seth, Robin J. Philp, Ally Lau, Kok Yee Jiun, Miranda Yap, Wei-Shou Hu

Biotechnology and Bioengineering. Jul 2007, Vol. 97, No. 4: 933-951

Wnt Pathway Anomalies in Developing Amygdalae of Turner Syndrome-like Mice

Adam S. Raefski, Benjamin R. Carone, Anupinder Kaur, Winfried Krueger, Michael J. O’Neill

Journal of Molecular Neuroscience. Jun 2007, Vol. 32, No. 2: 111-119

A Network of Genes Regulated by Light in Cyanobacteria

Rajeev Aurora, Yukako Hihara, Abhay K. Singh, Himadri B. Pakrasi

OMICS: A Journal of Integrative Biology. Jun 2007, Vol. 11, No. 2: 166-185

Abstract | Full Text PDF | Reprints | Permissions

Methods for Estimating and Mitigating Errors in Spotted, Dual-color DNA Microarrays

Tobias K. Karakach, Peter D. Wentzell

OMICS: A Journal of Integrative Biology. Jun 2007, Vol. 11, No. 2: 186-199

Abstract | Full Text PDF | Reprints | Permissions

Salinity adaptation and gene profiling analysis in the European eel (Anguilla anguilla) using microarray technology

S KALUJNAIA, I MCWILLIAM, V ZAGUINAIKO, A FEILEN, J NICHOLSON, N HAZON, C CUTLER, R BALMENT, A COSSINS, M HUGHES

General and Comparative Endocrinology. Jun 2007, Vol. 152, No. 2-3: 274-280

Improving cluster-based missing value estimation of DNA microarray data

Lígia P. Brás, José C. Menezes

Biomolecular Engineering. Jun 2007, Vol. 24, No. 2: 273-282

Systematic Approaches for Incorporating Control Spots and Data Quality Information to Improve Normalization of c DNA Microarray Data

D. Wang, C.-H. Zhang, M. B. Soares, J. Huang

Journal of Biopharmaceutical Statistics. May 2007, Vol. 17, No. 3: 415-431

A CENTENNIAL CELEBRATION FOR QUANTITATIVE GENETICS

Derek A. Roff

Evolution. May 2007, Vol. 61, No. 5: 1017-1032

Genome-Wide Reprogramming in Hybrids of Somatic Cells and Embryonic Stem Cells

Dominic J. Ambrosi, Borko Tanasijevic, Anupinder Kaur, Craig Obergfell, Rachel J. O'Neill, Winfried Krueger, Theodore P. Rasmussen

Stem Cells. May 2007, Vol. 25, No. 5: 1104-1113

An adaptive empirical Bayesian thresholding procedure for analysing microarray experiments with replication

Rebecca E. Walls, Stuart Barber, John T. Kent, Mark S. Gilthorpe

Journal of the Royal Statistical Society: Series C (Applied Statistics). May 2007, Vol. 56, No. 3: 271-291

Key aspects of analyzing microarray gene-expression data

James J Chen

Pharmacogenomics. May 2007, Vol. 8, No. 5: 473-482

Microarray analysis of 7029 gene expression patterns in burma mangrove under high-salinity stress

M MIYAMA, N HANAGATA

Plant Science. May 2007, Vol. 172, No. 5: 948-957

Statistics for proteomics: Experimental design and 2-DE differential analysis

Jean-François Chich, Olivier David, Fanny Villers, Brigitte Schaeffer, Didier Lutomski, Sylvie Huet

Journal of Chromatography B. Apr 2007, Vol. 849, No. 1-2: 261-272

Identification of differentially expressed genes and false discovery rate in microarray studies

Arief Gusnanto, Stefano Calza, Yudi Pawitan

Current Opinion in Lipidology. Apr 2007, Vol. 18, No. 2: 187-193

Assessment of reducing RNA input for Agilent oligo microarrays

E.M. van Schothorst, V. Pagmantidis, V.C.J. de Boer, J. Hesketh, J. Keijer

Analytical Biochemistry. Apr 2007, Vol. 363, No. 2: 315-317

Genomic characterization of multiple clinical phenotypes of cancer using multivariate linear regression models

S. Matsui, M. Ito, H. Nishiyama, H. Uno, H. Kotani, J. Watanabe, P. Guilford, A. Reeve, M. Fukushima, O. Ogawa

Bioinformatics. Mar 2007, Vol. 23, No. 6: 732-738

Analysis of Expression Data: An Overview

Anoop Grewal, Peter Lambert, Jordan Stockton

. Mar 2007

Comparison of statistical performance of univariate and bivariate mixed models for Affymetrix ^® probe level data

Wen-Ping Hsieh, Tzu-Ming Chu, Russ Wolfinger

Journal of Statistical Computation and Simulation. Mar 2007, Vol. 77, No. 3: 251-264

Transcriptional profiling of wheat caryopsis development using cDNA microarrays

Debbie L. Laudencia-Chingcuanco, Boryana S. Stamova, Frank M. You, Gerard R. Lazo, Diane M. Beckles, Olin D. Anderson

Plant Molecular Biology. Feb 2007, Vol. 63, No. 5: 651-668

Gene expression associated with compatible viral diseases in grapevine cultivars

C. Espinoza, A. Vega, C. Medina, K. Schlauch, G. Cramer, P. Arce-Johnson

Functional & Integrative Genomics. Feb 2007, Vol. 7, No. 2: 95-110

Water and salinity stress in grapevines: early and late changes in transcript and metabolite profiles

Grant R. Cramer, Ali Ergül, Jerome Grimplet, Richard L. Tillett, Elizabeth A. R. Tattersall, Marlene C. Bohlman, Delphine Vincent, Justin Sonderegger, Jason Evans, Craig Osborne, David Quilici, Karen A. Schlauch, David A. Schooley, John C. Cushman

Functional & Integrative Genomics. Feb 2007, Vol. 7, No. 2: 111-134

Heterosis associated gene expression in maize embryos 6 days after fertilization exhibits additive, dominant and overdominant pattern

Stephanie Meyer, Heike Pospisil, Stefan Scholten

Plant Molecular Biology. Feb 2007, Vol. 63, No. 3: 381-391

Qualification of Embryonal Carcinoma 2102Ep As a Reference for Human Embryonic Stem Cell Research

Richard Josephson, Carol J. Ording, Ying Liu, Soojung Shin, Uma Lakshmipathy, Araz Toumadje, Bradley Love, Jonathan D. Chesnut, Peter W. Andrews, Mahendra S. Rao, Jonathan M. Auerbach

Stem Cells. Feb 2007, Vol. 25, No. 2: 437-446

Genome-wide survey of the gene expression response to saprolegniasis in Atlantic salmon

Christian Roberge, David J. Páez, Orlane Rossignol, Helga Guderley, Julian Dodson, Louis Bernatchez

Molecular Immunology. Feb 2007, Vol. 44, No. 6: 1374-1383

Normalisation of Multicondition cDNA Macroarray Data

Nicola L. Dawes, Jarka Glassey

Comparative and Functional Genomics. Jan 2007, Vol. 2007: 1-12

Analysis and Management of Microarray Gene Expression Data

Gregory R. Grant, Elisabetta Manduchi, Christian J. Stoeckert

. Jan 2007

A conditionally immortalized cell line model for the study of human prostatic epithelial cell differentiation

Bernadette Daly-Burns, Tahirah N. Alam, Alan Mackay, Jeremy Clark, Christopher J. Shepherd, Siân Rizzo, Roger Tatoud, Michael J. O'Hare, John R. Masters, David L. Hudson

Differentiation. Jan 2007, Vol. 75, No. 1: 35-48

Nicotine causes age-dependent changes in gene expression in the adolescent female rat brain

Oksana O. Polesskaya, Karl J. Fryxell, Amita D. Merchant, Laura L. Locklear, Ko-Fei Ker, Craig G. McDonald, Amy K. Eppolito, Laura N. Smith, Tracey L. Wheeler, Robert F. Smith

Neurotoxicology and Teratology. Jan 2007, Vol. 29, No. 1: 126-140

Statistical Method for Implementing the Experimenter Effect in the Analysis of Gene Expression Data

Communications of the Korean statistical society. Dec 2006, Vol. 13, No. 3: 701-718

Comparison between SAGE and cDNA microarray for quantitative accuracy in transcript profiling analyses

Eun Mi Eom, Ji Yeors Lee, Hye Sang Park, Youn Jung Byun, Young Mie Ha-Lee, Dong Hee Lee

Journal of Plant Biology. Dec 2006, Vol. 49, No. 6: 498-506

UPSC-BASE - Populus transcriptomics online

Andreas Sjödin, Max Bylesjö, Oskar Skogström, Daniel Eriksson, Peter Nilsson, Patrik Rydén, Stefan Jansson, Jan Karlsson

The Plant Journal. Dec 2006, Vol. 48, No. 5: 806-817

Reproducibility Probability Score—incorporating measurement variability across laboratories for gene selection

Guixian Lin, Xuming He, Hanlee Ji, Leming Shi, Ronald W Davis, Sheng Zhong

Nature Biotechnology. Dec 2006, Vol. 24, No. 12: 1476-1477

Ranking analysis of microarray data: A powerful method for identifying differentially expressed genes

Yuan-De Tan, Myriam Fornage, Yun-Xin Fu

Genomics. Dec 2006, Vol. 88, No. 6: 846-854

Joint estimation of calibration and expression for high-density oligonucleotide arrays

A. L. Oberg, D. W. Mahoney, K. V. Ballman, T. M. Therneau

Bioinformatics. Oct 2006, Vol. 22, No. 19: 2381-2387

Human laminin-5 and laminin-10 mediated gene expression of prostate carcinoma cells

Robert Calaluce, Shaleen K. Beck, Elisabeth L. Bair, Ritu Pandey, Kevin A. Greer, Adam M. Hoying, James B. Hoying, David W. Mount, Raymond B. Nagle

The Prostate. Sep 2006, Vol. 66, No. 13: 1381-1390

DNA Microarray Data, Statistical Analysis of

Susmita Datta

. Aug 2006

Differential gene expression of wheat progeny with contrasting levels of transpiration efficiency

Gang-Ping Xue, C. Lynne McIntyre, Scott Chapman, Neil I. Bower, Heather Way, Antonio Reverter, Bryan Clarke, Ray Shorter

Plant Molecular Biology. Aug 2006, Vol. 61, No. 6: 863-881

Scanning microarrays at multiple intensities enhances discovery of differentially expressed genes

D. S. Skibbe, X. Wang, X. Zhao, L. A. Borsuk, D. Nettleton, P. S. Schnable

Bioinformatics. Aug 2006, Vol. 22, No. 15: 1863-1870

A robust statistical procedure to discover expression biomarkers using microarray genomic expression data

Yang-yun Zou, Jian Yang, Jun Zhu

Journal of Zhejiang University SCIENCE B. Aug 2006, Vol. 7, No. 8: 603-607

Analysis of microarray experiments of gene expression profiling

A TARCA, R ROMERO, S DRAGHICI

American Journal of Obstetrics and Gynecology. Aug 2006, Vol. 195, No. 2: 373-388

WaveRead: Automatic measurement of relative gene expression levels from microarrays using wavelet analysis

G BIDAUT, F MANION, C GARCIA, M OCHS

Journal of Biomedical Informatics. Aug 2006, Vol. 39, No. 4: 379-388

Combining multiple microarrays in the presence of controlling variables

T. Park, S.-G. Yi, Y. K. Shin, S. Lee

Bioinformatics. Jul 2006, Vol. 22, No. 14: 1682-1689

Biological microarray interpretation: The rules of engagement

Rainer Breitling

Biochimica et Biophysica Acta (BBA) - Gene Structure and Expression. Jul 2006, Vol. 1759, No. 7: 319-327

Construction of null statistics in permutation-based multiple testing for multi-factorial microarray experiments

X. Gao

Bioinformatics. Jun 2006, Vol. 22, No. 12: 1486-1494

Empirical Bayes analysis of variance component models for microarray data

S. Feng, R. D. Wolfinger, T. M. Chu, G. C. Gibson, L. A. McGraw

Journal of Agricultural, Biological, and Environmental Statistics. Jun 2006, Vol. 11, No. 2: 197-209

Gene expression analysis of mouse chromosome substitution strains

Keith R. Shockley, Gary A. Churchill

Mammalian Genome. Jun 2006, Vol. 17, No. 6: 598-614

Some Statistical Issues in Microarray Gene Expression Data

Matthew S. Mayo, Byron J. Gajewski, Jeffrey S. Morris

Radiation Research. Jun 2006, Vol. 165, No. 6: 745-748

From genetical genomics to systems genetics: potential applications in quantitative genomics and animal breeding

Haja N. Kadarmideen, Peter Rohr, Luc L.G. Janss

Mammalian Genome. Jun 2006, Vol. 17, No. 6: 548-564

The effects of different sample labelling methods on signal intensities of a 60-mer diagnostic microarray

Xiao-Yang Mo, Wen-Li Ma, Ling Li, Qiu-Lin Xu, Ya-Li Zhang, Wen-Ling Zheng

Journal of Virological Methods. Jun 2006, Vol. 134, No. 1-2: 36-40

A calibration method for estimating absolute expression levels from microarray data

K. Engelen, B. Naudts, B. De Moor, K. Marchal

Bioinformatics. May 2006, Vol. 22, No. 10: 1251-1258

maSigPro: a method to identify significantly differential expression profiles in time-course microarray experiments

A. Conesa, M. J. Nueda, A. Ferrer, M. Talon

Bioinformatics. May 2006, Vol. 22, No. 9: 1096-1102

A cDNA microarray approach to decipher sunflower (Helianthus annuus) responses to the necrotrophic fungus Phoma macdonaldii

