Final clinical analysis of pre-operative ipilimumab and nivolumab in locally advanced urothelial cancer and exploration of tumor-draining lymph node composition: The NABUCCO trial, Chantal F Stockem, Jeroen van Dorp, Nick van Dijk … Britt B M Suelmann, Michiel S van der Heijden; European journal of cancer (Oxford, England : 1990), 2025-09-11

NASP modulates histone turnover to drive PARP inhibitor resistance, Sarah C Moser, Anna Khalizieva, Josef Roehsner … Abdelghani Mazouzi, Jos Jonkers; Nature, 2025-08-13

Biomarker Analysis and Treatment Dynamics Following Preoperative Ipilimumab plus Nivolumab in Locally Advanced Urothelial Cancer from the Phase IB NABUCCO Study, Chantal F Stockem, Alberto Gil-Jimenez, Hamza Ali … Daniel J Vis, Michiel S van der Heijden; Clinical cancer research : an official journal of the American Association for Cancer Research, 2025-06-09

Whole genome sequencing of 378 prostate cancer metastases reveals tissue selectivity for mismatch deficiency with potential therapeutic implications, Daniel J Vis, Sander A L Palit, Marie Corradi … Wilbert Zwart, Andries M Bergman; Genome medicine, 2025-03-21

Cell-free DNA aneuploidy score as a dynamic early response marker in prostate cancer, Khrystany T Isebia, Anouk C de Jong, Lisanne F van Dessel … Maurice P H M Jansen, John W M Martens; Molecular oncology, 2025-03-14

Genomic and transcriptomic features of androgen receptor signaling inhibitor resistance in metastatic castration-resistant prostate cancer, Xiaolin Zhu, Tatyanah Farsh, Daniël Vis … Michiel S van der Heijden, Felix Y Feng; The Journal of clinical investigation, 2024-10-01

A pan-cancer screen identifies drug combination benefit in cancer cell lines at the individual and population level, Daniel J Vis, Patricia Jaaks, Nanne Aben … Mathew J Garnett, Lodewyk F A Wessels; Cell reports. Medicine, 2024-08-21

Platinum-Based Chemotherapy Induces Opposing Effects on Immunotherapy Response-Related Spatial and Stromal Biomarkers in the Bladder Cancer Microenvironment, Maksim A Chelushkin, Jeroen van Dorp, Sandra van Wilpe … Daniel J Vis, Michiel S van der Heijden; Clinical cancer research : an official journal of the American Association for Cancer Research, 2024-07-24

Spatial relationships in the urothelial and head and neck tumor microenvironment predict response to combination immune checkpoint inhibitors, Alberto Gil-Jimenez, Nick van Dijk, Joris L Vos … Michiel S van der Heijden, Lodewyk F A Wessels; Nature communications, 2024-03-22

Corrigendum to “Assessment of Predictive Genomic Biomarkers for Response to Cisplatin-based Neoadjuvant Chemotherapy in Bladder Cancer” [Eur Urol 2023;83:313-17], Alberto Gil-Jimenez, Jeroen van Dorp, Alberto Contreras-Sanz … Peter C Black, Michiel S van der Heijden; European urology, 2023-03-12

Assessment of Predictive Genomic Biomarkers for Response to Cisplatin-based Neoadjuvant Chemotherapy in Bladder Cancer, Alberto Gil-Jimenez, Jeroen van Dorp, Alberto Contreras-Sanz … Peter C Black, Michiel S van der Heijden; European urology, 2022-08-14

Effective drug combinations in breast, colon and pancreatic cancer cells, Patricia Jaaks, Elizabeth A Coker, Daniel J Vis … Lodewyk Wessels, Mathew J Garnett; Nature, 2022-02-24

The Tumor Immune Landscape and Architecture of Tertiary Lymphoid Structures in Urothelial Cancer, Nick van Dijk, Alberto Gil-Jimenez, Karina Silina … Bas W G van Rhijn, Michiel S van der Heijden; Frontiers in immunology, 2022-01-06

Predicting patient response with models trained on cell lines and patient-derived xenografts by nonlinear transfer learning, Soufiane M C Mourragui, Marco Loog, Daniel J Vis … Marcel J T Reinders, Lodewyk F A Wessels; Proceedings of the National Academy of Sciences of the United States of America, 2021-12-07

