2025
Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells.
D'Mello A, Murphy T, Wade M, Kirkham C, Kong Y, Tettelin H, Pettigrew M. Host-pathogen interaction profiling of nontypeable Haemophilus influenzae and Moraxella catarrhalis coinfection of bronchial epithelial cells. MSphere 2025, e0024225. PMID: 40492732, DOI: 10.1128/msphere.00242-25.Peer-Reviewed Original ResearchRegulation of quorum sensingTranscriptome profilingBioinformatics analysisCell culture modelBiological pathwaysIron-sulfur metabolismHost-pathogen interactionsHost biological pathwaysHost cell pathwaysIscR regulonChronic obstructive pulmonary diseaseEpithelial cellsQuorum sensingEpithelial cell infectionRNA-seqH292 cell lineHost pathwaysExacerbation of chronic obstructive pulmonary diseaseNontypeable Haemophilus influenzaeRNA sequencingHost cellsDifferential regulationCulture modelBronchial epithelial cellsMono-infection
2011
AlleleSeq: analysis of allele‐specific expression and binding in a network framework
Rozowsky J, Abyzov A, Wang J, Alves P, Raha D, Harmanci A, Leng J, Bjornson R, Kong Y, Kitabayashi N, Bhardwaj N, Rubin M, Snyder M, Gerstein M. AlleleSeq: analysis of allele‐specific expression and binding in a network framework. Molecular Systems Biology 2011, 7: msb201154. PMID: 21811232, PMCID: PMC3208341, DOI: 10.1038/msb.2011.54.Peer-Reviewed Original ResearchMeSH KeywordsAllelesCell LineChromosome MappingChromosomes, Human, XChromosomes, Human, YDatabases, GeneticDNA-Binding ProteinsGene Expression RegulationGene Regulatory NetworksGenome, HumanHumansMolecular Sequence AnnotationOligonucleotide Array Sequence AnalysisPolymorphism, Single NucleotideSequence Analysis, RNATranscription FactorsConceptsAllele-specific expressionGenome sequenceFunctional genomics data setsAllele-specific behaviorAllele-specific eventsDiploid genome sequenceChIP-seq data setsGenomic data setsGenomic sequence variantsPersonal genome sequencesAlignment of readsRNA-seqGenome ProjectPaternal alleleComputational pipelineReads mappingSequence variantsNetwork motifsVariation dataReference alleleAllelesReadsSequenceExpressionMaternally
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