Marion Alignan, Tarek Hewezi, Michel Petitprez, Gregory Dechamp-Guillaume, Laurent Gentzbittel

New Phytologist. May 2006, Vol. 170, No. 3: 523-536

Normalization Using Weighted Negative Second Order Exponential Error Functions (NeONORM) Provides Robustness Against Asymmetries in Comparative Transcriptome Profiles and Avoids False Calls

Sebastian Noth, Guillaume Brysbaert, Arndt Benecke

Genomics, Proteomics & Bioinformatics. May 2006, Vol. 4, No. 2: 90-109

Improving reliability and performance of DNA microarrays

Maria Sievertzon, Peter Nilsson, Joakim Lundeberg

Expert Review of Molecular Diagnostics. May 2006, Vol. 6, No. 3: 481-492

Expression Profiling of Botrytis cinerea Genes Identifies Three Patterns of Up-regulation in Planta and an FKBP12 Protein Affecting Pathogenicity

A GIOTI, A SIMON, P LEPECHEUR, C GIRAUD, J PRADIER, M VIAUD, C LEVIS

Journal of Molecular Biology. Apr 2006, Vol. 358, No. 2: 372-386

Bioinformatics

Ali Abbas, Lei Liu

. Apr 2006

Bioinformatics

Lei Liu, Ali Abbas

. Apr 2006

A new approach to intensity-dependent normalization of two-channel microarrays

A. R. Dabney, J. D. Storey

Biostatistics. Apr 2006, Vol. 8, No. 1: 128-139

Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays

Tarek Hewezi, Michel Petitprez, Laurent Gentzbittel

Planta. Apr 2006, Vol. 223, No. 5: 948-964

Parallelism in gene transcription among sympatric lake whitefish (Coregonus clupeaformis Mitchill) ecotypes

N. DEROME, P. DUCHESNE, L. BERNATCHEZ

Molecular Ecology. Apr 2006, Vol. 15, No. 5: 1239-1249

A Bayesian Multiple Testing of Detecting Differentially Expressed Genes in Two-sample Comparison Problem

Communications of the Korean statistical society. Apr 2006, Vol. 13, No. 1: 39-47

Natural genetic variation in whole-genome expression in Arabidopsis thaliana: the impact of physiological QTL introgression

THOMAS E. JUENGER, TIERNEY WAYNE, SANDRA BOLES, V. VAUGHAN SYMONDS, JOHN MCKAY, SEAN J. COUGHLAN

Molecular Ecology. Apr 2006, Vol. 15, No. 5: 1351-1365

Application of reliability coefficients in cDNA microarray data analysis

Wenqing He, Shelley B. Bull, Nalan Gokgoz, Irene Andrulis, Jay Wunder

Statistics in Medicine. Mar 2006, Vol. 25, No. 6: 1051-1066

Array-based methods for diagnosis and prevention of transplant rejection

Qiuheng Zhang, Elaine F Reed

Expert Review of Molecular Diagnostics. Mar 2006, Vol. 6, No. 2: 165-178

Application of microarray technology in primate behavioral neuroscience research

Adriaan M. Karssen, Jun Z. Li, Song Her, Paresh D. Patel, Fan Meng, Simon J. Evans, Marquis P. Vawter, Hiroaki Tomita, Prabhakara V. Choudary, William E. Bunney, Edward G. Jones, Stanley J. Watson, Huda Akil, Richard M. Myers, Alan F. Schatzberg, David M. Lyons

Methods. Mar 2006, Vol. 38, No. 3: 227-234

Ecological and evolutionary genomics of Saccharomyces cerevisiae

CHRISTIAN R. LANDRY, JEFFREY P. TOWNSEND, DANIEL L. HARTL, DUCCIO CAVALIERI

Molecular Ecology. Mar 2006, Vol. 15, No. 3: 575-591

Bayesian Modeling of Differential Gene Expression

Alex Lewin, Sylvia Richardson, Clare Marshall, Anne Glazier, Tim Aitman

Biometrics. Mar 2006, Vol. 62, No. 1: 10-18

Using endophenotypes for pathway clusters to map complex disease genes

Wen-Harn Pan, Ke-Shiuan Lynn, Chun-Houh Chen, Yi-Lin Wu, Chung-Yen Lin, Hsing-Yi Chang

Genetic Epidemiology. Feb 2006, Vol. 30, No. 2: 143-154

A Nonparametric Likelihood Ratio Test to Identify Differentially Expressed Genes from Microarray Data

Sankar Bokka, Sunil K Mathur

Applied Bioinformatics. Jan 2006, Vol. 5, No. 4: 267-276

Applications of genomic technologies to the study of organochlorine pesticide-induced reproductive toxicity in fish

Natàlia Garcia-Reyero, Nancy D. Denslow

Journal of Pesticide Science. Jan 2006, Vol. 31, No. 3: 252-262

The Use of Background Signal in the Transformation of cDNA-Microarray Measurements

Suzy Van Sanden, Tomasz Burzykowski

Applied Bioinformatics. Jan 2006, Vol. 5, No. 3: 161-172

Rapid parallel evolutionary changes of gene transcription profiles in farmed Atlantic salmon

CHRISTIAN ROBERGE, SIGURD EINUM, HELGA GUDERLEY, LOUIS BERNATCHEZ

Molecular Ecology. Jan 2006, Vol. 15, No. 1: 9-20

Associating phenotypes with molecular events: recent statistical advances and challenges underpinning microarray experiments

Yulan Liang, Arpad Kelemen

Functional & Integrative Genomics. Jan 2006, Vol. 6, No. 1: 1-13

[11] Analysis of Variance of Microarray Data

Julien F. Ayroles, Greg Gibson

. Jan 2006, Vol. 411: 214-233

The influence of missing value imputation on detection of differentially expressed genes from microarray data

I. Scheel, M. Aldrin, I. K. Glad, R. Sorum, H. Lyng, A. Frigessi

Bioinformatics. Dec 2005, Vol. 21, No. 23: 4272-4279

Microarray technology in the study of obesity and non-alcoholic fatty liver disease

Ancha Baranova, Karen Schlauch, Shobha Gowder, Rochelle Collantes, Vikas Chandhoke, Zobair M. Younossi

Liver International. Dec 2005, Vol. 25, No. 6: 1091-1096

Statistical methods for gene expression analysis

Shibing Deng, Tzu-Ming Chu, Young K. Truong, Russ D. Wolfinger

. Nov 2005

Expression Profiling Soybean Response to Pseudomonas syringae Reveals New Defense-Related Genes and Rapid HR-Specific Downregulation of Photosynthesis

Jijun Zou, Sandra Rodriguez-Zas, Mihai Aldea, Min Li, Jin Zhu, Delkin O. Gonzalez, Lila O. Vodkin, Evan DeLucia, Steven J. Clough

