Niranjan NAGARAJAN

 

RESEARCH

Our research primarily focuses on developing novel statistical and combinatorial algorithms to analyse massive genomic datasets and provide biological insights. A defining aspect of our computational genomics work is the use of parametric complexity analysis (Nagarajan & Pop, JCB 2009) and exact algorithms (Gao et al., RECOMB, JCB 2011; Wilm et al., NAR 2012) to design bioinformatics tools with provable performance guarantees. We primarily focus on addressing questions in three areas a) Sequence Analysis & Assembly b) Metagenomic Analysis and c) Integrative Genomics.

The genomics tools 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) Human Microbiome Studies

We develop analytical approaches that leverage advances in sequencing technologies (e.g. PacBio, Nanopore) to decipher the functional role of microbial communities resident in the human body. These are then combined within a systems biology framework to understand how host-microbiome interactions influence health and disease states. Our goal is to identify novel biomarkers and therapeutic targets to help restore microbial symbiosis. Areas of current work in the lab include (i) Role of skin microbiota in Atopic Dermatitis (w/ Dr. John Common) ii) Impact of antibiotic therapy on gut microbiome (w/ Dr. Barnaby Young) and iii) Microbial dysbiosis in cholangiocarcinoma (w/ Dr. Joanne Ngeow).

B) Personalized & Integrative Cancer Omics

We are designing systems to integrate diverse cancer omics datasets to identify driver mutations and effective drug combinations (w/ Dr. Iain Tan and Dr. Ramanuj Dasgupta). The goal is to make molecular profiling data useful for targeted and personalized therapy.

Lab Webpage

Selected Publications

• Bertrand D, Dris sler S, Chia BK, Koh JY, Li C, Suphavilai C, Tan IB, Nagarajan N^# "ConsensusDriver Improves upon Individual Algorithms for Predicting Driver Alterations in Different Cancer Types and Individual Patients." Cancer Res 2018 Jan 01 ; 78(1) : 290-301 Abstract
• Sović I, Šikić M, Wilm A, Fenlon SN, Chen S, Nagarajan N^# "Fast and sensitive mapping of nanopore sequencing reads with GraphMap." Nat Commun 2016 ; 7 : 11307 Abstract
• Lim KM, Li C, Chng KR, Nagarajan N^# "@MInter: automated text-mining of microbial interactions." Bioinformatics 2016 Jun 16 Epub 2016 Jun 16 Abstract
• Li C, Lim KM, Chng KR, Nagarajan N^# "Predicting microbial interactions through computational approaches." Methods 2016 Jun 1 ; 102 : 12-9 Epub 2016 Mar 26 Abstract
• Gao S, Bertrand D, Chia BK, Nagarajan N^# "OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees." Genome Biol 2016 ; 17(1) : 102 Epub 2016 May 11 Abstract
• Chng KR, Tay ASL, Li C, Ng AHQ, Wang J, Suri BK, Matta AS, McGovern N, Janela B, Wong XFC, Sio YY, Au BV, Wilm A, De Sessions PF, Lim TC, Tang MBY, Ginhoux F, Connolly JE, Lane EB, Chew FT, Common JEA^#, Nagarajan N^# "Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare" Nat Microbiol 2016 1:16106 doi:10.1038/nmicrobiol.2016.106
• Chng KR, Chan SH, Ng AHQ, Li C, Jusakul A, Bertrand D, Wilm A, Choo SP, Tan DMY, Lim KH, Soetinko R, Ong CK, Duda DG, Dima S, Popescu I, Wongkham C, Feng Z, Yeoh KH, Teh BT, Yongvanit P, Wongkham S, Bhudhisawasdi V, Khuntikeo N, Tan P, Pairojkul C^#, Ngeow J^#, Nagarajan N^# "Tissue microbiome profiling identifies an enrichment of specific enteric bacteria In Opisthorchis viverrini associated cholangiocarcinoma" EBioMedicine 2016 8:12-13
• Li C, Chng KR, Boey EJ, Ng AH, Wilm A, Nagarajan N^# "INC-Seq: accurate single molecule reads using nanopore sequencing." Gigascience 2016 Aug 02 ; 5(1) : 34 Abstract
• 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
• 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