Publications by authors named "Ruud H Brakenhoff"

100Publications

Annual malignant transformation rate of oral leukoplakia remains consistent: A long-term follow-up study.

Oral Oncol 2020 11 7;110:105014. Epub 2020 Oct 7.

Amsterdam UMC, location VUmc, Department of Oral and Maxillofacial Surgery / Oral Pathology, Cancer Center Amsterdam, Academic Centre for Dentistry Amsterdam (ACTA), P.O. Box 7057, 1007 MB Amsterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
November 2020

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery.

Genomics Proteomics Bioinformatics 2020 Apr 12;18(2):104-119. Epub 2020 Aug 12.

Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China. Electronic address:

View Article and Find Full Text PDF
April 2020

Comprehensive multiparameter genetic analysis improves circulating tumor DNA detection in head and neck cancer patients.

Oral Oncol 2020 Jun 23;109:104852. Epub 2020 Jun 23.

Department of Otolaryngology - Head and Neck Surgery, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
June 2020

Outcome prediction of head and neck squamous cell carcinoma by MRI radiomic signatures.

Eur Radiol 2020 Nov 4;30(11):6311-6321. Epub 2020 Jun 4.

Radiology and Nuclear Medicine, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, De Boelelaan 1117, 1081 HV, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
November 2020

Epithelial-to-mesenchymal transition is a prognostic marker for patient outcome in advanced stage HNSCC patients treated with chemoradiotherapy.

Radiother Oncol 2020 Jun 13;147:186-194. Epub 2020 May 13.

Division of Cell Biology, The Netherlands Cancer Institute, Amsterdam, The Netherlands; Department of Radiation Oncology, The Netherlands Cancer Institute, Amsterdam, The Netherlands. Electronic address:

View Article and Find Full Text PDF
June 2020

Chemopreventive targeted treatment of head and neck precancer by Wee1 inhibition.

Sci Rep 2020 02 11;10(1):2330. Epub 2020 Feb 11.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
February 2020

Digital pathology-aided assessment of tumor-infiltrating T lymphocytes in advanced stage, HPV-negative head and neck tumors.

Cancer Immunol Immunother 2020 Apr 24;69(4):581-591. Epub 2020 Jan 24.

Department of Pathology, University Medical Center Utrecht, Heidelberglaan 100, 3584 CX, Utrecht, The Netherlands.

View Article and Find Full Text PDF
April 2020

Incorporation of differentiated dysplasia improves prediction of oral leukoplakia at increased risk of malignant progression.

Mod Pathol 2020 06 2;33(6):1033-1040. Epub 2020 Jan 2.

Amsterdam UMC and Academic Centre for Dentistry Amsterdam (ACTA), Vrije Universiteit Amsterdam, Department of Oral and Maxillofacial Surgery/Oral Pathology, Cancer Center Amsterdam, de Boelelaan, 1117, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
June 2020

Development and Validation of a Novel and Rapid Molecular Detection Method for High-Risk Human Papillomavirus in Formalin-Fixed, Paraffin-Embedded Tumor Tissue.

J Mol Diagn 2020 02 16;22(2):262-271. Epub 2019 Dec 16.

Department of Otolaryngology-Head and Neck Surgery, Amsterdam University Medical Center, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
February 2020

Characterization of a head and neck cancer-derived cell line panel confirms the distinct TP53-proficient copy number-silent subclass.

Oral Oncol 2019 11 18;98:53-61. Epub 2019 Sep 18.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Section Tumor Biology, Cancer Center Amsterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
November 2019

Molecular Characterization of Locally Relapsed Head and Neck Cancer after Concomitant Chemoradiotherapy.

Clin Cancer Res 2019 12 22;25(23):7256-7265. Epub 2019 Aug 22.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head & Neck Surgery, Cancer Center Amsterdam, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
December 2019

Targeting the cell cycle in head and neck cancer by Chk1 inhibition: a novel concept of bimodal cell death.

