2021
Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India
Pandit B, Bhattacharjee S, Bhattacharjee B. Association of clade-G SARS-CoV-2 viruses and age with increased mortality rates across 57 countries and India. Infection Genetics And Evolution 2021, 90: 104734. PMID: 33508515, PMCID: PMC7839510, DOI: 10.1016/j.meegid.2021.104734.Peer-Reviewed Original ResearchConceptsIndication of population expansionNegative Tajima's D valuesAllele frequency spectrumTajima's D valuesSARS-CoV-2 sequencesAmino acid changesClade of virusesNucleotide diversityEvolutionary analysisLinkage disequilibriumPopulation expansionContribution of host factorsViral haplotypesClade GAcid changesSARS-CoV-2 variantsViral populationsHost factorsMortality rateVariantsViral factorsNetwork analysisCoronary heart diseaseSARS-CoV-2 virusVirus
2015
Limits and patterns of cytomegalovirus genomic diversity in humans
Renzette N, Pokalyuk C, Gibson L, Bhattacharjee B, Schleiss M, Hamprecht K, Yamamoto A, Mussi-Pinhata M, Britt W, Jensen J, Kowalik T. Limits and patterns of cytomegalovirus genomic diversity in humans. Proceedings Of The National Academy Of Sciences Of The United States Of America 2015, 112: e4120-e4128. PMID: 26150505, PMCID: PMC4522815, DOI: 10.1073/pnas.1501880112.Peer-Reviewed Original ResearchConceptsGenomic diversityHuman hostGenome-wide mutationsHuman cytomegalovirusRecombination rate mapsHCMV populationsViral genomic diversityGenome beingRegulatory proteinsViral populationsDiversityPolymorphismHostPatient samplesDiverse regionsGenomeNatural infectionLociCongenitally infected infantsGenesMutationsProteinInfected infantsGlycoproteinRecombination
2013
Differential Expression of HPV16 L2 Gene in Cervical Cancers Harboring Episomal HPV16 Genomes: Influence of Synonymous and Non-Coding Region Variations
Mandal P, Bhattacharjee B, Ghosh D, Mondal N, Chowdhury R, Roy S, Sengupta S. Differential Expression of HPV16 L2 Gene in Cervical Cancers Harboring Episomal HPV16 Genomes: Influence of Synonymous and Non-Coding Region Variations. PLOS ONE 2013, 8: e65647. PMID: 23762404, PMCID: PMC3675152, DOI: 10.1371/journal.pone.0065647.Peer-Reviewed Original ResearchMeSH KeywordsAdultAgedCapsid ProteinsCarcinoma, Squamous CellFemaleGene DosageGene Expression Regulation, ViralGenome, ViralHost-Pathogen InteractionsHuman papillomavirus 16HumansMicroRNAsMiddle AgedOncogene Proteins, ViralOpen Reading FramesPapillomavirus InfectionsPlasmidsPolymorphism, GeneticPromoter Regions, GeneticRNA, MessengerSequence Analysis, DNAUterine Cervical NeoplasmsConceptsNon-coding regionsHPV16 genomeSynonymous variationNon-malignant samplesHuman codonsL2 genesWhole-genome sequence analysisShort non-coding regionHPV16 isolatesGenome sequence analysisMiRNA binding sitesWeak promoter activityHsa-mir-548Gene copy numberCaCx casesEpisomal HPV16 genomesSequence variationCoding regionSequence analysisGenomeNon-codingViral genomeEpisomal viral genomesCopy numberL2 ORF
2011
Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants
Renzette N, Bhattacharjee B, Jensen J, Gibson L, Kowalik T. Extensive Genome-Wide Variability of Human Cytomegalovirus in Congenitally Infected Infants. PLOS Pathogens 2011, 7: e1001344. PMID: 21625576, PMCID: PMC3098220, DOI: 10.1371/journal.ppat.1001344.Peer-Reviewed Original ResearchConceptsRNA virusesReplication of RNA genomesGenome-wide variabilityPopulation genetic analysesRNA virus populationsHuman cytomegalovirusGenome wide studiesAmino acid levelsIntrahost populationsDsDNA genomeRNA genomeGenomic variabilityGenome typesPositive selectionGenetic analysisGenomeDNA virusesVirus populationsViral populationsWide studiesCongenital human cytomegalovirusImmune-mediated mechanismsCongenitally infected infantsSamples of neonatesFidelity replication
2008
Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis
Bhattacharjee B, Mandal N, Roy S, Sengupta S. Characterization of sequence variations within HPV16 isolates among Indian women: Prediction of causal role of rare non-synonymous variations within intact isolates in cervical cancer pathogenesis. Virology 2008, 377: 143-150. PMID: 18495198, DOI: 10.1016/j.virol.2008.04.007.Peer-Reviewed Original ResearchConceptsNon-synonymous changesCharacterization of sequence variationsPolymorphic variationDeleterious to protein functionHPV16 isolatesNon-synonymous variationsRare non-synonymous variationsDeleterious variationHaplotype backgroundNucleotide variationsSIFTS databaseDeleterious mutationsSequence variationSequence variantsProtein functionHPV16 genomeHaplotype analysisHaplotypesFunctional validationCervical cancer pathogenesisE-12IsolatesCaCx developmentCancer pathogenesisProductive infection
2006
CpG methylation of HPV 16 LCR at E2 binding site proximal to P97 is associated with cervical cancer in presence of intact E2
Bhattacharjee B, Sengupta S. CpG methylation of HPV 16 LCR at E2 binding site proximal to P97 is associated with cervical cancer in presence of intact E2. Virology 2006, 354: 280-285. PMID: 16905170, DOI: 10.1016/j.virol.2006.06.018.Peer-Reviewed Original ResearchConceptsLong control regionE2 binding sitesP97 promoterCervical cancerNormal controlsAssociated with cervical cancerCytologically normal controlsIntact E2 geneHuman papillomavirus type 16Binding sitesMspI restriction digestionRegulate transcriptionRepressor activityHPV-16CaCx samplesCpG methylationControl regionIntact E2Restriction digestionE7 genesType 16E2 geneCaCxMalignant samplesSite methylation