Characterizing the genetic basis of transcriptome diversity through RNA-sequencing of 922 individuals, Genome Research, vol.24, pp.14-24, 2014. ,
Personalized Medicine and Human Genetic Diversity. Cold Spring Harb Perspect Med, vol.4, pp.8581-8582, 2014. ,
Pharmacogenomics: translating functional genomics into rational therapeutics, 1999. ,
Ectopic Activation of Germline and Placental Genes Identifies Aggressive Metastasis-Prone Lung Cancers, Sci Transl Med. American Association for the Advancement of Science, vol.5, pp.186-66, 2013. ,
URL : https://hal.archives-ouvertes.fr/hal-01261754
Discovery and saturation analysis of cancer genes across 21 tumour types, Nature, vol.505, pp.495-501, 2014. ,
Multiplatform analysis of 12 cancer types reveals molecular classification within and across tissues of origin, Cell, vol.158, pp.929-973, 2014. ,
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2, Genome Biol, vol.15, p.25516281, 2014. ,
edgeR: a Bioconductor package for differential expression analysis of digital gene expression data, Bioinformatics, vol.26, pp.139-179, 2010. ,
limma powers differential expression analyses for RNA-sequencing and microarray studies, Nucleic Acids Research, vol.43, pp.47-54, 2015. ,
The limit fold change model: a practical approach for selecting differentially expressed genes from microarray data, BMC Bioinformatics. BioMed Central, vol.3, p.17, 2002. ,
Why Batch Effects Matter in Omics Data, and How to Avoid Them, Trends in Biotechnology. Elsevier Current Trends, vol.35, pp.498-507, 2017. ,
Selecting between-sample RNA-Seq normalization methods from the perspective of their assumptions, Briefings in Bioinformatics, vol.19, pp.776-92, 2018. ,
Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data, BMC Bioinformatics. BioMed Central, vol.16, p.347, 2015. ,
Developing a "personalome" for precision medicine: emerging methods that compute interpretable effect sizes from single-subject transcriptomes, Briefings in Bioinformatics, vol.63, p.2889, 2017. ,
Individual-level analysis of differential expression of genes and pathways for personalized medicine, Bioinformatics, vol.31, pp.62-70, 2015. ,
A rank-based algorithm of differential expression analysis for small cell line data with statistical control, Briefings in Bioinformatics, vol.20, pp.482-91, 2019. ,
Differential expression analysis for individual cancer samples based on robust within-sample relative gene expression orderings across multiple profiling platforms, Oncotarget, vol.7, pp.68909-68929, 2016. ,
Critical limitations of prognostic signatures based on risk scores summarized from gene expression levels: a case study for resected stage I non-small-cell lung cancer, Briefings in Bioinformatics, vol.17, pp.233-275, 2016. ,
A relative ordering-based predictor for tamoxifentreated estrogen receptor-positive breast cancer patients: multi-laboratory cohort validation, Breast Cancer Res. Treat, vol.142, p.24253811, 2013. ,
DEGseq: an R package for identifying differentially expressed genes from RNA-seq data, Bioinformatics, vol.26, pp.136-144, 2010. ,
Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package, Nucleic Acids Research, vol.43, p.140, 2015. ,
GFOLD: a generalized fold change for ranking differentially expressed genes from RNA-seq data, Bioinformatics, vol.28, pp.2782-2790, 2012. ,
Cancer statistics, Cancer Journal for Clinicians, vol.69, pp.7-34, 2019. ,
, Comprehensive molecular profiling of lung adenocarcinoma, Nature, vol.511, pp.543-50, 2014.
, Comprehensive genomic characterization of squamous cell lung cancers, Nature, vol.489, pp.519-544, 2012.
