List of works - Jacques Colinge

13 Functional Proteomics of Innate Immunity Signalling

A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN.

scientific article

A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations.

scientific article published on 24 December 2015

A Web Resource for Improved Analysis of AP-MS Protein Interaction Data

scientific article published in May 2013

A cellular screen identifies ponatinib and pazopanib as inhibitors of necroptosis.

scientific article

A chemical and phosphoproteomic characterization of dasatinib action in lung cancer

scientific article

A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF.

scientific article published on 3 June 2013

A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer.

scientific article published on 25 September 2011

A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor

scientific article published on 22 May 2017

A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling

scientific article published on 31 May 2012

A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib

scientific article

A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies

scientific article

A reversible gene trap collection empowers haploid genetics in human cells

scientific article published on 25 August 2013

A target-disease network model of second-generation BCR-ABL inhibitor action in Ph+ ALL

scientific article (publication date: 2013)

A time-resolved molecular map of the macrophage response to VSV infection

scientific article

Acid elution and one-dimensional shotgun analysis on an Orbitrap mass spectrometer: an application to drug affinity chromatography.

scientific article published in October 2009

Affinity purification strategies for proteomic analysis of transcription factor complexes.

scientific article published on 22 August 2013

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk

scientific article published on 31 March 2021

An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

scientific article published on 18 July 2011

An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome

scientific article

Application of modular response analysis to medium- to large-size biological systems

scientific article published on 20 April 2022

Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity

scientific article

Assessing peptide de novo sequencing algorithms performance on large and diverse data sets.

scientific article

Biallelic loss-of-function mutation in NIK causes a primary immunodeficiency with multifaceted aberrant lymphoid immunity.

scientific article

Building and exploring an integrated human kinase network: global organization and medical entry points.

scientific article

CD14 is a coreceptor of Toll-like receptors 7 and 9. ⬇️

scientific article

CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2.

scientific article

CLOUD – CeMM library of unique drugs.

scientific article

Cell-Cycle Regulation Accounts for Variability in Ki-67 Expression Levels.

scientific article

Charting the molecular network of the drug target Bcr-Abl

scientific article

Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets

scientific article published on 24 August 2007

Clinical significance of genetic aberrations in secondary acute myeloid leukemia

scientific article published on 7 August 2012

Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma

scientific article published on 06 May 2014

Data-Based Radiation Oncology: Design of Clinical Trials in the Toxicity Biomarkers Era.

scientific article

Deconvolution of targeted protein-protein interaction maps.

scientific article published on 10 July 2012

Detecting the impact of sequencing errors on SAGE data.

scientific article

Differential proteomics via probabilistic peptide identification scores

scientific article published on 01 January 2005

Distinct oncogenes drive different genome and epigenome alterations in human mammary epithelial cells

scientific article published on 10 June 2019

Distinct oncogenes drive distinct genome and epigenome alterations in human mammary epithelial cells

Early-onset inflammatory bowel disease and common variable immunodeficiency-like disease caused by IL-21 deficiency

scientific article published on 17 April 2014

Epigenetik in der Onkologie

Experimental characterization of the human non-sequence-specific nucleic acid interactome

scientific article

Experiments in searching small proteins in unannotated large eukaryotic genomes

scientific article published on 01 January 2005

Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia.

scientific article published on 19 December 2017

Functional dissection of the TBK1 molecular network

scientific article

Gene essentiality and synthetic lethality in haploid human cells

scientific journal article

General statistical modeling of data from protein relative expression isobaric tags.

scientific article

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

scientific article published on 18 October 2016

Germline RBBP6 mutations in familial myeloproliferative neoplasms.

scientific article published on 16 November 2015

Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions.

scientific article

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.

scientific article

IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA

scientific article

Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics

scientific article

Improved peptide charge state assignment.

scientific article

In Vivo Large-Scale Mapping of Protein Turnover in Human Cerebrospinal Fluid

scientific article published on 02 December 2019

In vitro and in silico processes to identify differentially expressed proteins

scientific article published on 01 August 2004

InSilicoSpectro: an open-source proteomics library.

scientific article published in March 2006

Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins

scientific article

Initial characterization of the human central proteome

scientific article

Interactome of two diverse RNA granules links mRNA localization to translational repression in neurons.

scientific article published on 19 December 2013

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

scientific article

Introduction to computational proteomics

scientific article

Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins

scientific article

MASPECTRAS 2: An integration and analysis platform for proteomic data.

scientific article

Machine Learning-Assisted Evaluation of Circulating DNA Quantitative Analysis for Cancer Screening

scientific article published on 29 July 2020

MetaBlasts: tracing protein tyrosine phosphatase gene family roots from Man to Drosophila melanogaster and Caenorhabditis elegans genomes.

scientific article published on August 2000

Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer.

scientific article

NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation

scientific article published on 29 September 2014

Notch inhibition overcomes resistance to tyrosine kinase inhibitors in EGFR-driven lung adenocarcinoma

scientific article published on 01 February 2020

OLAV-PMF: a novel scoring scheme for high-throughput peptide mass fingerprinting

scientific article

OLAV: towards high-throughput tandem mass spectrometry data identification

scientific article (publication date: August 2003)

