List of works - Lodewyk F A Wessels

The consensus molecular subtypes of colorectal cancer

scientific article

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

scientific article

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

scientific article

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

scientific article

Concordance among gene-expression-based predictors for breast cancer

scientific article

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

scientific article

Converting a breast cancer microarray signature into a high-throughput diagnostic test.

scientific article published on 30 October 2006

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

scientific article

MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling

scientific article

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

scientific article

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

scientific article

Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue

scientific article (publication date: 11 February 2011)

Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment

scientific article published on 2 September 2004

Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response

scientific article published on 8 August 2009

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

scientific article

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

scientific article

Changes in gene expression associated with response to neoadjuvant chemotherapy in breast cancer

scientific article published in May 2005

Predicting a local recurrence after breast-conserving therapy by gene expression profiling

scientific article published on January 2006

A protocol for building and evaluating predictors of disease state based on microarray data

scientific article published on 7 April 2005

Elevated APOBEC3B correlates with poor outcomes for estrogen-receptor-positive breast cancers

scientific article

Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model

scientific article

Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells

scientific article

Cross-validated Cox regression on microarray gene expression data

scientific article

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

scientific article

Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function

scientific article

Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data

scientific article

Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors

scientific article published on 01 December 2002

Genomic patterns resembling BRCA1- and BRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy

scientific article

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

scientific article

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

scientific article

Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients

scientific article

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

scientific article published on 2 May 2006

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data.

scientific article

Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness

scientific article published on October 27, 2011

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

scientific article published in April 2016

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

scientific article

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

scientific article

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

scientific article

Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach

scientific article

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients

scientific article published on 01 October 2019

Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes

scientific article

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

scientific article

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

scientific article

Somatic structural rearrangements in genetically engineered mouse mammary tumors

scientific article

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

scientific article

Multiscale representation of genomic signals

scientific article published on April 13, 2014

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

scientific article

Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

scientific article published on July 11, 2012

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

scientific article

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes

scientific article

List of works by Lodewyk F A Wessels

The consensus molecular subtypes of colorectal cancer

Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Large-scale genotyping identifies 41 new loci associated with breast cancer risk

Concordance among gene-expression-based predictors for breast cancer

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

Converting a breast cancer microarray signature into a high-throughput diagnostic test.

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

MED12 controls the response to multiple cancer drugs through regulation of TGF-β receptor signaling

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

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

Gene expression profiles from formalin fixed paraffin embedded breast cancer tissue are largely comparable to fresh frozen matched tissue

Gene expression profiling in follicular lymphoma to assess clinical aggressiveness and to guide the choice of treatment

Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

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

Changes in gene expression associated with response to neoadjuvant chemotherapy in breast cancer

Predicting a local recurrence after breast-conserving therapy by gene expression profiling

A protocol for building and evaluating predictors of disease state based on microarray data

Elevated APOBEC3B correlates with poor outcomes for estrogen-receptor-positive breast cancers

Transposon mutagenesis identifies genes driving hepatocellular carcinoma in a chronic hepatitis B mouse model

Ubiquitin E3 ligase Ring1b/Rnf2 of polycomb repressive complex 1 contributes to stable maintenance of mouse embryonic stem cells

Cross-validated Cox regression on microarray gene expression data

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

Dosage-dependent tumor suppression by histone deacetylases 1 and 2 through regulation of c-Myc collaborating genes and p53 function

Identification of cancer genes using a statistical framework for multiexperiment analysis of nondiscretized array CGH data

Molecular classification of breast carcinomas by comparative genomic hybridization: a specific somatic genetic profile for BRCA1 tumors

Genomic patterns resembling BRCA1- and BRCA2-mutated breast cancers predict benefit of intensified carboplatin-based chemotherapy

Identification of distinct miRNA target regulation between breast cancer molecular subtypes using AGO2-PAR-CLIP and patient datasets

Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability

Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients

A comparison of univariate and multivariate gene selection techniques for classification of cancer datasets

Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data.

Quantitative copy number analysis by Multiplex Ligation-dependent Probe Amplification (MLPA) of BRCA1-associated breast cancer regions identifies BRCAness

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

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

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

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

Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients

Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes

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

Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data

Somatic structural rearrangements in genetically engineered mouse mammary tumors

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

Multiscale representation of genomic signals

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

Integration of Clinical and Gene Expression Data Has a Synergetic Effect on Predicting Breast Cancer Outcome

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

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes