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List of works by Charles Auffray

"T2-high" in severe asthma related to blood eosinophil, exhaled nitric oxide and serum periostin

scientific article published on 03 January 2019

'The 39 steps' in gene expression profiling: critical issues and proposed best practices for microarray experiments

scientific article

2012 highlights in translational 'omics ⬇️

scientific article published on January 31, 2013

A Topological Data Analysis Network Model of Asthma Based on Blood Gene Expression Profiles

article

A Transcriptome-driven Analysis of Epithelial Brushings and Bronchial Biopsies to Define Asthma Phenotypes in U-BIOPRED

scientific article published on 15 February 2017

A computational framework for complex disease stratification from multiple large-scale datasets.

scientific article published on 29 May 2018

A functional and regulatory network associated with PIP expression in human breast cancer

scientific article

A minimum of four human class II α-chain genes are encoded in the HLA region of chromosome 6 ⬇️

scientific article published on July 14, 1983

A prioritization analysis of disease association by data-mining of functional annotation of human genes

scientific article

A transgenic mouse model engineered to investigate human brain-derived neurotrophic factor in vivo

scientific article

ALP and MLP distribution during myofibrillogenesis in cultured cardiomyocytes

scientific article

Affinity analysis of differentially expressed genes in hepatocytes expressing HCV core genotype 1b or 3a.

scientific article published on 3 June 2013

Alternative usage of 5' exons in the chicken nerve growth factor gene: refined characterization of a weakly expressed gene

scientific article

An integrative systems biology approach to understanding pulmonary diseases

scientific article published in June 2010

Application of 'omics technologies to biomarker discovery in inflammatory lung diseases

scientific article published on 08 February 2013

AsthmaMap: An expert-driven computational representation of disease mechanisms

scholarly article by Alexander Mazein et al published 30 July 2018 in Clinical & Experimental Allergy

Author Correction: COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 17 July 2020

Author Correction: Introducing PIONEER: a project to harness big data in prostate cancer research

scientific article published on 25 June 2020

Autism cornered: network analyses reveal mechanisms of autism spectrum disorders

scientific article published on 30 December 2014

Biochemical and transcriptomic analyses of two bovine skeletal muscles in Charolais bulls divergently selected for muscle growth

scientific article published on 16 March 2005

Bridging the gap between systems biology and medicine

scientific article published on 29 September 2009

COVID-19 Disease Map, building a computational repository of SARS-CoV-2 virus-host interaction mechanisms

scientific article published on 05 May 2020

COVID-19 and beyond: a call for action and audacious solidarity to all the citizens and nations, it is humanity’s fight

scientific article published in 2020

Characterization of a new human isoform of the enigma homolog family specifically expressed in skeletal muscle

scientific article

Characterization of tissue expression and full-length coding sequence of a novel human gene mapping at 3q12.1 and transcribed in oligodendrocytes

scientific article

Clinical and inflammatory characteristics of the European U-BIOPRED adult severe asthma cohort

scientific article published on 10 September 2015

Community-driven roadmap for integrated disease maps

scientific article published on 23 April 2018

Computational Methods and Bioinformatic Tools

Computational analysis of multimorbidity between asthma, eczema and rhinitis

scientific article

Computational disease modeling - fact or fiction?

scientific article

Contribution of airway eosinophils in airway wall remodeling in asthma: Role of MMP-10 and MET

scientific article published on 11 February 2019

Coordination of intrinsic, extrinsic, and endoplasmic reticulum-mediated apoptosis by imatinib mesylate combined with arsenic trioxide in chronic myeloid leukemia

scientific article published on 25 October 2005

Corrigendum to “Gene expression profiling of human satellite cells during muscular aging using cDNA arrays” [Gene 321 (2003) 145–154]

article

DNA Methylation in Newborns and Maternal Smoking in Pregnancy: Genome-wide Consortium Meta-analysis

scientific article published on 30 March 2016

DNA methylation in childhood asthma: an epigenome-wide meta-analysis

scientific article published on 26 February 2018

Drug specific resistance to oxaliplatin is associated with apoptosis defect in a cellular model of colon carcinoma

scientific article published on October 2002

Editorial: Systems biology and personalized medicine - the future is now.