Peptide fragment intensity statistical modeling

scientific article published on 23 August 2007

Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms

scientific article

Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling.

scientific article

Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens.

scientific article published on 16 October 2010

Quantitative proteomics of aqueous and vitreous fluid from patients with idiopathic epiretinal membranes

scientific article published on 29 November 2012

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

scientific article published on 20 March 2020

Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy

scientific article

Superoxide Dismutase 1 Protects Hepatocytes from Type I Interferon-Driven Oxidative Damage

scientific article

Systems Biology Analysis of Kinase Inhibitor Action in Leukemia Treatments

scientific article published on 07 September 2013

Systems biology analysis of protein-drug interactions.

scientific article published on 27 December 2011

Systems-pharmacology dissection of a drug synergy in imatinib-resistant CML.

scientific article

TLR 2 and CD14 mediate innate immunity and lung inflammation to staphylococcal Panton-Valentine leukocidin in vivo

scientific article published on 22 December 2010

TOPS: a versatile software tool for statistical analysis and visualization of combinatorial gene-gene and gene-drug interaction screens

scientific article

Target profiling of an antimetastatic RAPTA agent by chemical proteomics: relevance to the mode of action

scientific article published on 9 February 2015

Target profiling of an antimetastatic RAPTA agent by chemical proteomics: relevance to the mode of action† †Electronic supplementary information (ESI) available: Experimental, crystallographic, biological and mass spectrometric data, full list of pr

scientific article published on 9 February 2015

Targeting a cell state common to triple-negative breast cancers

scientific article

The Btk tyrosine kinase is a major target of the Bcr-Abl inhibitor dasatinib

scholarly article

The CRAPome: a contaminant repository for affinity purification-mass spectrometry data

scientific article

The Lipid-Modifying Enzyme SMPDL3B Negatively Regulates Innate Immunity

scientific journal article

The Prognostic Impact of the Aryl Hydrocarbon Receptor (AhR) in Primary Breast Cancer Depends on the Lymph Node Status ⬇️

scientific article published on 26 February 2019

The RNA-binding protein HuR/ELAVL1 regulates IFN-β mRNA abundance and the type I IFN response

scientific article published on 12 March 2015

The chemokine interleukin-8 and the surface activation protein CD69 are markers for Bcr-Abl activity in chronic myeloid leukemia.

scientific article published on 23 July 2008

The molecular landscape and microenvironment of salivary duct carcinoma reveal new therapeutic opportunities

scientific article published on 15 March 2020

The triggering receptor expressed on myeloid cells 2 inhibits complement component 1q effector mechanisms and exerts detrimental effects during pneumococcal pneumonia

scientific article

Transcriptomic and genomic heterogeneity in blastic plasmacytoid dendritic cell neoplasms: from ontogeny to oncogenesis

scientific article published in 2021

Using iTRAQ combined with tandem affinity purification to enhance low-abundance proteins associated with somatically mutated EGFR core complexes in lung cancer.

scientific article

Viral immune modulators perturb the human molecular network by common and unique strategies

scientific article

Virulence factor NSs of rift valley fever virus recruits the F-box protein FBXO3 to degrade subunit p62 of general transcription factor TFIIH

scientific article

[Radiomics: Definition and clinical development]

scientific article published on 03 September 2015

List of works by Jacques Colinge

13 Functional Proteomics of Innate Immunity Signalling

A Comprehensive Analysis of the Dynamic Response to Aphidicolin-Mediated Replication Stress Uncovers Targets for ATM and ATMIN.

A Surface Biotinylation Strategy for Reproducible Plasma Membrane Protein Purification and Tracking of Genetic and Drug-Induced Alterations.

A Web Resource for Improved Analysis of AP-MS Protein Interaction Data

A cellular screen identifies ponatinib and pazopanib as inhibitors of necroptosis.

A chemical and phosphoproteomic characterization of dasatinib action in lung cancer

A chemical biology approach identifies AMPK as a modulator of melanoma oncogene MITF.

A chemical-genetic screen reveals a mechanism of resistance to PI3K inhibitors in cancer.

A combinatorial screen of the CLOUD uncovers a synergy targeting the androgen receptor

A comparative proteomic study of human skin suction blister fluid from healthy individuals using immunodepletion and iTRAQ labeling

A computational approach to analyze the mechanism of action of the kinase inhibitor bafetinib

A miniaturized chemical proteomic approach for target profiling of clinical kinase inhibitors in tumor biopsies

A reversible gene trap collection empowers haploid genetics in human cells

A target-disease network model of second-generation BCR-ABL inhibitor action in Ph+ ALL

A time-resolved molecular map of the macrophage response to VSV infection

Acid elution and one-dimensional shotgun analysis on an Orbitrap mass spectrometer: an application to drug affinity chromatography.

Affinity purification strategies for proteomic analysis of transcription factor complexes.

An R package for generic modular response analysis and its application to estrogen and retinoic acid receptor crosstalk

An integrated chemical biology approach identifies specific vulnerability of Ewing's sarcoma to combined inhibition of Aurora kinases A and B.

