2024
Enhancing RBP Binding Site Prediction on Long RNA Sequences through Large Language Models
Guo J, Yang Y. Enhancing RBP Binding Site Prediction on Long RNA Sequences through Large Language Models. 2024, 00: 6998-7004. DOI: 10.1109/bibm62325.2024.10822773.Peer-Reviewed Original ResearchRNA-binding proteinsBinding site predictionRNA sequencingSite predictionRNA-binding protein binding sitesLong RNA sequencesRNA structureGene regulationSequence informationBase pairsSequence integrityBinding proteinBiological processesRNABinding sitesSequenceProteinProtein bindingSequence predictionLong sequencesGenesEnformerSitesBindingBiology
2023
Surgical management of peritoneal metastasis: Opportunities for pharmaceutical research
Wientjes M, