Thang Pham

DR.

20082019
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Research Output 2008 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

Proteome analysis of non-small cell lung cancer cell line secretomes and patient sputum reveals biofluid biomarker candidates for cisplatin response prediction

Böttger, F., Schaaij-Visser, T. B., de Reus, I., Piersma, S. R., Pham, T. V., Nagel, R., Brakenhoff, R. H., Thunnissen, E., Smit, E. F. & Jimenez, C. R., 2019, In : Journal of Proteomics. 196, p. 106-119

Research output: Contribution to journalArticleAcademicpeer-review

Tumor Heterogeneity Underlies Differential Cisplatin Sensitivity in Mouse Models of Small-Cell Lung Cancer

Böttger, F., Semenova, E. A., Song, J-Y., Ferone, G., van der Vliet, J., Cozijnsen, M., Bhaskaran, R., Bombardelli, L., Piersma, S. R., Pham, T. V., Jimenez, C. R. & Berns, A., 2019, In : Cell Reports. 27, 11, p. 3345-3358.e4

Research output: Contribution to journalArticleAcademicpeer-review

Open Access
2018

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

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
2017

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

2016

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

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

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

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

2014

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

Colorectal cancer derived organotypic spheroids maintain essential tissue characteristics but adapt their metabolism in culture

Rajcevic, U., Knol, J. C., Piersma, S. R., Bougnaud, S., Fack, F., Sundlisaeter, E., Sondenaa, K., Myklebust, R., Pham, T. V., Niclou, S. P. & Jimenez, C. R., 2014, In : Proteome Science. 12, 39.

Research output: Contribution to journalArticleAcademicpeer-review

Decoration of outer membrane vesicles with multiple antigens using an autotransporter approach.

Daleke, M. H., Felix, T., Soprova, Z., ten Hagen-Jongman ten, C. M., Vikström, D., Majlessi, L., Beskers, J., Follman, F., de Punder, K., van der Wel, N. N., Baumgarten, T., Pham, T. V., Piersma, S. R., Jimenez, C. R., van Ulsen, P., de Gier, J. W., Leclerc, C., Jong, W. S. & Luirink, S., 2014, In : Applied and Environmental Microbiology. 80, 18, p. 5854-5864

Research output: Contribution to journalArticleAcademicpeer-review

Mass Spectrometry-Based Serum and Plasma Peptidome Profiling for Prediction of Treatment Outcome in Patients With Solid Malignancies

Labots, M., Schutte, L. M., van der Mun, J. C., Pham, T. V., Jimenez, C. R. & Verheul, H. M. W., 2014, In : The Oncologist. 19, 10, p. 1028-1039

Research output: Contribution to journalArticleAcademicpeer-review

Proteomic analysis of cerebrospinal fluid extracellular vesicles: A comprehensive dataset

Chiasserini, D., van Weering, J. R. T., Piersma, S. R., Pham, T. V., Malekzadeh, A., Teunissen, C. E., de Wit, H. & Jimenez, C. R., 2014, In : Journal of Proteomics. 106, p. 191-204

Research output: Contribution to journalArticleAcademicpeer-review

Proteomics of differential extraction fractions enriched for chromatin-binding proteins from colon adenoma and carcinoma tissues

Knol, J. C., de Wit, M., Albrethsen, J., Piersma, S. R., Pham, T. V., Mongera, S., Carvalho, B., Fijneman, R. J. A., Meijer, G. A. & Jimenez, C. R., 2014, In : Biochimica et Biophysica Acta (BBA) - Proteins and Proteomics. 1844, 5, p. 1034-1043

Research output: Contribution to journalArticleAcademicpeer-review

2013

Differential Detergent Extraction of Mycobacterium marinum Cell Envelope Proteins Identifies an Extensively Modified Threonine-Rich Outer Membrane Protein with Channel Activity

van der Woude, A. D., Mahendran, K. R., Ummels, R., Piersma, S. R., Pham, T. V., Jimenez, C. R., de Punder, K., van der Wel, N. N., Winterhalter, M., Luirink, S., Bitter, W. & Houben, E. N. G., 2013, In : Journal of Bacteriology. 195, 9, p. 2050-2059

Research output: Contribution to journalArticleAcademicpeer-review

Maspin is a marker for early recurrence in primary stage III and IV colorectal cancer

Snoeren, N., Emmink, B. L., Koerkamp, M. J. G., van Hooff, S. R., Goos, J. A. C. M., Van Houdt, W. J., de Wit, M., Prins, A. M., Piersma, S. R., Pham, T. V., Belt, E. J. T. H., Bril, H., Stockmann, H. B., Meijer, G. A., van Hillegersberg, R., Holstege, FC., Jimenez, C. R., Fijneman, R. J. A., Kranenburg, O. W. & Rinkes, I. H. M. B., 2013, In : British Journal of Cancer. 109, 6, p. 1636-1647

Research output: Contribution to journalArticleAcademicpeer-review

Proteomic Profiling of Mycobacterium tuberculosis Identifies Nutrient-starvation-responsive Toxin-antitoxin Systems

Albrethsen, J., Agner, J., Piersma, S. R., Hojrup, P., Pham, T. V., Weldingh, K., Jimenez, C. R., Andersen, P. & Rosenkrands, I., 2013, In : Molecular and Cellular Proteomics. 12, 5, p. 1180-1191

Research output: Contribution to journalArticleAcademicpeer-review

Proteomics of Genetically Engineered Mouse Mammary Tumors Identifies Fatty Acid Metabolism Members as Potential Predictive Markers for Cisplatin Resistance

