Publications

FEBS letters

Genetic interactions, synthetic lethality and complexity in cancer vulnerability mapping-Insights and perspectives from the 2nd EuroDepMap symposium.

01-04-2026

Cancer discovery

Microbial Metabolic Pathways Guide Response to Immune Checkpoint Blockade Therapy.

12-01-2026

Nature

NASP modulates histone turnover to drive PARP inhibitor resistance.

01-09-2025

Science (New York, N.Y.)

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression.

03-07-2025

Genome biology

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.

09-05-2025

Clinical cancer research : an official journal of the American Association for Cancer Research

Platinum-Based Chemotherapy Induces Opposing Effects on Immunotherapy Response-Related Spatial and Stromal Biomarkers in the Bladder Cancer Microenvironment.

13-09-2024

iScience

Predictive gene expression profile for adjuvant taxane benefit in breast cancer in the MATADOR trial.

16-08-2024

The New England journal of medicine

Neoadjuvant Immunotherapy in Locally Advanced Mismatch Repair-Deficient Colon Cancer.

06-06-2024

Science (New York, N.Y.)

DNA damage induces p53-independent apoptosis through ribosome stalling.

17-05-2024

BMC bioinformatics

ecpc: an R-package for generic co-data models for high-dimensional prediction.

26-04-2023

Cancers

Homologous Recombination Deficiency and Cyclin E1 Amplification Are Correlated with Immune Cell Infiltration and Survival in High-Grade Serous Ovarian Cancer.

02-12-2022

Nature communications

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

30-11-2022

Statistics in medicine

Flexible co-data learning for high-dimensional prediction.

20-11-2021

Cell reports

The Cancer SENESCopedia: A delineation of cancer cell senescence.

27-07-2021

Genome medicine

Correction to: A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.

10-02-2021

Radiology

Radiogenomic Analysis of Breast Cancer by Linking MRI Phenotypes with Tumor Gene Expression.

01-08-2020

Nature communications

Multiple low dose therapy as an effective strategy to treat EGFR inhibitor-resistant NSCLC tumours.

22-06-2020

The EMBO journal

In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.

02-03-2020

Nature communications

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.

16-01-2020

Cancers

Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy.

29-03-2019

Briefings in bioinformatics

Principal component analysis of binary genomics data.

18-01-2019

Genome medicine

A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.

27-11-2018

Molecular & cellular proteomics : MCP

A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells.

01-10-2018

Oncotarget

Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma.

06-04-2018

Oncogene

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis.

18-01-2018

Oncoimmunology

Mammary tumor-derived CCL2 enhances pro-metastatic systemic inflammation through upregulation of IL1β in tumor-associated macrophages.

19-09-2017

Cell reports

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

29-08-2017

Genome biology

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.

16-12-2016

BMC systems biology

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

21-10-2016

Gastroenterology

Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells.

01-10-2016

Scientific reports

OncoScape: Exploring the cancer aberration landscape by genomic data fusion.

20-06-2016

Scientific reports

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

05-01-2016

Oncotarget

Fra-1 is a key driver of colon cancer metastasis and a Fra-1 classifier predicts disease-free survival.

22-12-2015

Chinese journal of cancer

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

14-09-2015

Nature chemical biology

Chemical profiling of the genome with anti-cancer drugs defines target specificities.

01-07-2015

Genome biology

CopywriteR: DNA copy number detection from off-target sequence data.

27-02-2015

Genomics data

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors.

01-12-2014

Cancer research

Complex formation and function of estrogen receptor α in transcription requires RIP140.

01-10-2014

PloS one

Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.

02-08-2014

PloS one

Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes.

22-02-2014

Nucleic acids research

Identifying subgroup markers in heterogeneous populations.

01-11-2013

Cell

Chromatin position effects assayed by thousands of reporters integrated in parallel.

15-08-2013

PloS one

Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.

22-05-2013

Nucleic acids research

A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

01-05-2013

Genome research

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

01-02-2013

Cancer research

Impact of intertumoral heterogeneity on predicting chemotherapy response of BRCA1-deficient mammary tumors.

01-05-2012

Genome research

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors.

01-12-2011

Annals of oncology : official journal of the European Society for Medical Oncology

An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients.

01-07-2011

BMC research notes

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data.

11-11-2010

BMC cancer

Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers.

24-08-2010

Genetic interactions, synthetic lethality and complexity in cancer vulnerability mapping-Insights and perspectives from the 2nd EuroDepMap symposium.