Molecular Plant-Microbe Interactions. Nov 2005, Vol. 18, No. 11: 1161-1174

The antiangiogenic tissue kallikrein pattern of endothelial cells in systemic sclerosis

Betti Giusti, Simona Serratì, Francesca Margheri, Laura Papucci, Luciana Rossi, Filippo Poggi, Alberto Magi, Angela Del Rosso, Marina Cinelli, Serena Guiducci, Bashar Kahaleh, Marco Matucci-Cerinic, Rosanna Abbate, Gabriella Fibbi, Mario Del Rosso

Arthritis & Rheumatism. Nov 2005, Vol. 52, No. 11: 3618-3628

A two-stage normalization method for partially degraded mRNA microarray data

L.-y. D. Liu, N. Wang, J. R. Lupton, N. D. Turner, R. S. Chapkin, L. A. Davidson

Bioinformatics. Nov 2005, Vol. 21, No. 21: 4000-4006

Impact of microarray technology in nutrition and food research

Bettina Spielbauer, Frank Stahl

Molecular Nutrition & Food Research. Oct 2005, Vol. 49, No. 10: 908-917

Comment

Jian Huang, Cun-Hui Zhang

Journal of the American Statistical Association. Sep 2005, Vol. 100, No. 471: 800-804

Functional genomics in farm animals – Microarray analysis

C BENDIXEN, J HEDEGAARD, P HORN

Meat Science. Sep 2005, Vol. 71, No. 1: 128-137

An expression index for Affymetrix GeneChips based on the generalized logarithm

L. Zhou

Bioinformatics. Aug 2005, Vol. 21, No. 21: 3983-3989

Identification of Rat Hippocampal mRNAs Altered by the Mitochondrial Toxicant, 3-NPA

BEATA D. PRZYBYLA-ZAWISLAK, BRETT T. THORN, SYED F. ALI, RICHARD A. DENNIS, ANTONINO AMATO, ASHRAF VIRMANI, ZBIGNIEW K. BINIENDA

Annals of the New York Academy of Sciences. Aug 2005, Vol. 1053, No. 1: 162-173

Evaluation of an Affymetrix High-density Oligonucleotide Microarray Platform as a Measurement System

Edwin R. van den Heuvel, Geert Geeven, Susanne Bauerschmidt, Jan E. M. Polman

Quality and Reliability Engineering International. Aug 2005, Vol. 21, No. 5: 491-508

Unravelling the functional interaction structure of a cellular network from temporal slope information of experimental data

Kwang-Hyun Cho, Sung-Young Shin, Sang-Mok Choo

FEBS Journal. Aug 2005, Vol. 272, No. 15: 3950-3959

Pathways to the analysis of microarray data

R. Keira Curtis, Matej Orešič, Antonio Vidal-Puig

Trends in Biotechnology. Aug 2005, Vol. 23, No. 8: 429-435

The use of cDNA microarray to identify differentially expressed labor-associated genes within the human myometrium during labor

M ESPLIN, M FAUSETT, M PELTIER, S HAMBLIN, R SILVER, D BRANCH, E ADASHI, D WHITING

American Journal of Obstetrics and Gynecology. Aug 2005, Vol. 193, No. 2: 404-413

Hotelling's T2 multivariate profiling for detecting differential expression in microarrays

Y. Lu, P.-Y. Liu, P. Xiao, H.-W. Deng

Bioinformatics. Jul 2005, Vol. 21, No. 14: 3105-3113

Stochastic Models Inspired by Hybridization Theory for Short Oligonucleotide Arrays

Zhijin Wu, Rafael A. Irizarry

Journal of Computational Biology. Jul 2005, Vol. 12, No. 6: 882-893

Abstract | Full Text PDF | Reprints | Permissions

Differential and trajectory methods for time course gene expression data

Y. Liang, B. Tayo, X. Cai, A. Kelemen

Bioinformatics. Jul 2005, Vol. 21, No. 13: 3009-3016

Quality pork genes and meat production

G PLASTOW, D CARRION, M GIL, J GARCIAREGUEIRO, M IFURNOLS, M GISPERT, M OLIVER, A VELARDE, M GUARDIA, M HORTOS

Meat Science. Jul 2005, Vol. 70, No. 3: 409-421

APPLICATIONS OF DNA MICROARRAYS IN BIOLOGY

Roland B. Stoughton

Annual Review of Biochemistry. Jun 2005, Vol. 74, No. 1: 53-82

Immune response in silico (IRIS): immune-specific genes identified from a compendium of microarray expression data

A R Abbas, D Baldwin, Y Ma, W Ouyang, A Gurney, F Martin, S Fong, M van Lookeren Campagne, P Godowski, P M Williams, A C Chan, H F Clark

Genes and Immunity. Jun 2005, Vol. 6, No. 4: 319-331

Molecular insight into the effects of hypothyroidism on the developing cerebellum

H DONG, M WADE, A WILLIAMS, A LEE, G DOUGLAS, C YAUK

Biochemical and Biophysical Research Communications. May 2005, Vol. 330, No. 4: 1182-1193

Gene expression signatures in neutrophils exposed to glucocorticoids: A new paradigm to help explain ?neutrophil dysfunction? in parturient dairy cows

J BURTON, S MADSEN, L CHANG, P WEBER, K BUCKHAM, R VANDORP, M HICKEY, B EARLEY

Veterinary Immunology and Immunopathology. May 2005, Vol. 105, No. 3-4: 197-219

Finite mixture model analysis of microarray expression data on samples of uncertain biological type with application to reproductive efficiency

N BING, I HOESCHELE, K YE, K EILERTSEN

Veterinary Immunology and Immunopathology. May 2005, Vol. 105, No. 3-4: 187-196

Bayesian Normalization and Identification for Differential Gene Expression Data

Dabao Zhang, Martin T. Wells, Christine D. Smart, William E. Fry

Journal of Computational Biology. May 2005, Vol. 12, No. 4: 391-406

Abstract | Full Text PDF | Reprints | Permissions

Evaluation of Nine Strategies for Analyzing a cDNA Toxicology Microarray Data Set

Juan Joanne Zhang, Tsong Yi, Lue Ping Zhao

Journal of Biopharmaceutical Statistics. May 2005, Vol. 15, No. 3: 403-418

Epigenetic Hypothesis Tests for Methylation and Acetylation in a Triple Microarray System

Lang Li, Huidong Shi, Constantin Yiannoutsos, Tim Hui-Ming Huang, Kenneth P. Nephew

Journal of Computational Biology. Apr 2005, Vol. 12, No. 3: 370-390

Abstract | Full Text PDF | Reprints | Permissions

Gene expression in tissue associated with extracellular matrix modified ePTFE

Mark A. Schwartz, Alice L. Stone, Kevin A. Greer, James B. Hoying, Stuart K. Williams

Journal of Biomedical Materials Research Part A. Apr 2005, Vol. 73A, No. 1: 30-38

