Publications
Staiger C, Cadot S, Kooter R, Dittrich M, Müller T, Klau GW, and Wessels LF. A critical evaluation of network and pathway based classifiers for outcome prediction in breast cancer. Plos One, 7, April 2012. [ http ]
Van Monsjou HS, Lopez-Yurda MI, Hauptmann M, Van den Brekel MW, Balm AJ, and Wreesmann VM. Oral and oropharyngeal squamous cell carcinoma in young patients: the Netherlands Cancer Institute experience. Head Neck, 2012. In press.
Kreeft AM, Smeele LE, Rasch CR, Hauptmann M, Rietveld DH, Leemans CR, and Balm AJ. Preoperative imaging and surgical margins in maxillectomy patients. Head Neck, 2012. In press. [ http ]
Devriese LA, Bosma AJ, Van den Heuvel MM, Heemsbergen W, Voest EE, and Schellens JH. Circulating tumor cell detection in advanced non-small cell lung cancer patients by multi-marker QPCR analysis. Lung Cancer, 2011. In press. [ http ]
Defraene G, Van den Bergh L, Al-Mamgani A, Haustermans K, Heemsbergen W, Van den Heuvel F, and Lebesque JV. The benefits of including clinical factors in rectal normal tissue complication probability modeling after radiotherapy for prostate cancer. Int J Radiat Oncol Biol Phys, 2011. In press. [ http ]
Ackerstaff AH, Rasch CR, Balm AJ, De Boer JP, Wiggenraad R, Rietveld DH, Gregor RT, Kroger R, Hauptmann M, Vincent A, and Hilgers FJ. Five-year quality of life results of the randomized clinical phase III (RADPLAT) trial, comparing concomitant intra-arterial versus intravenous chemoradiotherapy in locally advanced head and neck cancer. Head Neck, 2011. In press. [ http ]
Heemsbergen WD, Al-Mamgani A, Witte MG, Pos F, and Lebesque JV. In response to dr. Jereczek-Fossa and colleagues. Int J Radiat Oncol Biol Phys, 2011. In press.
Vollebergh MA, Nederlof PM, Wessels LF, Joosse SA, Van Beers E, Froklage F, Holtkamp M, Schrama JG, Wesseling J, Hauptmann M, De Bruin M, Rodenhuis M, and Linn SC. A clinical test for BRCAness: using array comparative genomic hybridization to predict benefit of high dose, platinum containing, chemotherapy in ER-low/HER2-negative breast cancer patients. Ann Oncol, 2011. In press.
Hoebers F, Heemsbergen W, Moor S, Lopez M, Klop M, Tesselaar M, and Rasch C. Reirradiation for head-and-neck cancer: delicate balance between effectiveness and toxicity. Int J Radiat Oncol Biol Phys, 81 (3):e111-118, 2011. [ http ]
Meulepas JM and Kiemeney LA voor de Werkgroep 'Monitoring van Kanker in Nederland' van de Signaleringscommissie Kanker van KWF Kankerbestrijding. Kanker in Nederland tot 2020 - Trends en prognoses. KWF Kankerbestrijding, Amsterdam, 2011. [ .pdf ]
De Jong J, De Ridder J, Van der Weyden L, Sun N, Van Uitert M, Berns A, Van Lohuizen M, Jonkers J, Adams DJ, and Wessels LF. Computational identification of insertional mutagenesis targets for cancer gene discovery. Nucl Acids Res, 39 (15):e105, 2011. [ http ]
Lamers-Kuijper E, Heemsbergen WD, Van Mourik A, and Rasch C. Sequentially delivered boost plans are superior to simultaneously delivered plans in head and neck cancer when the boost volume is located further away from the parotid glands. Radiother Oncol, 98 (1):51-56, 2011. [ http ]
