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: Principal Investigator at Incyte (Delaware, 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 Last known position: Quantitative Analyst at Complus Asset Management (Hong Kong)

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: Associate Professor at Masdar Institute (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 / Second job: Research Assistant Professor at University of Chicago (Dept of Medicine) / Last known position: Assistant Professor of Biosystems Informatics and Director of Translational Bioinformatics at University of Arizona (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 (Singapore)

  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 / Second jon: Assistant Professor at Michigan State University (Dept of Computer Science) / Last known position: Associate Professor and Chief, Dvision of Biomedical Informatics, Univbersity of Kentucky (College of Medicine)

  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 / Second job: Research Assistant Professor at Marshfield Clinic (WI, USA) / Last known position: Chief Scientific Officer, Insilicom LLC (FL, 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 / Last known position: Platform Leader (Computational Phenomics) at Genome Institute of Singapore

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 / Last known position: Head of R&D at DataRobot Inc (Singapore)

  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 (Singapore)

  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 / Last known position: Senior Manager (Biomedical Science) at Exploit Technologies (Singapore)

  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 / Second position: Professor at CAS Qingdao Institute of BioEnergy and Bioprocess Technology (China) / Last known position: Professor at Huazhong University of Science and Technology (College of Life Sciences and Technology) (Hubei, China)

  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 & David Hsu, January 2004--June 2008. Email: geoffkoh@yahoo.com.sg / First job: Research Fellow in Bioprocessing Technology Institute with Dong-Yup Lee / Last known position: VP (Research Support) at WorldQuant, Singapore

  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 / Second job: Research Fellow at SANBI with Vlad Bajic / Last known position: Asst Director at GSTF (Singapore)

  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 / Last known position: Guest Researcher at Osaka University Immunology Frontier Research Center (Osaka, Japan)

  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 / Second job: Senior Research Scientist at Eli Lilly (Indianapolis) / Last known position: Director of NGS Bioinformatics at LifeOmic (Indianapolis)

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 / Last known position: Engineering Director at Google (Zurich, Switzerland)

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 / Last known position: CEO at 9 Degrees Freedom (Singapore)

  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 / Second job: Senior Postdoctoral Fellow at MIT (Mass) / Last known position: Assistant Professor at National University of Singapore (Saw Swee Hock School of Public Health)

  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 / Last known position: Assistant Professor at UCLA Health

  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: Postdoctoral Fellow at CMU (Pitsburgh, PA) / Last known position: Research Assistant Professor at University of Pittsburgh (School of Medicine)

  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: Teaching Assistant at NUS SOC / Last known position: Lecturer at NUS SOC

  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: Quantitative Researcher at WorldQuant, Beijing / Second job: VP (Quantitative Research) at WorldQuant, Taipei / Last known position: VP (Portfolio Management) at WorldQuant, Singapore

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: Post-doc at the Institute of Molecular Bioscience, University of Queensland, with Prof Mark Ragan / Last known position: AI Engineer and Researcher at Maxwell Plus (Brisbane, Australia)

  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 (Singapore) / Last known position: Director of Software Development at CTAccel (Hong Kong)

  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 (Singapore) / Last known position: VP of Software at The Intelligent Warehouse (Singapore)

2013

  1. DO Huy Hoang, "Compressed Indexing Data Structures for Biological Sequences", PhD thesis submitted 2012, awarded 2013, National University of Singapore. Supervisor: Wing-Kin Sung, August 2007--November 2012. Email: hoangmit@gmail.com / First job: Postdoc at Genome Institute of Singapore / Last known position: Software Engineer at facebook

  2. GOH Wen Bin Wilson, "Computational Proteomics Using Network-Based Strategies", PhD thesis submitted 2013, awarded 2013, Imperial College London. Supervisors: Limsoon Wong & Marek Sergot, October 2009--June 2013. Email: gohwils@gmail.com / First job: Associate Professor at Tianjin University (China) / Last known position: Lecturer at Nanyang Technological University (School of Biological Sciences)

  3. KOH Chuan Hock, "Embracing Noise in Bioinformatics", PhD thesis submitted 2012, awarded 2013, National University of Singapore. Supervisor: Limsoon Wong, September 2008--September 2012. Email: kohchuanhock@gmail.com / First job: Developer at DeNA (Tokyo, Japan) / Second job: Data Scientist at Rakuten (Tokyo, Japan) / Last known position: Senior Data Scientist at Indeed.com (Tokyo, Japan)

  4. Sucheendra Kumar Palaniappan, "Probabilistic Verification and Analysis of Biopathway Dynamics", PhD thesis submitted 2012, awarded 2013, National University of Singapore. Supervisor: P. S. Thiagarajan, August 2008--March 2013. Email: sucheendrak@gmail.com / First job: Postdoc with Hiroaki Kitano @ RIKEN Centre for Integrative Medical Sciences

  5. WANG Yue, "Efficient Computational Techniques for Tag SNP Selection, Epistasis Analysis, and Genome-Wide Association Study", PhD thesis submitted 2012, awarded 2013, National University of Singapore. Supervisor: Limsoon Wong, September 2008--November 2012. Email: fayue1015@gmail.com / First job: Data Scientist at SingTel Living Analytics / Second job: Co-founder and COO at Igloohome, Singapore / Last known position: Founder and CEO at Populstay (Tokyo, Japan)

