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Research Output 2009 2019

  • 36 Article
  • 2 Meeting Abstract
  • 1 Research external, graduation external
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Article
2019

Fetal fraction evaluation in non-invasive prenatal screening (NIPS)

Hestand, M. S., Bessem, M., van Rijn, P., de Menezes, R. X., Sie, D., Bakker, I., Boon, E. M. J., Sistermans, E. A. & Weiss, M. M., 1 Feb 2019, In : European Journal of Human Genetics. 27, 2, p. 198-202 5 p.

Research output: Contribution to journalArticleAcademicpeer-review

HLA class II expression on tumor cells and low numbers of tumor-associated macrophages predict clinical outcome in oropharyngeal cancer

Cioni, B., Jordanova, E. S., Hooijberg, E., van der Linden, R., de Menezes, R. X., Tan, K., Willems, S., Elbers, J. B. W., Broeks, A., Bergman, A. M., Zuur, C. L. & de Boer, J. P., 1 Feb 2019, In : Head and Neck. 41, 2, p. 463-478 16 p.

Research output: Contribution to journalArticleAcademicpeer-review

Improvement of menopausal symptoms and the impact on work ability: A retrospective cohort pilot study

Geukes, M., Anema, J. R., van Aalst, M. P., de Menezes, R. X. & Oosterhof, H., 2019, In : Maturitas. 120, p. 23-28

Research output: Contribution to journalArticleAcademicpeer-review

2018

Abstract 1114: IGFBP7 reduces acute myeloid leukemia stem cell survival without affecting normal hematopoiesis

Cil, M., Vermue, E., Zweegman, S., Smit, M., Schuurhuis, G. J., Klootwijk, L. L. D. V., Menezes, R. X., Tsui, M-L., Smit, L., Rutten, A., Gils, N. V., Brocco, F., Roemer, M. G., Ossenkoppele, G. J., Verhagen, H. J., Rhenen, A. V., Janssen, J. J., Denkers, F. & Heukelom, S., 17 Aug 2018, In : Cancer Research. 78, 13 Supplement, p. 1114-1114 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

A functional siRNA screen identifies RhoGTPase-associated genes involved in thrombin-induced endothelial permeability

Amado-Azevedo, J., de Menezes, R. X., van Nieuw Amerongen, G. P., van Hinsbergh, V. W. M. & Hordijk, P. L., 2018, In : PLoS ONE. 13, 7, e0201231.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

A test for detecting differential indirect trans effects between two groups of samples

Chaturvedi, N., Menezes, R., Goeman, J. J. & van Wieringen, WN., 2018, In : Statistical Applications in Genetics and Molecular Biology.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

IGFBP7 Induces Differentiation and Loss of Survival of Human Acute Myeloid Leukemia Stem Cells without Affecting Normal Hematopoiesis

Verhagen, H. J. M. P., van Gils, N., Martiañez, T., van Rhenen, A., Rutten, A., Denkers, F., de Leeuw, D. C., Smit, M. A., Tsui, M-L., de Vos Klootwijk, L. L. E., Menezes, R. X., Çil, M., Roemer, M. G. M., Vermue, E., Heukelom, S., Zweegman, S., Janssen, J. J. W. M., Ossenkoppele, G. J., Schuurhuis, G. J. & Smit, L., 11 Dec 2018, In : Cell Reports. 25, 11, p. 3021-3035.e5

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

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

Bachas, C., Hodzic, J., van der Mijn, J. C., Stoepker, C., Verheul, H. M. W., Wolthuis, R. M. F., Felley-Bosco, E., van Wieringen, W. N., van Beusechem, V. W., Brakenhoff, R. H. & de Menezes, R. X., 20 Aug 2018, In : BMC Bioinformatics. 19, 1, p. 301

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Testing for pathway (in)activation by using Gaussian graphical models

van Wieringen, W. N., Peeters, C. F. W., de Menezes, R. X. & van de Wiel, M. A., 1 Nov 2018, In : Journal of the Royal Statistical Society. Series C: Applied Statistics. 67, 5, p. 1419-1436 18 p.

