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RESEARCH FOCUS
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Our research group utilizes a variety of genomic technologies including DNA microarrays, high-throughput sequencing, and bioinformatics to understand the genetic and molecular basis of host-pathogen interactions. Our disease focus is tropical infectious disease, as there are a number of tropical pathogens which cause serious disease in the region but for which little is known about their mechanism of virulence. We have been investigating the Gram negative saprophyte Burkholderia pseudomallei, the causative agent of meliodosis, an often fatal disease of humans and animals. The B. pseudomallei genome, at 7.2 Mb, is also one of the most complex microbial genomes sequenced to date.
We have found that B. pseudomallei is pathogenic to C. elegans, and that the mechanism of virulence is most likely conserved between nematodes and higher vertebrates. Using this assay, we have identified a number of novel virulence factors in the pathogen, and we are currently investigating if certain genetic or environmental factors can predispose a host towards an infection. We are also using whole-genome B. pseudomallei microarrays to study patterns of genomic variation in the natural environment.
We have also engaged in an intensive research program on cancer of the stomach, associated with the Duke-NUS Graduate Medical School (www.duke-nus.edu.sg)
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EDUCATION
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| 1992-2000 | Stanford University School of Medicine, MD PhD | | 1988-1992 | Harvard University, B.A. | | 1986-1987 | National Junior College, Singapore |
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PROFESSIONAL APPOINTMENTS
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| 2004 - Present | Group Leader, Genome Institute of Singapore |
| 2006- Present | Associate Professor, Duke-NUS Graduate Medical School Singapore |
| 2009 – Present | Director, Duke-NUS Genome Biology Facility |
| 2009 – Present | Research Associate Professor, Institute of Genome Sciences and Policy, Duke University |
| 2008 - Present | Program Leader, Genomic Oncology, Cancer Science Institute of Singapore (NUS) |
| 2006 - Present | Principal Investigator (Adjunct), National Cancer Centre, Singapore |
| 2003 - Present | Associate Professor (Adjunct), Dept of Physiology, National University of Singapore |
| 2004 - Present | Senior Research Fellow (Adjunct), Defence Medical and Environmental Research Institute, Defence Science Organization (DMERI@DSO), Singapore |
| 2005 - 2008 | Associate Professor (Adjunct), School of Computer Science, Nanyang Technological University, Singapore |
| 2002 – 2007 | Chief Scientific Officer, Agenica Research Pte Ltd (Joint Venture with NCCS, Mitsui Corp, and Shimadzu Corp) |
| 2002 - 2006 | Principal Investigator, National Cancer Centre, Singapore |
| 2003 - 2004 | Senior Research Fellow, Defence Medical and Environmental Research Institute (DMERI@DSO), Singapore |
| 2004 | Visiting Scientist, Broad Institute, Cambridge, MA |
| 2000 - 2003 | Research Scientist, Defence Medical Research Institute, Singapore |
| 2000 - 2002 | Senior Scientist, National Cancer Centre, Singapore |
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HONORS AND AWARDS
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| 1987 | President's Scholarship, Singapore |
| 1992 | Graduated summa cum laude (Highest Honors), Harvard University |
| 1992 | Phi Beta Kappa Society |
| 1992 | Fairchild Fellowship (for MSTP training), Stanford University |
| 1998 | Charles Yanofsky Award for Most Outstanding Graduate Thesis, Stanford University |
| 2001 | Young Scientist Award (Singapore National Academy of Sciences) |
| 2001 | NCC Academic Award for Best Intellectual Property Filing |
| 2002 | NCC Academic Award for Best New Research Programme |
| 2002 | Singapore Youth Award (National Youth Council) |
| 2002 | Best Business Plan and Executive Summary (Systome Therapeutics), Startup@Singapore National Techno-Venture Competition |
| 2004 | Singhealth Investigator Excellence Award |
| 2005 | AACR-ITO EN Scholar in Training Award, AACR 96th Annual Meeting |
| 2008 | Singapore Youth Award, Medal of Commendation (National Youth Council) |
| 2010 | AACR-Bristol-Myers Squibb Oncology Scholar-in-Training Award (for graduate student Iain Tan) |
| 2010 | ASCO Young Investigator Award (for graduate student Iain Tan) |
| 1987 | 1987 Loke Cheng Kim Scholarship, Singapore |
| 1988 | 1988 Detur Prize for Academic Excellence, Harvard University |
| 1991 | Signet Society, Harvard University |