Warmoes, M. O., Jaspers, J. E., Xu, G. T., Sampadi, B. K., Pham, T. V., Knol, J. C., Piersma, S. R., Boven, E., Jonkers, J., Rottenberg, S. & Jimenez, C. R., 2013, In : Molecular and Cellular Proteomics. 12, 5, p. 1319-1334

Research output: Contribution to journalArticleAcademicpeer-review

Surface proteomic analysis of osteosarcoma identifies EPHA2 as receptor for targeted drug delivery

Posthuma de Boer, J., Piersma, S. R., Pham, T. V., van Egmond, P. W., Knol, J. C., Cleton-Jansen, A. M., van Geer, M. A., van Beusechem, V. W., Kaspers, G. J. L., van Royen, B. J., Jimenez, C. R. & Helder, M. N., 2013, In : British Journal of Cancer. 109, 8, p. 2142-2154

Research output: Contribution to journalArticleAcademicpeer-review

The secretome of colon cancer stem cells contains drug-metabolizing enzymes

Emmink, B. L., Verheem, A., Van Houdt, W. J., Steller, E. J. A., Govaert, K. M., Pham, T. V., Piersma, S. R., Rinkes, I. H. M. B., Jimenez, C. R. & Kranenburg, O., 2013, In : Journal of Proteomics. 91, p. 84-96

Research output: Contribution to journalArticleAcademicpeer-review

2012

An accurate paired sample test for count data

Pham, T. V. & Jimenez, C. R., 2012, In : Bioinformatics. 28, 18, p. I596-I602

Research output: Contribution to journalArticleAcademicpeer-review

Label-free mass spectrometry-based proteomics for biomarker discovery and validation

Pham, T. V., Piersma, S. R., Oudgenoeg, G. & Jimenez, C. R., 2012, In : Expert review of molecular diagnostics. 12, 4, p. 343-359

Research output: Contribution to journalArticleAcademicpeer-review

Proteomics of Mouse BRCA1-deficient Mammary Tumors Identifies DNA Repair Proteins with Potential Diagnostic and Prognostic Value in Human Breast Cancer

Warmoes, M. O., Jaspers, J. E., Pham, T. V., Piersma, S. R., Oudgenoeg, G., Massink, M. P. G., Waisfisz, Q., Rottenberg, S., Boven, E., Jonkers, J. & Jimenez, C. R., 2012, In : Molecular and Cellular Proteomics. 11, 7, M111.013334.

Research output: Contribution to journalArticleAcademicpeer-review

Proximal Fluid Proteome Profiling of Mouse Colon Tumors Reveals Biomarkers for Early Diagnosis of Human Colorectal Cancer

Fijneman, R. J. A., de Wit, M., Pourghiasian, M., Piersma, S. R., Pham, T. V., Warmoes, M. O., Lavaei, M., Piso, C., Smit, F., Delis-van Diemen, P. M., van Turenhout, S. T., Terhaar sive Droste, J. S., Mulder, C. J. J., Blankenstein, M. A., Roobanus-Maandag, E. C., Smits, R., Fodde, R., van Hinsbergh, V. W. M., Meijer, G. A. & Jimenez, C. R., 2012, In : Clinical Cancer Research. 18, 9, p. 2613-2624

Research output: Contribution to journalArticleAcademicpeer-review

The Proteome of the Locus Ceruleus in Parkinson's Disease: Relevance to Pathogenesis

van Dijk, K. D., Berendse, H. W., Drukarch, B., Fratantoni, S. A., Pham, T. V., Piersma, S. R., Huisman, E., Breve, J. J. P., Groenewegen, H. J., Jimenez, C. R. & van de Berg, W. D. J., 2012, In : Brain Pathology. 22, 4, p. 485-498

Research output: Contribution to journalArticleAcademicpeer-review

2011

Comparative Proteomics of Colon Cancer Stem Cells and Differentiated Tumor Cells Identifies BIRC6 as a Potential Therapeutic Target

van Houdt, W., Emmink, B., Pham, T. V., Piersma, S., Verheem, A., de Vries, R., Fratantoni, S., Pronk, A., Clevers, H., Rinkes, B. I., Jimenez, C. R. & Kranenburg, O., 2011, In : Molecular and Cellular Proteomics. 10, 12, M111.011353.

Research output: Contribution to journalArticleAcademicpeer-review

Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry

Teunissen, C. E., Koel-Simmelink, M. J. A., Pham, T. V., Knol, J. C., Khalil, M., Trentini, A., Killestein, J., Nielsen, J. M., Vrenken, H., Popescu, V., Dijkstra, C. D. & Jimenez, C. R., 2011, In : Multiple Sclerosis. 17, 7, p. 838-850

Research output: Contribution to journalArticleAcademicpeer-review

2010

Comparative Protein Profiling Reveals Minichromosome Maintenance (MCM) Proteins As Novel Potential Tumor Markers for Meningiomas

Saydam, O., Senol, O., Visser, B. M., Pham, T. V., Piersma, S. R., Stemmer-Rachamimov, A. O., Würdinger, T., Peerdeman, S. M. & Jimenez, C. R., 2010, In : Journal of Proteome Research. 9, 1, p. 485-494

Research output: Contribution to journalArticleAcademicpeer-review

On the beta-binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics

Pham, T. V., Piersma, S. R., Warmoes, M. O. & Jimenez, C. R., 2010, In : Bioinformatics. 26, 3, p. 363-369

Research output: Contribution to journalArticleAcademicpeer-review