scientific article published in August 2012

Enabling multiscale modeling in systems medicine

scientific article

Epigenome-Wide Meta-Analysis of Methylation in Children Related to Prenatal NO2 Air Pollution Exposure

scientific article published on 22 July 2016

Epithelial dysregulation in obese severe asthmatics with gastro-oesophageal reflux

scientific article published on 27 June 2019

Erratum to: Making sense of big data in health research: towards an EU action plan

scientific article

Exposure to Traffic-Related Air Pollution and Serum Inflammatory Cytokines in Children

scientific article

Foreword: from the TRANSCRIPTOME conferences to the SYSTEMOSCOPE international consortium

scientific article published on October 2003

From functional genomics to systems biology: concepts and practices

scientific article published on October 2003

From genomic medicine to precision medicine: highlights of 2015.

scientific article published on 29 January 2016

Functional Annotation: extracting functional and regulatory order from microarrays

scientific article published on 25 May 2005

Gene expression profiling of human satellite cells during muscular aging using cDNA arrays

scientific article published in December 2003

Genome Medicine: past, present and future ⬇️

scientific article published on January 31, 2011

Genome-Wide Interaction Analysis of Air Pollution Exposure and Childhood Asthma with Functional Follow-up

scientific article published on 30 November 2016

HNF1alpha inactivation promotes lipogenesis in human hepatocellular adenoma independently of SREBP-1 and carbohydrate-response element-binding protein (ChREBP) activation

scientific article published on 22 March 2007

Host Transcription Profile In Nasal Epithelium And Whole Blood of Hospitalised Children under two years of age with Respiratory Syncytial Virus Infection

scientific article published on 27 September 2017

Human-like layout algorithms for signalling hypergraphs: outlining requirements

scholarly article by Martin Siebenhaller published in October 2018

IL-17-high asthma with features of a psoriasis immunophenotype

scientific article published on 15 April 2019

Identification and prospective stability of electronic nose (eNose)-derived inflammatory phenotypes in patients with severe asthma

scientific article published on 06 December 2018

Identification of genes involved in ceramide-dependent neuronal apoptosis using cDNA arrays

scientific article

Instability of sputum molecular phenotypes in U-BIOPRED severe asthma

scientific article published on 02 October 2020

Integration of Myeloblastosis Associated Virus proviral sequences occurs in the vicinity of genes encoding signaling proteins and regulators of cell proliferation

scientific article

Integrative annotation of 21,037 human genes validated by full-length cDNA clones

scientific article

Introducing PIONEER: a project to harness big data in prostate cancer research

scientific article published on 27 May 2020

Issues in Computational Methods for Functional Genomics and Systems Biology

Large-Scale Label-Free Quantitative Mapping of the Sputum Proteome

scientific article published on 8 May 2018

Longitudinally Stable, Clinically Defined Clusters of Patients with Asthma Independently Identified in the ADEPT and U-BIOPRED Asthma Studies

scientific article published in March 2016

Looking back at genomic medicine in 2011 ⬇️

scientific article published on January 30, 2012

M19 modulates skeletal muscle differentiation and insulin secretion in pancreatic β-cells through modulation of respiratory chain activity

scientific article

Making sense of big data in health research: Towards an EU action plan

scientific article

Matching gene expression with hypometabolism after cerebral ischemia in the nonhuman primate

scientific article published in October 2002

Mechanisms of the Development of Allergy (MeDALL): Introducing novel concepts in allergy phenotypes

scientific article

Modifications in the myogenic program induced by in vivo and in vitro aging

scientific article published in February 2005

Origins of systems biology in William Harvey's masterpiece on the movement of the heart and the blood in animals

scientific article (publication date: 17 April 2009)

P4 medicine needs P4 education.

