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Research Output 2006 2019

2019

Changes in the urinary extracellular vesicle proteome are associated with nephronophthisis-related ciliopathies

Stokman, M. F., Bijnsdorp, I. V., Schelfhorst, T., Pham, T. V., Piersma, S. R., Knol, J. C., Giles, R. H., Bongers, E. M. H. F., Knoers, N. V. A. M., Lilien, M. R., Jiménez, C. R. & Renkema, K. Y., 10 Feb 2019, In : Journal of Proteomics. 192, p. 27-36 10 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Human testis phosphoproteome reveals kinases as potential targets in spermatogenesis and testicular cancer

Castillo, J., Knol, J. C., Korver, C. M., Piersma, S. R., Pham, T. V., de Goeij-de Haas, R. R., van Pelt, A. M. M., Jimenez, C. R. & Jansen, B. J. H., 2019, In : Molecular and Cellular Proteomics. 18, p. S132-S144

Research output: Contribution to journalArticleAcademicpeer-review

INKA, an integrative data analysis pipeline for phosphoproteomic inference of active kinases

Beekhof, R., van Alphen, C., Henneman, A. A., Knol, J. C., Pham, T. V., Rolfs, F., Labots, M., Henneberry, E., le Large, T. Y., de Haas, R. R., Piersma, S. R., Vurchio, V., Bertotti, A., Trusolino, L., Verheul, H. M. & Jimenez, C. R., 2019, In : Molecular Systems Biology. 15, 4, p. e8250

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

The dichotomous role of the glycolytic metabolism pathway in cancer metastasis: Interplay with the complex tumor microenvironment and novel therapeutic strategies

el Hassouni, B., Granchi, C., Vallés-Martí, A., Supadmanaba, I. G. P., Bononi, G., Tuccinardi, T., Funel, N., Jimenez, C. R., Peters, G. J., Giovannetti, E. & Minutolo, F., 2019, In : Seminars in Cancer Biology.

Research output: Contribution to journalReview articleAcademicpeer-review

Urinary exosomal proteins as (pan-)cancer biomarkers: insights from the proteome

Erozenci, L. A., Böttger, F., Bijnsdorp, I. V. & Jimenez, C. R., 2019, In : FEBS Letters. 593, 13, p. 1580-1597

Research output: Contribution to journalArticleAcademicpeer-review

Cancer cells copy migratory behavior and exchange signaling networks via extracellular vesicles

Steenbeek, S. C., Pham, T. V., de Ligt, J., Zomer, A., Knol, J. C., Piersma, S. R., Schelfhorst, T., Huisjes, R., Schiffelers, R. M., Cuppen, E., Jimenez, C. R. & van Rheenen, J., 2018, In : EMBO Journal. 37, 15, e98357.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Consensus molecular subtype classification of colorectal adenomas

In collaboration with the NGS-ProToCol Consortium:, Komor, M. A., Bosch, L. J. W., Bounova, G., Bolijn, A. S., Delis-van Diemen, P. M., Rausch, C., Hoogstrate, Y., Stubbs, A. P., de Jong, M., Jenster, G., van Grieken, N. C. T., Carvalho, B., Wessels, L. F. A., Jimenez, C. R., Fijneman, R. J. A. & Meijer, G. A., 2018, In : Journal of Pathology. 246, 3, p. 266-276

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Correction: Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

Verweij, F. J., Bebelman, M. P., Jimenez, C. R., Garcia-Vallejo, J. J., Janssen, H., Neefjes, J., Knol, J. C., de Goeij-de Haas, R., Piersma, S. R., Baglio, S. R., Verhage, M., Middeldorp, J. M., Zomer, A., van Rheenen, J., Coppolino, M. G., Hurbain, I., Raposo, G., Smit, M. J., Toonen, R. F. G., van Niel, G. & 1 othersPegtel, D. M., 5 Mar 2018, In : Journal of Cell Biology. 217, 3, p. 1157

Research output: Contribution to journalErratumAcademicpeer-review

EspH is a hypervirulence factor for Mycobacterium marinum and essential for the secretion of the ESX-1 substrates EspE and EspF

Phan, T. H., van Leeuwen, L. M., Kuijl, C., Ummels, R., van Stempvoort, G., Rubio-Canalejas, A., Piersma, S. R., Jiménez, C. R., van der Sar, A. M., Houben, E. N. G. & Bitter, W., Aug 2018, In : PLoS Pathogens. 14, 8, p. e1007247

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Exploration of the platelet proteome in patients with early-stage cancer

Sabrkhany, S., Kuijpers, M. J. E., Knol, J. C., Olde Damink, S. W. M., Dingemans, A-M. C., Verheul, H. M., Piersma, S. R., Pham, T. V., Griffioen, A. W., oude Egbrink, M. G. A. & Jimenez, C. R., 2018, In : Journal of Proteomics. 177, p. 65-74