Ovarian Cancer-Specific BRCA-like Copy-Number Aberration Classifiers Detect Mutations Associated with Homologous Recombination Deficiency in the AGO-TR1 Trial, Philip C Schouten, Lisa Richters, Daniel J Vis … Sabine C Linn, Rita K Schmutzler; Clinical cancer research : an official journal of the American Association for Cancer Research, 2021-10-01

A kinome-centered CRISPR-Cas9 screen identifies activated BRAF to modulate enzalutamide resistance with potential therapeutic implications in BRAF-mutated prostate cancer, Sander A L Palit, Jeroen van Dorp, Daniel Vis … Wilbert Zwart, Michiel S van der Heijden; Scientific reports, 2021-07-02

Preoperative ipilimumab plus nivolumab in locoregionally advanced urothelial cancer: the NABUCCO trial, Nick van Dijk, Alberto Gil-Jimenez, Karina Silina … Bas W van Rhijn, Michiel S van der Heijden; Nature medicine, 2020-10-13

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, Julia D Wulfkuhle, Christina Yau, Denise M Wolf … Laura Van’t Veer, Emanuel F Petricoin; JCO precision oncology, 2020-09-11

Epigenetic profiling demarcates molecular subtypes of muscle-invasive bladder cancer, K E van der Vos, D J Vis, E Nevedomskaya … W Zwart, M S van der Heijden; Scientific reports, 2020-07-04

TLE3 loss confers AR inhibitor resistance by facilitating GR-mediated human prostate cancer cell growth, Sander Al Palit, Daniel Vis, Suzan Stelloo … Wilbert Zwart, Michiel S van der Heijden; eLife, 2019-12-20

Genomic data integration by WON-PARAFAC identifies interpretable factors for predicting drug-sensitivity in vivo, Yongsoo Kim, Tycho Bismeijer, Wilbert Zwart … Lodewyk F A Wessels, Daniel J Vis; Nature communications, 2019-11-08

Patient-derived organoids can predict response to chemotherapy in metastatic colorectal cancer patients, Salo N Ooft, Fleur Weeber, Krijn K Dijkstra … Hans Clevers, Emile E Voest; Science translational medicine, 2019-10-11

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality, Ewa Gogola, Alexandra A Duarte, Julian R de Ruiter … Jos Jonkers, Sven Rottenberg; Cancer cell, 2019-06-12

Selective Loss of PARG Restores PARylation and Counteracts PARP Inhibitor-Mediated Synthetic Lethality, Ewa Gogola, Alexandra A Duarte, Julian R de Ruiter … Jos Jonkers, Sven Rottenberg; Cancer cell, 2018-06-13

MAP3K1 and MAP2K4 mutations are associated with sensitivity to MEK inhibitors in multiple cancer models, Zheng Xue, Daniel J Vis, Alejandra Bruna … Lodewyk F A Wessels, René Bernards; Cell research, 2018-05-26

Pathogenic and targetable genetic alterations in 70 urachal adenocarcinomas, Henning Reis, Kristan E van der Vos, Christian Niedworok … Péter Nyirády, Tibor Szarvas; International journal of cancer, 2018-04-20

Identification of a Druggable Pathway Controlling Glioblastoma Invasiveness, Nora Pencheva, Mark C de Gooijer, Daniel J Vis … Olaf van Tellingen, René Bernards; Cell reports, 2017-07-07

Towards a global cancer knowledge network: dissecting the current international cancer genomic sequencing landscape, D J Vis, J Lewin, R G Liao … E Voest, Clinical Working Group of the Global Alliance for Genomics and Health; Annals of oncology : official journal of the European Society for Medical Oncology, 2017-04-29

Second-line Chemotherapy in Older Patients With Metastatic Urothelial Carcinoma: Pooled Analysis of 10 Second-line Studies, Samer Salah, Jae-Lyun Lee, Antonio Rozzi … Kouji Izumi, Jeremy Lewin; Clinical genitourinary cancer, 2017-01-10

