2017 

 Accepted manuscripts 

 

  • Frederik Johannes Verweij*, Maarten Paul Bebelman*, Connie Ramona Jimenez, Juan J Garcia-Vallejo, Hans Janssen , Jacques Neefjes , Jaco Knol , Richard de Goeij- de Haas , Sander Piersma , Rubina Baglio , Matthijs M Verhage , Jaap Middeldorp , Anoek Zomer , Jacco van Rheenen , Marc Coppolino , Ilse Hurbain , Graça Raposo , Martine Smit , Ruud Toonen , Guillaume van Niel, Michiel Pegtel.  Quantifying exosome release from MVBs in single cells reveals a modulatory role for GPCR signaling. J. Cell Biology 2017, provisionally accepted manuscript.
  • Linda JW Bosch#, Meike de Wit#, Thang V Pham, Veerle HM Coupé, Annemieke C Hiemstra, Sander R Piersma, Gideon Oudgenoeg, George L Scheffer, Sandra Mongera, Jochim Terhaar Sive Droste, Frank A Oort, Sietze T van Turenhout, Ilhame Ben Larbi, Joost Louwagie, Wim van Criekinge, Rene WM van der Hulst, Chris JJ Mulder, Beatriz Carvalho, Remond JA Fijneman, Connie R Jimenez*, Gerrit A Meijer* Novel stool-based protein biomarkers for improved colorectal cancer screening: a case-control study Annals of Internal Medicine 2017, accepted manuscript. #Shared first and *shared senior authors.

 

 Published manuscripts 

  • Van der Hiel B, Haanen JBAG, Stokkel MPM, Peeper DS, Jimenez CR, Beijnen JH, van de Wiel BA, Boellaard R, van den Eertwegh AJM; REPOSIT study group. 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. BMC Cancer. 2017 Sep 15;17(1):649.
  • Komor MA, Pham TV, Hiemstra AC, Piersma SR, Bolijn AS, Schelfhorst T, Delis-van Diemen PM, Tijssen M, Sebra RP, Ashby M, Meijer GA, Jimenez CR, Fijneman RJA. Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify. Mol Cell Proteomics. 2017 Oct;16(10):1850-1863.
  • Bijnsdorp IV, Maxouri O, Kardar A, Schelfhorst T, Piersma SR, Pham TV, Vis A, van Moorselaar RJ, Jimenez CR. Feasibility of urinary extracellular vesicle proteome profiling using a robust and simple, clinically applicable isolation method. J Extracell Vesicles. 2017 Apr 28;6(1):1313091.
  • Bridel C, Koel-Simmelink MJA, Peferoen L, Derada Troletti C, Durieux S, Gorter R, Nutma E, Gami P, Iacobaeus E, Brundin L, Kuhle J, Vrenken H, Killestein J, Piersma SR, Pham TV, De Vries HE, Amor S, Jimenez CR, Teunissen CE. Brain endothelial cell expression of SPARCL-1 is specific to chronic multiple sclerosis lesions and is regulated by inflammatory mediators in vitro. Neuropathol ApplNeurobiol. 2017 May 24. doi: 10.1111/nan.12412. [Epub ahead of print] PubMedPMID: 28543098.
  • Labots M, van der Mijn JC, Beekhof R, Piersma SR, de Goeij-de Haas RR, Pham TV, Knol JC, Dekker H, van Grieken NCT, Verheul HMW, Jiménez CR. Phosphotyrosine-based-phosphoproteomics scaled-down to biopsy level for analysis of individual tumor biology and treatment selection. J Proteomics. 2017 Jun6;162:99-107.
  • Le Large TYS, Bijlsma MF, Kazemier G, van Laarhoven HWM, Giovannetti E, Jimenez CR. Key biological processes driving metastatic spread of pancreatic cancer as identified by multi-omics studies. Semin Cancer Biol. 2017Jun;44:153-169.

 