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Large-Scale Urinary Proteome Dataset Across Tumor Types Reveals Candidate Biomarkers for Lung Cancer

Bijnsdorp, I. V. & Jimenez, C. R., 2018, In : EBioMedicine. 30, p. 5-6

Research output: Contribution to journalComment/Letter to the editorAcademic

Multidrug-resistant transporter expression does not always result in drug resistance

le Large, T. Y. S., el Hassouni, B., Kazemier, G., Piersma, S. R., van Laarhoven, H. W. M., Bijlsma, M. F., Jimenez, C. R. & Giovannetti, E., 2018, In : Cancer Science. 109, 10, p. 3360-3362 3 p.

Research output: Contribution to journalComment/Letter to the editorAcademic

Open Access

Mutations in ppe38 block PE-PGRS secretion and increase virulence of Mycobacterium tuberculosis

Ates, L. S., Dippenaar, A., Ummels, R., Piersma, S. R., van der Woude, A. D., van der Kuij, K., le Chevalier, F., Mata-Espinosa, D., Barrios-Payán, J., Marquina-Castillo, B., Guapillo, C., Jiménez, C. R., Pain, A., Houben, E. N. G., Warren, R. M., Brosch, R., Hernández-Pando, R. & Bitter, W., 2018, In : Nature Microbiology. 3, 2, p. 181-188

Research output: Contribution to journalArticleAcademicpeer-review

Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling

Verweij, F. J., Bebelman, M. P., Jimenez, C. R., Garcia-Vallejo, J. J., Janssen, H., Neefjes, J., Knol, J. C., de Goeij-de Haas, R., Piersma, S. R., Baglio, S. R., Verhage, M., Middeldorp, J. M., Zomer, A., van Rheenen, J., Coppolino, M. G., Hurbain, I., Raposo, G., Smit, M. J., Toonen, R. F. G., van Niel, G. & 1 othersPegtel, D. M., 5 Mar 2018, In : Journal of Cell Biology. 217, 3, p. 1129-1142 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Specific T Cell Responses against Minor Histocompatibility Antigens Cannot Generally Be Explained by Absence of Their Allelic Counterparts on the Cell Surface

Bijen, H. M., Hassan, C., Kester, M. G. D., Janssen, G. M. C., Hombrink, P., de Ru, A. H., Drijfhout, J. W., Meiring, H. D., de Jong, A. P., Falkenburg, J. H. F., Jimenez, C. R., Heemskerk, M. H. M. & van Veelen, P. A., 1 Jun 2018, In : Proteomics. 18, 12, 1700250.

Research output: Contribution to journalArticleAcademicpeer-review

Targeting miRNA-551b, a "Stemness"-like microRNA, to Eradicate AML (Stem) Cells

Martiáñez, T., Van Gils, N., De Leeuw, D. C., Vermue, E., Rutten, A., Denkers, F., Verhagen, H. J. M. P., Janssen, J. J. W. M., Ossenkoppele, G. J., Jimenez, C. & Smit, L., 21 Nov 2018, In : Blood. 132, Suppl 1

Research output: Contribution to journalMeeting AbstractAcademic

The cancer proteomic landscape and the HUPO Cancer Proteome Project

Jimenez, C. R., Zhang, H., Kinsinger, C. R. & Nice, E. C., 2018, In : Clinical Proteomics. 15, 1, 4.

Research output: Contribution to journalArticleAcademicpeer-review

Open Access

Tumor (phospho)proteomic and genomic profiling to guide selection of targeted therapy in patients with cancer

Labots, M., 2018, 210 p.

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

2017

Breast cancer: therapy and biomarker analysis

Lam, SW., 2017, 269 p.

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

Open Access

Combinatie van vier eiwitten verbetert screening darmkanker

Jimenez, CR., 2017, In : Tijdschrift Medisch Contact.

Research output: Contribution to journalArticleProfessional

Identification of differentially expressed splice variants by the proteogenomic pipeline splicify

Komor, M. A., Pham, T. V., Hiemstra, A. C., Piersma, S. R., Bolijn, A. S., Schelfhorst, T., Delis-Van Diemen, P. M., Tijssen, M., Sebra, R. P., Ashby, M., Meijer, G. A., Jimenez, C. R. & Fijneman, R. J. A., 1 Oct 2017, In : Molecular and Cellular Proteomics. 16, 10, p. 1850-1863 14 p.

Research output: Contribution to journalArticleAcademicpeer-review

Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies

Le Large, T. Y. S., Bijlsma, M. F., Kazemier, G., van Laarhoven, H. W. M., Giovannetti, E. & Jimenez, C. R., 1 Jun 2017, In : Seminars in Cancer Biology. 44, p. 153-169 17 p.

