Niranjan Nagarajan

Computational and Systems Biology, A*STAR

Affiliated withA*STAR

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JoVE Journal Publications

ArticleTotal : 1	Year
Publication title Cited by 20	2017

Other Publications

Article	Year
Automatic prediction of protein domains from sequence information using a hybrid learning system. Bioinformatics (Oxford, England)\| PubMed ID: 14962932	2004
Computing the P-value of the information content from an alignment of multiple sequences. Bioinformatics (Oxford, England)\| PubMed ID: 15961473	2005
Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone. Bioinformatics (Oxford, England)\| PubMed ID: 16873498	2006
FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments. Bioinformatics (Oxford, England)\| PubMed ID: 18180239	2008
Scaffolding and validation of bacterial genome assemblies using optical restriction maps. Bioinformatics (Oxford, England)\| PubMed ID: 18356192	2008
The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature\| PubMed ID: 18432245	2008
Statistical methods for detecting differentially abundant features in clinical metagenomic samples. PLoS computational biology\| PubMed ID: 19360128	2009
Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700. Journal of bacteriology\| PubMed ID: 19447908	2009
Parametric complexity of sequence assembly: theory and applications to next generation sequencing. Journal of computational biology : a journal of computational molecular cell biology\| PubMed ID: 19580519	2009
2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates. PloS one\| PubMed ID: 19636415	2009
Genomic characterization of the Yersinia genus. Genome biology\| PubMed ID: 20047673	2010
Alignment and clustering of phylogenetic markers--implications for microbial diversity studies. BMC bioinformatics\| PubMed ID: 20334679	2010
Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information. Journal of computational biology : a journal of computational molecular cell biology\| PubMed ID: 20377460	2010
Finishing genomes with limited resources: lessons from an ensemble of microbial genomes. BMC genomics\| PubMed ID: 20398345	2010
Sequencing and genome assembly using next-generation technologies. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 20835789	2010
GiRaF: robust, computational identification of influenza reassortments via graph mining. Nucleic acids research\| PubMed ID: 21177643	2011
Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes. Genome research\| PubMed ID: 21467267	2011
Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences. Journal of computational biology : a journal of computational molecular cell biology\| PubMed ID: 21929371	2011
A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer. Nature medicine\| PubMed ID: 22426421	2012
Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes. Nature genetics\| PubMed ID: 22484628	2012
Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly. Nature biotechnology\| PubMed ID: 22797562	2012
A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients. The Journal of infectious diseases\| PubMed ID: 22807519	2012
Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons. PloS one\| PubMed ID: 23029419	2012
LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets. Nucleic acids research\| PubMed ID: 23066108	2012
The draft genome of sweet orange (Citrus sinensis). Nature genetics\| PubMed ID: 23179022	2013
Whole-genome reconstruction and mutational signatures in gastric cancer. Genome biology\| PubMed ID: 23237666	2012
Sequence assembly demystified. Nature reviews. Genetics\| PubMed ID: 23358380	2013
Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences. PloS one\| PubMed ID: 23579286	2013
Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate. Genome announcements\| PubMed ID: 23814035	2013
Next-generation whole genome sequencing of dengue virus. Methods in molecular biology (Clifton, N.J.)\| PubMed ID: 24696338	2014
The Opisthorchis viverrini genome provides insights into life in the bile duct. Nature communications\| PubMed ID: 25007141	2014
Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls. Proceedings of the National Academy of Sciences of the United States of America\| PubMed ID: 25028492	2014
Systems consequences of amplicon formation in human breast cancer. Genome research\| PubMed ID: 25186909	2014
Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid. Genome announcements\| PubMed ID: 25278523	2014
BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads. Genome biology\| PubMed ID: 25406369	2014
The importance of study design for detecting differentially abundant features in high-throughput experiments. Genome biology\| PubMed ID: 25517037	2014
Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles. Nucleic acids research\| PubMed ID: 25572314	2015
High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer. Genome biology\| PubMed ID: 25808843	2015
Cloning and variation of ground state intestinal stem cells. Nature\| PubMed ID: 26040716	2015
Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity. Cell reports\| PubMed ID: 26146084	2015
Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission. PLoS neglected tropical diseases\| PubMed ID: 26325059	2015
Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints. PLoS neglected tropical diseases\| PubMed ID: 26327586	2015
Direct whole-genome deep-sequencing of human respiratory syncytial virus A and B from Vietnamese children identifies distinct patterns of inter- and intra-host evolution. The Journal of general virology\| PubMed ID: 26407694	2015
In vitro and in vivo correlates of physiological and neoplastic human Fallopian tube stem cells. The Journal of pathology\| PubMed ID: 26415052	2016
Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin. PLoS genetics\| PubMed ID: 26539826	2015
Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line. GigaScience\| PubMed ID: 26719794	2015
Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion. Nature communications\| PubMed ID: 26783136	2016
OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis. GigaScience\| PubMed ID: 26793302	2016
Predicting microbial interactions through computational approaches. Methods (San Diego, Calif.)\| PubMed ID: 27025964	2016
Fast and sensitive mapping of nanopore sequencing reads with GraphMap. Nature communications\| PubMed ID: 27079541	2016
OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees. Genome biology\| PubMed ID: 27169502	2016
In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation. Molecular cell\| PubMed ID: 27184079	2016
@MInter: automated text-mining of microbial interactions. Bioinformatics (Oxford, England)\| PubMed ID: 27312413	2016
Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma. EBioMedicine\| PubMed ID: 27428430	2016
INC-Seq: accurate single molecule reads using nanopore sequencing. GigaScience\| PubMed ID: 27485345	2016
Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare. Nature microbiology\| PubMed ID: 27562258	2016
Fast and accurate de novo genome assembly from long uncorrected reads. Genome research\| PubMed ID: 28100585	2017
Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries. Biotechnology for biofuels\| PubMed ID: 28174601	2017
Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis. Journal of endodontics\| PubMed ID: 28457636	2017