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COMMITTEE AND ADVISORY BOARD
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| 2003 | Member, Pro-term Committee, Duke-NUS Graduate Medical School |
| 2003 | Chair, Technology Scan Panel on Engineering Science in Medicine, Agency for Science, Technology and Research |
| 2004 | Chair, Scientific Committee, 4th World Melioidosis Congress |
| 2005-2007 | Chair, Life Sciences Virtual Grid Community, National Grid Office |
| 2005 | Working Committee, Molecular Pathology of Breast Cancer, International Agency for Research on Cancer (IARC), Lyon, France |
| 2006 | Member, International Advisory Committee, 5th World Melioidosis Congress |
| 2007 | Program Committee, AACR Centennial Conference |
| 2007 | Course Co-director, Molecules and Cells, Duke-NUS Graduate Medical School (Inaugural Class) |
| 2008 | Member, International Scientific Committee, International Society for Cellular Oncology |
| 2009 – Present | Member, Scientific Advisory Board, Eskitis Institute for Cell and Molecular Therapies, Griffith University, Australia |
| 2004 - Present | Member, Local Review Panel, Translational Research, Biomedical Research Council |
| 2007 - Present | Member, Bioethics Advisory Committee (National Committee) |
| 2007 - Present | Member, Local Review Panel, National Medical Research Council, Singapore |
| 2007 - Present | Member, Specialists Accreditation Board, Translational Medicine |
| 2008 – Present | Faculty Member, Singapore – MIT Computational and Systems Biology (CSB) Programme, NUS |
| 2003 - 2004 | Editorial Board Member, Cancer Reviews : Asia Pacific (World Scientific Press) |
| 2007 – Present | Associate Editor, BMC Medical Genomics (Biomed Central) |
| 2009- Present | Editorial Board Member, PLoS One |
| 2007 | Organizing Committee, AACR Centennial Conference on Translational Cancer Research, Singapore |
| 2009 | Session Chair, New Concepts in Organ Site Research (Gastric Cancer), 2010 American Association for Cancer Research Annual Meeting, Washington DC |
| 2009 | Member, International Scientific Committee, International Society for Cellular Oncology Meeting, Dresden, Germany |
| 2010 | Member, Gastric Cancer Advisory Committee, Bristol-Myers Squibb |
| 2004 - 2009 | Editorial Board Member, SGH Proceedings, Singapore |
| 2005 - 2009 | Associate Editor, Cancer Research (American Association for Cancer Research) |
| 2008 | Program Committee, AACR Centennial Conference, Singapore |
| 2010 | Member, Clinical Advisory Board, Siena Biotech |
| 2010 - present | Editoial Board Member, Cellular Oncology |
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EXTERNAL GRANT
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Sep 2009 - Sep 2010 |
Subaward from NUS as part of a research collaboration by
Bayer Schering Pharma (S$200,000)
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Oct 2007 - Sep 2012 |
TCR Flagship Programme “The Singapore gastric cancer consortium-improving outcomes for our patients”, PI (NCC Module) by
National Medical Research Council ($4,997,500)
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Oct 2005 – Sep 2008 |
Systematic Identification of Candidate Cancer and Biomarker Genes by High Resolution Mapping of Genomic Aberrations Using a Microarray Platform by
Singapore Cancer Syndicate, A-STAR ($850,062)
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Oct 2005 – Mar 2008 |
A Personalised and Adaptive Lliterature Curation System for the Biomedical Sciences by
National Grid Office ($280,400)
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July 2003 – June 2007 |
Regulation and Function of Lin-31, a gene important in RAS/MAPK signaling specificity during C. elegans vulval induction by
Biomedical Research Council ($800,000)
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Feb 2006 - Jan 2011 |
Systematic Identification of Oncogenic Cellular Pathways and Processes in Gastric Cancer for patient stratification and personalized therapy by
Biomedical Research Council, A-star ($1,890,000)
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Apr 2006 - Mar 2009 |
Establishment of the National Xenograft Therapeutic Program by
Singapore Cancer Syndicate, A-star ($920,000)
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Apr 2006 - Mar 2008 |
Functional characterization of PLA2G2A in gastric cancer by
Singhealth ($200,000)
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Apr 2006 - Jun 2010 |
Establishment of the National Xenograft Therapeutic Program by
Singapore Cancer Syndicate, A-star ($920,000)
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Apr 2003 – Mar 2006 |