Oncogenesis 2019 Jun 17;8(7):38. Epub 2019 Jun 17.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology/Head and Neck Surgery, Section Tumor Biology, Cancer Center Amsterdam, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
June 2019

Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction.

J Proteomics 2019 03 30;196:106-119. Epub 2019 Jan 30.

Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands. Electronic address:

View Article and Find Full Text PDF
March 2019

ACE: absolute copy number estimation from low-coverage whole-genome sequencing data.

Bioinformatics 2019 08;35(16):2847-2849

Pathology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
August 2019

Limited detection of human polyomaviruses in Fanconi anemia related squamous cell carcinoma.

PLoS One 2018 27;13(12):e0209235. Epub 2018 Dec 27.

Division of Oncology, Cancer and Blood Diseases Institute, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio, United States of America.

View Article and Find Full Text PDF
May 2019

Establishment and Genetic Landscape of Precancer Cell Model Systems from the Head and Neck Mucosal Lining.

Mol Cancer Res 2019 01 17;17(1):120-130. Epub 2018 Sep 17.

Amsterdam UMC, Vrije Universiteit Amsterdam, Otolaryngology-Head and Neck Surgery, Cancer Center Amsterdam, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
January 2019

Publisher Correction: The molecular landscape of head and neck cancer.

Nat Rev Cancer 2018 Oct;18(10):662

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, Netherlands.

View Article and Find Full Text PDF
October 2018

A review of the most promising biomarkers for early diagnosis and prognosis prediction of tongue squamous cell carcinoma.

Br J Cancer 2018 09 21;119(6):724-736. Epub 2018 Aug 21.

Department of Oral and Maxillofacial Surgery and Oral Pathology, Academic Centre for Dentistry, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
September 2018

Rscreenorm: normalization of CRISPR and siRNA screen data for more reproducible hit selection.

BMC Bioinformatics 2018 Aug 20;19(1):301. Epub 2018 Aug 20.

Department of Epidemiology and Biostatistics, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, 1007, MB, The Netherlands.

View Article and Find Full Text PDF
August 2018

The molecular landscape of head and neck cancer.

Nat Rev Cancer 2018 05 2;18(5):269-282. Epub 2018 Mar 2.

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center.

View Article and Find Full Text PDF
May 2018

Development and validation of a radiomic signature to predict HPV (p16) status from standard CT imaging: a multicenter study.

Br J Radiol 2018 Jun 22;91(1086):20170498. Epub 2018 Mar 22.

1 The D-Lab: Decision Support for Precision Medicine GROW - School for Oncology and Developmental Biology & MCCC Maastricht University Medical Centre+ Maastricht , Maastricht , Netherlands.

View Article and Find Full Text PDF
June 2018

Improved high-dimensional prediction with Random Forests by the use of co-data.

BMC Bioinformatics 2017 12 28;18(1):584. Epub 2017 Dec 28.

Department of Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, 1007 MB, The Netherlands.

View Article and Find Full Text PDF
December 2017

Targeting PLK1 as a novel chemopreventive approach to eradicate preneoplastic mucosal changes in the head and neck.

Oncotarget 2017 Nov 16;8(58):97928-97940. Epub 2017 May 16.

Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Cancer Center Amsterdam, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
November 2017

Risk Groups for Survival in HPV-Positive and HPV-Negative OPSCC.

Recent Results Cancer Res 2017;206:221-231

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
March 2017

Molecular Patterns and Biology of HPV-Associated HNSCC.

Recent Results Cancer Res 2017;206:37-56

Department of Otorhinolaryngology, Head and Neck Surgery, University of Giessen, Giessen, Germany.

View Article and Find Full Text PDF
March 2017

Applications of molecular diagnostics for personalized treatment of head and neck cancer: state of the art.

