2015
Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis
Roychowdhury T, Mandal S, Bhattacharya A. Analysis of IS6110 insertion sites provide a glimpse into genome evolution of Mycobacterium tuberculosis. Scientific Reports 2015, 5: 12567. PMID: 26215170, PMCID: PMC4517164, DOI: 10.1038/srep12567.Peer-Reviewed Original ResearchConceptsDifferent lineagesGenome-level variationCopy number patternsNext-generation sequencing platformsGenome evolutionUseful molecular markerAncestral insertionIndependent evolutionPhylogenetic treeGenome sequenceMycobacterium tuberculosis genomeInsertion siteSequencing platformsMolecular markersComputational pipelineRecombinational lossLineagesIS6110 insertion sitesTuberculosis genomeDifferent isolatesNGS dataInsertion regionInsertion data
2013
Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data
Roychowdhury T, Vishnoi A, Bhattacharya A. Next-Generation Anchor Based Phylogeny (NexABP): Constructing phylogeny from Next-generation sequencing data. Scientific Reports 2013, 3: 2634. PMID: 24022334, PMCID: PMC3769656, DOI: 10.1038/srep02634.Peer-Reviewed Original ResearchConceptsPhylogenetic analysisNext-generation sequencing datasetsWhole genome sequencesNGS dataNext-generation sequencing dataEvolutionary relationshipsStrains/isolatesPhylogenetic constructionDistinct lineagesReference genomeGenome sequenceSequencing datasetsSequencing dataEscherichia coliPhylogenyDifferent strainsVibrio choleraBootstrap analysisGenomeLineagesOrganismsColiInner branchesUnprecedented scalePathogens