A provisional set of references for preparation for CDATA-08
Cautions
Irreproducibility
Microarrays: retracing steps.
Coombes, Wang, Baggerly, Nat. Med.(2007)
The importance of experimental design in proteomic mass spectrometry experiments: some cautionary tales.
Hu, Coombes, Morris, et al., Briefings in functional genomics & proteomics(2005)
Batch effects
On the design and analysis of gene expression studies in human populations.
Akey, Biswas, Leek, et al., Nat. Genet.(2007)
Run batch effects potentially compromise the usefulness of genomic signatures for ovarian cancer.
Baggerly, Coombes, Neeley, J. Clin. Oncol.(2008)
Yeast
Cell cycle
Comprehensive identification of cell cycle-regulated genes of the yeast Saccharomyces cerevisiae by microarray hybridization.
Spellman, Sherlock, Zhang, et al., Mol. Biol. Cell(1998)
Transcriptional regulatory networks in Saccharomyces cerevisiae.
Lee, Rinaldi, Robert, et al., Science(2002)
Environmental stress response
Genomic expression programs in the response of yeast cells to environmental changes.
Gasch, Spellman, Kao, et al., Mol. Biol. Cell(2000)
Species divergence of TFBS
Divergence of transcription factor binding sites across related yeast species.
Borneman, Gianoulis, Zhang, et al., Science(2007)
Transcriptional regulation
Predictive modeling of genome-wide mRNA expression: from modules to molecules.
Bussemaker, Foat, Ward, Annual review of biophysics and biomolecular structure(2007)
Defining transcriptional networks through integrative modeling of mRNA expression and transcription factor binding data.
Gao, Foat, Bussemaker, BMC Bioinformatics(2004)
Post-transcriptional regulation
Profiling condition-specific, genome-wide regulation of mRNA stability in yeast.
Foat, Houshmandi, Olivas, et al., Proc. Natl. Acad. Sci. U.S.A.(2005)
Expression arrays
Theory: absolute mRNA concentrations
Absolute mRNA concentrations from sequence-specific calibration of oligonucleotide arrays.
Hekstra, Taussig, Magnasco, et al., Nucleic Acids Res.(2003)
Application: Breast cancer/stem compendium
An embryonic stem cell-like gene expression signature in poorly differentiated aggressive human tumors.
Ben-Porath, Thomson, Carey, et al., Nat. Genet.(2008)
Application: Pancreatic cancer/pathway addiction
Coordinated epidermal growth factor receptor pathway gene overexpression predicts epidermal growth factor receptor inhibitor sensitivity in pancreatic cancer.
Jimeno, Tan, Coffa, et al., Cancer Res.(2008)
Protein-DNA arrays
TF binding specificities
Compact, universal DNA microarrays to comprehensively determine transcription-factor binding site specificities.
Berger, Philippakis, Qureshi, et al., Nat. Biotechnol.(2006)
DNA microarray technologies for measuring protein-DNA interactions.
Bulyk, Curr. Opin. Biotechnol.(2006)
Harmen
DNA binding sites: representation and discovery.
Stormo, Bioinformatics(2000)
Expression plus genotyping
Early work
Mapping determinants of human gene expression by regional and genome-wide association.
Cheung, Spielman, Ewens, et al., Nature(2005)
GGtools: analysis of genetics of gene expression in bioconductor.
Carey, Morgan, Falcon, et al., Bioinformatics(2007)
Multiple populations
Common genetic variants account for differences in gene expression among ethnic groups.
Spielman, Bastone, Burdick, et al., Nat. Genet.(2007)
Population genomics of human gene expression.
Stranger, Nica, Forrest, et al., Nat. Genet.(2007)
Drosophila
Speed-mapping quantitative trait loci using microarrays.
Lai, Leips, Zou, et al., Nat. Methods(2007)
Ain't misbehavin' ? Genotype-environment interactions and the genetics of behavior.
Mackay, Anholt, Trends Genet.(2007)
Structural variation
Copy number: Breast cancer cell lines
A collection of breast cancer cell lines for the study of functionally distinct cancer subtypes.
Neve, Chin, Fridlyand, et al., Cancer Cell(2006)
Copy number: Glioma
Assessing the significance of chromosomal aberrations in cancer: methodology and application to glioma.
Beroukhim, Getz, Nghiemphu, et al., Proc. Natl. Acad. Sci. U.S.A.(2007)
Paired end mapping
Paired-end mapping reveals extensive structural variation in the human genome.
Korbel, Urban, Affourtit, et al., Science(2007)
High-throughput sequencing
Overview
Emerging technologies in DNA sequencing.
Metzker, Genome Res.(2005)
Primer: Sequencing--the next generation.
Rusk, Kiermer, Nat. Methods(2008)
Impact
The impact of next-generation sequencing technology on genetics.
Mardis, Trends Genet.(2008)
Statistics
Linear models
Linear models and empirical bayes methods for assessing differential expression in microarray experiments.
Smyth, Statistical applications in genetics and molecular biology(2004)
Motif finding
Extracting regulatory sites from the upstream region of yeast genes by computational analysis of oligonucleotide frequencies.
van Helden, André, Collado-Vides, J. Mol. Biol.(1998)
Regulatory element detection using correlation with expression.
Bussemaker, Li, Siggia, Nat. Genet.(2001)
Multiple testing
Identifying differentially expressed genes using false discovery rate controlling procedures.
Reiner, Yekutieli, Benjamini, Bioinformatics(2003)
GSEA
Gene set enrichment analysis: a knowledge-based approach for interpreting genome-wide expression profiles.
Subramanian, Tamayo, Mootha, et al., Proc. Natl. Acad. Sci. U.S.A.(2005)
Dissecting complex transcriptional responses using pathway-level scores based on prior information.
Bussemaker, Ward, Boorsma, BMC Bioinformatics(2007)
Extensions to gene set enrichment.
Jiang, Gentleman, Bioinformatics(2007)
Regularized LDA
Regularized linear discriminant analysis and its application in microarrays.
Guo, Hastie, Tibshirani, Biostatistics (Oxford, England)(2007)
Computing
Bioconductor
Bioconductor: open software development for computational biology and bioinformatics.
Gentleman, Carey, Bates, et al., Genome Biol.(2004)
Reproducible research
Reproducible research: a bioinformatics case study.
Gentleman, Statistical applications in genetics and molecular biology(2005)
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