 2016 

  • Labots M, Gotink KJ, Dekker H, Azijli K, van der Mijn JC, Huijts CM, Piersma SR, Jiménez CR, Verheul HM. Evaluation of a tyrosine kinase peptide microarray for tyrosine kinase inhibitor therapy selection in cancer. Exp Mol Med. 2016 Dec 16;48(12):e279.
  • Van Winden VJ, Ummels R, Piersma SR, Jiménez CR, Korotkov KV, Bitter W, Houben EN. Mycosins Are Required for the Stabilization of the ESX-1 and ESX-5 Type VII Secretion Membrane Complexes. MBio. 2016 Oct 18;7(5). pii: e01471-16.
  • Pham TV, Jimenez CR. Simulated linear test applied to quantitative proteomics. Bioinformatics. 2016 Sep 1;32(17):i702-i709. doi: 10.1093/bioinformatics/btw440. PubMed PMID: 27587692.
  • Warmoes M, Lam SW, der Groep PV, Jaspers JE, Smolders YH, de Boer L, Pham TV, Piersma SR, Rottenberg S, Boven E, Jonkers J, van Diest PJ, Jimenez CR. Secretome proteomics reveals candidate non-invasive biomarkers of BRCA1 deficiency in breast cancer. Oncotarget. 2016 Aug 23. doi: 10.18632/oncotarget.11535. [Epub ahead of print] PubMed PMID: 27566577.
  • Schouten M, Bielefeld P, Fratantoni SA, Hubens CJ, Piersma SR, Pham TV, Voskuyl RA, Lucassen PJ, Jimenez CR, Fitzsimons CP. Multi-omics profile of the mouse dentate gyrus after kainic acid-induced status epilepticus. Sci Data. 2016 Aug 16;3:160068.
  • van Linde ME, van der Mijn JC, Pham TV, Knol JC, Wedekind LE, Hovinga KE, Aliaga ES, Buter J, Jimenez CR, Reijneveld JC, Verheul HM. Evaluation of potential circulating biomarkers for prediction of response to chemoradiation in patients with glioblastoma. J Neurooncol. 2016 Sep;129(2):221-30.
  • Teunissen CE, Elias N, Koel-Simmelink MJ, Durieux-Lu S, Malekzadeh A, Pham TV, Piersma SR, Beccari T, Meeter LH, Dopper EG, van Swieten JC, Jimenez CR, Pijnenburg YA. Novel diagnostic cerebrospinal fluid biomarkers for pathologic subtypes of frontotemporal dementia identified by proteomics. Alzheimers Dement (Amst). 2016 Jan 19;2:86-94.
  • Rovithi M, Lind JS, Pham TV, Voortman J, Knol JC, Verheul HM, Smit EF, Jimenez CR. Response and toxicity prediction by MALDI-TOF-MS serum peptide profiling in patients with non-small cell lung cancer. Proteomics Clin Appl. 2016 Jul;10(7):743-9.
  • van der Mijn JC, Broxterman HJ, Knol JC, Piersma SR, De Haas RR, Dekker H, Pham TV, Van Beusechem VW, Halmos B, Mier JW, Jiménez CR, Verheul HM. Sunitinib activates Axl signaling in renal cell cancer. Int J Cancer. 2016 Jun 15;138(12):3002-10.
  • Jaco C. Knol, Inge de Reus, Tim Schelfhorst, Robin Beekhof, Meike de Wit, Sander R. Piersma, Thang V. Pham, Egbert F. Smit, Henk M.W. Verheul, Connie R. Jiménez. Peptide-mediated 'miniprep' isolation of extracellular vesicles is suitable for high-throughput proteomics. EuPA Open Proteomics Volume 11, June 2016, Pages 11–15. http://dx.doi.org/10.1016/j.euprot.2016.02.001
  • Wojtuszkiewicz A, Schuurhuis GJ, Kessler FL, Piersma SR, Knol JC, Pham TV, Jansen G, Musters RJ, van Meerloo J, Assaraf YG, Kaspers GJ, Zweegman S, Cloos J, Jimenez CR. Exosomes Secreted by Apoptosis-Resistant Acute Myeloid Leukemia (AML) Blasts Harbor Regulatory Network Proteins Potentially Involved in Antagonism of Apoptosis. Mol Cell Proteomics. 2016 Apr;15(4):1281-98.
  • Baglio SR, van Eijndhoven MA, Koppers-Lalic D, Berenguer J, Lougheed SM, Gibbs S, Léveillé N, Rinkel RN, Hopmans ES, Swaminathan S, Verkuijlen SA, Scheffer GL, van Kuppeveld FJ, de Gruijl TD, Bultink IE, Jordanova ES, Hackenberg M, Piersma SR, Knol JC, Voskuyl AE, Wurdinger T, Jiménez CR, Middeldorp JM, Pegtel DM. Sensing of latent EBV infection through exosomal transfer of 5'pppRNA. Proc Natl Acad Sci USA. 2016 Feb 2;113(5):E587-96.