Expert Rev Mol Diagn 2016 4;16(2):205-21. Epub 2016 Jan 4.

a Department of Otolaryngology-Head and Neck Surgery , VU University Medical Center , Amsterdam , The Netherlands.

View Article and Find Full Text PDF
November 2016

Defective sister chromatid cohesion is synthetically lethal with impaired APC/C function.

Nat Commun 2015 Oct 1;6:8399. Epub 2015 Oct 1.

Department of Clinical Genetics, section Oncogenetics, VU University Medical Center, Van der Boechorststraat 7, 1081 BT Amsterdam, The Netherlands.

View Article and Find Full Text PDF
October 2015

Sensitivity to chromosomal breakage as risk factor in young adults with oral squamous cell carcinoma.

J Oral Pathol Med 2016 Mar 26;45(3):189-92. Epub 2015 Aug 26.

Department of Otolaryngology - Head and Neck Surgery, Cancer Center Amsterdam, VU University Medical Center Amsterdam, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
March 2016

Noninvasive molecular screening for oral precancer in Fanconi anemia patients.

Cancer Prev Res (Phila) 2015 Nov 14;8(11):1102-11. Epub 2015 Aug 14.

Section Tumor Biology, Department of Otolaryngology-Head and Neck Surgery, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
November 2015

Molecular events in relapsed oral squamous cell carcinoma: Recurrence vs. secondary primary tumor.

Oral Oncol 2015 Aug 16;51(8):738-44. Epub 2015 May 16.

Department of Head and Neck Surgery and Otorhinolaryngology, A. C. Camargo Cancer Center and National Institute of Science and Technology on Oncogenomics (INCITO), São Paulo, Brazil.

View Article and Find Full Text PDF
August 2015

Direct benefit of vaccinating boys along with girls against oncogenic human papillomavirus: bayesian evidence synthesis.

BMJ 2015 May 12;350:h2016. Epub 2015 May 12.

Department of Epidemiology and Biostatistics, VU University Medical Centre, PO Box 7057, 1007 MB Amsterdam, Netherlands.

View Article and Find Full Text PDF
May 2015

Prevalence of human papillomavirus in laryngeal and hypopharyngeal squamous cell carcinomas in northern Spain.

Cancer Epidemiol 2015 Feb 29;39(1):37-41. Epub 2014 Nov 29.

Department of Otolaryngology, IUOPA, Hospital Universitario Central de Asturias, University of Oviedo, Oviedo, Spain.

View Article and Find Full Text PDF
February 2015

tigaR: integrative significance analysis of temporal differential gene expression induced by genomic abnormalities.

BMC Bioinformatics 2014 Oct 2;15:327. Epub 2014 Oct 2.

Department of Epidemiology and Biostatistics, VU University Medical Center, P,O, Box 7057, 1007 MB, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
October 2014

Molecular screening of oral precancer.

Oral Oncol 2013 Dec 9;49(12):1129-35. Epub 2013 Oct 9.

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands. Electronic address:

View Article and Find Full Text PDF
December 2013

Identification of lethal microRNAs specific for head and neck cancer.

Clin Cancer Res 2013 Oct 13;19(20):5647-57. Epub 2013 Aug 13.

Authors' Affiliations: Departments of Otolaryngology/Head-Neck Surgery, Epidemiology and Biostatistics, and Pathology, VU University Medical Center; Department of Mathematics, VU University; Division of Gene Regulation, The Netherlands Cancer Institute, Amsterdam; and InteRNA Technologies BV, Utrecht, The Netherlands.

View Article and Find Full Text PDF
October 2013

Treatment response of HPV-positive and HPV-negative head and neck squamous cell carcinoma cell lines.

Oral Oncol 2013 Jun 8;49(6):560-6. Epub 2013 Apr 8.

Department of Otolaryngology/Head-Neck Surgery, VU Medical Centre, PO Box 7057, 1007 MB Amsterdam, The Netherlands.

