Publications

Briefings in bioinformatics

Principal component analysis of binary genomics data.

18-01-2019

Bioinformatics (Oxford, England)

Modelling signalling networks from perturbation data.

01-12-2018

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

Nature communications

Integrative epigenetic taxonomy of primary prostate cancer.

21-11-2018

PloS one

Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association.

09-11-2018

The Journal of pathology

Consensus molecular subtype classification of colorectal adenomas.

01-11-2018

Molecular & cellular proteomics : MCP

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

01-10-2018

Cancer research

Transcriptomics and Transposon Mutagenesis Identify Multiple Mechanisms of Resistance to the FGFR Inhibitor AZD4547.

01-10-2018

Bioinformatics (Oxford, England)

iTOP: inferring the topology of omics data.

01-09-2018

Cell reports

Nuclear Receptor Nur77 Limits the Macrophage Inflammatory Response through Transcriptional Reprogramming of Mitochondrial Metabolism.

21-08-2018

JCO precision oncology

Evaluation of the HER/PI3K/AKT Family Signaling Network as a Predictive Biomarker of Pathologic Complete Response for Patients With Breast Cancer Treated With Neratinib in the I-SPY 2 TRIAL.

16-08-2018

Open biology

Mouse models in the era of large human tumour sequencing studies.

01-08-2018

Cancer research

Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines.

01-08-2018

Molecular oncology

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration.

01-08-2018

Cell research

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models.

01-07-2018

Cancer cell

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality.

11-06-2018

Oral oncology

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer.

01-06-2018

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

Insertional mutagenesis in a HER2-positive breast cancer model reveals ERAS as a driver of cancer and therapy resistance.

01-03-2018

Bioinformatics (Oxford, England)

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.

01-03-2018

Nature communications

Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer.

02-02-2018

Oncogene

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

18-01-2018

eLife

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.

18-01-2018

Cell

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity.

11-01-2018

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

Complementary Value of Contralateral Parenchymal Enhancement on DCE-MRI to Prognostic Models and Molecular Assays in High-risk ER⁺/HER2^- Breast Cancer.

01-11-2017

Oncoimmunology

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

19-09-2017

Nature

Identification of CMTM6 and CMTM4 as PD-L1 protein regulators.

07-09-2017

Cell reports

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

29-08-2017

Breast cancer research : BCR

The BRCA1ness signature is associated significantly with response to PARP inhibitor treatment versus control in the I-SPY 2 randomized neoadjuvant setting.

25-08-2017

Oncotarget

Predicting clinical benefit from everolimus in patients with advanced solid tumors, the CPCT-03 study.

15-08-2017

Urologic oncology

Description of the EuroTARGET cohort: A European collaborative project on TArgeted therapy in renal cell cancer-GEnetic- and tumor-related biomarkers for response and toxicity.

01-08-2017

Nature genetics

Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma.

01-08-2017

Nucleic acids research

Identifying transposon insertions and their effects from RNA-sequencing data.

07-07-2017

Cell reports

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness.

05-07-2017

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

Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.

01-05-2017

Oncotarget

Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer.

15-03-2017

Proceedings of the National Academy of Sciences of the United States of America

Estrogen receptor α wields treatment-specific enhancers between morphologically similar endometrial tumors.

21-02-2017

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

Scientific reports

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

23-11-2016

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

Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance.

01-11-2016

Oncotarget

Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition.

25-10-2016

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

Oncogene

Targeting the RB-E2F pathway in breast cancer.

15-09-2016

Bioinformatics (Oxford, England)

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

01-09-2016

Cell reports

PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma.

23-08-2016

Cell

A Landscape of Pharmacogenomic Interactions in Cancer.

28-07-2016

Nature communications

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.

11-07-2016

Cancer research

Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas.

01-07-2016

Molecular cancer therapeutics

Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R.

01-07-2016

Principal component analysis of binary genomics data.

Modelling signalling networks from perturbation data.

