Microarray data analysis: from disarray to consolidation and consensus

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PGC-1α-responsive genes involved in oxidative phosphorylation are coordinately downregulated in human diabetes

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Summaries of Affymetrix GeneChip probe level data

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Normalization for cDNA microarray data: a robust composite method addressing single and multiple slide systematic variation.

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The positive false discovery rate: a Bayesian interpretation and the q-value

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Microarray data normalization and transformation

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Multidimensionality of microarrays: Statistical challenges and (im)possible solutions

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Jun, Gal, Cd74, and C1qb as potential indicator for neuropathic pain

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Blood-based transcriptomics: leukemias and beyond

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Gene expression profiling of the uterus with embryos cloned by somatic cell nuclear transfer on day 30 of pregnancy

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Visualisation of the T cell differentiation programme by Canonical Correspondence Analysis of transcriptomes

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Transcriptome analysis identifies Bacillus anthracis genes that respond to CO2through an AtxA-dependent mechanism

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Detecting differentially expressed genes in heterogeneous diseases using half Student’s t-test

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A Fast and Simple Contact Printing Approach to Generate 2D Protein Nanopatterns

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Development of a peripheral blood transcriptomic gene signature to predict bronchopulmonary dysplasia

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Comparison of volatile aroma compounds in commercial surimi and their products from freshwater fish and marine fish and aroma fingerprints establishment based on metabolomics analysis methods

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Persistent proteomic alterations in the medial prefrontal cortex with abstinence from cocaine self‐administration

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Computational intelligence and machine learning in bioinformatics

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Using high-density exon arrays to profile gene expression in closely related species

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Syndecan-4 as a Biomarker to Predict Clinical Outcome for Glioblastoma Multiforme Treated with WT1 Peptide Vaccine

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Transcriptome-wide analysis of the Trypanosoma cruzi proliferative cycle identifies the periodically expressed mRNAs and their multiple levels of control

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Comprehensive evaluation of differential lncRNA and gene expression in patients with intervertebral disc degeneration

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Derivation of Cancer Diagnostic and Prognostic Signatures from Gene Expression Data

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Pathological Image Analysis Using the GPU: Stroma Classification for Neuroblastoma

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Genetics and Genomics

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When to use Quantile Normalization?Preprint

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An integrative approach for measuring semantic similarities using gene ontology

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FWCMR: A scalable and robust fuzzy weighted clustering based on MapReduce with application to microarray gene expression

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CEEMD-assisted bearing degradation assessment using tight clustering

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Proteomic Workflows for Biomarker Identification Using Mass Spectrometry — Technical and Statistical Considerations during Initial Discovery

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Diversity of Ca 2+ -Induced Morphology Revealed by Morphological Phenotyping of Ca 2+ -Sensitive Mutants of Saccharomyces cerevisiae

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Toxicogenomic Approaches in Developmental Toxicology Testing

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An Integrated Bioinformatics Analysis Repurposes an Antihelminthic Drug Niclosamide for Treating HMGA2-Overexpressing Human Colorectal Cancer

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Testing significance of features by lassoed principal components

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Clinical proteomics in neurodegenerative diseases

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Transcriptome Analysis of CHO Cell Size Increase During a Fed-Batch Process

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Screening Biomarkers of Prostate Cancer by Integrating microRNA and mRNA Microarrays

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Functional meta-analysis of double connectivity in gene coexpression networks in mammals

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Research Techniques Made Simple: Bioinformatics for Genome-Scale Biology

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Biomarker identification in clear cell renal cell carcinoma based on miRNA-seq and digital gene expression-seq data

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Identification of key genes and functions of circulating tumor cells in multiple cancers through bioinformatic analysis

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A Systems Biology Strategy on Differential Gene Expression Data Discloses Some Biological Features of Atrial Fibrillation

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A Test for Partial Differential Expression

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Testing the hypothesis of tissue selectivity: the intersection–union test and a Bayesian approach

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A simulation-approximation approach to sample size planning for high-dimensional classification studies

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Distinct transcriptional changes in non-small cell lung cancer patients associated with multi-antigenic RNActive® CV9201 immunotherapy

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Comprehensive RNA-Seq Profiling Reveals Temporal and Tissue-Specific Changes in Gene Expression in Sprague–Dawley Rats as Response to Heat Stress Challenges

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ExcellmiRDB for Translational Genomics: A Curated Online Resource for Extracellular MicroRNAs

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Global Quantitative Proteomic Profiling through 18O-Labeling in Combination with MS/MS Spectra Analysis

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SpRay: A visual analytics approach for gene expression data

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Formulating and testing hypotheses in functional genomics

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Reanalysis and integration of public microarray datasets reveals novel host genes modulated in leprosy

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Microarray studies in pulmonary arterial hypertension

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Blood cells transcriptomics as source of potential biomarkers of articular health improvement: effects of oral intake of a rooster combs extract rich in hyaluronic acid

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Age-related changes in gene expression in tissues of the sea urchin Strongylocentrotus purpuratus

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Glucose levels and genetic variants across transcriptional pathways: interaction effects with BMI

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Processes Underlying the Nutritional Programming of Embryonic Development by Iron Deficiency in the Rat