Vollebergh MA, Lips EH, Nederlof PM, Wessels LF, Schmidt MK, Van Beers EH, Cornelissen S, Holtkamp M, Froklage FE, De Vries EG, Schrama JG, Wesseling J Van de Vijver MJ, Van Tinteren H, De Bruin M, Hauptmann M, Rodenhuis S, and Linn SC. An aCGH classifier derived from BRCA1-mutated breast cancer and benefit of high-dose platinum-based chemotherapy in HER2-negative breast cancer patients. Ann Oncol, 22(7):1561-1570, 2011. [ http ]
Molloy TJ, Devriese LA, Helgason HH, Bosma AJ, Hauptmann M, Voest EE, Schellens JH, and Van't Veer LJ. A multi-marker QPCR-based platform for the detection of circulating tumor cells in patients with early-stage breast cancer. Br J Cancer, 104(12):1913-1919, 2011. [ http ]
Tamulonis C, Postma M, Marlow HQ, Magie CR, De Jong J, and Kaandorp J. A cell-based model of Nematostella vectensis gastrulation including bottle cell formation, invagination and zippering. Dev Biol, 351(1):217-228, 2011. [ http ]
Rasch CR, Hauptmann M, and Balm AJ. Response to “Robbins KT, Howell SB, Williams JS. Intra-arterial chemotherapy for advanced head and neck cancer: is there a verdict?”. Cancer, 117(4):874, 2011. [ http ]
Van der Pal HJ, Van Dalen EC, Hauptmann M, Kok WE, Caron HN, Van den Bos C, Oldenburger F, Koning CC, Van Leeuwen FE, and Kremer LC. Response to “Rosenberg H. Re: Cardiac function in 5-year survivors of childhood cancer: a long-term follow-up study.”. Arch Intern Med, 171(3):264-265, 2011. [ http ]
Knegjens JL, Pameijer FA, Hauptmann M, Balm AJ, Hoebers FJ, Kaanders JH De Bois JA, Verhoef LC, Wijers OB, Wiggenraad RG, Buter J, and Rasch CR. Tumor volume as outcome predictor in chemoradiation for advanced head and neck cancer. Head Neck, 33(3):375-382, 2011. [ http ]
Kok M, Zwart W, Holm C, Fles R, Hauptmann M, Van't Veer LJ, Wessels LF, Neefjes J, Stal O, Linn SC, Landberg G, and Michalides R. PKA-induced phosphorylation of ERalpha at serine 305 and high PAK1 levels is associated with sensitivity to tamoxifen in ER-positive breast cancer. Breast Cancer Res Treat, 125(1):1-12, 2011. [ http ]
Hauptmann M and Richardson DB. Response to “Sylvestre MP, Abrahamowicz M. Flexible modeling of the cumulative effects of time-dependent exposures on the hazard.”. Stat Med, 30(2):197, 2011. [ http ]
Meulepas JM, Newcomb PA, Burnett-Hartman AN, Hampton JM, and Trentham-Dietz A. Multivitamin supplement use and risk of invasive breast cancer. Public Health Nutr, 13(10):1540-1545, 2010. [ http ]
Ramsey SA, Knijnenburg TA, Kennedy KA, Zak DE, Gilchrist M, Gold ES, Johnson CD, Lampano AE, Litvak V, Navarro G, Stolyar T, Aderem A, and Shmulevich I. Genome-wide histone acetylation data improve prediction of mammalian transcription factor binding sites. Bioinformatics, 26(17):2071-2075, 2010. [ http | .pdf ]
Saleem RA, Long-O'Donnell R, Dilworth DJ, Armstrong AM, Jamakhandi AP, Wan Y, Knijnenburg TA, Niemisto A, Boyle J, Rachubinski RA, Shmulevich I, and Aitchison JD. Genome-wide analysis of effectors of peroxisome biogenesis. PLoS One, 5(8):e11953, 2010. [ http ]
