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Research Output 2006 2019

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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

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

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

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

Quantifying exosome secretion from single cells reveals a modulatory role for GPCR signaling (vol 217, pg 1129, 2018)

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., Mar 2018, In : Journal of Cell Biology. 217, 3

Research output: Contribution to journalArticleAcademicpeer-review

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

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
2017

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

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

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

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

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

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

Exosomal sorting of the viral oncoprotein LMP1 is restrained by TRAF2 association at signalling endosomes

Verweij, F. J., Heus, C., Kroeze, S., Cai, H. J., Kieff, E., Piersma, S. R., Jimenez, C. R., Middeldorp, J. M. & Pegtel, D. M., 2015, In : Journal of Extracellular Vesicles. 4, 26334.

Research output: Contribution to journalArticleAcademicpeer-review

Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines

Piersma, S. R., Knol, J. C., de Reus, I., Labots, M., Sampadi, B. K., Pham, T. V., Ishihama, Y., Verheul, H. M. W. & Jimenez, C. R., 2015, In : Journal of Proteomics. 127, p. 247-258

Research output: Contribution to journalArticleAcademicpeer-review

Genome-wide siRNA Screen Identifies the Radiosensitizing Effect of Downregulation of MASTL and FOXM1 in NSCLC

Nagel, C. R., Stigter-van Walsum, M., Buijze, M., van den Berg, J., van der Meulen, I. H., Hodzic, J., Piersma, S. R., Pham, T. V., Jimenez, C. R., van Beusechem, V. W. & Brakenhoff, R. H., 2015, In : Molecular Cancer Therapeutics. 14, 6, p. 1434-1444

Research output: Contribution to journalArticleAcademicpeer-review

MicroRNA-124 and-137 cooperativity controls caspase-3 activity through BCL2L13 in hippocampal neural stem cells

Schouten, M., Fratantoni, S. A., Hubens, C. J., Piersma, S. R., Pham, T. V., Bielefeld, P., Voskuyl, R. A., Lucassen, P. J., Jimenez, C. R. & Fitzsimons, C. P., 2015, In : Scientific Reports. 5, 12448.

Research output: Contribution to journalArticleAcademicpeer-review

miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo

Senol, O., Schaaij-Visser, T. B. M., Erkan, E. P., Dorfer, C., Lewandrowski, G., Pham, T. V., Piersma, S. R., Peerdeman, S. M., Strobel, T., Tannous, B., Saydam, N., Slavc, I., Knosp, E., Jimenez, C. R. & Saydam, O., 2015, In : Oncogene. 34, 14, p. 1790-1798

Research output: Contribution to journalArticleAcademicpeer-review

Neuroproteomics: Applications in Neuroscience and Neurology

Grinberg, L. T., Jimenez, C. R. & Li, K. W., 2015, In : Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1854, 7, p. 703-704

Research output: Contribution to journalArticleAcademicpeer-review

Proteomics of Colorectal Cancer in a Genomic Context: First Large-scale Mass Spectrometry-Based Analysis from the Cancer Genome Atlas

Jimenez, C. R. & Fijneman, R. J. A., 2015, In : Clinical Chemistry. 61, 9, p. 1126-1128

Research output: Contribution to journalArticleAcademicpeer-review

2014

Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes

Hassan, C., Kester, M. G. D., Oudgenoeg, G., De Ru, A. H., Janssen, G. M. C., Drijfhout, J. W., Spaapen, R. M., Jimenez, C. R., Heemskerk, M. H. M., Falkenburg, J. H. F. & van Veelen, P. A., 2014, In : Journal of Proteomics. 109, p. 240-244

Research output: Contribution to journalArticleAcademicpeer-review

Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer

van der Mijn, J. C., Sol, N., Mellema, W. W., Jimenez, C. R., Piersma, S. R., Dekker, H., Schulte, L. M., Smit, E. F., Broxterman, H. J., Skog, J., Tannous, B. A., Wurdinger, T. & Verheul, H. M., 2014, In : Journal of Extracellular Vesicles. 3, 25657.

Research output: Contribution to journalArticleAcademicpeer-review

Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector.

van der Woude, A. D., Stoop, E. J. M., Stiess, M., Wang, Q., Ummels, R., van Stempvoort, G., Piersma, S. R., Cascioferro, A., Jimenez, C. R., Houben, E. N. G., Luirink, J., Pieters, J., van der Sar, A. M. & Bitter, W., 2014, In : Cellular Microbiology. 16, 2, p. 280-295

Research output: Contribution to journalArticleAcademicpeer-review

Biomarker Study Everolimus, een studie van de Borstkanker Onderzoek Groep Nederland

Kruger, D. T., Beelen, S., Sleijfer, M. P. H. M., Jansen, C. R., Jimenez, C. R., Linn, S. C. & Boven, E., 2014, In : Kanker Breed. 6, 2

Research output: Contribution to journalArticlePopular

Breast cancer classification by proteomic technologies: Current state of knowledge

Lam, S. W., Jimenez, C. R. & Boven, E., 2014, In : Cancer Treatment Reviews. 40, 1, p. 129-138

Research output: Contribution to journalArticleAcademicpeer-review

BRI2-BRICHOS is increased in human amyloid plaques in early stages of Alzheimer's disease

del Campo, M., Hoozemans, J. J. M., Dekkers, L. L., Rozemuller, A. J. M., Korth, C., Muller-Schiffmann, A., Scheltens, P., Blankenstein, M. A., Jimenez, C. R., Veerhuis, R. & Teunissen, C. E., 2014, In : Neurobiology of Aging. 35, 7, p. 1596-1604

Research output: Contribution to journalArticleAcademicpeer-review

Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling

de Wit, M., Kant, H., Piersma, S. R., Pham, T. V., Mongera, S., van Berkel, M. P. A., Boven, E., Ponten, F., Meijer, G. A., Jimenez, C. R. & Fijneman, R. J. A., 2014, In : Journal of Proteomics. 99, p. 26-39

Research output: Contribution to journalArticleAcademicpeer-review