An orthogonal proteomic-genomic screen identifies AIM2 as a cytoplasmic DNA sensor for the inflammasome

Application of modular response analysis to medium- to large-size biological systems

Artemisinins Target GABAA Receptor Signaling and Impair α Cell Identity

Assessing peptide de novo sequencing algorithms performance on large and diverse data sets.

Biallelic loss-of-function mutation in NIK causes a primary immunodeficiency with multifaceted aberrant lymphoid immunity.

Building and exploring an integrated human kinase network: global organization and medical entry points.

CD14 is a coreceptor of Toll-like receptors 7 and 9. ⬇️

CD4(+) T cell lineage integrity is controlled by the histone deacetylases HDAC1 and HDAC2.

CLOUD – CeMM library of unique drugs.

Cell-Cycle Regulation Accounts for Variability in Ki-67 Expression Levels.

Charting the molecular network of the drug target Bcr-Abl

Chemical proteomic profiles of the BCR-ABL inhibitors imatinib, nilotinib, and dasatinib reveal novel kinase and nonkinase targets

Clinical significance of genetic aberrations in secondary acute myeloid leukemia

Comprehensive comparative and semiquantitative proteome of a very low number of native and matched epstein-barr-virus-transformed B lymphocytes infiltrating human melanoma

Data-Based Radiation Oncology: Design of Clinical Trials in the Toxicity Biomarkers Era.

Deconvolution of targeted protein-protein interaction maps.

Detecting the impact of sequencing errors on SAGE data.

Differential proteomics via probabilistic peptide identification scores

Distinct oncogenes drive different genome and epigenome alterations in human mammary epithelial cells

Distinct oncogenes drive distinct genome and epigenome alterations in human mammary epithelial cells

Early-onset inflammatory bowel disease and common variable immunodeficiency-like disease caused by IL-21 deficiency

Epigenetik in der Onkologie

Experimental characterization of the human non-sequence-specific nucleic acid interactome

Experiments in searching small proteins in unannotated large eukaryotic genomes

Functional analysis of Plasmodium falciparum subpopulations associated with artemisinin resistance in Cambodia.

Functional dissection of the TBK1 molecular network

Gene essentiality and synthetic lethality in haploid human cells

General statistical modeling of data from protein relative expression isobaric tags.

Genome-wide diversity and gene expression profiling of Babesia microti isolates identify polymorphic genes that mediate host-pathogen interactions

Germline RBBP6 mutations in familial myeloproliferative neoplasms.

Heme drives hemolysis-induced susceptibility to infection via disruption of phagocyte functions.

High-performance peptide identification by tandem mass spectrometry allows reliable automatic data processing in proteomics.

IFIT1 is an antiviral protein that recognizes 5'-triphosphate RNA

Identification of kinase inhibitor targets in the lung cancer microenvironment by chemical and phosphoproteomics

Improved peptide charge state assignment.

In Vivo Large-Scale Mapping of Protein Turnover in Human Cerebrospinal Fluid

In vitro and in silico processes to identify differentially expressed proteins

InSilicoSpectro: an open-source proteomics library.

Industrial-scale proteomics: from liters of plasma to chemically synthesized proteins

Initial characterization of the human central proteome

Interactome of two diverse RNA granules links mRNA localization to translational repression in neurons.

Interlaboratory reproducibility of large-scale human protein-complex analysis by standardized AP-MS

Introduction to computational proteomics

Isobar(PTM): a software tool for the quantitative analysis of post-translationally modified proteins

MASPECTRAS 2: An integration and analysis platform for proteomic data.

Machine Learning-Assisted Evaluation of Circulating DNA Quantitative Analysis for Cancer Screening

MetaBlasts: tracing protein tyrosine phosphatase gene family roots from Man to Drosophila melanogaster and Caenorhabditis elegans genomes.

Multiple and sequential data acquisition method: an improved method for fragmentation and detection of cross-linked peptides on a hybrid linear trap quadrupole Orbitrap Velos mass spectrometer.

NOTCH1 activation in breast cancer confers sensitivity to inhibition of SUMOylation

Notch inhibition overcomes resistance to tyrosine kinase inhibitors in EGFR-driven lung adenocarcinoma

OLAV-PMF: a novel scoring scheme for high-throughput peptide mass fingerprinting

OLAV: towards high-throughput tandem mass spectrometry data identification

Peptide fragment intensity statistical modeling

Perturbation of the mutated EGFR interactome identifies vulnerabilities and resistance mechanisms

Proteome-wide drug and metabolite interaction mapping by thermal-stability profiling.

Proteomic analysis of human cataract aqueous humour: Comparison of one-dimensional gel LCMS with two-dimensional LCMS of unlabelled and iTRAQ®-labelled specimens.

Quantitative proteomics of aqueous and vitreous fluid from patients with idiopathic epiretinal membranes

SingleCellSignalR: inference of intercellular networks from single-cell transcriptomics

Stereospecific targeting of MTH1 by (S)-crizotinib as an anticancer strategy

Superoxide Dismutase 1 Protects Hepatocytes from Type I Interferon-Driven Oxidative Damage