TANDEM: a two-stage approach to maximize interpretability of drug response models based on multiple molecular data types, Nanne Aben, Daniel J Vis, Magali Michaut … Magali Michaut, Lodewyk F A Wessels; Bioinformatics (Oxford, England), 2016-09-03

A Landscape of Pharmacogenomic Interactions in Cancer, Francesco Iorio, Theo A Knijnenburg, Daniel J Vis … Ultan McDermott, Mathew J Garnett; Cell, 2016-07-12

Multilevel models improve precision and speed of IC50 estimates, Daniel J Vis, Lorenzo Bombardelli, Howard Lightfoot … Mathew J Garnett, Lodewyk Fa Wessels; Pharmacogenomics, 2016-05-17

Facilitating a culture of responsible and effective sharing of cancer genome data, Lillian L Siu, Mark Lawler, David Haussler … Charles L Sawyers, Emile E Voest; Nature medicine, 2016-05-06

Integration of genomic, transcriptomic and proteomic data identifies two biologically distinct subtypes of invasive lobular breast cancer, Magali Michaut, Suet-Feung Chin, Ian Majewski … Carlos Caldas, Rene Bernards; Scientific reports, 2016-01-06

Subunit composition of VRAC channels determines substrate specificity and cellular resistance to Pt-based anti-cancer drugs, Rosa Planells-Cases, Darius Lutter, Charlotte Guyader … Sven Rottenberg, Thomas J Jentsch; The EMBO journal, 2015-11-05

Intra- and inter-tumor heterogeneity in a vemurafenib-resistant melanoma patient and derived xenografts, Kristel Kemper, Oscar Krijgsman, Paulien Cornelissen-Steijger … John B Haanen, Daniel S Peeper; EMBO molecular medicine, 2015-06-25

Correlated measurement error hampers association network inference, Mateusz Kaduk, Huub C J Hoefsloot, Daniel J Vis … Age K Smilde, Margriet M W B Hendriks; Journal of chromatography. B, Analytical technologies in the biomedical and life sciences, 2014-06-22

Network identification of hormonal regulation, Daniel J Vis, Johan A Westerhuis, Huub C J Hoefsloot … Margriet M W B Hendriks, Age K Smilde; PloS one, 2014-05-24

Inferring differences in the distribution of reaction rates across conditions, Diana M Hendrickx, Huub C J Hoefsloot, Margriet M W B Hendriks … Bas Teusink, Age K Smilde; Molecular bioSystems, 2012-07-12

Detecting regulatory mechanisms in endocrine time series measurements, Daniel J Vis, Johan A Westerhuis, Huub C J Hoefsloot … Margriet M W B Hendriks, Age K Smilde; PloS one, 2012-03-31

Genome-wide analysis of yeast stress survival and tolerance acquisition to analyze the central trade-off between growth rate and cellular robustness, Anna Zakrzewska, Gerco van Eikenhorst, Johanna E C Burggraaff … Stanley Brul, Gertien J Smits; Molecular biology of the cell, 2011-10-04

Dynamic metabolomic data analysis: a tutorial review, A K Smilde, J A Westerhuis, H C J Hoefsloot … F Roelfsema, J van der Greef; Metabolomics : Official journal of the Metabolomic Society, 2010-03-27

Endocrine pulse identification using penalized methods and a minimum set of assumptions, Daniel J Vis, Johan A Westerhuis, Huub C J Hoefsloot … Jan van der Greef, Age K Smilde; American journal of physiology. Endocrinology and metabolism, 2009-10-29

Phenotyping tea consumers by nutrikinetic analysis of polyphenolic end-metabolites, Ewoud J J van Velzen, Johan A Westerhuis, John P M van Duynhoven … Daniël J Vis, Age K Smilde; Journal of proteome research, 2009-04-21

Statistical validation of megavariate effects in ASCA, Daniel J Vis, Johan A Westerhuis, Age K Smilde … Age K Smilde, Jan van der Greef; BMC bioinformatics, 2007-09-01

T-profiler: scoring the activity of predefined groups of genes using gene expression data, André Boorsma, Barrett C Foat, Daniel Vis … Frans Klis, Harmen J Bussemaker; Nucleic acids research, 2005-06-28