He Y, Van't Veer L, Lopez-Yurda M, Van de Velde C, and Marijnen C. Do rectal cancer patients with PIK3CA mutations benefit from preoperative radiotherapy with regard to local recurrences? Clin Cancer Res, 16 (24):6179, 2010. [ http ]
Bruin S, Klijn C, Liefers GJ, Braaf LM, Joosse SA, Van Beers EH, Verwaal VJ, Morreau H, Wessels LF, Van Velthuysen ML, Tollenaar RA, and Van 't Veer LJ. Specific genomic aberrations in primary colorectal cancer are associated with liver metastases. BMC Cancer, 10(1):662, 2010. [ http ]
Lodder WL, Hauptmann M, Teertstra HJ, Van den Brekel MW, and Balm AJ. Respone to “Taylor SM, Drover C, MacEachern R, et al.: Is preoperative ultrasonography accurate in measuring tumor thickness and predicting the incidence of cervical metastasis in oral cancer?”. Oral Oncol, 46(8):627, 2010. [ http ]
Zhang L, Tang X, Rothman N, Vermeulen R, Ji Z, Shen M, Qiu C, Guo W, Liu S, Reiss B, Beane Freeman L, Ge Y, Hubbard AE, Hua M, Blair A, Galvan N, Ruan X, Alter BP, Xin KX, Li S, Moore LE, Kim S, Xie Y, Hayes RB, Azuma M, Hauptmann M, Xiong J, Stewart PA, Li L, Rappaport SM, Huang H, Fraumeni Jr JF, Smith MT, and Lan Q. Response to “Speit G, Gelbke HP, Pallapies D, Morfeld P. Occupational exposure to formaldehyde, hematotoxicity and leukemia-specific chromosome changes in cultured myeloid progenitor cells - Letter.”. Cancer Epidemiol Biomarkers Prev, 19(7):1884-1885, 2010. [ http ]
Yang TI, Minkema D, Elkhuizen PH, Heemsbergen WD, Van Mourik AM, and Van Vliet-Vroegindeweij C. Clinical applicability of cone-beam computed tomography in monitoring seroma volume change during breast irradiation. Int J Radiat Oncol Biol Phys, 78(1):119-126, 2010. [ http ]
De Ridder J, Gerrits A, Bot J, De Haan G, Reinders M, and Wessels LF. Inferring combinatorial association logic networks in multimodal genome-wide screens. Bioinformatics, 26(12):i149-157, 2010. [ http ]
Van Bemmel JG, Pagie L, Braunschweig U, Brugman W, Meuleman W, Kerkhoven RM, and Van Steensel B. The insulator protein SU(HW) fine-tunes nuclear lamina interactions of the Drosophila genome. PLoS One, 5(11):e15013, 2010. [ http ]
Holstege H, Van Beers E, Velds A, Liu X, Joosse S, Klarenbeek S, Schut E, Kerkhoven R, Klijn C, Wessels L, Nederlof P, and Jonkers J. Cross-species comparison of aCGH data from mouse and human BRCA1- and BRCA2-mutated breast cancers. BMC Cancer, 10(1):455, 2010. [ http ]
De Ronde JJ, Klijn C, Velds A, Holstege H, Reinders MJ, Jonkers J, and Wessels LF. KC-SMARTR: An R package for detection of statistically significant aberrations in multi-experiment aCGH data. BMC Res Notes, 3(1):298, 2010. [ http ]
Varela I*, Klijn C*, Stephens P, Mudie L, Stebbings L, Galappaththige D, Van der Gulden H, Schut E, Klarenbeek S, Campbell P, Wessels L, Stratton M, Jonkers J, Futreal PA, and Adams D. Somatic structural rearrangements in genetically engineered mouse mammary tumors. Genome Biol, 11(10):R100, 2010. (*Varela and Klijn contributed equally). [ http ]
Taskesen E, Beekman R, De Ridder J, Wouters BJ, Peeters JK, Touw IP, Reinders MJ, and Delwel R. HAT: Hypergeometric analysis of tiling-arrays with application to promoter-GeneChip data. BMC Bioinformatics, 11(1):275, 2010. [ http ]
