Publications

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

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

Defining chromosomal translocation risks in cancer.

28-06-2016

Scientific reports

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

20-06-2016

Oncotarget

Neoadjuvant tamoxifen synchronizes ERα binding and gene expression profiles related to outcome and proliferation.

07-06-2016

Pharmacogenomics

Multilevel models improve precision and speed of IC50 estimates.

01-05-2016

Cell

A Vulnerability of a Subset of Colon Cancers with Potential Clinical Utility.

07-04-2016

Oncotarget

Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

22-03-2016

Genomics data

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.

01-03-2016

European urology

ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy.

01-03-2016

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

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

Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients.

15-12-2015

The EMBO journal

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs.

14-12-2015

Nature medicine

The consensus molecular subtypes of colorectal cancer.

01-11-2015

EMBO molecular medicine

Androgen receptor profiling predicts prostate cancer outcome.

01-11-2015

Mobile genetic elements

Applications of DNA integrating elements: Facing the bias bully.

07-10-2015

Breast cancer research : BCR

Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response.

03-10-2015

Molecular oncology

BRCA1-like signature in triple negative breast cancer: Molecular and clinical characterization reveals subgroups with therapeutic potential.

01-10-2015

Cancer research

Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer.

01-10-2015

Bioinformatics (Oxford, England)

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

01-10-2015

Chinese journal of cancer

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

14-09-2015

EMBO molecular medicine

Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts.

01-09-2015

Molecular oncology

Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.

01-08-2015

Nature chemical biology

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

01-07-2015

Cell

Prospective derivation of a living organoid biobank of colorectal cancer patients.

07-05-2015

Cell research

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.

01-04-2015

Genome biology

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

27-02-2015

Cancer research

BRCA2-deficient sarcomatoid mammary tumors exhibit multidrug resistance.

15-02-2015

Experimental cell research

Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling.

15-01-2015

Nature genetics

A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.

01-01-2015

Genomics data

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

01-12-2014

Cell reports

Parallel in vivo and in vitro melanoma RNAi dropout screens reveal synthetic lethality between hypoxia and DNA damage response inhibition.

20-11-2014

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

Cancer research

USP9X downregulation renders breast cancer cells resistant to tamoxifen.

15-07-2014

Nature methods

Multiscale representation of genomic signals.

01-06-2014

Nature protocols

Using TRIP for genome-wide position effect analysis in cultured cells.

09-05-2014

Cell reports

Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon cancer through transcriptional induction of ERBB3.

10-04-2014

Nature

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma.

03-04-2014

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.

Defining chromosomal translocation risks in cancer.

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

Neoadjuvant tamoxifen synchronizes ERα binding and gene expression profiles related to outcome and proliferation.

Multilevel models improve precision and speed of IC50 estimates.

A Vulnerability of a Subset of Colon Cancers with Potential Clinical Utility.

Comparative analysis of human and mouse transcriptomes of Th17 cell priming.

Androgen receptor DNA binding and chromatin accessibility profiling in prostate cancer.

ERBB2 Mutations Characterize a Subgroup of Muscle-invasive Bladder Cancers with Excellent Response to Neoadjuvant Chemotherapy.

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.

Pretreatment microRNA Expression Impacting on Epithelial-to-Mesenchymal Transition Predicts Intrinsic Radiosensitivity in Head and Neck Cancer Cell Lines and Patients.

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs.

The consensus molecular subtypes of colorectal cancer.

Androgen receptor profiling predicts prostate cancer outcome.

Applications of DNA integrating elements: Facing the bias bully.

Next generation sequencing of triple negative breast cancer to find predictors for chemotherapy response.

BRCA1-like signature in triple negative breast cancer: Molecular and clinical characterization reveals subgroups with therapeutic potential.

Genome-Wide Identification and Characterization of Novel Factors Conferring Resistance to Topoisomerase II Poisons in Cancer.

xHeinz: an algorithm for mining cross-species network modules under a flexible conservation model.

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

Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts.

Robust BRCA1-like classification of copy number profiles of samples repeated across different datasets and platforms.

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

Prospective derivation of a living organoid biobank of colorectal cancer patients.

SMARCE1 suppresses EGFR expression and controls responses to MET and ALK inhibitors in lung cancer.

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

BRCA2-deficient sarcomatoid mammary tumors exhibit multidrug resistance.

Quantitative imaging of focal adhesion dynamics and their regulation by HGF and Rap1 signaling.

A conditional piggyBac transposition system for genetic screening in mice identifies oncogenic networks in pancreatic cancer.

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

Parallel in vivo and in vitro melanoma RNAi dropout screens reveal synthetic lethality between hypoxia and DNA damage response inhibition.

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.

USP9X downregulation renders breast cancer cells resistant to tamoxifen.

Multiscale representation of genomic signals.

Using TRIP for genome-wide position effect analysis in cultured cells.

Intrinsic resistance to MEK inhibition in KRAS mutant lung and colon cancer through transcriptional induction of ERBB3.

Reversible and adaptive resistance to BRAF(V600E) inhibition in melanoma.

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