2025
Physiologic mechanisms underlying polycystic kidney disease
Boletta A, Caplan M. Physiologic mechanisms underlying polycystic kidney disease. Physiological Reviews 2025, 105: 1553-1607. PMID: 39938884, PMCID: PMC12174308, DOI: 10.1152/physrev.00018.2024.Peer-Reviewed Original ResearchPrimary ciliaPolycystic kidney diseaseTrafficking of proteinsHuman ciliopathiesExtracellular signalsMultiple genesKidney diseaseProtein productionMolecular basisCell biologyMonogenic disordersCyst formationGenesRenal epithelial cellsProteinCiliaBiochemical informationApical surfaceEpithelial cellsFunctional expressionPhysiological propertiesWealth of informationPhysiological mechanismsCellsFibrocystin
2023
The Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms
Ladel L, Tan W, Jeyakanthan T, Sailo B, Sharma A, Ahuja N. The Promise of Epigenetics Research in the Treatment of Appendiceal Neoplasms. Cells 2023, 12: 1962. PMID: 37566041, PMCID: PMC10417136, DOI: 10.3390/cells12151962.Peer-Reviewed Original ResearchLarge-scale Investigations of AAC Usage Patterns: Trends, Autism, and Stacked Autoencoders
Atyabi A, Boccanfuso L, Snider J, Kim M, Barney E, Ahn Y, Li B, Dommer K, Shic F. Large-scale Investigations of AAC Usage Patterns: Trends, Autism, and Stacked Autoencoders. 2023, 00: 851-859. DOI: 10.1109/ccwc57344.2023.10099096.Peer-Reviewed Original ResearchAutism spectrum disorderAAC appSpeech-generating deviceUsage patternsLearning methodsDeep learning methodsStreams of dataUnsupervised learning methodIndividual usage patternsData modeling perspectiveNon-speech communicationData streamsData scienceStacked AutoencoderClassification accuracyModeling mechanismSpectrum disorderLanguage learningAlternative communication applicationPattern modelingAppsNumeric valuesFreeSpeechCommunication applicationsWealth of information
2022
Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila
Bosch J, Ugur B, Pichardo-Casas I, Rabasco J, Escobedo F, Zuo Z, Brown B, Celniker S, Sinclair D, Bellen H, Perrimon N. Two neuronal peptides encoded from a single transcript regulate mitochondrial complex III in Drosophila. ELife 2022, 11: e82709. PMID: 36346220, PMCID: PMC9681215, DOI: 10.7554/elife.82709.Peer-Reviewed Original ResearchConceptsSmall open reading framesClasses of genesShares sequence similarityOpen reading frameSequence similarityBicistronic transcriptBiological functionsPhenotypic analysisMitochondrial functionImportant regulatorThousands of peptidesNeuronal functionGenesWealth of informationTranscriptsAnimal lethalityPeptidesRecent studiesParalogsDrosophilaSmORFsMitochondriaRegulatorRegulatesNeuronal peptidesAntiviral Strategies Against SARS-CoV-2: A Systems Biology Approach
Prates ET, Garvin MR, Jones P, Miller JI, Sullivan KA, Cliff A, Gazolla JGFM, Shah MB, Walker AM, Lane M, Rentsch CT, Justice A, Pavicic M, Romero J, Jacobson D. Antiviral Strategies Against SARS-CoV-2: A Systems Biology Approach. Methods In Molecular Biology 2022, 2452: 317-351. PMID: 35554915, DOI: 10.1007/978-1-0716-2111-0_19.ChaptersConceptsSystems biology approachBiology approachHigh-performance computingArtificial intelligence methodologiesDiversity of informationIntelligence methodologiesStructural proteomicsSystem-level infrastructureMultiomics integrationCore frameworkViral pathogenesisAntiviral strategiesWealth of informationUnprecedented accessPathogensComputingComputational protocolPathogen detectionInformationProteomicsAdaptation analysisDevelopment of vaccinesProtocolInfrastructureNetwork
2018
Beyond genomics: understanding exposotypes through metabolomics