Hauptmann M and Ronckers CM. RE: A further plea for adherence to the principles underlying science in general and the epidemiologic enterprise in particular. Int J Epidemiol, 39(6):1677-1679, 2010. [ http ]
Vollebergh MA, Kappers I, Klomp HM, Buning-Kager JC, Korse CM, Hauptmann M, De Visser KE, Van den Heuvel MM, and Linn SC. Ligands of epidermal growth factor receptor and the insulin-like growth factor family as serum biomarkers for response to epidermal growth factor receptor inhibitors in patients with advanced non-small cell lung cancer. J Thorac Oncol, 5(12):1939-1948, 2010. [ http ]
Heemsbergen WD, Al-Mamgani A, Witte MG, Van Herk M, Pos FJ, and Lebesque JV. Urinary obstruction in prostate cancer patients from the Dutch trial (68 Gy vs. 78 Gy): relationships with local dose, acute effects and baseline characteristics. Int J Radiat Oncol Biol Phys, 78(1):19-25, 2010. [ http ]
Peric-Hupkes D, Meuleman W, Pagie L, Bruggeman SW, Solovei I, Brugman W, Graf S, Flicek P, Kerkhoven RM, van Lohuizen M, Reinders M, Wessels L, and van Steensel B. Molecular maps of the reorganization of genome-nuclear lamina interactions during differentiation. Mol Cell, 38(4):603-613, 2010. [ http ]
Van der Pal HJ, Van Dalen EC, Hauptmann M, Kok WE, Caron HN, Van den Bos C, Oldenburger F, Koning CC, Van Leeuwen FE, and Kremer LC. Cardiac function in 5-year survivors of childhood cancer: a long-term follow-up study. Arch Intern Med, 170(14):1247-1255, 2010. [ http ]
Lodder WL, Hauptmann M, Teertstra HJ, Van den Brekel MW, and Balm AJ. Re: Is preoperative ultrasonography accurate in measuring tumor thickness and predicting the incidence of cervical metastasis in oral cancer? Oral Oncol, 46(8):627, 2010. [ http ]
Borst GR, Ishikawa M, Nijkamp J, Hauptmann M, Shirato H, Bengua G, Onimaru R, De Bois JA, Lebesque JV, and Sonke JJ. Radiation pneumonitis after hypofractionated radiotherapy: evaluation of the LQ(L) model and different dose parameters. Int J Radiat Oncol Biol Phys, 77(5):1596-1603, 2010. [ http ]
Al-Mamgani A, Heemsbergen WD, Levendag PC, and Lebesque JV. Subgroup analysis of patients with localized prostate cancer treated within the Dutch-randomized dose escalation trial. Radiother Oncol, 96(1):13-18, 2010. [ http ]
Al-Mamgani A, Lebesque JV, Heemsbergen WD, Tans L, Kirkels WJ, Levendag PC, and Incrocci L. Controversies in the treatment of high-risk prostate cancer - what is the optimal combination of hormonal therapy and radiotherapy: a review of literature. Prostate, 70(7):701-709, 2010. [ http ]
Witte MG, Heemsbergen WD, Bohoslavsky R, Pos FJ, Al-Mamgani A, Lebesque JV, and Van Herk M. Relating dose outside the prostate with Freedom from Failure in the Dutch trial 68 Gy vs. 78 Gy. Int J Radiat Oncol Biol Phys, 77(1):131-138, 2010. [ http ]
Yang TI, Elkhuizen PH, Minkema D, Heemsbergen WD, Van Mourik AM, Cassee J, Hurkmans C, and Van Vliet-Vroegindeweij C. Clinical factors associated with seroma volume reduction in breast-conserving therapy for early-stage breast cancer: A multi-institutional analysis. Int J Radiat Oncol Biol Phys, 76(5):1325-1332, 2010. [ http ]
