Thang V Pham

Department of Clinical and Experimental Cardiology, Amsterdam Cardiovascular Sciences, Amsterdam UMC, University of Amsterdam, Heart Centre, Meibergdreef 9, 1105 AZ, Amsterdam, The Netherlands.

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February 2021

Loss of FLCN-FNIP1/2 induces a non-canonical interferon response in human renal tubular epithelial cells.

Elife 2021 Jan 18;10. Epub 2021 Jan 18.

Amsterdam UMC, location VUmc, Vrije Universiteit Amsterdam, Clinical Genetics, Cancer Center Amsterdam, Amsterdam, Netherlands.

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January 2021

Proteomic and Functional Studies Reveal Detyrosinated Tubulin as Treatment Target in Sarcomere Mutation-Induced Hypertrophic Cardiomyopathy.

Authors:

Maike Schuldt Jiayi Pei Magdalena Harakalova Larissa M Dorsch Saskia Schlossarek Michal Mokry Jaco C Knol Thang V Pham Tim Schelfhorst Sander R Piersma Cris Dos Remedios Michiel Dalinghaus Michelle Michels Folkert W Asselbergs Marie-Jo Moutin Lucie Carrier Connie R Jimenez Jolanda van der Velden Diederik W D Kuster

Circ Heart Fail 2021 Jan 12;14(1):e007022. Epub 2021 Jan 12.

Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Physiology, Amsterdam Cardiovascular Sciences, The Netherlands (M.S., L.M.D., J.v.d.V., D.W.D.K.).

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January 2021

Omics Analysis of Educated Platelets in Cancer and Benign Disease of the Pancreas.

Authors:

Giulia Mantini Laura L Meijer Ilias Glogovitis Sjors G J G In 't Veld Rosita Paleckyte Mjriam Capula Tessa Y S Le Large Luca Morelli Thang V Pham Sander R Piersma Adam E Frampton Connie R Jimenez Geert Kazemier Danijela Koppers-Lalic Thomas Wurdinger Elisa Giovannetti

Cancers (Basel) 2020 Dec 29;13(1). Epub 2020 Dec 29.

Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center (VUmc), 1081 HV Amsterdam, The Netherlands.

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December 2020

Quantitative analysis of CDX2 protein expression improves its clinical utility as a prognostic biomarker in stage II and III colon cancer.

Authors:

Sjoerd H den Uil Meike de Wit Robbert J C Slebos Pien M Delis-van Diemen Joyce Sanders Sander R Piersma Thang V Pham Veerle M H Coupé Herman Bril Hein B A C Stockmann Connie R Jimenez Gerrit A Meijer Remond J A Fijneman

Eur J Cancer 2021 Feb 17;144:91-100. Epub 2020 Dec 17.

Department of Pathology, The Netherlands Cancer Institute, Plesmanlaan 121, 1066 CX, Amsterdam, the Netherlands. Electronic address:

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February 2021

Feasibility of phosphoproteomics to uncover oncogenic signalling in secreted extracellular vesicles using glioblastoma-EGFRVIII cells as a model.

Authors:

Irene V Bijnsdorp Tim Schelfhorst Mark Luinenburg Frank Rolfs Sander R Piersma Richard R de Haas Thang V Pham Connie R Jimenez

J Proteomics 2021 02 8;232:104076. Epub 2020 Dec 8.

Amsterdam UMC, Vrije Universiteit Amsterdam, OncoProteomics Laboratory, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands; Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.

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February 2021

Computational Analysis of Phosphoproteomics Data in Multi-Omics Cancer Studies.

Authors:

Giulia Mantini Thang V Pham Sander R Piersma Connie R Jimenez

Proteomics 2021 Feb 8;21(3-4):e1900312. Epub 2020 Oct 8.

Department of Medical Oncology, OncoProteomics Laboratory, CCA 1-60, Amsterdam UMC VUmc-location, De Boelelaan 1117, Amsterdam, 1081 HV, The Netherlands.

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February 2021

DPHL: A DIA Pan-human Protein Mass Spectrometry Library for Robust Biomarker Discovery.