Distinct patterns of somatic genome alterations in lung adenocarcinomas and squamous cell carcinomas, Nat Genet, vol.48, pp.607-623, 2016. ,
Multiplatform-based molecular subtypes of non-small-cell lung cancer, Oncogene, vol.36, pp.1384-93, 2017. ,
The transcriptional landscape and mutational profile of lung adenocarcinoma, Genome Research, vol.22, pp.2109-2128, 2012. ,
Lung Cancers: Molecular Characterization, Clonal Heterogeneity and Evolution, and Cancer Stem Cells. Cancers (Basel), Multidisciplinary Digital Publishing Institute, vol.10, p.248, 2018. ,
Lung Cancer Biomarkers, Hematol. Oncol. Clin. North Am, vol.31, pp.13-29, 2017. ,
Comprehensive evaluation of published gene expression prognostic signatures for biomarker-based lung cancer clinical studies, Ann. Oncol, vol.28, pp.733-773, 2017. ,
Management of advanced non-small cell lung cancers with known mutations or rearrangements: latest evidence and treatment approaches, Ther Adv Respir Dis. SAGE PublicationsSage UK, vol.10, pp.113-142, 2016. ,
Subtype Classification of Lung Adenocarcinoma Predicts Benefit From Adjuvant Chemotherapy in Patients Undergoing Complete Resection, J. Clin. Oncol. American Society of Clinical Oncology, vol.33, pp.3439-3485, 2015. ,
International association for the study of lung cancer/american thoracic society/european respiratory society international multidisciplinary classification of lung adenocarcinoma, J Thorac Oncol, vol.6, pp.244-85, 2011. ,
URL : https://hal.archives-ouvertes.fr/inserm-00561753
The 2015 World Health Organization Classification of Lung Tumors: Impact of Genetic, Clinical and Radiologic Advances Since the 2004 Classification, J Thorac Oncol, vol.10, pp.1243-60, 2015. ,
Lung squamous cell carcinoma mRNA expression subtypes are reproducible, clinically important, and correspond to normal cell types, Clin. Cancer Res, vol.16, pp.4864-75, 2010. ,
Gene expression profiling reveals reproducible human lung adenocarcinoma subtypes in multiple independent patient cohorts, 2006. ,
Differential analysis of count data-the DESeq2 package, Genome Biology, 2014. ,
Non-small-cell lung cancers: a heterogeneous set of diseases, Nat. Rev. Cancer, vol.14, pp.535-581, 2014. ,
Integrative genomic profiling of large-cell neuroendocrine carcinomas reveals distinct subtypes of high-grade neuroendocrine lung tumors, Nat Commun, vol.9, p.29535388, 2018. ,
Landscape of transcriptional deregulation in lung cancer, BMC Genomics, vol.19, p.29866045, 2018. ,
SOX2 is an amplified lineagesurvival oncogene in lung and esophageal squamous cell carcinomas, Nat Genet, vol.41, pp.1238-1280, 2009. ,
Significance of p63 Amplification and Overexpression in Lung Cancer Development and Prognosis, Cancer Res. American Association for Cancer Research, vol.63, pp.7113-7134, 2003. ,
Targeting HER2 in the treatment of non-small cell lung cancer, Lung Cancer, vol.87, pp.220-225, 2015. ,
Molecular pathways and therapeutic targets in lung cancer, Oncotarget. Impact Journals, LLC, vol.5, pp.1392-433, 2014. ,
Comparative assessment of methods for the computational inference of transcript isoform abundance from RNA-seq data, Genome Biol. BioMed Central, vol.16, p.26201343, 2015. ,
Bias, robustness and scalability in single-cell differential expression analysis. Nat Meth, Nature Publishing Group, vol.15, pp.255-61, 2018. ,
Identification of Commonly Dysregulated Genes in Non-small-cell Lung Cancer by Integrated Analysis of Microarray Data and qRT-PCR Validation, Lung, vol.193, p.25851596, 2015. ,
Structure and function of the GINS complex, a key component of the eukaryotic replisome, Biochem. J, vol.425, pp.489-500, 2010. ,
PSF1, a DNA Replication Factor Expressed Widely in Stem and Progenitor Cells, Drives Tumorigenic and Metastatic Properties, Cancer Res. American Association for Cancer Research, vol.70, pp.1215-1239, 2010. ,
Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles, Nucleic Acids Research, vol.43, pp.44-48, 2015. ,
, Comprehensive Characterization of Cancer Driver Genes and Mutations. Cell, vol.173, pp.371-385, 2018.
fdrtool: a versatile R package for estimating local and tail area-based false discovery rates, Bioinformatics, vol.24, pp.1461-1463, 2008. ,
Efficient analysis of large-scale genome-wide data with two R packages: bigstatsr and bigsnpr, Bioinformatics, vol.34, pp.2781-2788, 2018. ,
Systematic and integrative analysis of large gene lists using DAVID bioinformatics resources, Nat Protoc. Nature Publishing Group, vol.4, pp.44-57, 2009. ,
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists, Nucleic Acids Research, vol.37, pp.1-13, 2009. ,
Differential expression analysis for sequence count data, Genome Biol, vol.11, 2010. ,