Genome Biology

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A new non-linear normalization method for reducing variability in DNA microarray experiments

Christopher Workman*, Lars J Jensen, Hanne Jarmer, Randy Berka, Laurent Gautier, Henrik B Nielser, Hans-Henrik Saxild, Claus Nielsen, Søren Brunak and Steen Knudsen

Genome Biology 2002, 3:research0048-research0048.16 doi:10.1186/gb-2002-3-9-research0048

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BioMed Central: 29 citations

Research article   Open Access

Bayesian integrated modeling of expression data: a case study on RhoG

Rashi Gupta, Dario Greco, Petri Auvinen, Elja Arjas BMC Bioinformatics 2010, 11:295 (1 June 2010)

Research article   Open Access

Hybridization thermodynamics of NimbleGen Microarrays

Ulrike Mueckstein, Germán G Leparc, Alexandra Posekany, Ivo Hofacker, David P Kreil BMC Bioinformatics 2010, 11:35 (19 January 2010)

Research article   Open Access

New insights into molecular pathways associated with flatfish ovarian development and atresia revealed by transcriptional analysis

Angèle Tingaud-Sequeira, François Chauvigné, Juanjo Lozano, María J Agulleiro, Esther Asensio, Joan Cerdà BMC Genomics 2009, 10:434 (15 September 2009)

Research article   Open Access

Comparative genomics in chicken and Pekin duck using FISH mapping and microarray analysis

Benjamin M Skinner, Lindsay BW Robertson, Helen G Tempest, Elizabeth J Langley, Dimitris Ioannou, Katie E Fowler, Richard PMA Crooijmans, Anthony D Hall, Darren K Griffin, Martin Völker BMC Genomics 2009, 10:357 (5 August 2009)

Method   Open Access Highly Accessed

A novel and universal method for microRNA RT-qPCR data normalization

Pieter Mestdagh, Pieter Van Vlierberghe, An De Weer, Daniel Muth, Frank Westermann, Frank Speleman, Jo Vandesompele Genome Biology 2009, 10:R64 (16 June 2009)

The mean expression value: a new method for accurate and reliable normalization of microRNA expression data from RT-qPCR experiments.

Methodology article   Open Access Highly Accessed

Improved ChIP-chip analysis by a mixture model approach

Wei Sun, Michael J Buck, Mukund Patel, Ian J Davis BMC Bioinformatics 2009, 10:173 (7 June 2009)

Methodology article   Open Access Highly Accessed

Comparative analysis of methods for gene transcription profiling data derived from different microarray technologies in rat and mouse models of diabetes

Steven P Wilder, Pamela J Kaisaki, Karène Argoud, Anita Salhan, Jiannis Ragoussis, Marie-Thérèse Bihoreau, Dominique Gauguier BMC Genomics 2009, 10:63 (5 February 2009)

Methodology article   Open Access

Use of normalization methods for analysis of microarrays containing a high degree of gene effects

Terri T Ni, William J Lemon, Yu Shyr, Tao P Zhong BMC Bioinformatics 2008, 9:505 (28 November 2008)

Research article   Open Access

Refined annotation and assembly of the Tetrahymena thermophila genome sequence through EST analysis, comparative genomic hybridization, and targeted gap closure

Robert S Coyne, Mathangi Thiagarajan, Kristie M Jones, Jennifer R Wortman, Luke J Tallon, Brian J Haas, Donna M Cassidy-Hanley, Emily A Wiley, Joshua J Smith, Kathleen Collins, Suzanne R Lee, Mary T Couvillion, Yifan Liu, Jyoti Garg, Ronald E Pearlman, Eileen P Hamilton, Eduardo Orias, Jonathan A Eisen, Barbara A Methé BMC Genomics 2008, 9:562 (26 November 2008)

Research article   Open Access

Genomic resources for a commercial flatfish, the Senegalese sole (Solea senegalensis): EST sequencing, oligo microarray design, and development of the Soleamold bioinformatic platform

Joan Cerdà, Jaume Mercadé, Juan Lozano, Manuel Manchado, Angèle Tingaud-Sequeira, Antonio Astola, Carlos Infante, Silke Halm, Jordi Viñas, Barbara Castellana, Esther Asensio, Pedro Cañavate, Gonzalo Martínez-Rodríguez, Francesc Piferrer, Josep V Planas, Francesc Prat, Manuel Yúfera, Olga Durany, Francesc Subirada, Elisabet Rosell, Tamara Maes BMC Genomics 2008, 9:508 (30 October 2008)

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Gene expression profiling of liver from dairy cows treated intra-mammary with lipopolysaccharide

Li Jiang, Peter Sørensen, Christine Røntved, Lotte Vels, Klaus L Ingvartsen BMC Genomics 2008, 9:443 (24 September 2008)

Research article   Open Access Highly Accessed

Transcription factor control of growth rate dependent genes in Saccharomyces cerevisiae: A three factor design

Alessandro Fazio, Michael C Jewett, Pascale Daran-Lapujade, Roberta Mustacchi, Renata Usaite, Jack T Pronk, Christopher T Workman, Jens Nielsen BMC Genomics 2008, 9:341 (18 July 2008)

Research article   Open Access Highly Accessed

Whole genome comparative studies between chicken and turkey and their implications for avian genome evolution

