Thang V. Pham (PhD, University of Amsterdam)

A:
Cancer Center Amsterdam, room 1-46
VU University Medical Center
De Boelelaan 1117, 1081 HV Amsterdam
The Netherlands

E: t.pham@vumc.nl
T: +31-20-444-6998
F: +31-20-444-3844


I am a researcher at the OncoProteomics Laboratory, Cancer Center Amsterdam, VU University Medical Center, and a guest at the bioinformatics unit of the faculty of Sciences, VU University Amsterdam. I am currently working on pattern recognition and proteomics techniques for cancer biomarker discovery, especially for early detection.

Research projects

Previously, I was in the field of object recognition and matching, tracking of background and foreground in surveillance videos, and biometric identification.

I was a member of the MultimediaN project working in collaboration with the NFI (the Netherlands Forensic Institute) (2004-2006).

I coordinated the participation of the University of Amsterdam in the European Network of Excellence MUSCLE (2005-2006).

I was a member of the MIA project working on multimedia indexing for content-based video retrieval (funded by TNO-TPD, 1999-2003).



Students
  • Sanne Ruis (master thesis, boosting algorithms and object recognition)
  • Gosia Migut (bachelor thesis, interest point detection)
  • Anita de Ruiter (bachelor thesis, significance analysis of MALDI data, with Elena Marchiori)
  • Frank Neezen (master level internship, pathway analysis in cancer proteomics, with Connie Jimenez and Remond Fijneman)
  • Maikel Wisman, Mathilde den Exter and Simon van Leeuwen (a proteomics minor project)


Publications

Thesis

Learning spatial relations for object recognition
Pham Viet Thang
PhD thesis, University of Amsterdam, 2005.
ISBN 90-5776131-9

Advisor and promoter: Prof. dr. ir. Arnold W.M. Smeulders.



Book chapters

Statistical analysis of spectral count data generated in label-free tandem mass spectrometry-based proteomics
T.V. Pham, C.R. Jimenez
Neuroproteomics. Editor: Ka Wan Li, 2011.

Computational analysis of high throughput MALDI-TOF-MS based peptide profiling
T.V. Pham, C.R. Jimenez
Accepted.



In journals

Face detection by aggregated Bayesian network classifiers
T.V. Pham, M. Worring, A.W.M. Smeulders
Pattern Recognition Letters, 23(4):451-461, February 2002.
| BibTex | pdf |
Datasets (one text line per pattern): face-train.raw.gz face-test.raw.gz nonface-train.raw.gz nonface-test.raw.gz


Object recognition with uncertain geometry and uncertain part detection
T.V. Pham and A.W.M. Smeulders
Computer Vision and Image Understanding, 99(2):241-258, 2005.
| BibTex | pdf |

Sparse representation for coarse and fine object recognition
T.V. Pham and A.W.M. Smeulders
IEEE Transactions on Pattern Analysis and Machine Intelligence, 28(4):555-567, 2006.
| BibTex | pdf | some slides |


Learning spatial relations in object recognition
T.V. Pham and A.W.M. Smeulders
Pattern Recognition Letters, 27(14):1673-1684, October 2006.
| pdf |


Endogeneous peptide profiling of cerebrospinal fluid by MALDI-TOF mass spectrometry: Optimization of magnetic bead-based peptide capture and analysis of preanalytical variables
C.R. Jimenez, M. Koel-Simmelink, T.V. Pham, L. van der Voort, C.E. Teunissen
Proteomics - Clinical Applications, 1(11):1385-1392, 2007.

High-throughput and targeted in-depth mass spectrometry-based approaches for biofluid profiling and biomarker discovery
C.R. Jimenez, S.R. Piersma, T.V. Pham
Biomarkers in Medicine , 1(4):541-565, December 2007.