Brown LM, Gridley G, Wu AH, Falk RT, Hauptmann M, Kolonel LN, West DW, Nomura AM, Pike MC, Hoover RN, and Ziegler RG. Low level alcohol intake, cigarette smoking and risk of breast cancer in Asian-American women. Breast Cancer Res Treat, 120:203-210, 2010. [ http ]
De Ronde JJ, Hannemann J, Halfwerk H, Mulder L, Straver ME, Vrancken Peeters MJ, Wesseling J, Van de Vijver M, Wessels LF, and Rodenhuis S. Concordance of clinical and molecular breast cancer subtyping in the context of preoperative chemotherapy response. Breast Cancer Res Treat, 119:119-126, 2010. [ http ]
Zhang L, Tang X, Rothman N, Vermeulen R, Ji Z, Shen M, Qiu C, Guo W, Liu S, Reiss B, Beane Freeman L, Ge Y, Hubbard AE, Hua M, Blair A, Galvan N, Ruan X, Alter BP, Xin KX, Li S, Moore LE, Kim S, Xie Y, Hayes RB, Azuma M, Hauptmann M, Xiong J, Stewart PA, Li L, Rappaport SM, Huang H, Fraumeni Jr JF, Smith MT, and Lan Q. Occupational exposure to formaldehyde, hematotoxicity and leukemia-specific chromosome changes in cultured myeloid progenitor cells. Cancer Epidemiol Biomarkers Prev, 19:80-88, 2010. [ http ]
De Jong MC, Pramana J, Knegjens JL, Balm AJ, Van den Brekel MW, Hauptmann M, Begg AC, and Rasch CR. HPV and high risk gene expression profiles predict response to chemoradiotherapy in head and neck cancer independent of clinical factors. Radiother Oncol, 95(3):365-370, 2010. [ http ]
Retel VP, Joore MA, Knauer M, Linn SC, Hauptmann M, and Van Harten WH. Cost-effectiveness of the 70-gene signature versus Sankt Gallen guidelines and Adjuvant Online for early breast cancer. Eur J Cancer, 46(8):1382-1391, 2010. [ http ]
Rasch CR, Hauptmann M, Schornagel J, Wijers O, Buter J, Gregor T, Wiggenraad R, De Boer JP, Ackerstaff AH, Kroger R, Hoebers FJ, and Balm AJ. Intra-arterial versus intravenous chemoradiation for advanced head and neck cancer: results of a randomized phase 3 trial. Cancer, 116(9):2159-2165, 2010. [ http ]
Knauer M, Mook S, Rutgers EJ, Bender RA, Hauptmann M, Van de Vijver M, Koornstra RH, Bueno de Mesquita JM, Linn SC, and Van 't Veer LJ. The predictive value of the 70-gene signature for adjuvant chemotherapy in early breast cancer. Breast Cancer Res Treat, 120:655-661, 2010. [ http ]
De Ronde J, Wessels LF, and Wesseling J. Molecular subtyping of breast cancer: ready to use? Lancet Oncol, 11:306-307, 2010. [ http ]
Broeks A, Braaf LM, Wessels LF, Van de Vijver M, De Bruin ML, Stovall M, Russell NS, Van Leeuwen FE, and Van 't Veer LJ. Radiation-associated breast tumors display a distinct gene expression profile. Int J Radiat Oncol Biol Phys, 76:540-547, 2010. [ http ]
Mattison J, Kool J, Uren AG, De Ridder J, Wessels L, Jonkers J, Bignell GR, Butler A, Rust AG, Brosch M, Wilson CH, Van der Weyden L, Largaespada DA, Stratton MR, Futreal PA, Van Lohuizen M, Berns A, Collier LS, Hubbard T, and Adams DJ. Novel candidate cancer genes identified by a large-scale cross-species comparative oncogenomics approach. Cancer Res, 70:883-895, 2010. [ http ]
