Senior Investigator

Niranjan NAGARAJAN, Ph.D.
Group Leader
Associate Director, Computational and Systems Biology
Research Focus

Advances in sequencing technology have made genomics a data-rich science with a diverse range of assays to study biological systems. Our research primarily focuses on developing novel statistical and combinatorial algorithms that significantly improve our ability to mine genomic data and provide biological insights. In particular, the group uses parametric complexity analysis (Nagarajan & Pop, 2009; JCB) and exact algorithms (Gao et al, 2011; RECOMB & JCB, Wilm et al, 2012; NAR) to design bioinformatics tools with proven performance guarantees. Our interest and expertise in Computational Genomics is in addressing three kinds of questions a) Sequence Analysis & Assembly b) Metagenomic Analysis and c) Inferring Evolutionary Models

The algorithms developed in the group cater to two broad application areas where we work with clinicians and domain experts to address opportune biological and clinical questions impacting human health:

A) Infectious Diseases & Human Microbiome Studies

High-throughput low-cost sequencing has made it possible to sequence large strain collections to study the genetic basis of a range of infectious diseases as well as track their evolution and transmission patterns in a clinical setting. Improved bioinformatics tools, to sort through and analyze genetic data, are therefore a key requirement and critical to the success of these endeavors. In collaboration with groups at GIS (Hibberd and Swaine Labs) and other academic (Wong Lab, NUS, Kingsford Lab, CMU), industrial (Tom Dawson, P&G) and clinical groups (NUH, TTSH) we work on analytical questions related to a) Viral Evolution and Transmission b) Antibiotic Resistance and Virulence Determinants and c) Role of Human Microbiome in Health and Disease.

B) Personalized & Integrative Cancer Omics

While recent cancer genome sequencing projects have provided significant new datasets and insights into the landscape of mutations (and also transcriptional and epigenomic changes) that are characteristic of various cancers, there are still several challenges in translating this information into targeted and personalized therapy. Our group collaborates with leading experts in Cancer Biology (Wa-McKeon Lab, GIS/JAX) and Cancer Genomics (Hillmer and Tan Lab, GIS/Duke-NUS/NCCS), and uses integrative analysis approaches to study mechanisms of oncogenesis and identify new (patient-specific) drug targets.


2000-2006 Ph.D. in Computer Science, Cornell University, Ithaca, NY, USA
2000-2004 M.Sc. in Computer Science, Cornell University, Ithaca, NY, USA
1996-2000 B.A. in Computer Science and Mathematics, Ohio Wesleyan University, Delaware, OH, USA
1994-1996 International Baccalaureate, International School of Paris, Paris, France

Professional Appointments

2013-Associate Director, Genome Institute of Singapore
2013-Group Leader, Genome Institute of Singapore
2011-2013Assistant Director, Genome Institute of Singapore
2010-Assistant Professor (Adjunct), Computer Science, National University of Singapore
2009-2013Senior Research Scientist, Genome Institute of Singapore
2007-2009Post-doctoral Fellow, Center for Bioinformatics and Computational Biology, University of Maryland
2000-2006Graduate Research Assistant, Cornell University

Honors and Awards

1996-2000 Presidential Fellowhip, Ohio Wesleyan University
1999 David H. Staley Outstanding Junior Prize
2000 Phi Beta Kappa
2000 Robert L. Wilson Prize in Mathematics
2006 Teaching Excellence Award, Cornell University

Committee and Advisory Board

2009-Associate Editor, BMC Bioinformatics
2013-Editorial Board, Biology Direct

External Grant

2013-2016Development and application of single virion sequencing to track viral evolution during disease progression and drug treatment by A*STAR JCO (S$ 749,500)
2013-2016Establishment of a humanized mouse model for study of bona fide hepatitis virus infection, immune responses and drug development by A*STAR JCO (S$4,798,132)
2012-2015A*STAR Industrial Microbiology Genome Informatics platform by A*STAR (S$ 3,599,000)
2012-2015Early warning for ovarian cancer: detecting premalignant lesions by NMRC (S$ 3,753,478)
2012-2014Cancer structural genomics and de novo assembly of polyploid genomes by A*STAR (S$ 536,051)
2012-2014Genomic and Transcriptomic investigation of Malassezia strains by A*STAR (S$ 230,765)
2011-2012Genome Technology Development by A*STAR (S$ 381,250)
2010-2014Molecular and structural characterization of the desalination mechanisms in euryhaline fish for the mimicry of seawater desalination by Environment and Water Industry Development Council (S$ 1,844,750)

Selected Publications

  1. Bertrand D, Chng KR, Sherbaf FG, Kiesel A, Chia BK, Sia YY, Huang SK, Hoon DS, Liu ET, Hillmer A, Nagarajan N "Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles." Nucleic Acids Res 2015 Jan 8 Abstract     

  2. Wang S, Chng KR, Wilm A, Zhao S, Yang KL, Nagarajan N, He J "Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls." Proc Natl Acad Sci U S A 2014 Jul 15 Abstract     

  3. Luo H, Li J, Chia BK, Robson P, Nagarajan N "The importance of study design for detecting differentially abundant features in high-throughput experiments." Genome Biol 2014 ; 15(12) : 527 Epub 2014 Dec 3 Abstract     

  4. Nagarajan N, Pop M "Sequence assembly demystified." Nat Rev Genet 2013 Jan 29 Epub 2013 Jan 29 Abstract     

  5. Ong SH, Kukkillaya VU, Wilm A, Lay C, Ho EX, Low L, Hibberd ML, Nagarajan N "Species Identification and Profiling of Complex Microbial Communities Using Shotgun Illumina Sequencing of 16S rRNA Amplicon Sequences." PLoS One 2013 ; 8(4) : e60811 Epub 2013 Apr 8 Abstract     

  6. Lam ET, Hastie A, Lin C, Ehrlich D, Das SK, Austin MD, Deshpande P, Cao H, Nagarajan N, Xiao M, Kwok PY "Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly." Nat Biotechnol 2012 Jul 15 Epub 2012 Jul 15 Abstract     

  7. Wilm A, Aw PP, Bertrand D, Yeo GH, Ong SH, Wong CH, Khor CC, Petric R, Hibberd ML, Nagarajan N "LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets." Nucleic Acids Res 2012 Oct 12 Abstract     

  8. Nagarajan N, Bertrand D, Hillmer AM, Zang ZJ, Yao F, Jacques PE, Teo AS, Cutcutache I, Zhang Z, Lee WH, Sia YY, Gao S, Ariyaratne PN, Ho A, Woo XY, Veeravali L, Ong CK, Deng N, Desai KV, Khor CC, Hibberd ML, Shahab A, Rao J, Wu M, Teh M, Zhu F, Chin SY, Pang B, So JB, Bourque G, Soong R, Sung WK, Teh BT, Rozen S, Ruan X, Yeoh KG, Tan PB, Ruan Y "Whole-genome reconstruction and mutational signatures in gastric cancer." Genome Biol 2012 Dec 13 ; 13(12) : R115 Epub 2012 Dec 13 Abstract     

  9. Gao S, Sung WK, Nagarajan N "Opera: Reconstructing Optimal Genomic Scaffolds with High-Throughput Paired-End Sequences." J Comput Biol 2011 Sep 19 Abstract     

  10. Nagarajan N, Kingsford C "GiRaF: robust, computational identification of influenza reassortments via graph mining." Nucleic Acids Res 2010 Dec 21 Abstract     

Complete Publications List

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