  6. ZHANG Zhizhuo, "Study of Protein-DNA Interaction Using New Generation Data", PhD thesis submitted 2013, awarded 2013, National University of Singapore. Supervisor: Wing-Kin Sing, ???--March 2013. Email: zzz2010@gmail.com / First job: Postdoctoral Associate at MIT with Manolis Kellis / Last known position: Senior Machine Learning Scientist at 4Catalyzer (CT, USA)

  7. ZHOU Hufeng, "Computational Studies of Host-Pathogen Protein-Protein Interactions---A Case Study of the H. Sapiens-M. tuberculosis H37Rv System", PhD thesis submitted 2013, awarded 2013, National University of Singapore. Supervisor: Limsoon Wong, September 2009--July 2013. Email: zhf8608@gmail.com / First job: Research Fellow at Harvard Medical School with Elliott Kieff / Last known position: Instructor at Harvard Medical School

2014

  1. Benjamin Mate GYORI, "Probabilistic approaches to modeling uncertainty in biological pathway dynamics", PhD thesis submitted 2014, awarded 2014. National University of Singapore. Supervisor: David Hsu, January 2010--July 2014. Email: ben.gyori@gmail.com / First job: Postdoctoral Fellow at Harvard Medical School Department of Systems Biology with Peter Sorger.

  2. JIN Jingjing, "Investigating lipid and secondary metabolisms in plants by next-generation sequencing", PhD thesis submitted 2014, awarded 2014. National University of Singapore. Supervisors: Limsoon Wong & Nam-Hai Chua, January 2010--July 2014. Email: jjjscuedu@gmail.com / First job: Research Fellow at Temasek Lifesciences Lab / Last known position: ??? at Zhengzhou Tabacco Research Institute (China)

  3. Chandana Tikiri Bandara Tennakoon, "Fast and accurate mapping of next generation sequencing data", PhD thesis submitted 2013, awarded 2014. National University of Singapore. Supervisor: Wing-Kin Sung, start???---??? 2013. First job: Postdoc in A*STAR SICS.

2015

  1. CHANG Cheng Wei, "Cofactor prediction using ChIP-Sequencing Data", PhD thesis submitted 2014, awarded 2015. National University of Singapore. Supervisors: Wing-Kin Sung & Edwin Cheung, August 2008---July 2014. Email: ??? / First job: ???

  2. LIM Jing Quan, "Accurate alignment of sequencing reads from various genomic origins", PhD thesis submitted 2014. National University of Singapore. Supervisor: Wing-Kin Sung, ???---July 2014. Email: ??? / First job: Research Fellow at National Cancer Centre Singapore

  3. LIM Junliang Kevin, "Using biological networks and gene-expression profiles for the analysis of diseases", PhD thesis submitted 2014. National Uinversity of Singapore. Supervisor: Limsoon Wong, August 2010---November 2014. Email: kevlim83@gmail.com / First job: Research fellow at Duke NUS / Last known position: ??? at Wilmar Labs NUS

  4. Michal Wozniak, "Computational aspects of the presence of drug resistance mechanisms", PhD thesis submitted 2015. University of Warsaw. Supervisor: Jerzy Tiuryn & Limsoon Wong, September 2009---March 2015. Email: mw219725@gmail.com / First job: ???

  5. YONG Chern Han, "Discovering dynamic protein complexes from static interactomes: Three challenges", PhD thesis submitted 2014, awarded 2015. National University of Singapore. Supervisor: Limsoon Wong, January 2009---November 2014. Email: radiocherny@gmail.com / First job: Research fellow at Duke NUS.

2017

  1. NGUYEN Nam Ninh, "Computational methods for reconstruction and enhancement of genome-scale metabolic networks", PhD thesis submitted 2016, awarded 2017. National University of Singapore. Supervisor: Hon Wai Leong, start???---??? 2016. Email: ??? / First job: Software Engineer at Squarepoint Capital (Singapore)

  2. LU Bingxin, "Analyzing lateral gene transfer with machine learning and phylogenetic methods", PhD thesis submitted 2017, awarded 2017. National University of Singapore. Supervisor: Hon Wai Leong, start???---??? 2017. Email: ??? / First job: Postdoc at Genome Institute of Singapore

2018

  1. Abha BELORKAR, "Gene expression analysis in the presence of heterogeneity", PhD thesis submitted 2018, awarded 2018. National University of Singapore. Supervisor: Limsoon Wong, August 2014---January 2018. Email: abha.b.nus@gmail.com / First job: Postdoc at University of Pennsyvania with Li-San Wang

2019

  1. Stefano PERNA, "Data-driven techniques for knowledge discovery in regulomics", PhD thesis submitted 2019, awarded 2019. Politecnico di Milano. Supervisor: Stefano Ceri & Limsoon Wong, ??? 2016---February 2019. Email: stefano.perna@polimi.it / First job: ???

  2. Chayaporn Suphavilai (Nok), "Predicting cancer drug response using a recommender system", PhD thesis submitted 2019. National University of Singapore. Supervisors: Niranjan Nagarajan & Limsoon Wong, May 2015---February 2019. Email: ??? / First job: ???

  3. LI Chenhao, "Predicting microbial interactions with modelling approaches", PhD thesis submitted 2019. National University of Singapore. Supervisors: Niranjan Nagarajan & Limsoon Wong, May 2015---February 2019. Email: ??? / First job: ???

2020

  1. XIE Luyu, "Evaluation and improvement of genome assembly", PhD thesis submitted 2019. National University of Singapore. Supervisor: Limsoon Wong, August 2014---November 2019. Email: x86@u.nus.edu / First job: Postdoc with Teh Bin Tean at Dukr-NUS

Lab Coordinator: Limsoon Wong / Last updated: 16 March 2019.