Niranjan Nagarajan

Automatic prediction of protein domains from sequence information using a hybrid learning system.

Computing the P-value of the information content from an alignment of multiple sequences.

Apples to apples: improving the performance of motif finders and their significance analysis in the Twilight Zone.

FAST: Fourier transform based algorithms for significance testing of ungapped multiple alignments.

Scaffolding and validation of bacterial genome assemblies using optical restriction maps.

The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus).

Statistical methods for detecting differentially abundant features in clinical metagenomic samples.

Complete genome sequence of Aggregatibacter (Haemophilus) aphrophilus NJ8700.

Parametric complexity of sequence assembly: theory and applications to next generation sequencing.

2009 Swine-origin influenza A (H1N1) resembles previous influenza isolates.

Genomic characterization of the Yersinia genus.

Alignment and clustering of phylogenetic markers--implications for microbial diversity studies.

Finding biologically accurate clusterings in hierarchical tree decompositions using the variation of information.

Finishing genomes with limited resources: lessons from an ensemble of microbial genomes.

Sequencing and genome assembly using next-generation technologies.

GiRaF: robust, computational identification of influenza reassortments via graph mining.

Comprehensive long-span paired-end-tag mapping reveals characteristic patterns of structural variations in epithelial cancer genomes.

Opera: reconstructing optimal genomic scaffolds with high-throughput paired-end sequences.

A common BIM deletion polymorphism mediates intrinsic resistance and inferior responses to tyrosine kinase inhibitors in cancer.

Exome sequencing of gastric adenocarcinoma identifies recurrent somatic mutations in cell adhesion and chromatin remodeling genes.

Genome mapping on nanochannel arrays for structural variation analysis and sequence assembly.

A randomized, double-blind placebo controlled trial of balapiravir, a polymerase inhibitor, in adult dengue patients.

Long span DNA paired-end-tag (DNA-PET) sequencing strategy for the interrogation of genomic structural mutations and fusion-point-guided reconstruction of amplicons.

LoFreq: a sequence-quality aware, ultra-sensitive variant caller for uncovering cell-population heterogeneity from high-throughput sequencing datasets.

The draft genome of sweet orange (Citrus sinensis).

Whole-genome reconstruction and mutational signatures in gastric cancer.

Sequence assembly demystified.

Species identification and profiling of complex microbial communities using shotgun Illumina sequencing of 16S rRNA amplicon sequences.

Genome Sequencing of Four Strains of Rickettsia prowazekii, the Causative Agent of Epidemic Typhus, Including One Flying Squirrel Isolate.

Next-generation whole genome sequencing of dengue virus.

The Opisthorchis viverrini genome provides insights into life in the bile duct.

Genomic characterization of three unique Dehalococcoides that respire on persistent polychlorinated biphenyls.

Systems consequences of amplicon formation in human breast cancer.

Draft Genome Sequence of Polychlorinated Biphenyl-Dechlorinating Dehalococcoides mccartyi Strain SG1, Which Carries a Circular Putative Plasmid.

BAsE-Seq: a method for obtaining long viral haplotypes from short sequence reads.

The importance of study design for detecting differentially abundant features in high-throughput experiments.

Patient-specific driver gene prediction and risk assessment through integrated network analysis of cancer omics profiles.

High-depth sequencing of over 750 genes supports linear progression of primary tumors and metastases in most patients with liver-limited metastatic colorectal cancer.

Cloning and variation of ground state intestinal stem cells.

Recurrent Fusion Genes in Gastric Cancer: CLDN18-ARHGAP26 Induces Loss of Epithelial Integrity.

Tracking Dengue Virus Intra-host Genetic Diversity during Human-to-Mosquito Transmission.

Analysis of Dengue Virus Genetic Diversity during Human and Mosquito Infection Reveals Genetic Constraints.

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.

In vitro and in vivo correlates of physiological and neoplastic human Fallopian tube stem cells.

Genus-Wide Comparative Genomics of Malassezia Delineates Its Phylogeny, Physiology, and Niche Adaptation on Human Skin.

Single-molecule optical genome mapping of a human HapMap and a colorectal cancer cell line.

Mutational spectrum of Barrett's stem cells suggests paths to initiation of a precancerous lesion.

OPTIMA: sensitive and accurate whole-genome alignment of error-prone genomic maps by combinatorial indexing and technology-agnostic statistical analysis.

Predicting microbial interactions through computational approaches.

Fast and sensitive mapping of nanopore sequencing reads with GraphMap.

OPERA-LG: efficient and exact scaffolding of large, repeat-rich eukaryotic genomes with performance guarantees.

In Vivo Mapping of Eukaryotic RNA Interactomes Reveals Principles of Higher-Order Organization and Regulation.

@MInter: automated text-mining of microbial interactions.

Tissue Microbiome Profiling Identifies an Enrichment of Specific Enteric Bacteria in Opisthorchis viverrini Associated Cholangiocarcinoma.

INC-Seq: accurate single molecule reads using nanopore sequencing.

Whole metagenome profiling reveals skin microbiome-dependent susceptibility to atopic dermatitis flare.

Fast and accurate de novo genome assembly from long uncorrected reads.

Development of a genetically programed vanillin-sensing bacterium for high-throughput screening of lignin-degrading enzyme libraries.

Transcriptomics Analysis Reveals Putative Genes Involved in Biofilm Formation and Biofilm-associated Drug Resistance of Enterococcus faecalis.