2015 

  • Tutakhel OA, Jeleń S, Valdez-Flores M, Dimke H, Piersma SR, Jimenez CR, Deinum J, Lenders JW, Hoenderop JG, Bindels RJ. Alternative splice variant of the thiazide-sensitive NaCl cotransporter: a novel player in renal salt handling.Am J Physiol Renal Physiol. 2015 Nov 11:ajprenal.00429.2015.
  • Schouten M, Fratantoni SA, Hubens CJ, Piersma SR, Pham TV, Bielefeld P, Voskuyl RA, Lucassen PJ, Jimenez CR, Fitzsimons CP. MicroRNA-124 and -137 cooperativity controls caspase-3 activity through BCL2L13 in hippocampal neural stem cells.Sci Rep. 2015 Jul 24;5:12448.
  • Ates LS, Ummels R, Commandeur S, van de Weerd R, Sparrius M, Weerdenburg E, Alber M, Kalscheuer R, Piersma SR, Abdallah AM, Abd El Ghany M, Abdel-Haleem AM, Pain A, Jiménez CR, Bitter W, Houben EN. Essential Role of the ESX-5 Secretion System in Outer Membrane Permeability of Pathogenic Mycobacteria.PLoS Genet. 2015 May 4;11(5):e1005190.
  • van der Mijn JC, Labots M, Piersma SR, Pham TV, Knol JC, Broxterman HJ, Verheul HM, Jiménez CR. Evaluation of different phospho-tyrosine antibodies for label-free phosphoproteomicsJ Proteomics. 2015 Sep 8;127(Pt B):259-63.
  • Verweij FJ, de Heus C, Kroeze S, Cai H, Kieff E, Piersma SR, Jimenez CR, Middeldorp JM, Pegtel DM. Exosomal sorting of the viral oncoprotein LMP1 is restrained by TRAF2 association at signalling endosomes.J Extracell Vesicles. 2015 Apr 10;4:26334
  • Grinberg LT, Jimenez CR, Li KW. Neuroproteomics: applications in neuroscience and neurology.Biochim Biophys Acta. 2015 Jul;1854(7):703-4.
  • Piersma SR, Knol JC, de Reus I, Labots M, Sampadi BK, Pham TV, Ishihama Y, Verheul HM, Jimenez CR. Feasibility of label-free phosphoproteomics and application to base-line signaling of colorectal cancer cell lines.J Proteomics. 2015 Sep 8;127(Pt B):247-58.
  • Nagel R, Stigter-van Walsum M, Buijze M, van den Berg J, van der Meulen IH, Hodzic J, Piersma SR, Pham TV, Jimenez CR, van Beusechem VW, Brakenhoff RH. Genome-wide siRNA screen identifies the radiosensitizing effect of downregulation of MASTL and FOXM1 in NSCLC. Mol Cancer Ther. 2015 Mar 25. pii: molcanther.0846.2014. [Epub ahead of print] PubMed PMID: 25808837.
  • Jimenez CR, Fijneman RJ. Proteomics of Colorectal Cancer in a Genomic Context: First Large-Scale Mass Spectrometry-Based Analysis from the Cancer Genome Atlas. Clin Chem. 2015 Feb 26. pii: clinchem.2014.234807. [Epub ahead of print] PubMed PMID: 25722459.

2014 

  • Van der Mijn JC, Sol N, Mellema W, Jimenez CR, Piersma SR, Dekker H, Schutte LM, Smit EF, Broxterman HJ, Skog J, Tannous BA, Wurdinger T, Verheul HM. Analysis of AKT and ERK1/2 protein kinases in extracellular vesicles isolated from blood of patients with cancer. J Extracell Vesicles. 2014 Dec 8;3:25657. doi: 10.3402/jev.v3.25657. eCollection 2014. PubMed PMID: 25491250; PubMed Central PMCID: PMC4261239.
  • Emmink BL, Laoukili J, Kipp AP, Koster J, Govaert KM, Fatrai S, Verheem A, Steller EJ, Brigelius-Flohe R, Jimenez CR, Borel Rinkes IH, Kranenburg O. GPx2 suppression of H2O2 stress links the formation of differentiated tumor mass to metastatic capacity in colorectal cancer. Cancer Res. 2014 Sep 26. pii: canres.1645.2014. [Epub ahead of print]
  • Labots M, Schütte LM, van der Mijn JC, Pham TV, Jiménez CR, Verheul HM. Mass Spectrometry-Based Serum and Plasma Peptidome Profiling for Prediction of Treatment Outcome in Patients With Solid Malignancies. Oncologist. 2014 Oct;19(10):1028-1039. Epub 2014 Sep 3. Review.
  • Rajcevic U, Knol JC, Piersma S, Bougnaud S, Fack F, Sundlisaeter E, Søndenaa K, Myklebust R, Pham TV, Niclou SP, Jiménez CR. Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture. Proteome Sci. 2014 Jul 11;12:39.
  • Hassan C, Kester MG, Oudgenoeg G, de Ru AH, Janssen GM, Drijfhout JW, Spaapen RM, Jiménez CR, Heemskerk MH, Falkenburg JH, van Veelen PA. Accurate quantitation of MHC-bound peptides by application of isotopically labeled peptide MHC complexes. J. Proteomics 2014 Jul 19;109C:240-244.
  • Daleke-Schermerhorn MH, Felix T, Soprova Z, Ten Hagen-Jongman CM, Vikström D, Majlessi L, Beskers J, Follmann F, de Punder K, van der Wel NN, Baumgarten T, Pham TV, Piersma SR, Jiménez CR, van Ulsen P, de Gier JW, Leclerc C, Jong WS, Luirink J. Decoration of outer membrane vesicles with multiple antigens by using an autotransporter approach. Appl Environ Microbiol. 2014 Sep;80(18):5854-65.
  • Senol O, Schaaij-Visser TB, Erkan EP, Dorfer C, Lewandrowski G, Pham TV, Piersma SR, Peerdeman SM, Ströbel T, Tannous B, Saydam N, Slavc I, Knosp E, Jimenez CR, Saydam O. miR-200a-mediated suppression of non-muscle heavy chain IIb inhibits meningioma cell migration and tumor growth in vivo. Oncogene. 2014 May 26;0.
  • Jimenez CR, Verheul HM. Mass spectrometry-based proteomics: from cancer biology to protein biomarkers, drug targets, and clinical applications. Am Soc Clin Oncol Educ Book. 2014;34:e504-10. doi: 10.14694/EdBook_AM.2014.34.e504. PubMed PMID: 24857147.
  • Chiasserini D, van Weering JR, Piersma SR, Pham TV, Malekzadeh A, Teunissen CE, de Wit H, Jiménez CR. Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset. J Proteomics. 2014 Apr 24;106C:191-204.
  • Del Campo M, Hoozemans JJ, Dekkers LL, Rozemuller AJ, Korth C, Müller-Schiffmann A, Scheltens P, Blankenstein MA, Jimenez CR, Veerhuis R, Teunissen CE. BRI2-BRICHOS is increased in human amyloid plaques in early stages of Alzheimer's disease. Neurobiol Aging. 2014 Jul;35(7):1596-604.
  • De Wit M, Kant H, Piersma SR, Pham TV, Mongera S, van Berkel MP, Boven E, Pontén F, Meijer GA, Jimenez CR*, Fijneman RJ*. Colorectal cancer candidate biomarkers identified by tissue secretome proteome profiling. J Proteomics. 2014 Jan 10; 99C: 269-39. *Shared senior authorship.
  • Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: Current state of knowledge. Cancer Treat Rev. 2014 Feb; 40(1): 129-38.

