PhD Theses
A partial list of PhD theses submitted by graduate students of the lab and other affiliated students. To include a thesis, please contact Limsoon Wong (wongls@comp.nus.edu.sg)

2005

  1. CAO Xia, "Approximate searching in genomic databases", PhD thesis submitted 2005, awarded 2005, National University of Singapore. (Supervisors: Beng Chin Ooi & Anthony Tung, ??? 2001--??? 2005) Email: xia.cao@gmail.com / First job: Research Fellow at Univ of Michigan (Pathology Dept) with Alexey Nesvizhskii

  2. LIU Huiqing, "Effective use of data mining technologies on biological and clinical data", PhD thesis submitted 2004, awarded 2005, National University of Singapore. (Supervisor: Limsoon Wong, January 2000--October 2004) DNAFSMiner Server / Email: huiqing_liu@yahoo.com / First job: Postdoc at Univ of Georgia (Dept of Biochemistry and Molecular Biology) with Ying Xu / Second job: Research Assistant Professor at BioMaPS Institute for Quantitative Biology / Last known position: Senior Scientist at Centocor Inc (NJ, USA)

  3. LIU Tiefei, "Learning gene network using Bayesian network framework", PhD thesis submitted 2005, awarded 2005, National University of Singapore. (Supervisor: Wing-Kin Sung, Pei-lin Mao, ??? 2000--??? 2005) Email: liutf.cn@gmail.com / First job: Postdoc at NUS (Dept of Biochemistry) with Maxey Chung

2006

  1. Zeyar Aung, "Computational analysis of 3D protein structures", PhD thesis submitted 2005, awarded 2006, National University of Singapore. (Supervisor: Kian Lee Tan, January 2001--October 2006) Email: zeyarag@gmail.com / First job: Research Fellow at Institute for Infocomm Research (Knowledge Discovert Dept) with Jinyan Li / Last known position: Assistant Professor at Masdar Institute of Science and Technology (Abu Dhabi, UAE).

  2. LI Haiquan, "Efficient discovery of binding motif pairs from protein-protein interactions", PhD thesis submitted 2006, awarded 2006, National University of Singapore. (Supervisor: Jinyan Li, Wee Sun Lee, July 2002--July 2006) Email: hamanlee@gmail.com / First job: Research Associate at Noble Foundation with Patrick Zhao / Last known position: Research Assistant Professor at University of Chicago (Dept of Medicine).

  3. TAN Zhenqiang, "Querying and mining in biological databases", PhD thesis submitted 2006, awarded 2006, National University of Singapore. (Supervisor: Anthony Tung, ??? 2001--January 2006) Email: tanzq@mozat.com / First job: COO at MOZAT (startup)

  4. XU Xin, "Data mining techniques in gene expression data analysis", PhD thesis submitted 2006, awarded 2006, National University of Singapore. (Supervisor: Anthony Tung, ???--July 2006) Email: xu.xin@alumni.nus.edu.sg / First job: Postdoc at NUS (Dept of Biological Sciences) with Martti Tammi

2007

  1. CHEN Jin, "Systematic assessment of protein interaction data using graph topology approaches", PhD thesis submitted 2007, awarded 2007, National University of Singapore. (Supervisors: Wynne Hsu, Mong Li Lee, & See-Kiong Ng, January 2002--February 2007) Email: chenjin@gmail.com / First job: Postdoc at Stanford University (Dept of Plant Biology) with Sue Rhee / Last known position: Assistant Professor at Michigan State University (Dept of Computer Science)

  2. Rajesh Chowdhary, "Modeling and recognition of histone promoters on genome-wide scale by Bayesian networks", PhD thesis submitted 2006, awarded 2007, National University of Singapore. (Supervisors: Vladimir Bajic & Limsoon Wong, January 2003--September 2006) Email: rajeshchowdhary@gmail.com / First job: Postdoc at Harvard University (Dept of Statistics) with Jun Liu / Last known position: Research Assistant Professor at Marshfield Clinic (WI, USA)

  3. JI Liping, "Mining localized co-expressed gene patterns from microarray data", PhD thesis submitted 2007, awarded 2007, National University of Singapore. (Supervisor: Kian Lee Tan, July 2002--January 2007) Email: jiliping@stanford.edu / First job: Postdoc at Stanford University (Dept of Plant Biology) with Sue Rhee / Last known position: Associate professor at Harbin Institute of Technology, China

  4. Judice KOH, "Correlation-based methods for biological data cleaning", PhD thesis submitted 2007, awarded 2007, National University of Singapore. (Supervisor: Mong Li Lee, July 2002--March 2007) Email: judice.koh@utoronto.ca / First job: Postdoc at University of Toronto (Terrence Donnelly Centre for Cellular and Biomolecular Research) with Charles Boone

2008

  1. CHUA Hon Nian, "Graph-based methods for protein function prediction", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisors: Limsoon Wong & Wing-Kin Sung, August 2003--July 2007) FSWeight V2.1 Software / PCP V1.0 Software / Email: hnchua@i2r.a-star.edu.sg / First job: Research Fellow at Institute for Infocomm Research (Knowledge Discovert Dept) with See-Kiong Ng

  2. LIN Li, "Efficient Mining of Haplotype Patterns for Disease Prediction", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisor: Leong Tze Yun, July 2000--December 2007) Email: llin@unisim.edu.sg / First Job: Lecturer (SIM University, School of Business) / Last known position: Research Fellow, Institute of High Performance Computing

  3. Stanley NG, "Computational identification of novel microRNAs using intrinsic RNA folding measures", PhD thesis submitted 2008, awarded 2008, National University of Singapore. (Supervisor: Santosh Mishra & Limsoon Wong, January 2004--January 2008) Email: stanley_ng@immunol.a-star.edu.sg / First job: Research Fellow at Singapore Immunology Network with Ee Chee Ren

  4. NING Kang, "Algorithms for peptide and PTM identification using tandem mass spectrometry", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisor: Hon Wai Leong and Louxin Zhang, August 2003--November 2007) Email: albertnk@gmail.com / First job: Research Fellow in University of Michigan (Pathology Dept) with Alexey Nesvizhskii

  5. KOH Geoffrey, "Pathway Models Decomposition and Composition Techniques for Parameter Estimation", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisor: P. S. Thiagarajan and David Hsu, January 2004--June 2008) Email: geoffkoh@yahoo.com.sg / First job: Research Fellow in Bioprocessing Technology Institute with Dong-Yup Lee

  6. Vijayaraghava Seshadri Sundararajan, "Progressive data mining: An exploration of using whole-dataset feature selection in building classifiers on three biological problems", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisor: Limsoon Wong, January 2002--June 2007) Email: chanusuba@gmail.com / First job: Research Fellow at NUS (Dept of Preventive Dentistry) with Steven Hsu / Last known position: Research Fellow at SANBI with Vlad Bajic

  7. Edward Wijaya, "Integrative methods for discovering generic cis-regulatory motifs", PhD thesis submitted 2008, awarded 2008, National University of Singapore. (Supervisor: Wing-Kin Sung, August 2003--March 2008) Email: ewijaya@gmail.com / First job: Postdoc at AIST Japan (CBRC) with Paul Horton.

  8. WONG Swee Seong, "String matching and indexing with suffix data structures", PhD thesis submitted 2007, awarded 2008, National University of Singapore. (Supervisor: Wing-Kin Sung & Limsoon Wong, August 2003--August 2007) CPS Software / Email: wong_swee_seong@lilly.com / First job: Senior Associate Scientist at Lily Singapore Center for Drug Discovery

2009

  1. Vipin Narang, "Gene Regulatory Element Prediction with Bayesian Networks", PhD thesis submitted 2008, awarded 2009, National University of Singapore. (Supervisor: Wing-Kin Sung & Ankush Mittal, January 2003--July 2008) Email: narangv@gis.a-star.edu.sg / First job: Research Scientist at Genome Institute of Singapore.

  2. Anshul Nigham, "Algorithms for Analyzing Protein Conformational Flexibility with Noisy Data", PhD thesis submitted 2008, awarded 2009, Singapore-MIT Alliance. (Supervisor: David Hsu & Tomas Lozano-Perez, ???--June 2008) Email: nigham@gmail.com / First job: Software Developer at IBM (Singapore).

  3. Francis NG, "Algorithms for multi-point range query and reverse nearest neighbour search", PhD thesis submitted 2009, awarded 2009, National University of Singapore. (Supervisor: Hon Wai Leong, ???--March 2009). Email: ??? / First job: ???

