Nature Search

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi
Wendell Jones
Weida Tong
ResearchOpen Access03 Jul 2007
Nature Precedings

P: 1
The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Leming Shi
Wendell Jones
Weida Tong
ResearchOpen Access02 Jul 2007
Nature Precedings

P: 1
Shift in the urinary metabolome associated with 2,3,7,8-tetrachlorodibenzo-p-dioxin activation of the hepatic aryl hydrocarbon receptor

Warren J. Sink
Russell Fling
Tim Zacharewski
ResearchOpen Access18 Jul 2025
Scientific Reports

Volume: 15, P: 1-19
A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

Gene expression is highly variable between tissues, and changes during development and with age. Here, the authors provide a comprehensive RNA-Seq analysis of the rat transcriptome, spanning eleven organs, four developmental stages and both sexes.

Ying Yu
James C. Fuscoe
Charles Wang
ResearchOpen Access10 Feb 2014
Nature Communications

Volume: 5, P: 1-11
Geographical genomics of human leukocyte gene expression variation in southern Morocco

Greg Gibson and colleagues report an analysis of gene expression variation in relation to environmental geography and ethnicity in blood leukocyte samples from individuals in rural and urban southern Morocco. The study determined the contributions of geography and ethnicity to associations between genotypes and transcript abundance.

Youssef Idaghdour
Wendy Czika
Greg Gibson
Research06 Dec 2009
Nature Genetics

Volume: 42, P: 62-67
The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster

Wei Jin
Rebecca M. Riley
Greg Gibson
Research26 Nov 2001
Nature Genetics

Volume: 29, P: 389-395
A framework for automated scalable designation of viral pathogen lineages from genomic data

Automated and scalable designation of virus lineages based on a heuristic approach can help to determine and curate virus lineages from large genomic datasets and inform nomenclature.

Jakob McBroome
Adriano de Bernardi Schneider
Russell Corbett-Detig
ResearchOpen Access05 Feb 2024
Nature Microbiology

Volume: 9, P: 550-560
Reanalysis of Richter et al. (2010) on reproducibility

Russell D Wolfinger
Correspondence29 Apr 2013
Nature Methods

Volume: 10, P: 373-374
A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

The Sequencing Quality Control (SEQC) consortium shows that junction discovery and differential gene expression profiling with RNA-seq can be robust but transcript-level and absolute measurements remain challenging.

Zhenqiang Su
Paweł P Łabaj
Leming Shi
Research24 Aug 2014
Nature Biotechnology

Volume: 32, P: 903-914
The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

The Microarray Quality Control consortium pitted 36 teams against each other to evaluate methods for creating genomic classifiers, computational tools for interpreting gene expression profiles. The performance of the classifiers on blinded validation data—and metadata on the analytic methods—reveal the challenges facing the field.

Leming Shi
Gregory Campbell
Russell D Wolfinger
Research30 Jul 2010
Nature Biotechnology

Volume: 28, P: 827-838
The international MAQC Society launches to enhance reproducibility of high-throughput technologies

Leming Shi
Rebecca Kusko
Weida Tong
Correspondence08 Dec 2017
Nature Biotechnology

Volume: 35, P: 1127-1128
Evaluation of external RNA controls for the assessment of microarray performance

Weida Tong
Anne Bergstrom Lucas
Leming Shi
Research09 Aug 2006
Nature Biotechnology

Volume: 24, P: 1132-1139
Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project

Tucker A Patterson
Edward K Lobenhofer
Russell D Wolfinger
Research08 Sept 2006
Nature Biotechnology

Volume: 24, P: 1140-1150

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The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

The Reproducibility of Lists of Differentially Expressed Genes in Microarray Studies

Shift in the urinary metabolome associated with 2,3,7,8-tetrachlorodibenzo-p-dioxin activation of the hepatic aryl hydrocarbon receptor

A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages

Geographical genomics of human leukocyte gene expression variation in southern Morocco

The contributions of sex, genotype and age to transcriptional variance in Drosophila melanogaster

A framework for automated scalable designation of viral pathogen lineages from genomic data

Reanalysis of Richter et al. (2010) on reproducibility

A comprehensive assessment of RNA-seq accuracy, reproducibility and information content by the Sequencing Quality Control Consortium

The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models

The international MAQC Society launches to enhance reproducibility of high-throughput technologies

Evaluation of external RNA controls for the assessment of microarray performance

Performance comparison of one-color and two-color platforms within the Microarray Quality Control (MAQC) project

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