2013 

  • Knol JC, de Wit M, Albrethsen J, Piersma SR, Pham TV, Mongera S, Carvalho B, Fijneman RJA, Meijer GA, Jiménez CR. Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues. Biochim Biophys Acta - Proteins and Proteomics (2013).
  • Bijnsdorp IV, Geldof AA, Lavaei M, Piersma SR, van Moorselaar RJA, Jimenez CR. ITGA3 and ITGB1 interfere with non-cancerous prostate cell functions and are increased in urine exosomes of metastatic prostate cancer patients. J Extracell Vesicles. 2013 Dec 23;2.
  • Van der Woude AD, Stoop EJ, Stiess M, Wang S, Ummels R, van Stempvoort G, Piersma SR, Cascioferro A, Jiménez CR, Houben EN, Luirink J, Pieters J, van der Sar AM, Bitter W. Analysis of SecA2-dependent substrates in Mycobacterium marinum identifies protein kinase G (PknG) as a virulence effector. Cell Microbiol. 2013 Oct 9.
  • Kooij V, Zhang P, Piersma SR, Sequeira V, Boontje NM, Wijnker PJ, Jiménez CR, Jaquet KE, Dos Remedios C, Murphy AM, Van Eyk JE, van der Velden J, Stienen GJ. PKCα-Specific Phosphorylation of the Troponin Complex in Human Myocardium: A Functional and Proteomics Analysis. PLoS One. 2013 Oct 7;8(10): e74847.
  • Snoeren N, Emmink BL, Koerkamp MJ, van Hooff SR, Goos JA, van Houdt WJ, de Wit M, Prins AM, Piersma SR, Pham TV, Belt EJ, Bril H, Stockmann HB, Meijer GA, van Hillegersberg R, Holstege FC, Jimenez CR, Fijneman RJ, Kranenburg OW, Rinkes IH. Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer. PLoS One. 2013 Sep 17;109(6): 1636-47.
  • DeBoer JP, Piersma SR, Pham TV, Knol JC, van Beusechem VW, Kaspers GJL, van Royen BJ, Jiménez CR, Helder MN*. Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery. British Journal of Cancer (2013). *Shared senior authorship.
  • Lam SW, Jimenez CR, Boven E. Breast cancer classification by proteomic technologies: Current state of knowledge. Cancer Treat Rev. (2013).
  • Petersen K, Rajcevic U, Abdul Rahim SA, Jonassen I, Kalland KH, Jimenez CR, Bjerkvig R, Niclou SP. Gene set based integrated data analysis reveals phenotypic differences in a brain cancer model. PLoS One 8(7):e68288 (2013).
  • Emmink BL, Verheem A, Van Houdt WJ, Steller EJ, Govaert KM, Pham TV, Piersma SR, Borel Rinkes IH, Jimenez CR*, Kranenburg O*. The secretome of colon cancer stem cells contains drug-metabolizing enzymes. J Proteomics 91C:84-96 (2013). *Shared senior authorship.
  • De Vries-van Leeuwen IJ, da Costa Pereira D, Flach KD, Piersma SR, Haase C, Bier D, Yalcin Z, Michalides R, Feenstra KA, Jiménez CR, de Greef TF, Brunsveld L, Ottmann C, Zwart W, de Boer AH. Interaction of 14-3-3 proteins with the estrogen receptor alpha F domain provides a drug target interface. Proc Natl Acad Sci U S A 110(22):8894-9 (2013).
  • Piersma SR, Warmoes MO, de Wit M, de Reus I, Knol JC, Jiménez CR. Whole gel processing procedure for GeLC-MS/MS based proteomics. Proteome Sci. 11(1):17 (2013).
  • van der Woude AD, Mahendran KR, Ummels R, Piersma SR, Pham TV, Jiménez CR, de Punder K, van der Wel NN, Winterhalter M, Luirink J, Bitter W, Houben EN. Differential detergent extraction of mycobacterium marinum cell envelope proteins identifies an extensively modified threonine-rich outer membrane protein with channel activity. J Bacteriol. 195(9):2050-9 (2013).
  • Warmoes M, Jaspers JE, Xu G, Sampadi BK, Pham TV, Knol JC, Piersma SR, Boven E, Jonkers J, Rottenberg S*, Jimenez CR*. Proteomics of genetically engineered mouse mammary tumors identifies fatty acid metabolism members as potential predictive markers for cisplatin resistance. Mol Cell Proteomics 12(5):1319-34 (2013). *Shared senior authorship.
  • Schaaij-Visser TB, de Wit M, Lam SW, Jiménez CR. The cancer secretome, current status and opportunities in the lung, breast and colorectal cancer context. Biochim Biophys Acta. (2013). doi:pii: S1570-9639(13)00040-X. 10.1016/j.bbapap.2013.01.029.
  • Albrethsen J, Agner J, Piersma SR, Højrup P, Pham TV, Weldingh K, Jimenez CR, Andersen P, Rosenkrands I. Proteomic profiling of Mycobacterium tuberculosis identifies nutrient-starvation-responsive toxin-antitoxin systems. Mol Cell Proteomics 12(5):1180-91 (2013).
  • de Wit M, Fijneman RJA, Verheul HMW, Meijer GA, Jimenez CR. Proteomics in colorectal cancer translational research: biomarker discovery for clinical applications. Clin Biochem. 46(6):466-79 (2013).