View Article and Find Full Text PDF
June 2013

Potentially novel options for treatment of HPV-attributable head and neck cancer.

Cell Cycle 2013 Apr 19;12(7):1020-1. Epub 2013 Mar 19.

Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, Netherlands.

View Article and Find Full Text PDF
April 2013

Functional genetic screens identify genes essential for tumor cell survival in head and neck and lung cancer.

Clin Cancer Res 2013 Apr 26;19(8):1994-2003. Epub 2013 Feb 26.

AuDepartment of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
April 2013

Molecular diagnosis of minimal residual disease in head and neck cancer patients.

Cell Oncol (Dordr) 2012 Oct 4;35(5):367-75. Epub 2012 Sep 4.

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, PO Box 7057, 1007 MB, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
October 2012

Generation of precursor cell lines from preneoplastic fields surrounding head and neck cancers.

Head Neck 2013 Apr 19;35(4):568-74. Epub 2012 Jun 19.

Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center Amsterdam, The Netherlands.

View Article and Find Full Text PDF
April 2013

Prognostic value of DNA ploidy status in patients with oral leukoplakia.

Oral Oncol 2011 Oct 30;47(10):956-60. Epub 2011 Aug 30.

Dept. of Oral and Maxillofacial Surgery and Oral Pathology, ACTA/VU University Medical Center, 1007 MB Amsterdam, The Netherlands.

View Article and Find Full Text PDF
October 2011

Cancer. Another NOTCH for cancer.

Science 2011 Aug;333(6046):1102-3

Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, 1007 MB Amsterdam, Netherlands.

View Article and Find Full Text PDF
August 2011

Advances and applications of oral cancer basic research.

Oral Oncol 2011 Sep 29;47(9):783-91. Epub 2011 Jul 29.

Department of Otolaryngology-Head and Neck Surgery, Jewish General Hospital, McGill University, Montreal, Canada.

View Article and Find Full Text PDF
September 2011

To DNA or not to DNA? That is the question, when it comes to molecular subtyping for the clinic!

Clin Cancer Res 2011 Aug 14;17(15):4959-64. Epub 2011 Jun 14.

Departments of Pathology and Epidemiology and Biostatistics, Section Tumor Biology, Department of Otolaryngology/Head-Neck Surgery, Cancer Center Amsterdam, The Netherlands.

View Article and Find Full Text PDF
August 2011

Prognostic significance of truncating TP53 mutations in head and neck squamous cell carcinoma.

Clin Cancer Res 2011 Jun 5;17(11):3733-41. Epub 2011 Apr 5.

Departments of Otolaryngology/Head-Neck Surgery, Epidemiology and Biostatistics, and Pathology, VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
June 2011

Protein signatures associated with tumor cell dissemination in head and neck cancer.

J Proteomics 2011 Apr 22;74(4):558-66. Epub 2011 Jan 22.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, CH Utrecht, The Netherlands.

View Article and Find Full Text PDF
April 2011

The molecular biology of head and neck cancer.

Nat Rev Cancer 2011 Jan 16;11(1):9-22. Epub 2010 Dec 16.

Department of Otolaryngology-Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
January 2011

Immortalization of oral keratinocytes by functional inactivation of the p53 and pRb pathways.

Int J Cancer 2011 Apr 24;128(7):1596-605. Epub 2010 May 24.

Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
April 2011

Adenovirus retargeting to surface expressed antigens on oral mucosa.

J Gene Med 2010 Apr;12(4):365-76

Department of Otolaryngology/Head-Neck Surgery, Section Tumor Biology, VU University Medical Centre, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
April 2010

Molecular analysis of surgical margins in head and neck cancer: more than a marginal issue.

Oral Oncol 2010 Jul 26;46(7):485-91. Epub 2010 Feb 26.

Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
July 2010

Intensity-based analysis of dual-color gene expression data as an alternative to ratio-based analysis to enhance reproducibility.