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

Integrative epigenetic taxonomy of primary prostate cancer.

Role of variant allele fraction and rare SNP filtering to improve cellular DNA repair endpoint association.

Consensus molecular subtype classification of colorectal adenomas.

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

Transcriptomics and Transposon Mutagenesis Identify Multiple Mechanisms of Resistance to the FGFR Inhibitor AZD4547.

iTOP: inferring the topology of omics data.

Nuclear Receptor Nur77 Limits the Macrophage Inflammatory Response through Transcriptional Reprogramming of Mitochondrial Metabolism.

Evaluation of the HER/PI3K/AKT Family Signaling Network as a Predictive Biomarker of Pathologic Complete Response for Patients With Breast Cancer Treated With Neratinib in the I-SPY 2 TRIAL.

Mouse models in the era of large human tumour sequencing studies.

Integrative Modeling Identifies Key Determinants of Inhibitor Sensitivity in Breast Cancer Cell Lines.

Loss of androgen receptor signaling in prostate cancer-associated fibroblasts (CAFs) promotes CCL2- and CXCL8-mediated cancer cell migration.

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models.

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality.

Comparative genomic analysis of oral versus laryngeal and pharyngeal cancer.

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.

Insertional mutagenesis in a HER2-positive breast cancer model reveals ERAS as a driver of cancer and therapy resistance.

Bayesian data integration for quantifying the contribution of diverse measurements to parameter estimates.

Characterizing steroid hormone receptor chromatin binding landscapes in male and female breast cancer.

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

Loss of functional BAP1 augments sensitivity to TRAIL in cancer cells.

A Living Biobank of Breast Cancer Organoids Captures Disease Heterogeneity.

Complementary Value of Contralateral Parenchymal Enhancement on DCE-MRI to Prognostic Models and Molecular Assays in High-risk ER+/HER2- Breast Cancer.

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

Identification of CMTM6 and CMTM4 as PD-L1 protein regulators.

Genomic Determinants of Protein Abundance Variation in Colorectal Cancer Cells.

The BRCA1ness signature is associated significantly with response to PARP inhibitor treatment versus control in the I-SPY 2 randomized neoadjuvant setting.

Predicting clinical benefit from everolimus in patients with advanced solid tumors, the CPCT-03 study.

Description of the EuroTARGET cohort: A European collaborative project on TArgeted therapy in renal cell cancer-GEnetic- and tumor-related biomarkers for response and toxicity.

Insertional mutagenesis identifies drivers of a novel oncogenic pathway in invasive lobular breast carcinoma.

Identifying transposon insertions and their effects from RNA-sequencing data.

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness.

Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape.

Systematic functional perturbations uncover a prognostic genetic network driving human breast cancer.

Estrogen receptor α wields treatment-specific enhancers between morphologically similar endometrial tumors.

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

Logic models to predict continuous outputs based on binary inputs with an application to personalized cancer therapy.

Loss of ARID1A Activates ANXA1, which Serves as a Predictive Biomarker for Trastuzumab Resistance.

Large variety in a panel of human colon cancer organoids in response to EZH2 inhibition.

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

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

Targeting the RB-E2F pathway in breast cancer.

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types.

PTEN Loss in E-Cadherin-Deficient Mouse Mammary Epithelial Cells Rescues Apoptosis and Results in Development of Classical Invasive Lobular Carcinoma.

A Landscape of Pharmacogenomic Interactions in Cancer.

RUBIC identifies driver genes by detecting recurrent DNA copy number breaks.

Comparative Cistromics Reveals Genomic Cross-talk between FOXA1 and ERα in Tamoxifen-Associated Endometrial Carcinomas.

Sensitizing Triple-Negative Breast Cancer to PI3K Inhibition by Cotargeting IGF1R.

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Complementary Value of Contralateral Parenchymal Enhancement on DCE-MRI to Prognostic Models and Molecular Assays in High-risk ER⁺/HER2^- Breast Cancer.