Normalization of two-channel microarray experiments: a semiparametric approach

J. E. Eckel, C. Gennings, T. M. Therneau, L. D. Burgoon, D. R. Boverhof, T. R. Zacharewski

Bioinformatics. Apr 2005, Vol. 21, No. 7: 1078-1083

Identifying differentially expressed genes from microarray experiments via statistic synthesis

Y. H. Yang, Y. Xiao, M. R. Segal

Bioinformatics. Apr 2005, Vol. 21, No. 7: 1084-1093

Computational Biology and Toxicogenomics

Kathleen Marchal, Kristof Engelen, Frank De Smet, Bart De Moor

. Mar 2005: 37-92

Weighted analysis of microarray gene expression using maximum-likelihood

D. J. Bakewell, E. Wit

Bioinformatics. Mar 2005, Vol. 21, No. 6: 723-729

Systemic response to aphid infestation by Myzus persicae in the phloem of Apium graveolens

Fanchon Divol, Fran

oise Vilaine, Sandra Thibivilliers, Jo

lle Amselem, Jean-Christophe Palauqui, Chantal Kusiak, Sylvie Dinant

Plant Molecular Biology. Mar 2005, Vol. 57, No. 4: 517-540

Bayesian Clustering of Prostate Cancer Patients by Using a Latent Class Poisson Model

Korean Journal of Applied Statistics. Mar 2005, Vol. 18, No. 1: 1-13

Discriminate gene lists derived from cDNA microarray profiles of limited samples permit distinguishing mesenchymal neoplasia ex vivo

David E. Joyner, Mark L.Wade, Aniko Szabo, Jeffrey Bastar, Cheryl M. Coffin, Karen H. Albritton, Philip S. Bernard, R. Lor Randall

Journal of Cancer Research and Clinical Oncology. Mar 2005, Vol. 131, No. 3: 137-146

Print-tip Normalization for DNA Microarray Data

Korean Journal of Applied Statistics. Mar 2005, Vol. 18, No. 1: 115-127

An experimental evaluation of a loop versus a reference design for two-channel microarrays

V. Vinciotti, R. Khanin, D. D'Alimonte, X. Liu, N. Cattini, G. Hotchkiss, G. Bucca, O. de Jesus, J. Rasaiyaah, C. P. Smith, P. Kellam, E. Wit

Bioinformatics. Feb 2005, Vol. 21, No. 4: 492-501

A two-step strategy for detecting differential gene expression in cDNA microarray data

Yan Lu, Jun Zhu, Pengyuan Liu

Current Genetics. Feb 2005, Vol. 47, No. 2: 121-131

ArrayVigil: A Methodology for Statistical Comparison of Gene Signatures Using Segregated-one-tailed (SOT) Wilcoxon's Signed-rank Test

Haseeb Ahmad Khan

Journal of Molecular Biology. Jan 2005, Vol. 345, No. 4: 645-649

Laboratory variability does not preclude identification of biological functions impacted by hydroxyurea

Arne Müller, Eric Boitier, Ting Hu, Gregory J. Carr, Anne-Céline Le Fèvre, Jean-Pierre Marchandeau, Manoli Flor, Felicia Jefferson, Marilyn J. Aardema, Véronique Thybaud

Environmental and Molecular Mutagenesis. Jan 2005, Vol. 46, No. 4: 221-235

Gene expression profiling of ovine skin and wool follicle development using a combined ovine–bovine skin cDNA microarray

B. J. Norris, N. I. Bower, W. J. M. Smith, G. R. Cam, A. Reverter

Australian Journal of Experimental Agriculture. Jan 2005, Vol. 45, No. 8: 867

Reassessing Design and Analysis of two-Colour Microarray Experiments Using Mixed Effects Models

Guilherme J. M. Rosa, Juan P. Steibel, Robert J. Tempelman

Comparative and Functional Genomics. Jan 2005, Vol. 6, No. 3: 123-131

Development of a coral cDNA array to examine gene expression profiles in exposed to environmental stress

S EDGE, M MORGAN, D GLEASON, T SNELL

Marine Pollution Bulletin. Jan 2005, Vol. 51, No. 5-7: 507-523

Model-based analysis of microarray data: Exploration of differentially expressed genes between two cell types based on a two-dimensional mixed normal model

Megu Ohtaki, Keiko Otani, Kenichi Satoh, Toshihiko Kawamura, Keiko Hiyama, Masahiko Nishiyama

Japanese Journal of Biometrics. Jan 2005, Vol. 26, No. 1: 31-48

GENOMICS AND BIOINFORMATICS

Spencer Muse

. Jan 2005: 799-831

Parametric Robust Regression Analysis of Contaminated Data

Tsung-Shan Tsou, Kuang-Fu Cheng

Communications in Statistics - Theory and Methods. Dec 2004, Vol. 33, No. 8: 1887-1898

Microarray Data Visualization and Analysis with the Longhorn Array Database (LAD)

Patrick J. Killion, Vishwanath R. Iyer

. Dec 2004

Design and analysis of experiments with high throughput biological assay data

David M. Rocke

Seminars in Cell & Developmental Biology. Dec 2004, Vol. 15, No. 6: 703-713

Microarrays—Standard Operating Procedures

Thorsten Forster, Peter Ghazal

. Dec 2004: 824-830

Statistical Analysis of a Loop Designed Microarray Experiment Data

Korean Journal of Applied Statistics. Nov 2004, Vol. 17, No. 3: 419-430

DNA microarrays — techniques and applications in microbial systems

T. Majtán, G. Bukovská, J. Timko

Folia Microbiologica. Nov 2004, Vol. 49, No. 6: 635-664

Median-of-Subsets Normalization of Intensities for cDNA Array Data

Robert R. Delongchamp, Cruz Velasco, Mehdi Razzaghi, Angela Harris, Dan Casciano

DNA and Cell Biology. Oct 2004, Vol. 23, No. 10: 653-659

Abstract | Full Text PDF | Reprints | Permissions

Combining genome-wide and targeted gene expression profiling in drug discovery: microarrays and real-time PCR

Daniel A. Brazeau

Drug Discovery Today. Oct 2004, Vol. 9, No. 19: 838-845

Correspondence analysis of microarray time-course data in case?control design

Q TAN

Journal of Biomedical Informatics. Oct 2004, Vol. 37, No. 5: 358-365

ESTs, cDNA microarrays, and gene expression profiling: tools for dissecting plant physiology and development

Rob Alba, Zhangjun Fei, Paxton Payton, Yang Liu, Shanna L. Moore, Paul Debbie, Jonathan Cohn, Mark D'Ascenzo, Jeffrey S. Gordon, Jocelyn K. C. Rose, Gregory Martin, Steven D. Tanksley, Mondher Bouzayen, Molly M. Jahn, Jim Giovannoni

The Plant Journal. Sep 2004, Vol. 39, No. 5: 697-714

New insights into ADPKD molecular pathways using combination of SAGE and microarray technologies