Authors:

Tiansheng Zhu Yi Zhu Yue Xuan Huanhuan Gao Xue Cai Sander R Piersma Thang V Pham Tim Schelfhorst Richard R G D Haas Irene V Bijnsdorp Rui Sun Liang Yue Guan Ruan Qiushi Zhang Mo Hu Yue Zhou Winan J Van Houdt Tessa Y S Le Large Jacqueline Cloos Anna Wojtuszkiewicz Danijela Koppers-Lalic Franziska Böttger Chantal Scheepbouwer Ruud H Brakenhoff Geert J L H van Leenders Jan N M Ijzermans John W M Martens Renske D M Steenbergen Nicole C Grieken Sathiyamoorthy Selvarajan Sangeeta Mantoo Sze S Lee Serene J Y Yeow Syed M F Alkaff Nan Xiang Yaoting Sun Xiao Yi Shaozheng Dai Wei Liu Tian Lu Zhicheng Wu Xiao Liang Man Wang Yingkuan Shao Xi Zheng Kailun Xu Qin Yang Yifan Meng Cong Lu Jiang Zhu Jin'e Zheng Bo Wang Sai Lou Yibei Dai Chao Xu Chenhuan Yu Huazhong Ying Tony K Lim Jianmin Wu Xiaofei Gao Zhongzhi Luan Xiaodong Teng Peng Wu Shi'ang Huang Zhihua Tao Narayanan G Iyer Shuigeng Zhou Wenguang Shao Henry Lam Ding Ma Jiafu Ji Oi L Kon Shu Zheng Ruedi Aebersold Connie R Jimenez Tiannan Guo

Genomics Proteomics Bioinformatics 2020 Apr 12;18(2):104-119. Epub 2020 Aug 12.

Zhejiang Provincial Laboratory of Life Sciences and Biomedicine, Westlake University, Hangzhou 310024, China; Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou 310024, China; Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou 310024, China. Electronic address:

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April 2020

Microdissected pancreatic cancer proteomes reveal tumor heterogeneity and therapeutic targets.

Authors:

Tessa Ys Le Large Giulia Mantini Laura L Meijer Thang V Pham Niccola Funel Nicole Ct van Grieken Bart Kok Jaco Knol Hanneke Wm van Laarhoven Sander R Piersma Connie R Jimenez G Kazemier Elisa Giovannetti Maarten F Bijlsma

JCI Insight 2020 08 6;5(15). Epub 2020 Aug 6.

Laboratory for Experimental Oncology and Radiobiology, Amsterdam University Medical Centers, University of Amsterdam, Cancer Center Amsterdam, Amsterdam, Netherlands.

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August 2020

Identification of novel cerebrospinal fluid biomarker candidates for dementia with Lewy bodies: a proteomic approach.

Mol Neurodegener 2020 06 18;15(1):36. Epub 2020 Jun 18.

Neurochemistry Laboratory and Biobank, Department of Clinical Chemistry, Amsterdam Neuroscience, Vrije Universiteit Amsterdam, Amsterdam UMC, Amsterdam, The Netherlands.

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June 2020

Phosphotyrosine-based Phosphoproteomics for Target Identification and Drug Response Prediction in AML Cell Lines.

Authors:

Carolien van Alphen Jacqueline Cloos Robin Beekhof David G J Cucchi Sander R Piersma Jaco C Knol Alex A Henneman Thang V Pham Johan van Meerloo Gert J Ossenkoppele Henk M W Verheul Jeroen J W M Janssen Connie R Jimenez

Mol Cell Proteomics 2020 05 26;19(5):884-899. Epub 2020 Feb 26.

Amsterdam UMC, Vrije Universiteit Amsterdam, Medical Oncology, Cancer Center; Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands

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May 2020

Kinase Inhibitor Treatment of Patients with Advanced Cancer Results in High Tumor Drug Concentrations and in Specific Alterations of the Tumor Phosphoproteome.

Authors:

Mariette Labots Thang V Pham Richard J Honeywell Jaco C Knol Robin Beekhof Richard de Goeij-de Haas Henk Dekker Maarten Neerincx Sander R Piersma Johannes C van der Mijn Donald L van der Peet Martijn R Meijerink Godefridus J Peters Nicole C T van Grieken Connie R Jiménez Henk M W Verheul

Cancers (Basel) 2020 Feb 1;12(2). Epub 2020 Feb 1.

Department of Medical Oncology, RadboudUMC, Radboud University, Geert Grooteplein Zuid 8, 6525 GA Nijmegen, The Netherlands.

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February 2020

Combined Expression of Plasma Thrombospondin-2 and CA19-9 for Diagnosis of Pancreatic Cancer and Distal Cholangiocarcinoma: A Proteome Approach.

