List of works - Lodewyk F A Wessels

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

scientific article published in April 2016

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

scientific article published on 2 May 2006

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

scientific article published on 16 January 2020

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

scientific article published on 7 April 2005

Analysis of mass spectrometry data using sub-spectra

scientific article

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

scientific article

Applications of DNA integrating elements: Facing the bias bully

scientific article

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

scientific article

Biclustering sparse binary genomic data

scientific article

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

scientific article

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

scientific article published in May 2005

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes

scientific article

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

scientific article

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

scientific article

Concordance among gene-expression-based predictors for breast cancer

scientific article

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

scientific article published on 8 August 2009

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

scientific article published on 30 October 2006

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

scientific article

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

scientific article

Cross-validated Cox regression on microarray gene expression data

scientific article

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

scientific article

Detection of Colorectal Cancer by Serum and Tissue Protein Profiling: A Prospective Study in a Population at Risk

scientific article

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

scientific article

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

scientific article

Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward Androgen Independence

scientific article published in 2022

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

scientific article

Erratum: Corrigendum: The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

scientific article published in Nature

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

scientific article

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

scientific article published in 2022

Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

scientific article published on 25 January 2021

Functional Genomic Identification of Predictors of Sensitivity and Mechanisms of Resistance to Multivalent Second-Generation TRAIL-R2 Agonists

scientific article published on 01 April 2022

Functional categorization of BRCA1 variants of uncertain clinical significance in homologous recombination repair complementation assays

scientific article published on 16 June 2020

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

Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer

scientific article published on 09 June 2022

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

scientific article

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

scientific article

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

scientific article

Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach

scientific article

Identifying subgroup markers in heterogeneous populations

scientific article published on 22 September 2013

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

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

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

scientific article

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

scientific article

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

scientific article

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

scientific article

Knowledge driven decomposition of tumor expression profiles

scientific article

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

scientific article

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

scientific article

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

scientific article

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

scientific article

MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling

scientific article published in 2022

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

scientific article

Module-based outcome prediction using breast cancer compendia

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

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

scientific article published on 22 June 2020

Multiscale representation of genomic signals

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

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors

scientific article published on 01 July 2019

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

scientific article

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

scientific article published on 01 October 2019

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

scientific article

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

scientific article published on January 2006

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

scientific article

Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning

scientific article published on 06 December 2021

Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer: the NABUCCO trial

scientific article published on 12 October 2020

Publisher Correction: Truncated FGFR2 is a clinically actionable oncogene in multiple cancers

correction of a scholarly 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

Response of metastatic mouse invasive lobular carcinoma to mTOR inhibition is partly mediated by the adaptive immune system

scientific article published on 12 February 2020

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

scientific article

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

scientific article published on 20 March 2015

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

scientific article

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

scientific article

Somatic structural rearrangements in genetically engineered mouse mammary tumors

scientific article

Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

scientific article

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

scientific article

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

scientific article

The consensus molecular subtypes of colorectal cancer

scientific article

The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

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

γδ T cells are effectors of immunotherapy in cancers with HLA class I defects

scientific article published in 2023

List of works by Lodewyk F A Wessels

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

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

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

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

Analysis of mass spectrometry data using sub-spectra

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

Applications of DNA integrating elements: Facing the bias bully

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

Biclustering sparse binary genomic data

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

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

Co-occurrence analysis of insertional mutagenesis data reveals cooperating oncogenes

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

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

Concordance among gene-expression-based predictors for breast cancer

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

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

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

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

Cross-validated Cox regression on microarray gene expression data

Detecting statistically significant common insertion sites in retroviral insertional mutagenesis screens

Detection of Colorectal Cancer by Serum and Tissue Protein Profiling: A Prospective Study in a Population at Risk

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

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

Drug-Induced Epigenomic Plasticity Reprograms Circadian Rhythm Regulation to Drive Prostate Cancer toward Androgen Independence

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

Erratum: Corrigendum: The deubiquitinase USP9X suppresses pancreatic ductal adenocarcinoma

Exploiting combinatorial cultivation conditions to infer transcriptional regulation

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

Few-shot learning creates predictive models of drug response that translate from high-throughput screens to individual patients

Functional Genomic Identification of Predictors of Sensitivity and Mechanisms of Resistance to Multivalent Second-Generation TRAIL-R2 Agonists

Functional categorization of BRCA1 variants of uncertain clinical significance in homologous recombination repair complementation assays

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

Genomic analysis defines clonal relationships of ductal carcinoma in situ and recurrent invasive breast cancer

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

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

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

Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach

Identifying subgroup markers in heterogeneous populations

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

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

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

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

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

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

Knowledge driven decomposition of tumor expression profiles

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

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

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

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

MYC promotes immune-suppression in triple-negative breast cancer via inhibition of interferon signaling

MicroRNA sequence and expression analysis in breast tumors by deep sequencing

Module-based outcome prediction using breast cancer compendia

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

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

Multiscale representation of genomic signals

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

PRECISE: a domain adaptation approach to transfer predictors of drug response from pre-clinical models to tumors

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

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

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

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

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

Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning

Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer: the NABUCCO trial

Publisher Correction: Truncated FGFR2 is a clinically actionable oncogene in multiple cancers

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

Response of metastatic mouse invasive lobular carcinoma to mTOR inhibition is partly mediated by the adaptive immune system

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

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

SIRAC: Supervised Identification of Regions of Aberration in aCGH datasets

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

Somatic structural rearrangements in genetically engineered mouse mammary tumors

Specific genomic aberrations in primary colorectal cancer are associated with liver metastases

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

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

The consensus molecular subtypes of colorectal cancer