  4. Vinsensius B. Vega, "Inferring regulatory signal from genomic data", PhD thesis submitted 2008, awarded 2009, National University of Singapore. (Supervisors: Wing-Kin Sung, January 2004--October 2008; Philip Long, August 2001--December 2003). Email: vega@alum.comp.nus.edu.sg / First job: Research Scientist at Genome Institute of Singapore.

2010

  1. Donny SOH, "Understanding Pathways", PhD thesis submitted 2009, awarded 2010, Imperial College London. (Supervisors: Yike Guo & Limsoon Wong, December 2004--November 2009). Email: donnysoh@gmail.com / First job: Research Fellow at Institute for Infocomm Research (Knowledge Discovery Dept) with See-Kiong Ng

  2. FENG Mengling, "Frequent Pattern Space Maintenance: Theories and Algorithms", PhD thesis submitted 2009, awarded 2010, Nanyang Technological University. (Supervisors: Limsoon Wong, Yap Peng Tan, Jinyan Li, April 2004--April 2009) TRUM V1.0 Software / PSM 2.0 Software / Email: mornin@gmail.com / First job: Research Fellow at Institute for Infocomm Research (Knowledge Discovery Dept) with See-Kiong Ng

  3. Charlie LEE, "Bioinformatics Applications for Virology Research", PhD thesis submitted 2010, awarded 2010, National University of Singapore. (Supervisor: Wing-Kin Sung, Jan 2006--May 2010). Email: leewhc@gis.a-star.edu.sg / First job: Research Fellow at Genome Institute of Singapore

2011

  1. Hugo Willy, "On Interaction Motif Inference from Biomolecular Interactions: Riding the Growth of the High Throughput Sequential and Structural Data", PhD thesis submitted 2010, awarded 2011, National University of Singapore. (Supervisors: Wing-Kin Sung, See-Kiong Ng, Aug 2003--Dec 2010). Email: hugowill@comp.nus.edu.sg / First job: Research Fellow at NUS

  2. OOI Nick Sern Brandon, "Molecular and Computational Approaches to Understanding Keloid Scarring", PhD thesis submitted 2010, awarded 2011, National University of Singapore. (Supervisors: Phan Toan Thang, P. S. Thiagarajan, Aug 2004--Dec 2010). Email: brandon_ooi@rp.sg / First job: Academic Staff at Republic Polytechnic

  3. LIU Bing, "Probabilistic Approximation and Analysis Techniques for Bio-Pathway Models", PhD thesis submitted 2010, awarded 2011, National University of Singapore. (Supervisors: P. S. Thiagarajan, David Hsu, Aug 2006--Dec 2010). Email: liubing1020@gmail.com / First job: Research Fellow at NUS

  4. CHONG Ket Fah, "New Models and Algorithms for De Novo Peptide Sequencing of Multicharge MS/MS Spectra", PhD thesis submitted 2010, awarded 2011, National University of Singapore. (Supervisor: Hon Wai Leong, Jan 2002--Dec 2010). Email: chongket@comp.nus.edu.sg / First job: ???

  5. DONG Difeng, "Relapse Prediction in Childhood Acute Lymphoblastic Leukemia by Time-Series Gene Expression Profiling", PhD thesis submitted 2011, awarded 2011, National University of Singapore. (Supervisor: Limsoon Wong, December 2005--May 2011). Email: dong.difeng@gmail.com / First job: Research Fellow at NUS

2012

  1. Sriganesh Maniganahalli Srihari, "Integrating Biological Insights with Topological Characteristics for Improved Complex Prediction from Protein Interaction Networks", PhD thesis submitted 2012, awarded 2012, National University of Singapore. (Supervisor: Hon Wai Leong, January 2008--January 2012). Email: sriganesh.m.s@gmail.com / First job: ???

  2. CHIANG Tsung-Han, "Markov Dynamic Models for Long-Timescale Protein Motion", PhD thesis submitted 2011, awarded 2012, National University of Singapore. (Supervisor: David Hsu, October 2006--December 2011). Email: th.chiang@gmail.com / First job: Software Engineer at Eidyia (startup)

  3. Melvin ZHANG, "Algorithms for Conserved Gene Cluster Discovery and Ortholog Assignment", PhD thesis submitted 2011, awarded 2012, National University of Singapore. (Supervisor: Hon Wai Leong, start???--April 2012). Email: ??? / First job: Programmer at Hoiio.com (startup)

Lab Coordinator: Limsoon Wong / Last updated: 9 May 2012.