Microbial Metabolic Pathways Guide Response to Immune Checkpoint Blockade Therapy.

NASP modulates histone turnover to drive PARP inhibitor resistance.

Zincore, an atypical coregulator, binds zinc finger transcription factors to control gene expression.

Endometrial tumorigenesis involves epigenetic plasticity demarcating non-coding somatic mutations and 3D-genome alterations.

Platinum-Based Chemotherapy Induces Opposing Effects on Immunotherapy Response-Related Spatial and Stromal Biomarkers in the Bladder Cancer Microenvironment.

Predictive gene expression profile for adjuvant taxane benefit in breast cancer in the MATADOR trial.

Neoadjuvant Immunotherapy in Locally Advanced Mismatch Repair-Deficient Colon Cancer.

DNA damage induces p53-independent apoptosis through ribosome stalling.

ecpc: an R-package for generic co-data models for high-dimensional prediction.

Homologous Recombination Deficiency and Cyclin E1 Amplification Are Correlated with Immune Cell Infiltration and Survival in High-Grade Serous Ovarian Cancer.

Extensive androgen receptor enhancer heterogeneity in primary prostate cancers underlies transcriptional diversity and metastatic potential.

Flexible co-data learning for high-dimensional prediction.

The Cancer SENESCopedia: A delineation of cancer cell senescence.

Correction to: A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.

Radiogenomic Analysis of Breast Cancer by Linking MRI Phenotypes with Tumor Gene Expression.

Multiple low dose therapy as an effective strategy to treat EGFR inhibitor-resistant NSCLC tumours.

In situ CRISPR-Cas9 base editing for the development of genetically engineered mouse models of breast cancer.

A network analysis to identify mediators of germline-driven differences in breast cancer prognosis.

Genetic Factors Associated with a Poor Outcome in Head and Neck Cancer Patients Receiving Definitive Chemoradiotherapy.

Principal component analysis of binary genomics data.

A role for the unfolded protein response stress sensor ERN1 in regulating the response to MEK inhibitors in KRAS mutant colon cancers.

A System-wide Approach to Monitor Responses to Synergistic BRAF and EGFR Inhibition in Colorectal Cancer Cells.

Fanconi anemia and homologous recombination gene variants are associated with functional DNA repair defects in vitro and poor outcome in patients with advanced head and neck squamous cell carcinoma.

Endogenous androgen receptor proteomic profiling reveals genomic subcomplex involved in prostate tumorigenesis.

Mammary tumor-derived CCL2 enhances pro-metastatic systemic inflammation through upregulation of IL1β in tumor-associated macrophages.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

A novel independence test for somatic alterations in cancer shows that biology drives mutual exclusivity but chance explains most co-occurrence.

BCM: toolkit for Bayesian analysis of Computational Models using samplers.

Deletion of Polycomb Repressive Complex 2 From Mouse Intestine Causes Loss of Stem Cells.

OncoScape: Exploring the cancer aberration landscape by genomic data fusion.

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer.

Fra-1 is a key driver of colon cancer metastasis and a Fra-1 classifier predicts disease-free survival.

A multilevel pan-cancer map links gene mutations to cancer hallmarks.

Chemical profiling of the genome with anti-cancer drugs defines target specificities.

CopywriteR: DNA copy number detection from off-target sequence data.

Genome-wide epigenetic profiling of breast cancer tumors treated with aromatase inhibitors.

Complex formation and function of estrogen receptor α in transcription requires RIP140.

Lack of genomic heterogeneity at high-resolution aCGH between primary breast cancers and their paired lymph node metastases.

Breast cancer subtype specific classifiers of response to neoadjuvant chemotherapy do not outperform classifiers trained on all subtypes.

Identifying subgroup markers in heterogeneous populations.

Chromatin position effects assayed by thousands of reporters integrated in parallel.

Analysis of tumor heterogeneity and cancer gene networks using deep sequencing of MMTV-induced mouse mammary tumors.

A scale-space method for detecting recurrent DNA copy number changes with analytical false discovery rate control.

Constitutive nuclear lamina-genome interactions are highly conserved and associated with A/T-rich sequence.

Impact of intertumoral heterogeneity on predicting chemotherapy response of BRCA1-deficient mammary tumors.

High-throughput semiquantitative analysis of insertional mutations in heterogeneous tumors.

An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients.

KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data.

Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers.

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