2012

  • Pham TV, Jimenez CR. An accurate paired sample test for count data. Bioinformatics 28(18):i596-i602 (2012).
  • Houben EN, Bestebroer J, Ummels R, Wilson L, Piersma SR, Jiménez CR, Ottenhoff TH, Luirink J, Bitter W. Composition of the type VII secretion system membrane complex. Mol Microbiol. 86(2):472-84 (2012).
  • Daleke MH, van der Woude AD, Parret AH, Ummels R, de Groot AM, Watson D, Piersma SR, Jiménez CR, Luirink J, Bitter W, Houben EN. Specific Chaperones for the Type VII Protein Secretion Pathway. J Biol Chem 287(38):31939-47 (2012).
  • Kranenburg O, Emmink BL, Knol J, van Houdt WJ, Rinkes IH, Jimenez CR. Proteomics in studying cancer stem cell biology. Expert Rev Proteomics 9(3):325-36 (2012).
  • Bogels M, Braster R, Nijland PG, Gul N, van de Luijtgaarden W, Fijneman RJA, Meijer GA, Jimenez CR, Beelen RHJ, van Egmond M. Carcinoma origin dictates differential skewing of monocyte function. OncoImmunology 1(7): 1-12 (2012).
  • Pham TV, Piersma SR, Oudgenoeg G, Jimenez CR. Label-free mass spectrometry-based proteomics for biomarker discovery and validation. Expert Reviews Mol. Diagnostics 12(4): 343-359 (2012).
  • Fijneman RJ, de Wit M, Pourghiasian M, Piersma SR, Pham TV, Warmoes MO, Lavaei M, Piso C, Smit F, Delis-van Diemen PM, van Turenhout ST, Terhaar Sive Droste JS, Mulder CJ, Blankenstein MA, Robanus-Maandag EC, Smits R, Fodde R, van Hinsbergh VW, Meijer GA and Jimenez CR. Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer. Clin. Cancer Res. 18(9): 2613-2624 (2012).
  • van Dijk KD, Berendse HW, Drukarch B, Fratantoni SA, Pham TV, Piersma SR, Huisman E, Brevé JJP, Groenewegen HJ, Jimenez CR*, van de Berg WDJ*. The proteome of the locus ceruleus in Parkinson's disease: relevance to pathogenesis. Brain Pathol. 22(4):485-98 (2012).
  • Warmoes M, Jaspers JE, Pham TV, Piersma SR, Oudgenoeg G, Massink MP, Waisfisz Q, Rottenberg S, Boven E, Jonkers J and Jimenez CR. Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with diagnostic and prognostic value in human breast cancer. Mol. Cell Proteomics 11: M111.013334 (2012).
  • de Wit M, Jimenez CR, Carvalho B, Belien JA, Delis-van Diemen PM, Mongera S, Piersma SR, Vikas M, Navani S, Pontén F, Meijer GA, Fijneman RJ. Cell surface proteomics identifies glucose transporter type 1 and prion protein as candidate biomarkers for colorectal adenoma-to-carcinoma progression. Gut 61(6):855-64 (2012).