Hervé Husson, Partha Manavalan, Viatcheslav R. Akmaev, Ryan J. Russo, Brian Cook, Brenda Richards, Dana Barberio, Dongyu Liu, Xiaohong Cao, Gregory M. Landes

Genomics. Sep 2004, Vol. 84, No. 3: 497-510

Balancing false positives and false negatives for the detection of differential expression in malignancies

F De Smet, Y Moreau, K Engelen, D Timmerman, I Vergote, B De Moor

British Journal of Cancer. Aug 2004

Design and Analysis of Microarray Studies for Obesity Research

Kyoungmi Kim, Maria DeLuca, Grier Page, Marie-Pierre St-Onge, Kui Zhang, David Allison, Steven Heymsfield

. Aug 2004, Vol. 20040951: 145-203

Sample Size for Identifying Differentially Expressed Genes in Microarray Experiments

Sue-Jane Wang, James J. Chen

Journal of Computational Biology. Aug 2004, Vol. 11, No. 4: 714-726

Abstract | Full Text PDF | Reprints | Permissions

A Genomic Predictor of Oral Squamous Cell Carcinoma

Mark E. Whipple, Eduardo Mendez, D Gregory Farwell, S Nicholas Agoff, Chu Chen

The Laryngoscope. Aug 2004, Vol. 114, No. 8: 1346-1354

Possible sources of dye-related signal correlation bias in two-color DNA microarray assays

W Gregory Cox, Matthew P Beaudet, Jakyoung Y Agnew, Jerry L Ruth

Analytical Biochemistry. Aug 2004, Vol. 331, No. 2: 243-254

The TAO-Gen Algorithm for Identifying Gene Interaction Networks with Application to SOS Repair in E. coli

Takeharu Yamanaka, Hiroyoshi Toyoshiba, Hideko Sone, Frederick M. Parham, Christopher J. Portier

Environmental Health Perspectives. Jul 2004, Vol. 112, No. 16: 1614-1621

Study of Arabidopsis thalianaresistome in response to cucumber mosaic virus infection using whole genome microarray

Rajendra Marathe, Zhong Guan, Radhamani Anandalakshmi, Hongyu Zhao, S. Dinesh-Kumar

Plant Molecular Biology. Jul 2004, Vol. 55, No. 4: 501-520

Characterization of heterogeneity in the molecular pathogenesis of lupus nephritis from transcriptional profiles of laser-captured glomeruli

Karin S. Peterson, Jing-Feng Huang, Jessica Zhu, Vivette D’Agati, Xuejun Liu, Nancy Miller, Mark G. Erlander, Michael R. Jackson, Robert J. Winchester

Journal of Clinical Investigation. Jun 2004, Vol. 113, No. 12: 1722-1733

Evidence of systematic expressed sequence tag IMAGE clone cross-hybridization on cDNA microarrays

Dan Handley, Nicoleta Serban, David Peters, Robert O'Doherty, Melvin Field, Larry Wasserman, Peter Spirtes, Richard Scheines, Clark Glymour

Genomics. Jun 2004, Vol. 83, No. 6: 1169-1175

Modeling Microarray Data Using a Threshold Mixture Model

Goran Kauermann, Paul Eilers

Biometrics. Jun 2004, Vol. 60, No. 2: 376-387

Discovery of the a-1 Microglobulin Complex in Urine Sample Patients with Cadmium Intoxication

Rosdiana Natzir .

Journal of Medical Sciences(Faisalabad). Mar 2004, Vol. 4, No. 3: 198-202

Novel tumor necrosis factor ?-regulated genes in rheumatoid arthritis

Huang-Ge Zhang, Karren Hyde, Grier P. Page, Jacob P. L. Brand, Juling Zhou, Shaohua Yu, David B. Allison, Hui-Chen Hsu, John D. Mountz

Arthritis & Rheumatism. Feb 2004, Vol. 50, No. 2: 420-431

Regulatory gene expression in skeletal muscle of highly endurance-trained humans

M. Wittwer, R. Billeter, H. Hoppeler, M. Fluck

Acta Physiologica Scandinavica. Feb 2004, Vol. 180, No. 2: 217-227

Use of expressed sequence tag analysis and cDNA microarrays of the filamentous fungus Aspergillus nidulans

A Sims

Fungal Genetics and Biology. Feb 2004, Vol. 41, No. 2: 199-212

Gene-specific dye bias in microarray reference designs

Alan A. Dombkowski, Bryan J. Thibodeau, Susan L. Starcevic, Raymond F. Novak

FEBS Letters. Feb 2004, Vol. 560, No. 1-3: 120-124

Dye-Bias Correction in Dual-Labeled cDNA Microarray Gene Expression Measurements

Barry A. Rosenzweig, P. Scott Pine, Olen E. Domon, Suzanne M. Morris, James J. Chen, Frank D. Sistare

Environmental Health Perspectives. Jan 2004, Vol. 112, No. 4: 480-487

Replicated studentized-deviate detection applied to the identification of differentially expressed genes in TNF-α-stimulated cells

Qing-Wei Zhang, Nobukazu Ono, Yoshiyuki Takahara, Hiroshi Tanaka

Gene. Jan 2004, Vol. 324: 89-96

Which to use? - microarray data analysis in input and output data processing

Qingwei Zhang, Rie Ushijima, Takatoshi Kawai, Hiroshi Tanaka

Chem-Bio Informatics Journal. Jan 2004, Vol. 4, No. 2: 56-72

Phenotype Characterisation Using Integrated Gene Transcript, Protein and Metabolite Profiling

Matej Ore??i??, Clary B Clish, Eugene J Davidov, Elwin Verheij, Jack Vogels, Louis M Havekes, Eric Neumann, Aram Adourian, Stephen Naylor, Jan van der Greef, Thomas Plasterer

Applied Bioinformatics. Jan 2004, Vol. 3, No. 4: 205-217

Allelic variations in gene expression

Hai Yan, Wei Zhou

Current Opinion in Oncology. Jan 2004, Vol. 16, No. 1: 39-43

Leydig cell gene expression: effects of age and caloric restriction

Haolin Chen, Rafael A Irizarry, Lindi Luo, Barry R Zirkin

Experimental Gerontology. Jan 2004, Vol. 39, No. 1: 31-43

Microarrays in biology and medicine

Supratim Choudhuri

Journal of Biochemical and Molecular Toxicology. Jan 2004, Vol. 18, No. 4: 171-179

Proteomics and mass spectrometry in nutrition research

H Kim

Nutrition. Jan 2004, Vol. 20, No. 1: 155-165

A Generalized Additive Model For Microarray Gene Expression Data Analysis

Chen-An Tsai, Huey-Miin Hsueh, James J. Chen

Journal of Biopharmaceutical Statistics. Jan 2004, Vol. 14, No. 3: 553-573

Statistical Approaches in the Analysis of Gene Expression Data Derived from Bone Regeneration Specific cDNA Microarrays