Research output: Contribution to journalArticleAcademicpeer-review

The FA/BRCA Pathway Identified as the Major Predictor of Cisplatin Response in Head and Neck Cancer by Functional Genomics

Martens-de Kemp, S. R., Brink, A., van der Meulen, I. H., de Menezes, R. X., Te Beest, D. E., Leemans, C. R., van Beusechem, V. W., Braakhuis, B. J. M. & Brakenhoff, R. H., Mar 2017, In : Molecular Cancer Therapeutics. 16, 3, p. 540-550 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

2016

Analysing multiple types of molecular profiles simultaneously: connecting the needles in the haystack

Menezes, R. X., Mohammadi, L., Goeman, J. J. & Boer, J. M., 9 Feb 2016, In : BMC Bioinformatics. 17, 77.

Research output: Contribution to journalArticleAcademicpeer-review

Testing for association between RNA-Seq and high-dimensional data

Rauschenberger, A., Jonker, M. A., van de Wiel, M. A. & Menezes, R. X., 8 Mar 2016, In : BMC Bioinformatics. 17, 118.

Research output: Contribution to journalArticleAcademicpeer-review

2015

A cell-based high-throughput screening assay for radiation susceptibility using automated cell counting

Hodzic, J., Dingjan, I., Maas, M. J. P., van der Meulen-Muileman, I. H., Menezes, R. X., Heukelom, S., Verheij, M., Gerritsen, W. R., Geldof, A. A., van Triest, B. & van Beusechem, V. W., 2015, In : Radiation Oncology. 10, 55.

Research output: Contribution to journalArticleAcademicpeer-review

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

de Lange, J., Faramarz, A., Oostra, A. B., Menezes, R. X., van der Meulen, I. H., Rooimans, M. A., Rockx, D. A., Brakenhoff, R. H., van Beusechem, V. W., King, R. W., de Winter, J. P. & Wolthuis, R. M. F., 2015, In : Nature Communications. 6, 8399.

Research output: Contribution to journalArticleAcademicpeer-review

Evidence for Immune Response, Axonal Dysfunction and Reduced Endocytosis in the Substantia Nigra in Early Stage Parkinson's Disease.

Dijkstra, A. A., Ingrassia, A., Menezes, R. X., van Kesteren, R. E., Rozemuller, A. J., Heutink, P. & van de Berg, W. D. J., 2015, In : PLoS ONE. 10, 6, e0128651.

Research output: Contribution to journalArticleAcademicpeer-review

Oncogenic Role of miR-15a-3p in 13q Amplicon-Driven Colorectal Adenoma-to-Carcinoma Progression

de Groen, F. L. M., Timmer, L. M., Menezes, R. X., Diosdado, B., Hooijberg, E., Meijer, G. A., Steenbergen, R. D. M. & Carvalho, B., 2015, In : PLoS ONE. 10, 7, e0132495.

Research output: Contribution to journalArticleAcademicpeer-review

2014

A test for comparing two groups of samples when analyzing multiple omics profiles

Chaturvedi, N., Goeman, J. J., Boer, J. M., van Wieringen, W. N. & Menezes, R., 2014, In : BMC Bioinformatics. 15, 236.

Research output: Contribution to journalArticleAcademicpeer-review

Fused lasso algorithm for Cox proportional hazards and binomial logit models with application to copy number profiles

Chaturvedi, N., Menezes, R. & Goeman, J. J., 2014, In : Biometrical Journal. 56, 3, p. 477-492

Research output: Contribution to journalArticleAcademicpeer-review

Nontemplated Nucleotide Additions Distinguish the Small RNA Composition in Cells from Exosomes

Lalic, D., Hackenberg, M., Bijnsdorp, I. V., van Eijndhoven, M. A. J., Sadek, P., Sie, D. L. S., Zini, N., Middeldorp, J. M., Ylstra, B., Menezes, R., Wurdinger, T., Meijer, G. A. & Pegtel, D. M., 2014, In : Cell Reports. 8, 6, p. 1649-1658

Research output: Contribution to journalArticleAcademicpeer-review

2013

Affordable Luciferase Reporter Assay for Cell-Based High-Throughput Screening

van Olst, E., Vermeulen, C., Menezes, R., Howell, M., Smit, E. F. & van Beusechem, V. W., 2013, In : Journal of Biomolecular Screening. 18, 4, p. 453-461

Research output: Contribution to journalArticleAcademicpeer-review

Epigenetic drug combination induces genome-wide demethylation and altered gene expression in neuro-ectodermal tumor-derived cell lines