BMC Genomics 2010 Feb 17;11:112. Epub 2010 Feb 17.

Neuroregeneration Laboratory, Netherlands Institute for Neuroscience, Meibergdreef 47, 1105 BA Amsterdam, the Netherlands.

View Article and Find Full Text PDF
February 2010

Protein biomarker discovery for head and neck cancer.

J Proteomics 2010 Sep 4;73(10):1790-803. Epub 2010 Feb 4.

Biomolecular Mass Spectrometry and Proteomics Group, Netherlands Proteomics Centre, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

View Article and Find Full Text PDF
September 2010

Gene expression profiling in head and neck squamous cell carcinoma.

Curr Opin Otolaryngol Head Neck Surg 2010 Apr;18(2):67-71

Department of Otolaryngology - Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
April 2010

Evaluation of cornulin, keratin 4, keratin 13 expression and grade of dysplasia for predicting malignant progression of oral leukoplakia.

Oral Oncol 2010 Feb 29;46(2):123-7. Epub 2009 Dec 29.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands.

View Article and Find Full Text PDF
February 2010

Differential Proteomics Identifies Protein Biomarkers That Predict Local Relapse of Head and Neck Squamous Cell Carcinomas.

Clin Cancer Res 2009 Dec;15(24):7666-7675

Authors' Affiliations: Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, and Netherlands Proteomics Centre, Utrecht, the Netherlands; Departments of Otolaryngology/Head-Neck Surgery, Epidemiology and Biostatistics, and Oral and Maxillofacial Surgery/Pathology, Academic Centre for Dentistry Amsterdam (ACTA), VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
December 2009

Human papilloma virus in head and neck cancer: the need for a standardised assay to assess the full clinical importance.

Eur J Cancer 2009 Nov 18;45(17):2935-9. Epub 2009 Sep 18.

Section Tumor Biology, Department of Otolaryngology/Head-Neck Surgery, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
November 2009

Genetic classification of oral and oropharyngeal carcinomas identifies subgroups with a different prognosis.

Cell Oncol 2009 ;31(4):291-300

Section Tumor Biology, Department of Otolaryngology/Head-Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands.

View Article and Find Full Text PDF
September 2009

Comparative proteome analysis to explore p53 pathway disruption in head and neck carcinogenesis.

J Proteomics 2009 Jul 13;72(5):803-14. Epub 2009 May 13.

Biomolecular Mass Spectrometry and Proteomics Group, Bijvoet Center for Biomolecular Research and Utrecht Institute for Pharmaceutical Sciences, Utrecht University, The Netherlands.

View Article and Find Full Text PDF
July 2009

Genomic profiles associated with early micrometastasis in lung cancer: relevance of 4q deletion.

Clin Cancer Res 2009 Mar 10;15(5):1566-74. Epub 2009 Feb 10.

Institute of Tumor Biology and Department of General, Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany.

View Article and Find Full Text PDF
March 2009

Screening for oral precancer with noninvasive genetic cytology.

Cancer Prev Res (Phila) 2009 Feb 27;2(2):128-33. Epub 2009 Jan 27.

Department of Oral and Maxillofacial Surgery and Oral Pathology, VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
February 2009

Comparative evaluation of genetic assays to identify oral pre-cancerous fields.

J Oral Pathol Med 2008 Nov 14;37(10):599-606. Epub 2008 Aug 14.

Department of Oromaxillofacial Surgery and Oral Pathology, VU University Medical Center, Amsterdam, the Netherlands.

View Article and Find Full Text PDF
November 2008

Detection, clinical relevance and specific biological properties of disseminating tumour cells.

Nat Rev Cancer 2008 May;8(5):329-40

Institute of Tumour Biology, Center of Experimental Medicine, University Medical Center Hamburg Eppendorf, Martinistrasse 52, Hamburg, Germany.

View Article and Find Full Text PDF
May 2008