Darren K Griffin, Lindsay B Robertson, Helen G Tempest, Alain Vignal, Valérie Fillon, Richard PMA Crooijmans, Martien AM Groenen, Svetlana Deryusheva, Elena Gaginskaya, Wilfrid Carré, David Waddington, Richard Talbot, Martin Völker, Julio S Masabanda, Dave W Burt BMC Genomics 2008, 9:168 (14 April 2008)

Research   Open Access Highly Accessed

Time-course analysis of genome-wide gene expression data from hormone-responsive human breast cancer cells

Margherita Mutarelli, Luigi Cicatiello, Lorenzo Ferraro, Olì MV Grober, Maria Ravo, Angelo M Facchiano, Claudia Angelini, Alessandro Weisz BMC Bioinformatics 2008, 9(Suppl 2):S12 (26 March 2008)

Research article   Open Access Highly Accessed

Normalization of oligonucleotide arrays based on the least-variant set of genes

Stefano Calza, Davide Valentini, Yudi Pawitan BMC Bioinformatics 2008, 9:140 (5 March 2008)

Methodology article   Open Access Highly Accessed

Using Generalized Procrustes Analysis (GPA) for normalization of cDNA microarray data

Huiling Xiong, Dapeng Zhang, Christopher J Martyniuk, Vance L Trudeau, Xuhua Xia BMC Bioinformatics 2008, 9:25 (16 January 2008)

Software   Open Access Highly Accessed

GEDI: a user-friendly toolbox for analysis of large-scale gene expression data

André Fujita, João R Sato, Carlos E Ferreira, Mari C Sogayar BMC Bioinformatics 2007, 8:457 (19 November 2007)

Research article   Open Access

Androgen-induced masculinization in rainbow trout results in a marked dysregulation of early gonadal gene expression profiles

Daniel Baron, Jérôme Montfort, Rémi Houlgatte, Alexis Fostier, Yann Guiguen BMC Genomics 2007, 8:357 (4 October 2007)

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Prediction of highly expressed genes in microbes based on chromatin accessibility

Hanni Willenbrock, David W Ussery BMC Molecular Biology 2007, 8:11 (13 February 2007)

Bacterial genes are highly expressed if their DNA structure tends to exclude chromatin, an association that is much better at predicting expression levels than codon usage perhaps because the DNA is accessible to transcriptional machinery.

Research   Open Access Highly Accessed

An environmental signature for 323 microbial genomes based on codon adaptation indices

Hanni Willenbrock, Carsten Friis, Agnieszka S Juncker, David W Ussery Genome Biology 2006, 7:R114 (7 December 2006)

The correlation of two methods for estimating codon adaptation indices applied to more than 300 bacterial species shows that codon usage preference provides an environmental signature by which it is possible to group bacteria according to their lifestyle

Research   Open Access

Metabolic network driven analysis of genome-wide transcription data from Aspergillus nidulans

Helga David, Gerald Hofmann, Ana Oliveira, Hanne Jarmer, Jens Nielsen Genome Biology 2006, 7:R108 (15 November 2006)

Genome-wide transcription analysis of Aspergillus nidulans grown on different carbon sources and a reconstruction of the complete metabolic network of this filamentous fungi are presented.

Software   Open Access Highly Accessed

AMDA: an R package for the automated microarray data analysis

Mattia Pelizzola, Norman Pavelka, Maria Foti, Paola Ricciardi-Castagnoli BMC Bioinformatics 2006, 7:335 (6 July 2006)

Software   Open Access

SBEAMS-Microarray: database software supporting genomic expression analyses for systems biology

Bruz Marzolf, Eric W Deutsch, Patrick Moss, David Campbell, Michael H Johnson, Timothy Galitski BMC Bioinformatics 2006, 7:286 (6 June 2006)

Research article   Open Access Highly Accessed

Comparison of normalization methods for CodeLink Bioarray data

Wei Wu, Nilesh Dave, George C Tseng, Thomas Richards, Eric P Xing, Naftali Kaminski BMC Bioinformatics 2005, 6:309 (28 December 2005)

Research article   Open Access Highly Accessed

Evaluation of normalization methods for cDNA microarray data by k-NN classification

Wei Wu, Eric P Xing, Connie Myers, I Saira Mian, Mina J Bissell BMC Bioinformatics 2005, 6:191 (26 July 2005)

Of forty-one strategies for removing dye biases in microarray data that were tested by k-NN leave-one-out-validation, three two-step processes, which removed intensity-dependent bias and local spatial effects, reduced classification errors most consistently and effectively across all data sets.

Methodology article   Open Access Highly Accessed

Quality assessment of microarrays: Visualization of spatial artifacts and quantitation of regional biases

Mark Reimers, John N Weinstein BMC Bioinformatics 2005, 6:166 (1 July 2005)

Methodology article   Open Access

Two-stage normalization using background intensities in cDNA microarray data

Dankyu Yoon, Sung-Gon Yi, Ju-Han Kim, Taesung Park BMC Bioinformatics 2004, 5:97 (21 July 2004)

Methodology article   Open Access

Improving the statistical detection of regulated genes from microarray data using intensity-based variance estimation

Jason Comander, Sripriya Natarajan, Michael A Gimbrone, Guillermo García-Cardeña BMC Genomics 2004, 5:17 (27 February 2004)

Methodology article   Open Access Highly Accessed

Three-parameter lognormal distribution ubiquitously found in cDNA microarray data and its application to parametric data treatment

Tomokazu Konishi BMC Bioinformatics 2004, 5:5 (13 January 2004)