2011

  • Bosch LJ, Carvalho B, Fijneman RJ, Jimenez CR, Pinedo HM, van EM and Meijer GA. Molecular tests for colorectal cancer screening. Clin. Colorectal Cancer 10: 8-23 (2011).
  • Emmink BL, Van Houdt WJ, Vries RG, Hoogwater FJ, Govaert KM, Verheem A, Nijkamp MW, Steller EJ, Jimenez CR, Clevers H, Borel Rinkes IH and Kranenburg O. Differentiated human colorectal cancer cells protect tumor-initiating cells from irinotecan. Gastroenterology 141: 269-278 (2011).
  • Gast MC, Zapatka M, van TH, Bontenbal M, Span PN, Tjan-Heijnen VC, Knol JC, Jimenez CR, Schellens JH and Beijnen JH. Postoperative serum proteomic profiles may predict recurrence-free survival in high-risk primary breast cancer. J. Cancer Res. Clin. Oncol. 137: 1773-1783 (2011).
  • Knol JC and Jimenez CR. MALDI-TOF serum profiling using semiautomated serum peptide capture with magnetic reversed phase (C18) beads. Methods Mol. Biol. 790: 3-16 (2011).
  • Skvortsov S, Jimenez CR, Knol JC, Eichberger P, Schiestl B, Debbage P, Skvortsova I and Lukas P. Radioresistant head and neck squamous cell carcinoma cells: intracellular signaling, putative biomarkers for tumor recurrences and possible therapeutic targets. Radiother. Oncol. 101: 177-182 (2011).
  • Teunissen CE, Koel-Simmelink MJ, Pham TV, Knol JC, Khalil M, Trentini A, Killestein J, Nielsen J, Vrenken H, Popescu V, Dijkstra CD and Jimenez CR. Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry. Mult. Scler. 17: 838-850 (2011).
  • Teunissen CE, Tumani H, Bennett JL, Berven FS, Brundin L, Comabella M, Franciotta D, Federiksen JL, Fleming JO, Furlan R, Hintzen RQ, Hughes SG, Jimenez CR, Johnson MH, Killestein J, Krasulova E, Kuhle J, Magnone MC, Petzold A, Rajda C, Rejdak K, Schmidt HK, van P, V, Waubant E, Wolf C, Deisenhammer F, Giovannoni G and Hemmer B. Consensus Guidelines for CSF and Blood Biobanking for CNS Biomarker Studies. Mult. Scler. Int. 2011: 246412 (2011).
  • van Dijk KD, Berendse HW, Drukarch B, Fratantoni SA, Pham TV, Piersma SR, Huisman E, Breve JJ, Groenewegen HJ, Jimenez CR and van de Berg WD. The Proteome of the Locus Ceruleus in Parkinson's Disease: Relevance to Pathogenesis. Brain Pathol. (2011).
  • Van Houdt WJ, Emmink BL, Pham TV, Piersma SR, Verheem A, Vries RG, Fratantoni SA, Pronk A, Clevers H, Borel Rinkes IH, Jimenez CR and Kranenburg O. Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target. Mol. Cell Proteomics. 10: M111 (2011).