Identification of Novel Cancer Subtypes and Genetic Identifiers Using Genome-Level Targeted Technologies by
, Biomedical Research Council ($1,550,800)
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PATENTS
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2008 |
EP1668151B1 :
Materials and Methods Related to Breast Cancer Dia (Granted)
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2008 |
160726 :
Materials and Methods Related to Breast Cancer Dia (Granted)
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2006 |
200404696-7 :
Materials and Methods for Cancer Diagnosis (Granted)
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SELECTED PUBLICATIONS
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1. Nandi T, Ong C, Singh AP, Boddey J, Atkins T, Sarkar-Tyson M, Essex-Lopresti AE, Chua HH, Pearson T, Kreisberg JF, Nilsson C, Ariyaratne P, Ronning C, Losada L, Ruan Y, Sung WK, Woods D, Titball RW, Beacham I, Peak I, Keim P, Nierman WC, Tan P "A genomic survey of positive selection in Burkholderia pseudomallei provides insights into the evolution of accidental virulence." PLoS Pathog 2010 ; 6(4) : e1000845 Epub 2010 Apr 1
Abstract
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2. Bernice Meng Qi Sim, Narisara Chantratita, Vanaporn Wuthiekanun, Janjira Thaipadungpanit, Sarinna Tumupa, Chi Ho Lin, Tannistha Nandi, Hui Hoon Chua, Yichun Liu, Edward J. Feil, Mindy Glass, Gladys Tan, Sharon J. Peacock, Patrick Tan (2010) Genomic Acquisition of Virulence Factors by Natural Isolates of Burkholderia. Genome Biology 11:R89
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3. Chi Ho Lin, Guillaume Bourque, and Patrick Tan (2008) A Comparative Synteny Map of Burkholderia Species Links Large-scale Genome Rearrangements to Fine-scale Nucleotide Variation in Prokaryotes. Molecular Biology and Evolution, 25(3):549-558
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4. Sharon J. Peacock, Herbert P. Schweizer, David A.B. Dance, Theresa L. Smith, Jay E. Gee, Vanaporn Wuthiekanun, David DeShazer, Ivo Steinmetz, Patrick Tan and Bart J. Currie (2008) Consensus guidelines on the management of accidental laboratory exposure to Burkholderia pseudomallei and Burkholderia mallei. Emerging Infectious Diseases. Available from http://www.cdc.gov/EID/content/14/7/07-1501.htm DOI: 10.3201/eid1407.071501
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5. Siew Hoon Sim, Yiting Yu, Chi Ho Lin, R. Krishna M. Karuturi, Vanaporn Wuthiekanun, Apichai Tuanyok, Hui Hoon Chua, Catherine Ong, Sivalingam Suppiah Paramalingam, Gladys Tan, Lynn Tang, Gary Lau, Eng Eong Ooi, Donald Woods, Edward Feil, Sharon J. Peacock, and Patrick Tan (2008) The Core and Accessory Genomes of Burkholderia pseudomallei: Implications for Human Melioidosis. PLoS Pathogens. 4(10): e1000178.
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6. Yu Y, Kim HS, Chua HH, Lin CH, Sim SH, Lin D, Derr A, Engels R, DeShazer D, Birren B, Nierman WC, Tan P. (2006) Genomic patterns of pathogen evolution revealed by comparison of Burkholderia pseudomallei, the causative agent of melioidosis, to avirulent Burkholderia thailandensis. BMC Microbiology 6, 46 (Designated a “Highly Accessed” Article)
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7. Fiona Rodrigues, Mitali Sarkar-Tyson, Sarah V Harding, Siew Hoon Sim, Hui Hoon Chua, Chi Ho Lin, Xu Han, R Krishna M Karuturi, Ken Sung, Kun Yu, Wei Chen, Timothy P Atkins, Richard W Titball, and Patrick Tan (2006) A Global Map of Growth Regulated Gene Expression in Burkholderia pseudomallei, the Causative Agent of Melioidosis, J. Bacteriology 188, 8178-8188 (COVER IMAGE)
Supplemental Data File
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8. Keli Ou, Catherine Ong, Shze Yung Koh, Fiona Rodrigues, Siew Hoon Sim, Daniel Wong, Chia Huey Ooi, Kim Chong Ng, Hiroyuki Jikuya, Chin Chin Yau, Sou Yen Soon, Djohan Kesuma, May Ann Lee, and Patrick Tan (2005) Integrative Genomic, Transcriptional, and Proteomic Diversity in Natural Isolates of the Human Pathogen Burkholderia pseudomallei, J. Bacteriology 187, 4276-4285 (Impact factor: 3.993)
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9. Catherine Ong, Ooi Chia Huey, Dongling Wang, Hweeling Chong, Ng Kim Chong, Fiona Rodrigues, May Ann Lee, and Patrick Tan (2004) Patterns of Large-Scale Genomic Variation in Virulent and Avirulent Burkholderia Species, Genome Research 14, 2295-2307
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10. Gan, YH, Chua, KL, Chua, HH, Chong, HL, and Tan, P (2002) Identification of Novel Virulence Factors In Burkholderia Pseudomallei Using a C. Elegans Pathogenesis Model. Molecular Microbiology 44(5), 1185-1197
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