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RESEARCH FOCUS
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Advances in sequencing technology have changed the landscape of research in Computationally Biology providing researchers with a flood of information about biological sequences. Our research focuses on statistical and algorithmic approaches to make sense of this data and provide biological insights. Some of the areas that we work on include:
1) Genome Assembly - Our ability to study various genomes is dependent on computational tools to reconstruct genomes from noisy experimental data. In recent years, new sequencing technologies have presented both a challenge and an opportunity for the design of new assembly tools and strategies. In our group we look at both de novo and comparative approaches for using sequencing and mapping information to reconstruct various Microbial and Eukaryotic genomes.
2) Pan-genomics - Analyzing and cataloguing genomic differences between individuals of a species (or strains of a microbial species or genus) is critical for understanding the genomic basis for various phenotypes. These differences can be subtle and can sometimes be in unexpected places (repeat elements, intronic regions etc.) and in our work we develop statistical approaches to identify such differences with high confidence.
3) Metagenomics is a new area of study geared towards understanding of microbial communities and their impact on diverse environments - from the human body to entire marine ecosystems. Our work is geared towards the design of novel tools to aid in the analysis of metagenomic datasets (both marker sequences as well as whole genome shotgun sequences).
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EDUCATION
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| 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 |
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PROFESSIONAL APPOINTMENTS
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| 2009- | Senior Research Scientist, Genome Institute of Singapore |
| 2007-2009 | Post-doctoral Fellow, Center for Bioinformatics and Computational Biology, University of Maryland |
| 2000-2006 | Graduate Research Assistant, Cornell University |
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HONORS AND AWARDS
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| 1996-2000 | Presidential Fellowhip, Ohio Wesleyan University |
| 1999 | David H. Staley Outstanding Junior Prize |
| 2000 | Robert L. Wilson Prize in Mathematics |
| 2006 | Teaching Excellence Award, Cornell University |
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COMMITTEE AND ADVISORY BOARD
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| 2009- | Associate Editor, BMC Bioinformatics |
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SELECTED PUBLICATIONS
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1. White JR, Navlakha S, Nagarajan N, Ghodsi MR, Kingsford C, Pop M "Alignment and clustering of phylogenetic markers - implications for microbial diversity studies." BMC Bioinformatics 2010 Mar 24 ; 11(1) : 152 Epub 2010 Mar 24
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2. Kingsford Carl*, Nagarajan Niranjan*, Salzberg Steven L "2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates." PLoS ONE 2009 ; 4(7) : e6402 Epub 2009 Jul 28. * Joint first authors
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3. Nagarajan Niranjan, Pop Mihai "Parametric complexity of sequence assembly: theory and applications to next generation sequencing." J. Comput. Biol. 2009 Jul ; 16(7) : 897-908
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4. Saket Navlakha, James White, Niranjan Nagarajan, Mihai Pop, Carl Kingsford "Finding biologically accurate clusterings in hierarchical decompostions using the variation of information." RECOMB 2009
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5. Nagarajan Niranjan, Read Timothy D, Pop Mihai "Scaffolding and validation of bacterial genome assemblies using optical restriction maps." Bioinformatics 2008 May 15 ; 24(10) : 1229-35 Epub 2008 Mar 20
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6. Niranjan Nagarajan and Carl Kingsford "Uncovering genomic reassortments among Influenza strains by enumerating maximal bicliques." IEEE BIMB 2008.
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7. Ng Patrick, Nagarajan Niranjan, Jones Neil, Keich Uri "Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone." Bioinformatics 2006 Jul 15 ; 22(14) : e393-401
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8. Niranjan Nagarajan, Patrick Ng, Uri Keich "Refining motif finders with E-value calculations." RECOMB Regulatory Genomics 2006
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9. Nagarajan Niranjan, Jones Neil, Keich Uri "Computing the P-value of the information content from an alignment of multiple sequences." Bioinformatics 2005 Jun ; 21 Suppl 1 : i311-8
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10. Nagarajan Niranjan, Yona Golan "Automatic prediction of protein domains from sequence information using a hybrid learning system." Bioinformatics 2004 Jun 12 ; 20(9) : 1335-60 Epub 1970 Jan 1
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COMPLETE PUBLICATION LIST
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