Authors:

Tessa Y S Le Large Laura L Meijer Rosita Paleckyte Lenka N C Boyd Bart Kok Thomas Wurdinger Tim Schelfhorst Sander R Piersma Thang V Pham Nicole C T van Grieken Barbara M Zonderhuis Freek Daams Hanneke W M van Laarhoven Maarten F Bijlsma Connie R Jimenez Elisa Giovannetti Geert Kazemier

Oncologist 2020 04 14;25(4):e634-e643. Epub 2020 Jan 14.

Department of Surgery, Cancer Center Amsterdam, Amsterdam University Medical Center, VU University, Amsterdam, The Netherlands.

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April 2020

iq: an R package to estimate relative protein abundances from ion quantification in DIA-MS-based proteomics.

Authors:

Thang V Pham Alex A Henneman Connie R Jimenez

Bioinformatics 2020 04;36(8):2611-2613

OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam 1081 HV, The Netherlands.

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April 2020

Proteins in stool as biomarkers for non-invasive detection of colorectal adenomas with high risk of progression.

Authors:

Malgorzata A Komor Linda Jw Bosch Veerle Mh Coupé Christian Rausch Thang V Pham Sander R Piersma Sandra Mongera Chris Jj Mulder Evelien Dekker Ernst J Kuipers Mark A van de Wiel Beatriz Carvalho Remond Ja Fijneman Connie R Jimenez Gerrit A Meijer Meike de Wit

J Pathol 2020 03 13;250(3):288-298. Epub 2020 Jan 13.

Department of Pathology, The Netherlands Cancer Institute, Amsterdam, The Netherlands.

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March 2020

Proteomic Analysis of miR-195 and miR-497 Replacement Reveals Potential Candidates that Increase Sensitivity to Oxaliplatin in MSI/P53wt Colorectal Cancer Cells.

Authors:

Dennis Poel Lenka N C Boyd Robin Beekhof Tim Schelfhorst Thang V Pham Sander R Piersma Jaco C Knol Connie R Jimenez Henk M W Verheul Tineke E Buffart

Cells 2019 09 19;8(9). Epub 2019 Sep 19.

Department of Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, VU University Medical Center, 1081HV Amsterdam, The Netherlands.

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September 2019

Proteomic analysis of gemcitabine-resistant pancreatic cancer cells reveals that microtubule-associated protein 2 upregulation associates with taxane treatment.

Authors:

Tessa Ya Sung Le Large Btissame El Hassouni Niccola Funel Bart Kok Sander R Piersma Thang V Pham Kenneth P Olive Geert Kazemier Hanneke W M van Laarhoven Connie R Jimenez Maarten F Bijlsma Elisa Giovannetti

Ther Adv Med Oncol 2019 10;11:1758835919841233. Epub 2019 May 10.

Medical Oncology, Amsterdam UMC, Vrije Universiteit Amsterdam, Cancer Center Amsterdam, De Boelelaan 1117, Amsterdam, Netherlands.

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May 2019

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

Authors:

Franziska Böttger Ekaterina A Semenova Ji-Ying Song Giustina Ferone Jan van der Vliet Miranda Cozijnsen Rajith Bhaskaran Lorenzo Bombardelli Sander R Piersma Thang V Pham Connie R Jimenez Anton Berns

Cell Rep 2019 06;27(11):3345-3358.e4

Oncode Institute, Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands; Division of Molecular Genetics, The Netherlands Cancer Institute, 1066 CX Amsterdam, the Netherlands. Electronic address:

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June 2019

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

Authors:

Robin Beekhof Carolien van Alphen Alex A Henneman Jaco C Knol Thang V Pham Frank Rolfs Mariette Labots Evan Henneberry Tessa Ys Le Large Richard R de Haas Sander R Piersma Valentina Vurchio Andrea Bertotti Livio Trusolino Henk Mw Verheul Connie R Jimenez

Mol Syst Biol 2019 May 24;15(5):e8981. Epub 2019 May 24.

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May 2019

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

Authors:

Robin Beekhof Carolien van Alphen Alex A Henneman Jaco C Knol Thang V Pham Frank Rolfs Mariette Labots Evan Henneberry Tessa Ys Le Large Richard R de Haas Sander R Piersma Valentina Vurchio Andrea Bertotti Livio Trusolino Henk Mw Verheul Connie R Jimenez

Mol Syst Biol 2019 04 12;15(4):e8250. Epub 2019 Apr 12.