Kool J, Uren AG, Martins CP, Sie D, De Ridder J, Turner G, Van Uitert M, Matentzoglu K, Lagcher W, Krimpenfort P, Gadiot J, Pritchard C, Lenz J, Lund AH, Jonkers J, Rogers J, Adams DJ, Wessels L, Berns A, and Van Lohuizen M. Insertional mutagenesis in mice deficient for p15Ink4b, p16Ink4a, p21Cip1, and p27Kip1 reveals cancer gene interactions and correlations with tumor phenotypes. Cancer Res, 70:520-531, 2010. [ http ]
Klijn C, Bot J, Adams DJ, Reinders M, Wessels L, and Jonkers J. Identification of networks of co-occurring, tumor-related DNA copy number changes using a genome-wide scoring approach. PLoS Comput Biol, 6:e1000631, 2010. [ http ]
Horlings HM, Lai C, Nuyten DS, Halfwerk H, Kristel P, Van Beers E, Joosse SA, Klijn C, Nederlof PM, Reinders MJ, Wessels LF, and Van de Vijver MJ. Integration of DNA copy number alterations and prognostic gene expression signatures in breast cancer patients. Clin Cancer Res, 16:651-663, 2010. [ http ]
Hauptmann M, Stewart PA, Lubin JH, Beane Freeman LE, Hornung RW, Herrick RF, Hoover RN, Fraumeni JF Jr, Blair A, and Hayes RB. Response to “Cole P, Adami HO, Trichopoulos D, Mandel J. Re: Mortality from lymphohematopoietic malignancies and brain cancer among embalmers exposed to formaldehyde.”. J Natl Cancer Inst, 102(19):1519-1520, 2009. [ http ]
Staiger C, Hinneburg A, and Klösgen RB. Diversity in degrees of freedom of mitochondrial transit peptides. Mol Biol Evol, 26(8):1773-1780, Aug 2009. [ http ]
Knijnenburg TA. Inferring the influence of cultivation parameters on transcriptional regulation. PhD thesis, Delft University of Technology, 2009. [ .pdf ]
Knijnenburg TA, Daran JM, Van den Broek MA, Daran-Lapujade PA, De Winde JH, Pronk JT, Reinders MJ, and Wessels LF. Combinatorial effects of environmental parameters on transcriptional regulation in Saccharomyces cerevisiae: a quantitative analysis of a compendium of chemostat-based transcriptome data. BMC Genomics, 10:53, 2009. [ http | .pdf ]
Knijnenburg TA, Wessels LF, Reinders MJ, and Shmulevich I. Fewer permutations, more accurate P-values. Bioinformatics, 25(12):i161-i168, 2009. [ http | .pdf ]
Abeel T, De Ridder J, and Peixoto L. Highlights from the 5th International Society for Computational Biology Student Council Symposium at the 17th Annual International Conference on Intelligent Systems for Molecular Biology and the 8th European Conference on Computational Biology. BMC Bioinformatics, 10(Suppl 13):I1, 2009. [ http ]
Kreike B, Halfwerk H, Armstrong N, Bult P, Foekens JA, Veltkamp SC, Nuyten DS, Bartelink H, and Van de Vijver MJ. Local recurrence after breast-conserving therapy in relation to gene expression patterns in a large series of patients. Clin Cancer Res, 15(12):4181-4190, 2009. [ http ]
Gast MC, Van Dulken EJ, Van Loenen TK, Kingma-Vegter F, Westerga J, Flohil CC, Knol JC, Jimenez CR, Van Gils CH, Wessels LF, Schellens JH, and Beijnen JH. Detection of breast cancer by surface-enhanced laser desorption/ionization time-of-flight mass spectrometry tissue and serum protein profiling. Int J Biol Markers, 24:130-141, 2009.
Gast MC, Van Gils CH, Wessels LF, Harris N, Bonfrer JM, Rutgers EJ, Schellens JH, and Beijnen JH. Serum protein profiling for diagnosis of breast cancer using SELDI-TOF MS. Oncol Rep, 22:205-213, 2009.