Jungnam Joo, Hongshik Ahn, Frank Lombardo, Michael Hadjiargyrou, Wei Zhu

Journal of Biopharmaceutical Statistics. Jan 2004, Vol. 14, No. 3: 607-628

Identification of Differentially Expressed Genes with Multivariate Outlier Analysis

Hong-Ya Zhao, Patrick Y. K. Yue, Kai-Tai Fang

Journal of Biopharmaceutical Statistics. Jan 2004, Vol. 14, No. 3: 629-646

Microarray Platforms: Introduction and Application to Neurobiology

Stanislav L. Karsten, Lili C. Kudo, Daniel H. Geschwind

. Jan 2004, Vol. 60: 1-23

On parametric empirical Bayes methods for comparing multiple groups using replicated gene expression profiles

C. M. Kendziorski, M. A. Newton, H. Lan, M. N. Gould

Statistics in Medicine. Dec 2003, Vol. 22, No. 24: 3899-3914

Linear Models for Microarray Data Analysis: Hidden Similarities and Differences

M. Kathleen Kerr

Journal of Computational Biology. Dec 2003, Vol. 10, No. 6: 891-901

Abstract | Full Text PDF | Reprints | Permissions

A novel approach for high-quality microarray processing using third-dye array visualization technology

Xujing Wang, Nan Jiang, Xin Feng, Yizhou Xie, P.J. Tonellato, S. Ghosh, M.J. Hessner

IEEE Transactions on Nanobioscience. Dec 2003, Vol. 2, No. 4: 193-201

Microarray image enhancement by denoising using stationary wavelet transform

X.H. Wang, R.S.H. Istepanian, Yong Hua Song

IEEE Transactions on Nanobioscience. Dec 2003, Vol. 2, No. 4: 184-189

Fundamentals of cDNA microarray data analysis

Yuk Fai Leung, Duccio Cavalieri

Trends in Genetics. Nov 2003, Vol. 19, No. 11: 649-659

Comparison and meta-analysis of microarray data: from the bench to the computer desk

Yves Moreau, Stein Aerts, Bart De Moor, Bart De Strooper, Michal Dabrowski

Trends in Genetics. Oct 2003, Vol. 19, No. 10: 570-577

Towards deciphering phloem: a transcriptome analysis of the phloem of Apium graveolens

F. Vilaine, J.-C. Palauqui, J. Amselem, C. Kusiak, R. Lemoine, S. Dinant

The Plant Journal. Oct 2003, Vol. 36, No. 1: 67-81

Application of functional genomics in allergy and clinical immunology

R. Pawliczak, J. H. Shelhamer

Allergy. Oct 2003, Vol. 58, No. 10: 973-980

Array rank order regression analysis for the detection of gene copy-number changes in human cancer

C Cheng

Genomics. Aug 2003, Vol. 82, No. 2: 122-129

Randomization tests for small samples: an application for genetic expression data

Gary L. Gadbury, Grier P. Page, Moonseong Heo, John D. Mountz, David B. Allison

Journal of the Royal Statistical Society: Series C (Applied Statistics). Jul 2003, Vol. 52, No. 3: 365-376

Temporal responses of Arabidopsis root architecture to phosphate starvation: evidence for the involvement of auxin signalling

Y. AL-GHAZI, B. MULLER, S. PINLOCHE, T. J. TRANBARGER, P. NACRY, M. ROSSIGNOL, F. TARDIEU, P. DOUMAS

Plant, Cell and Environment. Jul 2003, Vol. 26, No. 7: 1053-1066

Identification of genes differentially expressed during aflatoxin biosynthesis in Aspergillus flavus and Aspergillus parasiticus

G OBrian

Fungal Genetics and Biology. Jul 2003, Vol. 39, No. 2: 118-127

Bayesian Estimation of Transcript Levels Using a General Model of Array Measurement Noise

Ron O. Dror, Jonathan G. Murnick, Nicola J. Rinaldi, Voichita D. Marinescu, Ryan M. Rifkin, Richard A. Young

Journal of Computational Biology. Jun 2003, Vol. 10, No. 3-4: 433-452

Abstract | Full Text PDF | Reprints | Permissions

Microarrays: How Many Do You Need?

Alexander Zien, Juliane Fluck, Ralf Zimmer, Thomas Lengauer

Journal of Computational Biology. Jun 2003, Vol. 10, No. 3-4: 653-667

Abstract | Full Text PDF | Reprints | Permissions

The Design and Analysis of Microarray Experiments: Applications in Parasitology

David A. Morrison, John T. Ellis

DNA and Cell Biology. Jun 2003, Vol. 22, No. 6: 357-394

Abstract | Full Text PDF | Reprints | Permissions

Resampling-based multiple testing for microarray data analysis

Youngchao Ge, Sandrine Dudoit, Terence P. Speed

Test. Jun 2003, Vol. 12, No. 1: 1-77

Variances Are Not Always Nuisance Parameters

Raymond J. Carroll

Biometrics. Jun 2003, Vol. 59, No. 2: 211-220

Statistical Methods for Analyzing Microarray Feature Data with Replications

Yaning Yang, Josephine Hoh, Clemens Broger, Martin Neeb, Joanne Edington, Klaus Lindpaintner, Jurg Ott

Journal of Computational Biology. Apr 2003, Vol. 10, No. 2: 157-169

Abstract | Full Text PDF | Reprints | Permissions

Genes regulated by learning in the hippocampus

Tarek A. Leil, Alex Ossadtchi, Thomas E. Nichols, Richard M. Leahy, Desmond J. Smith

Journal of Neuroscience Research. Mar 2003, Vol. 71, No. 6: 763-768

Arabidopsis gene expression changes during cyst nematode parasitism revealed by statistical analyses of microarray expression profiles

David P. Puthoff, Dan Nettleton, Steven R. Rodermel, Thomas J. Baum

The Plant Journal. Mar 2003, Vol. 33, No. 5: 911-921

A PPLICATION OF M ICROARRAY T ECHNOLOGY IN E NVIRONMENTAL AND C OMPARATIVE P HYSIOLOGY

Andrew Y. Gracey, Andrew R. Cossins

Annual Review of Physiology. Mar 2003, Vol. 65, No. 1: 231-259

Gene expression data: The technology and statistical analysis

B. A. Craig, M. A. Black, R. W. Doerge

Journal of Agricultural, Biological, and Environmental Statistics. Mar 2003, Vol. 8, No. 1: 1-28

Gene expression profiling in islet biology and diabetes research

Ernesto Bernal-Mizrachi, Corentin Cras-M

neur, Mitsuru Ohsugi, M. Alan Permutt

Diabetes/Metabolism Research and Reviews. Jan 2003, Vol. 19, No. 1: 32-42

Global Analysis of Cell Type-Specific Gene Expression

David W. Galbraith

Comparative and Functional Genomics. Jan 2003, Vol. 4, No. 2: 208-215

Normalization Methods for Analysis of Microarray Gene-Expression Data

Yi-Ju Chen, Ralph Kodell, Frank Sistare, Karol Thompson, Suzanne Morris, James Chen