Research output: Contribution to journalReview articleAcademicpeer-review

Mechanisms in the cellular defense against oxidative stress

Corbin, MV., 2017, 171 p.

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

Open Access

Novel Stool-Based Protein Biomarkers for Improved Colorectal Cancer Screening: A Case-Control Study

Bosch, L. J. W., De Wit, M., Pham, T. V., Coupé, V. M. H., Hiemstra, A. C., Piersma, S. R., Oudgenoeg, G., Scheffer, G. L., Mongera, S., Droste, J. T. S., Oort, F. A., Van Turenhout, S. T., Larbi, I. B., Louwagie, J., Van Criekinge, W., Van Der Hulst, R. W. M., Mulder, C. J. J., Carvalho, B., Fijneman, R. J. A., Jimenez, C. R. & 1 othersMeijer, G. A., 19 Dec 2017, In : Annals of Internal Medicine. 167, 12, p. 855-866 12 p.

Research output: Contribution to journalArticleAcademicpeer-review

Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection

Labots, M., van der Mijn, J. C., Beekhof, R., Piersma, S. R., de Goeij-de Haas, R. R., Pham, T. V., Knol, J. C., Dekker, H., van Grieken, N. C. T., Verheul, H. M. W. & Jiménez, C. R., 6 Jun 2017, In : Journal of Proteomics. 162, p. 99-107 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Vemurafenib plus cobimetinib in unresectable stage IIIc or stage IV melanoma: response monitoring and resistance prediction with positron emission tomography and tumor characteristics (REPOSIT): study protocol of a phase II, open-label, multicenter study

van der Hiel, B., Haanen, J. B. A. G., Stokkel, M. P. M., Peeper, D. S., Jimenez, C. R., Beijnen, J. H., van de Wiel, B. A., Boellaard, R., van den Eertwegh, A. J. M. & REPOSIT study group, 15 Sep 2017, In : BMC Cancer. 17, 1, p. 649

Research output: Contribution to journalArticleAcademicpeer-review

2016

Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling

Tutakhel, O. A. Z., Jelen, S., Valdez-Flores, M., Dimke, H., Piersma, S. R., Jimenez, C. R., Deinum, J., Lenders, J. W., Hoenderop, J. G. J. & Bindels, R. J. M., 1 Feb 2016, In : American Journal of Physiology. Renal Physiology. 310, 3, p. F204-F216

Research output: Contribution to journalArticleAcademicpeer-review

Evaluation of potential circulating biomarkers for prediction of response to chemoradiation in patients with glioblastoma

van Linde, M. E., van der Mijn, J. C., Pham, T. V., Knol, J. C., Wedekind, L. E., Hovinga, K. E., Aliaga, E. S., Buter, J., Jimenez, C. R., Reijneveld, J. C. & Verheul, H. M. W., Sep 2016, In : Journal of Neuro-Oncology. 129, 2, p. 221-230

Research output: Contribution to journalArticleAcademicpeer-review

Innovatieve metingen en markers voor prostaatkanker prognose met behulp van blaasjes uit urine- Improve

Jenster, G., van Royen, M., Martens, E., Jimenez, CR., Bijnsdorp, IV., Schalken, JA., Verhaegh, G., Kreutzer, M. & van Steijn, V., 2016, Magazine van Prostaatkankerstichting.nl. 2 p.

Research output: Book/ReportReportPopular

Leukemia cells teach eachother not to self-destruct

Jimenez, CR., Wojtuszkiewicz, AM. & Cloos, J., May 2016, 5 ed. ASBMB Today.

Research output: Book/ReportReportProfessional

Multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus

Schouten, M., Bielefeld, P., Fratantoni, S. A., Hubens, C. J., Piersma, S. R., Pham, T. V., Voskuyl, R. A., Lucassen, P. J., Jimenez, C. R. & Fitzsimons, C. P., 16 Aug 2016, In : Scientific data. 3, p. 160068

Research output: Contribution to journalArticleAcademicpeer-review

Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes

van Winden, V. J. C., Ummels, R., Piersma, S. R., Jimenez, C. R., Korotkov, K. V., Bitter, W. & Houben, E. N. G., 2016, In : mBio. 7, 5

Research output: Contribution to journalArticleAcademicpeer-review

New biomarkers and treatment strategies in renal cell cancer

van der Mijn, J. C., 2016

Research output: ThesisResearch VU University Amsterdam, graduation VU University AmsterdamAcademic

Novel diagnostic cerebrospinal fluid biomarkers for pathologic subtypes of frontotemporal dementia identified by proteomics

Teunissen, C. E., Elias, N., Koel-Simmelink, M. J. A., Durieux-Lu, S., Malekzadeh, A., Pham, T. V., Piersma, S. R., Beccari, T., Meeter, L. H. H., Dopper, E. G. P., van Swieten, J. C., Jimenez, C. R. & Pijnenburg, Y. A. L., 2016, In : Alzheimer's & Dementia: Diagnosis, Assessment & Disease Monitoring. 2, p. 86-94 9 p.