2010

  • Albrethsen J, Knol JC, Piersma SR, Pham TV, de Wit M, Mongera S, Carvalho B, Verheul HM, Fijneman RJ, Meijer GA and Jimenez CR. Subnuclear proteomics in colorectal cancer: identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression. Mol. Cell Proteomics. 9: 988-1005 (2010).
  • Fratantoni SA, Piersma SR and Jimenez CR. Comparison of the performance of two affinity depletion spin filters for quantitative proteomics of CSF: Evaluation of sensitivity and reproducibility of CSF analysis using GeLC-MS/MS and spectral counting. Proteomics. Clin. Appl. 4: 613-617 (2010).
  • Jimenez CR, Knol JC, Meijer GA and Fijneman RJ. Proteomics of colorectal cancer: overview of discovery studies and identification of commonly identified cancer-associated proteins and candidate CRC serum markers. J. Proteomics. 73: 1873-1895 (2010).
  • Jimenez CR and Slijper M. Current status of cancer proteomics, how far are we from clinical applications? J. Proteomics. 73: 1787-1789 (2010).
  • Pham TV, Piersma SR, Warmoes M and Jimenez CR. On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics. Bioinformatics. 26: 363-369 (2010).
  • Piersma SR, Labots M, Verheul HM and Jimenez CR. Strategies for kinome profiling in cancer and potential clinical applications: chemical proteomics and array-based methods. Anal. Bioanal. Chem. 397: 3163-3171 (2010).
  • Piersma SR, Fiedler U, Span S, Lingnau A, Pham TV, Hoffmann S, Kubbutat MH and Jimenez CR. Workflow comparison for label-free, quantitative secretome proteomics for cancer biomarker discovery: method evaluation, differential analysis, and verification in serum. J. Proteome. Res. 9: 1913-1922 (2010).
  • Sani M, Houben EN, Geurtsen J, Pierson J, de PK, van ZM, Wever B, Piersma SR, Jimenez CR, Daffe M, Appelmelk BJ, Bitter W, van der Wel N and Peters PJ. Direct visualization by cryo-EM of the mycobacterial capsular layer: a labile structure containing ESX-1-secreted proteins. PLoS. Pathog. 6: e1000794 (2010).
  • Saydam O, Senol O, Schaaij-Visser TB, Pham TV, Piersma SR, Stemmer-Rachamimov AO, Wurdinger T, Peerdeman SM and Jimenez CR. Comparative protein profiling reveals minichromosome maintenance (MCM) proteins as novel potential tumor markers for meningiomas. J. Proteome. Res. 9: 485-494 (2010).
  • Spitzer P, Klafki HW, Blennow K, Buee L, Esselmann H, Herruka SK, Jimenez C, Klivenyi P, Lewczuk P, Maler JM, Markus K, Meyer HE, Morris C, Muller T, Otto M, Parnetti L, Soininen H, Schraen S, Teunissen C, Vecsei L, Zetterberg H and Wiltfang J. cNEUPRO: Novel Biomarkers for Neurodegenerative Diseases. Int. J. Alzheimers. Dis. 2010: (2010).
  • van Dijk KD, Teunissen CE, Drukarch B, Jimenez CR, Groenewegen HJ, Berendse HW and van de Berg WD. Diagnostic cerebrospinal fluid biomarkers for Parkinson's disease: a pathogenetically based approach. Neurobiol. Dis. 39: 229-241 (2010).

2009

  • Abdallah AM, Verboom T, Weerdenburg EM, Gey van Pittius NC, Mahasha PW, Jimenez C, Parra M, Cadieux N, Brennan MJ, Appelmelk BJ and Bitter W. PPE and PE_PGRS proteins of Mycobacterium marinum are transported via the type VII secretion system ESX-5. Mol. Microbiol. 73: 329-340 (2009).
  • Albrethsen J, Knol JC and Jimenez CR. Unravelling the nuclear matrix proteome. J. Proteomics. 72: 71-81 (2009).
  • Checinska A, Giaccone G, Rodriguez JA, Kruyt FA and Jimenez CR. Comparative proteomics analysis of caspase-9-protein complexes in untreated and cytochrome c/dATP stimulated lysates of NSCLC cells. J. Proteomics. 72: 575-585 (2009).
  • 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).
  • Jimenez CR. Sorting and zooming: subcellular proteomics is booming! J. Proteomics. 72: 1-3 (2009).
  • Piersma SR, Broxterman HJ, Kapci M, de Haas RR, Hoekman K, Verheul HM and Jimenez CR. Proteomics of the TRAP-induced platelet releasate. J. Proteomics. 72: 91-109 (2009).
  • Rajcevic U, Niclou SP and Jimenez CR. Proteomics strategies for target identification and biomarker discovery in cancer. Front Biosci. 14: 3292-3303 (2009).
  • Rajcevic U, Petersen K, Knol JC, Loos M, Bougnaud S, Klychnikov O, Li KW, Pham TV, Wang J, Miletic H, Peng Z, Bjerkvig R, Jimenez CR and Niclou SP. iTRAQ-based proteomics profiling reveals increased metabolic activity and cellular cross-talk in angiogenic compared with invasive glioblastoma phenotype. Mol. Cell Proteomics. 8: 2595-2612 (2009).
  • Tefsen B, van Stijn CM, van den Broek M, Kalay H, Knol JC, Jimenez CR and van D, I. Chemoenzymatic synthesis of multivalent neoglycoconjugates carrying the helminth glycan antigen LDNF. Carbohydr. Res. 344: 1501-1507 (2009).
  • van Dijk FS, Nesbitt IM, Zwikstra EH, Nikkels PG, Piersma SR, Fratantoni SA, Jimenez CR, Huizer M, Morsman AC, Cobben JM, van Roij MH, Elting MW, Verbeke JI, Wijnaendts LC, Shaw NJ, Hogler W, McKeown C, Sistermans EA, Dalton A, Meijers-Heijboer H and Pals G. PPIB mutations cause severe osteogenesis imperfecta. Am. J. Hum. Genet. 85: 521-527 (2009).
  • Voortman J, Pham TV, Knol JC, Giaccone G and Jimenez CR. Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profiling. Proteome. Sci. 7: 34 (2009).

