2020
DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring
Zhang J, Liu J, Lee D, Lou S, Chen Z, Gürsoy G, Gerstein M. DiNeR: a Differential graphical model for analysis of co-regulation Network Rewiring. BMC Bioinformatics 2020, 21: 281. PMID: 32615918, PMCID: PMC7333332, DOI: 10.1186/s12859-020-03605-3.Peer-Reviewed Original ResearchConceptsCo-regulation networkCo-regulatory networkNetwork rewiringDisease regulatorsGenome-wide binding profilesGM12878 cell lineRNA polymerase IITumor suppressor BRCA1Transcription factor bindsChIP-seq dataDifferential graphical modelsBinding profileComplete binding profilesKey TFsPolymerase IIHub regulatorsPhenotypic variationFactor bindsGene expressionExpression changesCancerous stateRisk genesRegulatorCell linesCoordinated manner
2018
Oligodendrocyte precursor survival and differentiation requires chromatin remodeling by Chd7 and Chd8
Marie C, Clavairoly A, Frah M, Hmidan H, Yan J, Zhao C, Van Steenwinckel J, Daveau R, Zalc B, Hassan B, Thomas JL, Gressens P, Ravassard P, Moszer I, Martin DM, Lu QR, Parras C. Oligodendrocyte precursor survival and differentiation requires chromatin remodeling by Chd7 and Chd8. Proceedings Of The National Academy Of Sciences Of The United States Of America 2018, 115: e8246-e8255. PMID: 30108144, PMCID: PMC6126750, DOI: 10.1073/pnas.1802620115.Peer-Reviewed Original ResearchConceptsChromatin remodelersProliferation-differentiation balanceNormal developmentChromatin accessibility analysisOligodendrocyte precursor cellsChromatin closingChromatin remodelingChromatin openingTranscriptional repressionGenetic interactionsUncharacterized functionGenetic reprogrammingRisk-associated genesTranscriptional activationKey regulatorNeurodevelopmental defectsPrecursor survivalLineage cellsCHD7RemodelersOligodendrocyte lineage cellsPrecursor cellsGlioma formationBinding profileCHD8The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors
Kudron MM, Victorsen A, Gevirtzman L, Hillier LW, Fisher WW, Vafeados D, Kirkey M, Hammonds AS, Gersch J, Ammouri H, Wall ML, Moran J, Steffen D, Szynkarek M, Seabrook-Sturgis S, Jameel N, Kadaba M, Patton J, Terrell R, Corson M, Durham TJ, Park S, Samanta S, Han M, Xu J, Yan KK, Celniker SE, White KP, Ma L, Gerstein M, Reinke V, Waterston R. The ModERN Resource: Genome-Wide Binding Profiles for Hundreds of Drosophila and Caenorhabditis elegans Transcription Factors. Genetics 2018, 208: 937-949. PMID: 29284660, PMCID: PMC5844342, DOI: 10.1534/genetics.117.300657.Peer-Reviewed Original ResearchConceptsIndividual transcription factorsTranscription factorsModel organismsGenome-wide binding profilesMajor model organismsKey model organismDifferent transcription factorsTissue-specific patternsFly genomeWorm genomeChromatin immunoprecipitationStock CenterRegulatory pathwaysRegulatory sitesCaenorhabditisDrosophilaOrganismsGenomeBinding profileGenesModENCODESitesGFPImmunoprecipitationVast numberMeta regression: Relationship between antipsychotic receptor binding profiles and side-effects
Olten B, Bloch MH. Meta regression: Relationship between antipsychotic receptor binding profiles and side-effects. Progress In Neuro-Psychopharmacology And Biological Psychiatry 2018, 84: 272-281. PMID: 29410000, DOI: 10.1016/j.pnpbp.2018.01.023.Peer-Reviewed Original ResearchConceptsRisk of sedationExtrapyramidal side effectsM4 receptorsReceptor binding profileWeight gainAntipsychotic medicationSide effectsGeneric inverse variance methodReceptor affinityAffinity of antipsychoticsIndividual antipsychotic medicationsInverse variance methodTreatment of schizophreniaExtrapyramidal symptomsQTc prolongationM1 receptorsProlactin increaseQT prolongationAntipsychotic agentsH1 receptorsHigh riskMedicationsSedationBinding profileReceptors
2016
The zinc‐metallothionein redox system in human retina and RPE
Alvarez L, García M, Rodríguez S, Fernández B, Pereiro R, Sanz‐Medel A, Coca‐Prados M, González‐Iglesias H. The zinc‐metallothionein redox system in human retina and RPE. Acta Ophthalmologica 2016, 94 DOI: 10.1111/j.1755-3768.2016.0560.Peer-Reviewed Original ResearchHuman RPE cellsInflammatory cytokinesNeuroprotective functionOxidative stress processesEye sectionsNeural retinaHuman donorsRPE cellsRetinaHuman retinaHuman eyeRPEMT proteinExogenous zincCellular zinc homeostasisCellular modelZinc homeostasisMain regulatorStoichiometric transitionsEyesBinding profileProtein binding profileProtein synthesisLesser levelsMetallothionein
2013
Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs
Kudron M, Niu W, Lu Z, Wang G, Gerstein M, Snyder M, Reinke V. Tissue-specific direct targets of Caenorhabditis elegans Rb/E2F dictate distinct somatic and germline programs. Genome Biology 2013, 14: r5. PMID: 23347407, PMCID: PMC4053757, DOI: 10.1186/gb-2013-14-1-r5.Peer-Reviewed Original ResearchConceptsRb/E2FLin-35Target genesGenome-wide binding profilesGene expressionTissue-specific gene regulationLin-35 mutantsDistinct cell fatesSmall RNA pathwaysEffector target genesDirect target geneBinding profileGermline programHPL-2Chromatin associationH3K36 methylationRNA pathwaysCSR-1Germline transformationC. elegansGene regulationCell fateE2FDirect targetMultiple tissues
1996
Structure-Function Studies of Murine MIP-2, the Homologue of Melanoma Growth Stimulating Activity/gro-α and IL-8
Lolis E, Jerva L. Structure-Function Studies of Murine MIP-2, the Homologue of Melanoma Growth Stimulating Activity/gro-α and IL-8. NATO ASI Series 1996, 183-194. DOI: 10.1007/978-3-642-61180-3_17.Peer-Reviewed Original ResearchHuman melanoma cellsProtein 2Structure-function studiesAnalysis of sequencesLigand-receptor complexesMurine MIP-2Melanoma cellsThree-dimensional structureMurine homologueGene productsAmino terminusMutational analysisInflammatory protein-2Molecular mechanismsIL-8MIP-2High affinityProteinAutocrine growth factorBinding profileHomologuesMetastatic potentialGrowth factorMelanoma growthType B receptors
1992
Modulation of vascular cell behavior by transforming growth factors β
Madri J, Bell L, Merwin J. Modulation of vascular cell behavior by transforming growth factors β. Molecular Reproduction And Development 1992, 32: 121-126. PMID: 1637550, DOI: 10.1002/mrd.1080320207.Peer-Reviewed Original ResearchConceptsVascular cell typesCell typesCellular responsesCell surfaceTGF-beta receptorsVascular cell behaviorGrowth factor βDistinct bioassaysDifferent isoformsCell migrationCell behaviorInhibition of proliferationVascular cell responsesSmooth muscle cellsUnique binding profileAngiogenic assaysIsoformsBinding profileCell populationsBovine aortic endothelialFactor βMuscle cellsType IBASMCsAortic endothelial
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