Individual-level analysis of differential expression of genes and pathways for personalized medicine

Fold change rank ordering statistics: a new method for detecting differentially expressed genes

(2014) Doulaye Dembélé et al.   BMC BIOINFORMATICS

Correlating transcriptional networks to breast cancer survival: a large-scale coexpression analysis

(2013) Colin Clarke et al.   CARCINOGENESIS

Separate enrichment analysis of pathways for up- and downregulated genes

(2013) G. Hong et al.   Journal of the Royal Society Interface

Gene-pair expression signatures reveal lineage control

(2013) Merja Heinäniemi et al.   NATURE METHODS

Identifying subgroup markers in heterogeneous populations

(2013) Jorma J. de Ronde et al.   NUCLEIC ACIDS RESEARCH

Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers

(2013) S. Rousseaux et al.   Science Translational Medicine

Batch effect removal methods for microarray gene expression data integration: a survey

(2012) C. Lazar et al.   BRIEFINGS IN BIOINFORMATICS

Protein arginine methyltransferase 5 is a potential oncoprotein that upregulates G1 cyclins/cyclin-dependent kinases and the phosphoinositide 3-kinase/AKT signaling cascade

(2012) Tong-You W. Wei et al.   CANCER SCIENCE

Biomarker Discovery in Non-Small Cell Lung Cancer: Integrating Gene Expression Profiling, Meta-analysis, and Tissue Microarray Validation

(2012) J. Botling et al.   CLINICAL CANCER RESEARCH

Revealing weak differential gene expressions and their reproducible functions associated with breast cancer metastasis

(2012) Jinfeng Zou et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

Weighted Change-Point Method for Detecting Differential Gene Expression in Breast Cancer Microarray Data

(2012) Yao Wang et al.   PLoS One

DNA replication stress response involving PLK1, CDC6, POLQ, RAD51 and CLASPIN upregulation prognoses the outcome of early/mid-stage non-small cell lung cancer patients

(2012) C Allera-Moreau et al.   Oncogenesis

Identification of Genes Upregulated in ALK-Positive and EGFR/KRAS/ALK-Negative Lung Adenocarcinomas

(2011) H. Okayama et al.   CANCER RESEARCH

Robust Gene Expression Signature from Formalin-Fixed Paraffin-Embedded Samples Predicts Prognosis of Non-Small-Cell Lung Cancer Patients

(2011) Y. Xie et al.   CLINICAL CANCER RESEARCH

Extensive increase of microarray signals in cancers calls for novel normalization assumptions

(2011) Dong Wang et al.   COMPUTATIONAL BIOLOGY AND CHEMISTRY

DNA methylation profiling reveals a predominant immune component in breast cancers

(2011) Sarah Dedeurwaerder et al.   EMBO Molecular Medicine

Pregnancy-induced chromatin remodeling in the breast of postmenopausal women

(2011) Jose Russo et al.   INTERNATIONAL JOURNAL OF CANCER

Identification of early molecular markers for breast cancer

(2011) Céline Kretschmer et al.   Molecular Cancer

Integration of transcript expression, copy number and LOH analysis of infiltrating ductal carcinoma of the breast

(2010) Lesleyann Hawthorn et al.   BMC CANCER

Identification of a Novel Biomarker, SEMA5A, for Non-Small Cell Lung Carcinoma in Nonsmoking Women

(2010) T.-P. Lu et al.   CANCER EPIDEMIOLOGY BIOMARKERS & PREVENTION

Gene expression profiling reveals novel biomarkers in nonsmall cell lung cancer

(2010) Abel Sanchez-Palencia et al.   INTERNATIONAL JOURNAL OF CANCER

Subtle variations in Pten dose determine cancer susceptibility

(2010) Andrea Alimonti et al.   NATURE GENETICS

Tackling the widespread and critical impact of batch effects in high-throughput data

(2010) Jeffrey T. Leek et al.   NATURE REVIEWS GENETICS

Gene Expression-Based Classification of Non-Small Cell Lung Carcinomas and Survival Prediction

(2010) Jun Hou et al.   PLoS One

Large-Scale Analysis of Network Bistability for Human Cancers

(2010) Tetsuya Shiraishi et al.   PLoS Computational Biology

Proliferative genes dominate malignancy-risk gene signature in histologically-normal breast tissue

(2009) Dung-Tsa Chen et al.   BREAST CANCER RESEARCH AND TREATMENT

Gene expression signatures in breast cancer distinguish phenotype characteristics, histologic subtypes, and tumor invasiveness

(2009) Vincente Pedraza et al.   CANCER

CENPA overexpression promotes genome instability in pRb-depleted human cells

(2009) Angela Amato et al.   Molecular Cancer

Novel Rank-Based Statistical Methods Reveal MicroRNAs with Differential Expression in Multiple Cancer Types

(2009) Roy Navon et al.   PLoS One

Cancer outlier detection based on likelihood ratio test

(2008) Jianhua Hu   BIOINFORMATICS