2021
Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization
Lou S, Li T, Liu J, Gerstein M. Gene Tracer: a smart, interactive, voice-controlled Alexa skill For gene information retrieval and browsing, mutation annotation and network visualization. Bioinformatics 2021, 37: 2998-3000. PMID: 33792640, PMCID: PMC8479666, DOI: 10.1093/bioinformatics/btab107.Peer-Reviewed Original ResearchConceptsAlexa skillAmazon Alexa skillInformation retrievalMutation annotationsVoice recognitionInteractive inputVisualization experienceDemonstration videoNetwork visualizationSupplementary dataGenome browserUsersMore flexibilityGene informationInformationQueriesBrowserBrowsingVideoKeyboardTechnological advancesRetrievalAnnotationNetworkBioinformatics
2020
TopicNet: a framework for measuring transcriptional regulatory network change
Lou S, Li T, Kong X, Zhang J, Liu J, Lee D, Gerstein M. TopicNet: a framework for measuring transcriptional regulatory network change. Bioinformatics 2020, 36: i474-i481. PMID: 32657410, PMCID: PMC7355251, DOI: 10.1093/bioinformatics/btaa403.Peer-Reviewed Original ResearchConceptsRegulatory network changesTranscription factorsCellular statesDifferent regulatory programsCollection of genesDifferent cellular statesParticular cellular stateParticular transcription factorsRegulatory network connectivityKey transcription factorGene expression dataChromatin immunoprecipitationRegulatory networksCell statesExpression dataRegulatory programsHuman cellsDifferential survivalDiverse groupSupplementary dataDynamic changesLoss of targetImmunoprecipitationGenesActivity differences