scientific article

Participatory medicine: a driving force for revolutionizing healthcare

scientific article

Pathway discovery using transcriptomic profiles in adult-onset severe asthma

scientific article

Personalized respiratory medicine: exploring the horizon, addressing the issues. Summary of a BRN-AJRCCM workshop held in Barcelona on June 12, 2014

scientific article

Prediction of chronic lung allograft dysfunction: a systems medicine challenge

scientific article published in March 2014

Predictive, preventive, personalized and participatory medicine: back to the future

scientific article

Protein subnetwork markers improve prediction of cancer outcome

scientific article published on 16 October 2007

Recon2Neo4j: applying graph database technologies for managing comprehensive genome-scale networks

scientific article

Report on EU-USA workshop: how systems biology can advance cancer research (27 October 2008)

scientific article

Representing and querying disease networks using graph databases

scientific article

Revolutionizing medicine in the 21st century through systems approaches

scientific article published on 20 July 2012

STON: exploring biological pathways using the SBGN standard and graph databases

scientific article

Scale Relativity: an Extended Paradigm for Physics and Biology?

Scale relativity theory and integrative systems biology: 1. Founding principles and scale laws

scientific article published on 02 October 2007

Scale relativity theory and integrative systems biology: 2 Macroscopic quantum-type mechanics

scientific article (publication date: May 2008)

Self-organized living systems: conjunction of a stable organization with chaotic fluctuations in biological space-time

scientific article

Severe asthma exists despite suppressed tissue inflammation: findings of the U-BIOPRED study

scientific article published on 6 October 2016

Sex-linked recombination variation and distribution of disease-related genes

article

Sharing knowledge: a new frontier for public-private partnerships in medicine

scientific article published on 4 March 2009

Sputum proteomics and airway cell transcripts of current and ex-smokers with severe asthma in U-BIOPRED: an exploratory analysis.

scientific article published on 12 April 2018

Stratification of asthma phenotypes by airway proteomic signatures

scientific article published on 28 March 2019

Systems Medicine: The Future of Medical Genomics, Healthcare, and Wellness

scientific article published on January 2016

Systems analysis of transcriptome and proteome in retinoic acid/arsenic trioxide-induced cell differentiation/apoptosis of promyelocytic leukemia

scientific article

Systems biologists seek fuller integration of systems biology approaches in new cancer research programs

scientific article

Systems medicine and integrated care to combat chronic noncommunicable diseases

scientific article

Systems medicine approaches for the definition of complex phenotypes in chronic diseases and ageing. From concept to implementation and policies

scientific article published on January 2014

Systems medicine disease maps: community-driven comprehensive representation of disease mechanisms.

scientific article published on 2 June 2018

Systems medicine, personalized health and therapy

scientific article

Systems medicine: the future of medical genomics and healthcare

scientific article

T-helper cell type 2 (Th2) and non-Th2 molecular phenotypes of asthma using sputum transcriptomics in U-BIOPRED.

scientific article

Ten years of Genome Medicine

The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

scientific article

The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms

scientific article

The P4 Health Spectrum - A Predictive, Preventive, Personalized and Participatory Continuum for Promoting Healthspan

scientific article

The beta-catenin pathway is activated in focal nodular hyperplasia but not in cirrhotic FNH-like nodules

scientific article published on 18 April 2008

The cytoskeleton-associated PDZ-LIM protein, ALP, acts on serum response factor activity to regulate muscle differentiation

scientific article published on March 2007

The road from systems biology to systems medicine

scientific article published on 11 January 2013

Towards a European health research and innovation cloud (HRIC)

scientific article published on 19 February 2020

Towards standardization of RNA quality assessment using user-independent classifiers of microcapillary electrophoresis traces

scientific article

Transforming growth factor-beta1-modulated cerebral gene expression

scientific article published in September 2002

U-BIOPRED clinical adult asthma clusters linked to a subset of sputum omics

scientific article

Understanding the complexity of IgE-related phenotypes from childhood to young adulthood: a Mechanisms of the Development of Allergy (MeDALL) seminar

scientific article published on 03 March 2012

Volatile Organic Compounds Breathprinting of U-BIOPRED Severe Asthma smokers/ex-smokers cohort

article

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