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Tools for Interpreting Large-scale Protein Profiling in Microbiology

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Selective discussion and transparency in microarray research findings for cancer outcomes

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Development and application of a DNA microarray-based yeast two-hybrid system

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Molecular evidence‐based medicine

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Introduction to Sequencing the Brain Transcriptome

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Laplace Approximated EM Microarray Analysis: An Empirical Bayes Approach for Comparative Microarray Experiments

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Identification of potential hub genes associated with skin wound healing based on time course bioinformatic analyses

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A Faster cDNA Microarray Gene Expression Data Classifier for Diagnosing Diseases

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The use of neuroproteomics in drug abuse research

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UVB Radiation Induces Persistent Activation of Ribosome and Oxidative Phosphorylation Pathways

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Genomic studies in ageing research: the need to integrate genetic and gene expression approaches

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Genes and biochemical pathways in human skeletal muscle affecting resting energy expenditure and fuel partitioning

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Widespread inference of weighted microRNA-mediated gene regulation in cancer transcriptome analysis

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Comparison of variable selection methods for high-dimensional survival data with competing events

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Transcriptome analysis for the scale-down of a CHO cell fed-batch process

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Male Sex Interspecies Divergence and Down Regulation of Expression of Spermatogenesis Genes in Drosophila Sterile Hybrids

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Differential expression of DNA repair genes in Hispanic women with breast cancer.

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The Effect of Edge Bundling and Seriation on Sensemaking of Biclusters in Bipartite Graphs

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Early days: genomics and human responses to infection

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An integrative gene selection with association analysis for microarray data classification

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Comparative evaluation of set-level techniques in predictive classification of gene expression samples

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SVM-RCE-R-OPT: Optimization of Scoring Function for SVM-RCE-R

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RNA isolation for transcriptomics of human and mouse small skin biopsies

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Optically Encoded Particles and Their Applications in Multiplexed Biomedical Assays

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Advances in the application of high-throughput sequencing in invertebrate virology

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Melittin Constrains the Expression of Identified Key Genes Associated with Bladder Cancer

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Detecting outlier microarray arrays by correlation and percentage of outliers spots.

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Systems Biology Approach to Identify Gene Network Signatures for Colorectal Cancer

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An evaluation framework for statistical tests on microarray data

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A new molecular breast cancer subclass defined from a large scale real-time quantitative RT-PCR study

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Transcriptional correlates of memory maintenance following long-term sensitization of Aplysia californicaPreprint

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Functional studies on transfected cell microarray analysed by linear regression modelling

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Tumor suppressor ATP4B serve as a promising biomarker for worsening of gastric atrophy and poor differentiation

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An analytical pipeline to support robust research on the ecology, evolution, and function of floral volatiles

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BIRCH: An Automated Workflow for Evaluation, Correction, and Visualization of Batch Effect in Bottom-Up Mass Spectrometry-Based Proteomics Data

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Multi-study Integration of Brain Cancer Transcriptomes Reveals Organ-Level Molecular Signatures

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Dose-Dependent Effects of Morphine Exposure on mRNA and microRNA (miR) Expression in Hippocampus of Stressed Neonatal Mice

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Improving the power for detecting overlapping genes from multiple DNA microarray-derived gene lists

Deng, X., Xu, J., & Wang, C. (2008) · BMC Bioinformatics · doi:10.1186/1471-2105-9-s6-s14 · Cited by 18

A procedure to statistically evaluate agreement of differential expression for cross-species genomics

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Rapid modulation of gene expression profiles in the telencephalon of male goldfish following exposure to waterborne sex pheromones

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Rewritable remote encoding and decoding of miniature multi-bit magnetic tags for high-throughput biological analysis

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Equivalence testing in microarray analysis: similarities in the transcriptome of human atherosclerotic and nonatherosclerotic macrophages

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The Effect of Nicotinamide on Gene Expression in a Traumatic Brain Injury Model

Anderson, G., Peterson, T. C., Farin, F., Bammler, T., Beyer, R., Kantor, E., & Hoane, M. R. (2013) · Frontiers in Neuroscience · doi:10.3389/fnins.2013.00021 · Cited by 18

Identification of candidate genes in atopic dermatitis based on bioinformatic methods

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Homogeneous Inflammatory Gene Profiles Induced in Human Dermal Fibroblasts in Response to the Three Main Species of Borrelia burgdorferi sensu lato

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Leukocyte Dynamics Influence Reference Gene Stability in Whole Blood: Data-Driven qRT-PCR Normalization Is a Robust Alternative for Measurement of Transcriptional Biomarkers

O’Connell, G. C., Treadway, M. B., Petrone, A. B., Tennant, C. S., Lucke-Wold, N., Chantler, P. D., & Barr, T. L. (2017) · Laboratory Medicine · doi:10.1093/labmed/lmx035 · Cited by 18

Microarray analysis of gender- and parasite-specific gene transcription in Strongyloides ratti☆

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Gene expression microarray data analysis demystified

Roberts, P. C. (2008) · Biotechnology annual review · doi:10.1016/s1387-2656(08)00002-1 · Cited by 29

Exploring statistical methods for analysis of microarray data

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Statistical analysis of gene expression microarray data

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Computational analysis of microarray data

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