Gast MC, Van Gils CH, Wessels LF, Harris N, Bonfrer JM, Rutgers EJ, Schellens JH, and Beijnen JH. Influence of sample storage duration on serum protein profiles assessed by surface-enhanced laser desorption/ionisation time-of-flight mass spectrometry (SELDI-TOF MS). Clin Chem Lab Med, 47:694-705, 2009. [ http ]
Joosse SA, Van Beers EH, Tielen IH, Horlings H, Peterse JL, Hoogerbrugge N, Ligtenberg MJ, Wessels LF, Axwijk P, Verhoef S, Hogervorst FB, and Nederlof PM. Prediction of BRCA1-association in hereditary non-BRCA1/2 breast carcinomas with array-CGH. Breast Cancer Res Treat, 116:479-489, 2009. [ http ]
Kok M, Koornstra RH, Margarido TC, Fles R, Armstrong NJ, Linn SC, Van 't Veer LJ, and Weigelt B. Mammosphere-derived gene set predicts outcome in patients with ER-positive breast cancer. J Pathol, 218:316-326, 2009. [ http ]
Kok M, Holm-Wigerup C, Hauptmann M, Michalides R, Stal O, Linn S, and Landberg G. Estrogen receptor-α phosphorylation at serine-118 and tamoxifen response in breast cancer. J Natl Cancer Inst, 101:1725-1729, 2009. [ http ]
Borst GR, Ishikawa M, Nijkamp J, Hauptmann M, Shirato H, Onimaru R, Van den Heuvel MM, Belderbos J, Lebesque JV, and Sonke JJ. Radiation pneumonitis in patients treated for malignant pulmonary lesions with hypofractionated radiation therapy. Radiother Oncol, 91:307-313, 2009. [ http ]
Hauptmann M, Stewart PA, Lubin JH, Beane Freeman LE, Hornung RW, Herrick RF, Hoover RN, Fraumeni JF Jr, Blair A, and Hayes RB. Mortality from lymphohematopoietic malignancies and brain cancer among embalmers exposed to formaldehyde in the funeral industry. J Natl Cancer Inst, 101:1696-1708, 2009. [ .pdf ]
Van den Belt-Dusebout AW, Aleman BM, Besseling G, De Bruin ML, Hauptmann M, Van 't Veer MB, De Wit R, Ribot JG, Noordijk EM, Kerst JM, Gietema JA, and Van Leeuwen FE. Roles of radiation dose and chemotherapy in the etiology of stomach cancer as a second malignancy. Int J Radiat Oncol Biol Phys, 75:1420-1429, 2009. [ http ]
Hamming-Vrieze O, Balm AJ, Heemsbergen WD, Hooft van Huysduynen T, and Rasch CR. Regional control of melanoma neck node metastasis after selective neck dissection with or without adjuvant radiotherapy. Arch Otolaryngol Head Neck Surg, 135:795-800, 2009. [ http ]
Al-Mamgani A, Heemsbergen WD, Peeters ST, and Lebesque JV. Role of intensity-modulated radiotherapy in reducing toxicity in dose escalation for localized prostate cancer. Int J Radiat Oncol Biol Phys, 73:685-691, 2009. [ http ]
Meuleman W, Engwegen JY, Gast MC, Wessels LF, and Reinders MJ. Analysis of mass spectrometry data using sub-spectra. BMC Bioinformatics, 10 Suppl 1(S51), 2009. [ http ]
Beane Freeman LE, Blair A, Lubin JH, Stewart PA, Hayes RB, Hoover RN, and Hauptmann M. Mortality from lymphohematopoietic malignancies among workers in formaldehyde industries: update of the NCI cohort. J Natl Cancer Inst, 101:751-761, 2009. [ .pdf ]
Van den Broek GB, Wildeman M, Rasch CR, Armstrong N, Schuuring E, Begg AC, Looijenga LH, Scheper R, Van der Wal JE, Menkema L, Van Diest PJ, Balm AJ, Van Velthuysen ML, and Van den Brekel MW. Molecular markers predict outcome in squamous cell carcinoma of the head and neck after concomitant cisplatin-based chemoradiation. Int J Cancer, 124:2643-2650, 2009. [ http ]
Wildeman MA, Gibcus JH, Hauptmann M, Begg AC, Van Velthuysen ML, Hoebers FJ, Mastik MF, Schuuring E, Van der Wal JE, and Van den Brekel MW. Radiotherapy in laryngeal carcinoma: can a panel of 13 markers predict response? Laryngoscope, 119:316-322, 2009. [ http ]
Van Vliet MH, Wessels LF, and Reinders MJ. Knowledge driven decomposition of tumor expression profiles. BMC Bioinformatics, 10(Suppl 1):S20, 2009. [ http ]
Holm C, Kok M, Michalides R, Fles R, Koornstra RH, Wesseling J, Hauptmann M, Neefjes J, Peterse JL, Stal O, Landberg G, and Linn SC. Phosphorylation of the oestrogen receptor alpha at serine 305 and prediction of tamoxifen resistance in breast cancer. J Pathol, 217:372-379, 2009. [ http ]
Kok M, Linn SC, Van Laar RK, Jansen MP, Van den Berg TM, Delahaye LJ, Glas AM, Peterse JL, Hauptmann M, Foekens JA, Klijn JG, Wessels LF, Van't Veer LJ, and Berns EM. Comparison of gene expression profiles predicting progression in breast cancer patients treated with tamoxifen. Breast Cancer Res Treat, 113:275-283, 2009. [ http ]
Lopez Yurda MI. Four essays on applied microeconometrics. PhD thesis, Tinbergen Institute, Vrije Universiteit Amsterdam, 2009. TI 452.