Quadratic boosting
T.V. Pham and A.W.M. Smeulders
Pattern Recognition, 41(1):331-341, January 2008.
| pdf |


Support vector machine approach to separate control and breast cancer serum samples
T.V. Pham, M.A. van de Wiel, C.R. Jimenez
Statistical Applications in Genetics and Molecular Biology, Vol. 7 : Iss. 2, Article 11, January 2008.
| pdf | software |


Prediction of outcome of non-small cell lung cancer patients treated with chemotherapy and bortezomib by time-course MALDI-TOF-MS serum peptide profiling
J. Voortman*, T.V. Pham*, J.C. Knol, G. Giaccone, C.R. Jimenez.
Proteome Science 2009, 7:34. (* equal contribution)
| pdf |


iTRAQ based proteomic profiling reveals increased metabolic activity and cellular crosstalk in angiogenic compared to invasive Glioblastoma phenotype
U. Rajcevic, K. Petersen, J.C. Knol, M. Loos, S. Bougnaud, O. Klychnikov, K.W. Li, T.V. Pham, J. Wang, H. Miletic, Z. Peng, R. Bjerkvig, C.R. Jimenez, S.P. Niclou
Molecular and Cellular Proteomics, 8(11):2595-2612, November 2009.

Comparative protein profiling reveals minichromosome maintenance (MCM) proteins as novel potential tumor markers for meningiomas
O. Saydam, O. Senol, T.B. Schaaij-Visser, T.V. Pham, S.R. Piersma, A.O. Stemmer-Rachamimov, T. Wurdinger, S.M. Peerdeman, C.R. Jimenez
Journal of Proteome Research, 9(1):485-494, January 2010.

Sub-nuclear proteomics in colorectal cancer: Identification of proteins enriched in the nuclear matrix fraction and regulation in adenoma to carcinoma progression
J. Albrethsen, J.C. Knol, S.R. Piersma, T.V. Pham, M. de Wit, S. Mongera, B. Carvalho, H.M. Verheul, R.J. Fijneman, G.A. Meijer, C.R. Jimenez
Molecular and Cellular Proteomics, 9:988-1005, 2010.


Workflow comparison for in-depth, quantitative secretome proteomics for cancer biomarker discovery: Method evaluation, differential analysis and verification in serum
S.R. Piersma, U. Fiedler, S. Span, A. Lingnau, T.V. Pham, S. Hoffmann, M.H.G. Kubbutat, C.R. Jimenez
Journal of Proteome Research, 9:1913-1922, 2010.

On the beta binomial model for analysis of spectral count data in label-free tandem mass spectrometry-based proteomics
T.V. Pham, S.R. Piersma, M. Warmoes, C.R. Jimenez
Bioinformatics, 26(3):363-369, 2010.
| journal link | software |


Comparative proteomics of colon cancer stem cells and differentiated tumor cells identifies BIRC6 as a potential therapeutic target
W.J. van Houdt, B.L. Emmink, T.V. Pham, S.R. Piersma, A. Verheem, R.G. Vries, S.A. Fratantoni, A. Pronk, H. Clevers, I.H. Borel Rinkes, C.R. Jimenez, O. Kranenburg
Molecular and Cellular Proteomics, 10(12):M111.011353, 2011.


Identification of biomarkers for diagnosis and progression of MS by MALDI-TOF mass spectrometry
C.E. Teunissen, M.J. Koel-Simmelink, T.V. Pham, J.C. Knol, M. Khalil, A. Trentini, J. Killestein, J. Nielsen, H. Vrenken, V. Popescu, C.D. Dijkstra, C.R. Jimenez
Multiple Sclerosis Journal, 17(7):838-850, 2011.


The proteome of the locus ceruleus in Parkinson's disease: relevance to pathogenesis
K.D. van Dijk, H.W. Berendse, B. Drukarch, S.A. Fratantoni, T.V. Pham, S.R. Piersma, E. Huisman, J.J. Breve, H.J. Groenewegen, C.R. Jimenez, W.D. van de Berg
Brain Pathology, 22(4):485-98, 2012.


Proteomics of mouse BRCA1-deficient mammary tumors identifies DNA repair proteins with diagnostic and prognostic value in human breast cancer
M. Warmoes, J.E. Jaspers, T.V. Pham, S.R. Piersma, G. Oudgenoeg, M.P. Massink, Q. Waisfisz, S. Rottenberg, E. Boven, J. Jonkers, C.R. Jimenez
Molecular and Cellular Proteomics, 11(7):M111.013334, 2012.

Best poster prize in "EMBO Cancer Proteomics 2011: Systems Biology, Developmental Models & Data Integration", Dublin, Ireland.

Highly rated abstract at the 2010 American Association for Cancer Research meeting in Washington DC, USA.