Medical Oncology, Cancer Center Amsterdam, Amsterdam UMC, Vrije Universiteit Amsterdam, Amsterdam, The Netherlands

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April 2019

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

Authors:

Franziska Böttger Tieneke B Schaaij-Visser Inge de Reus Sander R Piersma Thang V Pham Remco Nagel Ruud H Brakenhoff Erik Thunnissen Egbert F Smit Connie R Jimenez

J Proteomics 2019 03 30;196:106-119. Epub 2019 Jan 30.

Amsterdam UMC, Vrije Universiteit Amsterdam, Department of Medical Oncology, Cancer Center Amsterdam, 1081 HV Amsterdam, the Netherlands. Electronic address:

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March 2019

Human Testis Phosphoproteome Reveals Kinases as Potential Targets in Spermatogenesis and Testicular Cancer.

Authors:

Judit Castillo Jaco C Knol Cindy M Korver Sander R Piersma Thang V Pham Richard R de Goeij-de Haas Ans M M van Pelt Connie R Jimenez Bastiaan J H Jansen

Mol Cell Proteomics 2019 03 25;18(Suppl 1):S132-S144. Epub 2019 Jan 25.

From the ‡Lead Pharma BV, Pivot Park, Kloosterstraat 9, 5349 AB Oss, The Netherlands;

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March 2019

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

Authors:

Marijn F Stokman Irene V Bijnsdorp Tim Schelfhorst Thang V Pham Sander R Piersma Jaco C Knol Rachel H Giles Ernie M H F Bongers Nine V A M Knoers Marc R Lilien Connie R Jiménez Kirsten Y Renkema

J Proteomics 2019 02 30;192:27-36. Epub 2018 Jul 30.

Department of Genetics, Center for Molecular Medicine, University Medical Center Utrecht, Utrecht, the Netherlands. Electronic address:

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February 2019

Selection of Protein Kinase Inhibitors Based on Tumor Tissue Kinase Activity Profiles in Patients with Refractory Solid Malignancies: An Interventional Molecular Profiling Study.

Authors:

Mariette Labots Johannes C Van der Mijn Henk Dekker Rita Ruijter Thang V Pham Hans J Van der Vliet Jacobus J M Van der Hoeven Gerrit A Meijer Henk M W Verheul

Oncologist 2018 10 17;23(10):1135-e118. Epub 2018 Jul 17.

Department of Medical Oncology, Cancer Center Amsterdam, VU University Medical Center, Amsterdam, The Netherlands

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October 2018

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

Authors:

Sander C Steenbeek Thang V Pham Joep de Ligt Anoek Zomer Jaco C Knol Sander R Piersma Tim Schelfhorst Rick Huisjes Raymond M Schiffelers Edwin Cuppen Connie R Jimenez Jacco van Rheenen

EMBO J 2018 08 14;37(15). Epub 2018 Jun 14.

Molecular Pathology, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands

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August 2018

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

Authors:

Siamack Sabrkhany Marijke J E Kuijpers Jaco C Knol Steven W M Olde Damink Anne-Marie C Dingemans Henk M Verheul Sander R Piersma Thang V Pham Arjan W Griffioen Mirjam G A Oude Egbrink Connie R Jimenez

J Proteomics 2018 04 10;177:65-74. Epub 2018 Feb 10.

OncoProteomics Laboratory, Department of Medical Oncology, Cancer Center Amsterdam, VU Medical Center, Amsterdam, The Netherlands. Electronic address:

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April 2018

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

Ann Intern Med 2017 Dec 21;167(12):855-866. Epub 2017 Nov 21.

From Netherlands Cancer Institute, Amsterdam; VU University Medical Center, Amsterdam; MDxHealth, Herstal, and Ghent University, Ghent, Belgium; and Kennemer Gasthuis, Haarlem, the Netherlands.

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December 2017

Identification of Differentially Expressed Splice Variants by the Proteogenomic Pipeline Splicify.

Authors:

Malgorzata A Komor Thang V Pham Annemieke C Hiemstra Sander R Piersma Anne S Bolijn Tim Schelfhorst Pien M Delis-van Diemen Marianne Tijssen Robert P Sebra Meredith Ashby Gerrit A Meijer Connie R Jimenez Remond J A Fijneman

Mol Cell Proteomics 2017 10 26;16(10):1850-1863. Epub 2017 Jul 26.

From the ‡Translational Gastrointestinal Oncology, Department of Pathology, Netherlands Cancer Institute, Amsterdam, the Netherlands;

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October 2017

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