2018
De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski
Biswal DK, Roychowdhury T, Pandey P, Tandon V. De novo genome and transcriptome analyses provide insights into the biology of the trematode human parasite Fasciolopsis buski. PLOS ONE 2018, 13: e0205570. PMID: 30325945, PMCID: PMC6191129, DOI: 10.1371/journal.pone.0205570.Peer-Reviewed Original ResearchConceptsShort interspersed elementsTranscriptome dataTranscriptome analysisDe novo genomeDraft genome assemblyGiant intestinal flukeNext-generation sequencing technologiesGeneration sequencing technologyNovo genomeRNAi pathwayGenome assemblyTransposable elementsEcological diversityImportant biological characteristicsInterspersed elementsGenome analysisProtein kinaseOverall transcriptomeSequencing technologiesTrematode parasitesFasciolopsis buskiEnergy metabolismIntestinal flukesSuitable diagnostic systemOrganismsClassification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences
Roychowdhury T, Singh VK, Bhattacharya A. Classification of pathogenic microbes using a minimal set of single nucleotide polymorphisms derived from whole genome sequences. Genomics 2018, 111: 205-211. PMID: 29432978, DOI: 10.1016/j.ygeno.2018.02.004.Peer-Reviewed Original ResearchConceptsIntra-species genomic variationsPathogenic microbesClassification of organismsWhole genome sequencesContext-specific mannerGenome sequencePhenotypic diversityGenomic variationSingle nucleotide polymorphismsMolecular markersNGS technologiesEscherichia coliNucleotide polymorphismsSpecific mannerE. coliSNPsPathogen classificationMicrobesOrganismsWealth of dataColiMinimal setImportant rolePhylogroupsDiversity
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