Research output: Contribution to journalArticleAcademicpeer-review

Peptide-mediated ‘miniprep’ isolation of extracellular vesicles is suitable for high-throughput proteomics

Knol, J. C., de Reus, I., Schelfhorst, T., Beekhof, R., de Wit, M., Piersma, SR., Pham, TV., Smit, EF., Verheul, HMW. & Jimenez, CR., Jun 2016, In : EuPA Open Proteomics. 11, p. 11-15

Research output: Contribution to journalArticleAcademicpeer-review

Response and toxicity prediction by MALDI-TOF-MS serum peptide profiling in patients with non-small cell lung cancer

Rovithi, M., Lind, J. S. W., Pham, T. V., Voortman, J., Knol, J. C., Verheul, H. M. W., Smit, E. F. & Jimenez, C. R., Jul 2016, In : Proteomics. Clinical applications. 10, 7, p. 743-749

Research output: Contribution to journalArticleAcademicpeer-review

Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer

Warmoes, M., Lam, S. W., van der Groep, P., Jaspers, J. E., Smolders, Y. H. C. M., de Boer, L., Pham, T. V., Piersma, S. R., Rottenberg, S., Boven, E., Jonkers, J., van Diest, P. J. & Jimenez, C. R., 27 Sep 2016, In : Oncotarget. 7, 39, p. 63537-63548

Research output: Contribution to journalArticleAcademicpeer-review

Sensing of latent EBV infection through exosomal transfer of 5'pppRNA

Baglio, S. R., van Eijndhoven, M. A. J., Koppers-Lalic, D., Berenguer, J., Lougheed, S. M., Gibbs, S., Leveille, N., Rinkel, R. N. P. M., Hopmans, E. S., Swaminathan, S., Verkuijlen, S. A. W. M., Scheffer, G. L., van Kuppeveld, F. J. M., de Gruijl, T. D., Bultink, I. E. M., Jordanova, E. S., Hackenberg, M., Piersma, S. R., Knol, J. C., Voskuyl, A. E. & 4 othersWurdinger, T., Jimenez, C. R., Middeldorp, J. M. & Pegtel, D. M., 2 Feb 2016, In : Proceedings of the National Academy of Sciences of the United States of America. 113, 5, p. E587-E596

Research output: Contribution to journalArticleAcademicpeer-review

Simulated linear test applied to quantitative proteomics

Pham, T. V. & Jimenez, C. R., 1 Sep 2016, In : Bioinformatics. 32, 17, p. 702-709

Research output: Contribution to journalArticleAcademicpeer-review

Sunitinib activates Axl signaling in renal cell cancer

van der Mijn, J. C., Broxterman, H. J., Knol, J. C., Piersma, S. R., De Haas, R. R., Dekker, H., Pham, T. V., Van Beusechem, V. W., Halmos, B., Mier, J. W., Jimenez, C. R. & Verheul, H. M. W., 15 Jun 2016, In : International Journal of Cancer. 138, 12, p. 3002-3010

Research output: Contribution to journalArticleAcademicpeer-review

Translationele OncoProteomics, over (fosfo)peptide fingerprints

Jimenez, CR., 14 Dec 2016, VU-DARE.

Research output: Book/ReportInaugural speechOther research output

Wetenschappers kijken in de toekomst

Jimenez, CR., 2016, Zorgkrant ZH Amstelland. 1 p.

Research output: Book/ReportReportPopular

2015

Abstract 4764: Transfer of regulatory protein networks via extracellular vesicles as a candidate mechanism of apoptosis-resistance in acute myeloid leukemia

Assaraf, Y. G., Zweegman, S., Cloos, J., Jansen, G., Knol, J., Schuurhuis, G. J., Jimenez, C. R., Piersma, S., Kessler, F. L., Wojtuszkiewicz, A. & Kaspers, G. L., 1 May 2015, In : Cancer Research. 74, 19 Supplement, p. 4764-4764 1 p.

Research output: Contribution to journalArticleAcademicpeer-review

Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria.

Ates, L. S., Ummels, R., Commandeur, S., van de Weerd, R., Sparrius, M., Weerdenburg, E., Alber, M., Kalscheuer, R., Piersma, S. R., Abdallah, A., Abd El Ghany, M., Abdel-Haleem, A. M., Pain, A., Jimenez, C. R., Bitter, W. & Houben, E. N. G., 2015, In : PLoS Genetics. 4, 11, 5.

Research output: Contribution to journalArticleAcademicpeer-review