Proximal fluid proteome profiling of mouse colon tumors reveals biomarkers for early diagnosis of human colorectal cancer
R.J. Fijneman, M. de Wit M, M. Pourghiasian, S.R. Piersma, T.V. Pham, M.O. Warmoes, M. Lavaei, C. Piso, F. Smit, P.M. Delis-van Diemen, S.T. van Turenhout, J.S. Terhaar Sive Droste, C.J. Mulder, M.A. Blankenstein, E.C. Robanus-Maandag, R. Smits, R. Fodde, V.W. van Hinsbergh, G.A. Meijer, C.R. Jimenez
Clinical Cancer Research, 18(9):2613-24, 2012.


Label-free mass spectrometry-based proteomics for biomarker discovery and validation
T.V. Pham, S.R. Piersma, G. Oudgenoeg, C.R. Jimenez
Expert Review of Molecular Diagnostics, 12(4):343-359, 2012.



An accurate paired sample test for count data
T.V. Pham, C.R. Jimenez
Bioinformatics, 28(18):i596-i602, 2012.
| journal link | software |



In conferences and workshops

Face detection by aggregated Bayesian network classifiers
T.V. Pham, M. Worring, A.W.M. Smeulders
In P. Perner, editor, Machine Learning and Data Mining in Pattern Recognition, volume 2123 of Lecture Notes in Artificial Intelligence , pages 249-262. Springer, July 2001.
| BibTex | ps | pdf |

Statistical strategy for object class recognition using part detectors
T.V. Pham, A.W.M. Smeulders
In A. Leonardis, H. Bischof (eds.) SLCV04. Statistical Learning in Computer Vision, ECCV 2004 workshop, Prague, Czech Republic, pages 33-48. May 2004.
>> Also published in Proceedings of the ASCI conference 2002 , pages 143-150, 2002. Best Poster Award.
| ps | ps.gz | pdf |

AdaBoost learning of shape and color features for object recognition
T.V. Pham, A.W.M. Smeulders, S. Ruis
In ICML 2005 Workshop on Machine Learning Techniques for Processing Multimedia Content, Bonn, Germany.
| pdf |



Efficient projection pursuit density estimation for background subtraction
T.V. Pham and A.W.M. Smeulders
In Proceedings of the Sixth IEEE International Workshop on Visual Surveillance, 2006, Graz, Austria.
| pdf |



Metric tree partitioning and Taylor approximation for fast support vector classification
T.V. Pham and A.W.M. Smeulders
In Proceedings of the International Conference on Pattern Recognition, 2006, Hong Kong.
| pdf |



A multi-camera visual surveillance system for tracking of reoccurrences of people
T.V. Pham, M. Worring and A.W.M. Smeulders
In Proceedings of the first ACM/IEEE International Conference on Distributed Smart Cameras (ICDSC-07), 2007, Vienna, Austria.
| pdf |



OplAnalyzer: a toolbox for MALDI-TOF mass spectrometry data analysis
T.V. Pham and C.R. Jimenez
In Proceedings of the International Conference on Mass-Data Analysis of Images and Signals in Medicine, Biotechnology, Chemistry, and Food Industry MDA, 2008, Germany.
| pdf |



Refereed research abstracts

Time-course MALDI-TOF-MS serum peptide profiling of non-small cell lung cancer patients treated with bortezomib, cisplatin and gemcitabine
J. Voortman*, T.V. Pham*, J.C. Knol, G. Giaccone, and C.R. Jimenez.
In Proceedings of American Society of Clinical Oncology (ASCO) 2008 Annual Meeting, Chicago, USA. Oral presentation . (* equal contribution)

CSF proteomics to identify candidate biomarkers for multiple sclerosis
C. Teunissen, M. Koel-Simmelink, T.V. Pham, L. van der Voort, and C.R. Jimenez
In Proceedings of the 7th Annual World Congress HUPO 2008, Amsterdam, the Netherlands.

Addressing the angiogenic switch by studying tumor-host interactions in a model of glioma
U. Rajcevic, J.C. Knol, M. Loos, K. Li, O. Klychnikov, R. Bjerkvig, T.V. Pham, K. Petersen, S.P. Niclou, and C.R. Jimenez
In Proceedings of the 7th Annual World Congress HUPO 2008, Amsterdam, the Netherlands.