Journal of Biopharmaceutical Statistics. Jan 2003, Vol. 13, No. 1: 57-74

Statistical Techniques for Microarray Data: A Partial Overview

Susmita Datta

Communications in Statistics: Theory and Methods. Jan 2003, Vol. 32, No. 1: 263-280

Treatment of Microarray Experiments as Split-Plot Designs

Michael Emptage, Buffy Hudson-Curtis, Kapil Sen

Journal of Biopharmaceutical Statistics. Jan 2003, Vol. 13, No. 2: 159-178

Gene expression profiling: methodological challenges, results, and prospects for addiction research

Jonathan D. Pollock

Chemistry and Physics of Lipids. Dec 2002, Vol. 121, No. 1-2: 241-256

Genomic interrogation of mechanism(s) underlying cellular responses to toxicants

R AMIN, H HAMADEH, P BUSHEL, L BENNETT, C AFSHARI, R PAULES

Toxicology. Dec 2002, Vol. 181-182: 555-563

The pathology of brucellosis reflects the outcome of the battle between the host genome and the genome

L ADAMS

Veterinary Microbiology. Dec 2002, Vol. 90, No. 1-4: 553-561

Power and sample size for DNA microarray studies

Mei-Ling Ting Lee, G. A. Whitmore

Statistics in Medicine. Dec 2002, Vol. 21, No. 23: 3543-3570

Of Meis and men: Lessons from a microarray study of teratogen action

Kimberly E. Docterman, Susan M. Smith

Teratology. Nov 2002, Vol. 66, No. 5: 217-223

DNA array-based method for detection of large rearrangements in theBRCA1 gene

Andrey Frolov, Amanda H. Prowse, Lisa Vanderveer, Betsy Bove, Hong Wu, Andrew K. Godwin

Genes, Chromosomes and Cancer. Nov 2002, Vol. 35, No. 3: 232-241

I MPACT OF G ENOMIC T ECHNOLOGIES ON S TUDIES OF B ACTERIAL G ENE E XPRESSION

Virgil Rhodius, Tina K. Van Dyk, Carol Gross, Robert A. LaRossa

Annual Review of Microbiology. Oct 2002, Vol. 56, No. 1: 599-624

Identifying and Quantifying Sources of Variation in Microarray Data Using High-Density cDNA Membrane Arrays

Kevin R. Coombes, W. Edward Highsmith, Tammy A. Krogmann, Keith A. Baggerly, David N. Stivers, Lynne V. Abruzzo

Journal of Computational Biology. Aug 2002, Vol. 9, No. 4: 655-669

Abstract | Full Text PDF | Reprints | Permissions

Bayesian Hierarchical Model for Identifying Changes in Gene Expression from Microarray Experiments

Philippe Broët, Sylvia Richardson, François Radvanyi

Journal of Computational Biology. Aug 2002, Vol. 9, No. 4: 671-683

Abstract | Full Text PDF | Reprints | Permissions

DNA M ICROARRAY T ECHNOLOGY : Devices, Systems, and Applications

Michael J. Heller

Annual Review of Biomedical Engineering. Aug 2002, Vol. 4, No. 1: 129-153

The value of microarray techniques for quantitative gene profiling in molecular diagnostics

Stephen A Bustin, Sina Dorudi

Trends in Molecular Medicine. Jun 2002, Vol. 8, No. 6: 269-272

Role of gene expression microarray analysis in finding complex disease genes

Chi C. Gu, D.C. Rao, Gary Stormo, Chindo Hicks, Michael A. Province

Genetic Epidemiology. Jun 2002, Vol. 23, No. 1: 37-56

Computational selection of distinct class- and subclass-specific gene expression signatures

P Bushel

Journal of Biomedical Informatics. Jun 2002, Vol. 35, No. 3: 160-170

Statistical intelligence: effective analysis of high-density microarray data

Sorin Draghici

Drug Discovery Today. May 2002, Vol. 7, No. 11: S55-S63

Statistical issues with microarrays: processing and analysis

Robert Nadon, Jennifer Shoemaker

Trends in Genetics. May 2002, Vol. 18, No. 5: 265-271

Microarrays in ecology and evolution: a preview

Greg Gibson

Molecular Ecology. Jan 2002, Vol. 11, No. 1: 17-24

The Curse of Normalization

Olaf Wolkenhauer, Carla Möller-Levet, Fatima Sanchez-Cabo

Comparative and Functional Genomics. Jan 2002, Vol. 3, No. 4: 375-379

A novel mechanism for the regulation of osteoblast differentiation: Transcription of periostin, a member of the fasciclin I family, is regulated by the bHLH transcription factor, twist

Akira Oshima, Hideyuki Tanabe, Tao Yan, Gina N. Lowe, Carlotta A. Glackin, Akira Kudo

Journal of Cellular Biochemistry. Jan 2002, Vol. 86, No. 4: 792-804

Heterologous Array Analysis in Pinaceae: Hybridization of Pinus taeda cDNA Arrays with cDNA from Needles and Embryogenic Cultures of P. taeda, P. sylvestris or Picea abies

Leonel van Zyl, Sara von Arnold, Peter Bozhkov, Yongzhong Chen, Ulrika Egertsdotter, John MacKay, Ronald R. Sederoff, Jing Shen, Lyubov Zelena, David H. Clapham

Comparative and Functional Genomics. Jan 2002, Vol. 3, No. 4: 306-318

Models for microarray gene expression data

Mei-Ling Ting Lee, Weining Lu, G. A. Whitmore, David Beier

Journal of Biopharmaceutical Statistics. Jan 2002, Vol. 12, No. 1: 1-19

Identifying Differentially Expressed Genes in cDNA Microarray Experiments

Keith A. Baggerly, Kevin R. Coombes, Kenneth R. Hess, David N. Stivers, Lynne V. Abruzzo, Wei Zhang

Journal of Computational Biology. Nov 2001, Vol. 8, No. 6: 639-659

Abstract | Full Text PDF | Reprints | Permissions

Microarrays: handling the deluge of data and extracting reliable information

K Hess

Trends in Biotechnology. Nov 2001, Vol. 19, No. 11: 463-468

GENE EXPRESSION PROFILINGMethods and Clinical Applications in Oncology

E RAETZ

Hematology/Oncology Clinics of North America. Oct 2001, Vol. 15, No. 5: 911-930

Progress in the Application of DNA Microarrays

Edward K. Lobenhofer, Pierre R. Bushel, Cynthia A. Afshari, Hisham K. Hamadeh

Environmental Health Perspectives. Aug 2001, Vol. 109, No. 9: 881-891

Current Awareness on Comparative and Functional Genomics

Comparative and Functional Genomics. Jan 2001, Vol. 2, No. 6: 401-412

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Using Bayesian Networks to Analyze Expression Data

Nir Friedman, Michal Linial, Iftach Nachman, Dana Pe'er

Journal of Computational Biology. August 2000: 601-620.

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