2008

  • Engwegen JY, Alberts M, Knol JC, Jimenez CR, Depla AC, Tuynman H, van Heukelem HA, Snel P, Smits ME, Cats A, Schellens JH and Beijnen JH. Influence of variations in sample handling on SELDI-TOF MS serum protein profiles for colorectal cancer. Proteomics. Clin. Appl. 2: 936-945 (2008).
  • Hamacher M, Stephan C, Hardt T, Eisenacher M, Henkel A, Wiltfang J, Jimenez CR, Park YM, Marcus K and Meyer HE. Applications in brain proteomics: 8(th) HUPO Brain Proteome Project Workshop 7 October 2007, Seoul, Korea. Proteomics. 8: 1750-1753 (2008).
  • Jimenez CR. Mass spectrometry-based proteomics: trends in tools and strategies. Eur. Pharm. Rev. 2008: 24-25 (2008).
  • Li KW and Jimenez CR. Synapse proteomics: current status and quantitative applications. Expert. Rev. Proteomics. 5: 353-360 (2008).
  • Pham TV, van de Wiel MA and Jimenez CR. Support vector machine approach to separate control and breast cancer serum samples. Stat. Appl. Genet. Mol. Biol. 7: Article11 (2008).
  • Pham TV and Jimenez CR. OplAnalyzer: a toolbox for MALDI-TOF mass spectrometry data analysis. In: Advances in Mass Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry and Food Industry, Third International Conference, MDA 2008, Leipzig, Germany, Proceedings Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 5108: 73-81 (2008).

2007

  • Jiménez CR. Mass spectrometry-based proteomics: trends in tools and strategies. Eur. Pharm. Revs. p24-25 (2007).
  • Codrea MC, Jimenez CR, Piersma S, Heringa J and Marchiori E. Robust peak detection and alignment of nanoLC-FT mass spectrometry data. In: Evolutionary Computation, Machine Learning and Data Mining in Bioinformatics: 5th European Conference, EvoBIO 2007, Valencia, Spain, Proceedings (Marchiori E, Moore JH and Rajapakse JC, eds.), Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 4447: 35-46 (2007).
  • Codrea MC, Jimenez CR, Heringa J and Marchiori E. Tools for computational processing of LC-MS datasets: a user's perspective. Comput. Methods Programs Biomed. 86: 281-290 (2007).
  • Jimenez CR, Piersma S and Pham TV. High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery. Biomark. Med. 1: 541-565 (2007).
  • Jimenez CR, El FZ, Knol JC, Hoekman K, Kruyt FA, Giaccone G, Smit AB and Li KW. Automated serum peptide profiling using novel magnetic C18 beads off-line coupled to MALDI-TOF-MS. Proteomics. Clin. Appl. 1: 598-604 (2007).
  • Jimenez CR, Koel-Simmelink M, Pham TV, van d, V and Teunissen CE. Endogeneous peptide profiling of cerebrospinal fluid by MALDI-TOF mass spectrometry: Optimization of magnetic bead-based peptide capture and analysis of preanalytical variables. Proteomics. Clin. Appl. 1: 1385-1392 (2007).

2006

  • Eiras S, Narolska NA, van Loon RB, Boontje NM, Zaremba R, Jimenez CR, Visser FC, Stooker W, van d, V and Stienen GJ. Alterations in contractile protein composition and function in human atrial dilatation and atrial fibrillation. J. Mol. Cell Cardiol. 41: 467-477 (2006).
  • Llamas MA, Sparrius M, Kloet R, Jimenez CR, Vandenbroucke-Grauls C and Bitter W. The heterologous siderophores ferrioxamine B and ferrichrome activate signaling pathways in Pseudomonas aeruginosa. J. Bacteriol. 188: 1882-1891 (2006).
  • Marchiori E, Jimenez CR, West-Nielsen M and Heegaard N. Robust SVM-based biomarker selection with noisy mass spectrometric proteomic data. In: Applications of Evolutionary Computing: EvoBIO, Fourth European Workshop on Evolutionary Bioinformatics, Budapest, Hungary, Proceedings (Rothlauf F, Branke J, Cagnoni S, Costa E, Cotta R, Drechsler R, Lutton E, Machado P, Moore JH, Romero J, Smith GD, Squillero G and Takagi H, eds.), Springer-Verlag, Berlin Heidelberg, Lect. Notes Comput. Sci. 3907: 79-90 (2006).
  • Jiménez CR, Spijker S, de Schipper S, Lodder JC, Janse C, Geraerts WPM, van Minnen J, Syed NI, Burlingame AL, Smit AB, Li KW. Peptidomics of a single identified neuron reveals diversity of multiple neuropeptides with convergent actions on cellular excitability. J. Neurosci. 26:518-529 (2006).
  • Li KW, Jiménez CR, Hornshaw MP, Van der Schors RC, Schoffelmeer ANM, Smit AB. Intermittent administration of morphine alters protein expression in rat nucleus accumbens. Proteomics 6(6)(2006).
  • Van den Oever MC, Spijker S, Li KW, Jiménez CR, Koya E, Van der Schors RC, Gouwenberg Y, Binnekade R, De Vries TJ, Schoffelmeer ANM, Smit AB. A proteomics approach to identify long-term molecular changes in rat medial prefrontal cortex resulting from sucrose self-administration. J. Prot. Res. 5:147-154 (2006).