Duijkers, F. A. M., Menezes, R., Goossens-Beumer, I. J., Stumpel, D. J. P. M., Admiraal, P., Pieters, R., Meijerink, J. P. P. & van Noesel, M. M., 2013, In : Cellular Oncology. 36, 5, p. 351-362

Research output: Contribution to journalArticleAcademicpeer-review

General power and sample size calculations for high-dimensional genomic data

van Iterson, M., van de Wiel, M., Boer, J. M. & Menezes, R., 2013, In : Statistical Applications in Genetics and Molecular Biology. 12, 4, p. 449-467

Research output: Contribution to journalArticleAcademicpeer-review

Integrated analysis of microRNA and mRNA expression: adding biological significance to microRNA target predictions

van Iterson, M., Bervoets, S., de Meijer, E. J., Buermans, H. P., 't Hoen, P. A. C., Menezes, R. & Boer, J. M., 2013, In : Nucleic Acids Research. 41, 15, e146.

Research output: Contribution to journalArticleAcademicpeer-review

2012

Matching of array CGH and gene expression microarray features for the purpose of integrative genomic analyses

van Wieringen, W. N., Unger, K., Leday, G. G. R., Krijgsman, O., Xavier de Menezes, R., Ylstra, B. & van de Wiel, M. A., 2012, In : BMC Bioinformatics. 13, p. 80 80.

Research output: Contribution to journalArticleAcademicpeer-review

Targeting JNK-interacting-protein-1 (JIP1) sensitises osteosarcoma to doxorubicin

Posthuma de Boer, J., van Egmond, P. W., Helder, M. N., Xavier de Menezes, R., Cleton-Jansen, A. M., Belien, J. A. M., Verheul, H. M. W., van Royen, B. J., Kaspers, G. J. L. & van Beusechem, V. W., 2012, In : Oncotarget. 3, 10, p. 1169-1181

Research output: Contribution to journalArticleAcademicpeer-review

2011

Evaluation of gene expression signatures predictive of cytogenetic and molecular subtypes of pediatric acute myeloid leukemia

Balgobind, B. V., van den Heuvel-Eibrink, M., Xavier de Menezes, R., Reinhardt, D., Hollink, I. H. I. M., Arentsen-Peters, S. T. C. J. M., van Wering, E. R., Kaspers, G. J. L., Cloos, J., De Bont, E. S. J. M., Cayuela, J. M., Baruchel, A., Meyer, C., Marschalek, R., Trka, J., Stary, J., Beverloo, B. H., Pieters, R., Zwaan, C. M. & den Boer, M. L., 2011, In : Haematologica. 96, 2, p. 221-230

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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Hypermethylation of specific microRNA genes in MLL-rearranged infant acute lymphoblastic leukemia: major matters at a micro scale

Stumpel, D. J. P. M., Schotte, D., Lange-Turenhout, E., Schneider, P., Seslija, L., Xavier de Menezes, R., Marquez, V. E., Pieters, R., den Boer, M. L. & Stam, R. W., 2011, In : Leukemia. 25, 3, p. 429-439

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA characterize genetic diversity and drug resistance in pediatric acute lymphoblastic leukemia

Schotte, D., Xavier de Menezes, R., Moqadam, F. A., Khankahdani, L. M., Lange-Turenhout, E., Chen, C. F., Pieters, R. & den Boer, M. L., 2011, In : Haematologica. 96, 5, p. 703-711

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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mRNA degradation controls differentiation state-dependent differences in transcript and splice variant abundance

't Hoen, P. A. C., Hirsch, M., de Meijer, E. J., Menezes, R. X., van Ommen, G. B. & den Dunnen, J. T., 2011, In : Nucleic Acids Research. 39, 2, p. 556-566

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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2010

Filtering, FDR and power

van Iterson, M., Boer, J. M. & Xavier de Menezes, R., 2010, In : BMC Bioinformatics. 11, p. 450 11 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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2009

Relative power and sample size analysis on gene expression profiling data

van Iterson, M., 't Hoen, P. A. C., Pedotti, P., Hooiveld, G. J. E. J., den Dunnen, J. T., van Ommen, G. J. B., Boer, J. M. & Menezes, R. X., 2009, In : BMC Genomics. 10

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
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