Van den Berg GJ, Lindeboom M, and Lopez M. Inequality in individual mortality and economic conditions earlier in life. Soc Sci Med, 69(9):1360-1367, 2009. [ http ]
Knijnenburg TA, Wessels LF, and Reinders MJ. Combinatorial influence of environmental parameters on transcription factor activity. Bioinformatics, 24(13):i172-i181, 2008. [ http | .pdf ]
Knijnenburg TA, Wessels LF, and Reinders MJ. Creating gene set activity profiles with time-series expression data. Int J Bioinform Res Appl, 4(3):306-323, 2008. [ .pdf ]
Hoebers FJ, Pameijer FA, De Bois J, Heemsbergen WD, Balm AJ, Schornagel JH, and Rasch CR. Prognostic value of primary tumor volume after concurrent chemoradiation with daily low-dose cisplatin for advanced-stage head and neck carcinoma. Head Neck, 30:1216-1223, 2008. [ http ]
Smitsmans MH, Pos FJ, De Bois J, Heemsbergen WD, Sonke JJ, Lebesque JV, and Van Herk M. The influence of a dietary protocol on cone beam CT-guided radiotherapy for prostate cancer patients. Int J Radiat Oncol Biol Phys, 71:1279-1286, 2008. [ http ]
Al-Mamgani A, Van Putten WL, Heemsbergen WD, Van Leenders GJ, Slot A, Dielwart MF, Incrocci L, and Lebesque JV. Update of Dutch multicenter dose-escalation trial of radiotherapy for localized prostate cancer. Int J Radiat Oncol Biol Phys, 72:980-988, 2008. [ http ]
Pietersen AM, Horlings HM, Hauptmann M, Langerod A, Ajouaou A, Cornelissen-Steijger P, Wessels LF, Jonkers J, Van de Vijver MJ, and Van Lohuizen M. EZH2 and BMI1 inversely correlate with prognosis and TP53 mutation in breast cancer. Breast Cancer Res, 10:R109, 2008. [ http ]
Hooning MJ, Aleman BM, Hauptmann M, Baaijens MH, Klijn JG, Noyon R, Stovall M, and Van Leeuwen FE. Roles of radiotherapy and chemotherapy in the development of contralateral breast cancer. J Clin Oncol, 26:5561-5568, 2008. [ http ]
Reyal F, Van Vliet MH, Armstrong N, Horlings H, De Visser KE, Kok M, Teschendorff AE, Mook S, Salmon R, Van de Vijver MJ, and Wessels LF. A comprehensive analysis of nine prognostic signatures reveals the high predictive capacity of proliferation, immune response and RNA splicing modules in breast cancer. Breast Cancer Res, 10:R93, 2008. [ http ]
Meuleman W, Engwegen JY, Gast MC, Beijnen JH, Reinders MJ, and Wessels LF. Comparison of normalisation methods for surface-enhanced laser desorption and ionisation (SELDI) time-of-flight (TOF) mass spectrometry data. BMC Bioinformatics, 9(88), 2008. [ http ]
Van Vliet M, Reyal F, Horlings H, Van de Vijver MJ, Reinders M, and Wessels L. Pooling breast cancer datasets has a synergetic effect on classification performance and improves signature stability. BMC Genomics, 9:375, 2008. [ http ]
Van Uitert M, Meuleman W, and Wessels L. Biclustering sparse binary genomic data. J Comput Biol, 15:1329-1345, 2008. [ http ]
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