Intensity-based differential analysis of complex protein mixtures using two-dimensional (2DLC and GELC) datasets coupled to MS/MS
T.V. Pham, S.R. Piersma, and C.R. Jimenez
In Proceedings of the 7th Annual World Congress HUPO 2008, Amsterdam, the Netherlands.

Label-free multi-dimensional nanoLC-MS/MS-based proteomics of CSF for biomarker discovery in mild cognitive impairment and Alzheimer's disease
S. Fratantoni, S.R. Piersma, T.V. Pham, C.E. Teunissen, and C.R. Jimenez
In Proceedings of Proteomics and Metabolomics Biomarker Discovery in CSF, 2009, Rotterdam, the Netherlands.

On the beta binomial model for spectral count data in label-free tandem mass spectrometry-based proteomics
T.V. Pham, S.R. Piersma, M. Warmoes, and C.R. Jimenez
In Proceedings of the 17th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB) and the 8th European Conference on Computational Biology (ECCB), 2009, Stockholm, Sweden.

Enrichment of tumorigenic stem-like cells in biopsy spheroids from colorectal cancer
U. Rajcevic, S.R. Piersma, S. Bougnaud, T.V. Pham, P. Enger, R. Bjerkvig, C.R. Jimenez, and S.P. Niclou
In Proceedings of the 8th Annual World Congress HUPO 2009, Toronto, Canada. Oral presentation .

Proximal fluid proteome profiling of human colorectal cancer tissue reveals candidate biomarkers for CRC screening
R.J.A. Fijneman, H. Kant, M. de Wit, S.R. Piersma, T.V. Pham, M. Warmoes, S. Mongera, H.M.W. Verheul, G.A. Meijer, C.R. Jimenez
In Proceedings of the American Association for Cancer Research (AACR) 101st Annual Meeting 2010, Washington DC, USA.

Quantitative proteomics of genetic mouse models for human breast cancer: Identification of BRCA1-associated proteins involved in DNA-repair
M.O. Warmoes, J. Jaspers, M.P.G. Massink, T.V. Pham, S.R. Piersma, E. Boven, H. Meijer-Heijboer, Q. Waisfisz, J. Jonkers, C.R. Jimenez
In Proceedings of the American Association for Cancer Research (AACR) 101st Annual Meeting 2010, Washington DC, USA.

Progress in CSF biomarker discovery for mild cognitive impairment and Alzheimer's disease by label-free quantitative proteomics
T.V. Pham, S. Fratantoni, S.R. Piersma, C.R. Jimenez
In Proceedings of the 9th Annual World Congress HUPO 2010, Sydney, Australia. Oral presentation

Strategies for analyzing spectral count data in label-free tandem mass spectrometry-based proteomics
T.V. Pham, C.R. Jimenez
In Proceedings of the 9th Annual World Congress HUPO 2010, Sydney, Australia.

Secretome proteomics to identify indicators for lung cancer treatment response prediction and monitoring
T.B. Schaaij-Visser, N. Proost, R. Nagel, S.R. Piersma, T.V. Pham, R.H. Brakenhoff, A. Berns, C.R. Jimenez
In Proceedings of the American Association for Cancer Research (AACR) 102nd Annual Meeting 2011, Orlando, USA.

Label-free mass spectrometry-based proteomics for biomarker discovery and validation in tissues and biofluids
C.R. Jimenez, R.J.A. Fijneman, M. de Wit, L. Bosch, S.R. Piersma, T.V. Pham, B. Carvalho, S. Mongera, HMW Verheul, G.A. Meijer
European Journal of Cancer, vol. 47, Suppl. 1, 2011.

Stool proteomics reveals new candidate biomarkers for colorectal cancer screening
L.J. Bosch, M. de Wit, G. Oudgenoeg, A.C. Hiemstra, S. Mongera, S.R. Piersma, T.V. Pham, N.C. van Grieken, J.S.T. Droste, F.A. Oort, S.T. van Turenhout, I. Ben Larbi, C.J. Mulder, B. Carvalho, C.R. Jimenez, R.J. Fijneman, G.A. Meijer
In Proceedings of the American Association for Cancer Research (AACR) 103rd Annual Meeting 2012, Chicago, USA.


Technical reports

Face detection methods: a critical evaluation
T.V. Pham and M. Worring
In ISIS Technical Report Series, University of Amsterdam, vol. 11, 2000.
| ps | pdf |




-- Updated 2012.