Rattray NJW, Deziel NC, Wallach JD, Khan SA, Vasiliou V, Ioannidis JPA, Johnson CH. Beyond genomics: understanding exposotypes through metabolomics. Human Genomics 2018, 12: 4. PMID: 29373992, PMCID: PMC5787293, DOI: 10.1186/s40246-018-0134-x.Peer-Reviewed Original ResearchConceptsGene-environment interactionsChallenges of metabolomicsIntegration of genomicsHuman genomeMultiple genetic variantsGenetic variationGenomic technologiesAssociation studiesMetabolic traitsMetabolite productionMetabolic processesIndividual phenotypesMetabolome-wide association studyProtein synthesisHuman population levelGenetic variantsBiological impactGenomicsDisease mechanismsMetabolomic informationWealth of informationPopulation levelSmall moleculesMetabolomicsTraits
2016
Recurrent genetic defects in classical Hodgkin lymphoma cell lines
Hudnall SD, Meng H, Lozovatsky L, Li P, Strout M, Kleinstein SH. Recurrent genetic defects in classical Hodgkin lymphoma cell lines. Leukemia & Lymphoma 2016, 57: 2890-2900. PMID: 27121023, DOI: 10.1080/10428194.2016.1177179.Peer-Reviewed Original ResearchConceptsMitosis-related genesSingle nucleotide variantsCHL cell linesCell linesRecurrent genetic defectsPathogenic single nucleotide variantsHL cell linesMitotic genesChromosome duplicationClassical Hodgkin lymphoma cell linesGenomic instabilityGenetic analysisWhole-exome sequencingNucleotide variantsGenesHodgkin's lymphoma cell linesLymphoma cell linesNumber variantsKaryotypic analysisGenetic defectsWealth of informationPoor growthVariantsDuplicationLinesChapter 23 hiPSC Models Relevant to Schizophrenia
Hartley B, Hadas Y, Brennand K. Chapter 23 hiPSC Models Relevant to Schizophrenia. Techniques In The Behavioral And Neural Sciences 2016, 23: 391-406. DOI: 10.1016/b978-0-12-800981-9.00023-7.ChaptersPluripotent stem cellsStem cellsPutative causal genesSpecific cellular phenotypesInduced pluripotent stem cellsGenomic lociTranscriptome sequencingRegulatory networksCausal genesCellular phenotypesGenetic manipulationMolecular mechanismsGenetic insultsFull complementPatient cellsEfficient derivationDisease initiationWealth of informationEnvironmental factorsRisk allelesCellsHuman brain tissueModel RelevantGross levelEtiology of schizophrenia
2011
AURA: Atlas of UTR Regulatory Activity
Dassi E, Malossini A, Re A, Mazza T, Tebaldi T, Caputi L, Quattrone A. AURA: Atlas of UTR Regulatory Activity. Bioinformatics 2011, 28: 142-144. PMID: 22057158, DOI: 10.1093/bioinformatics/btr608.Peer-Reviewed Original ResearchConceptsUntranslated regionMRNA untranslated regionsRegulatory activitySingle nucleotide variationsRegulatory annotationsPhylogenetic conservationIntuitive web interfaceNucleotide variationsGene expressionRNA sequencesComprehensive catalogSupplementary dataWealth of informationWeb interfaceSpecialized databasesBioinformaticsFull accessStructure dataAtlasConservationFunctional descriptionAnnotationSupplementary informationSequenceExpression
2006
Pathophysiology of leukocyte–tissue interactions
Molteni R, Fabbri M, Bender JR, Pardi R. Pathophysiology of leukocyte–tissue interactions. Current Opinion In Cell Biology 2006, 18: 491-498. PMID: 16904306, DOI: 10.1016/j.ceb.2006.08.001.Peer-Reviewed Original Research
1997
Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web
Panzer S, Cooley L, Miller P. Using explicitly represented biological relationships for database navigation and searching via the World-Wide Web. Bioinformatics 1997, 13: 281-290. PMID: 9183533, DOI: 10.1093/bioinformatics/13.3.281.Peer-Reviewed Original ResearchConceptsWorld Wide WebCGI scriptsDatabase navigationDatabase schemaBiological databasesRetrieval capabilitiesHypertext linksPrototype databaseRelated entitiesDatabase entriesDifferent entitiesPublic useWebWealth of informationDatabaseHyperlinksInformationNavigationBiological relationshipsEntitiesSchemaRequestsScriptsCapabilityNew type
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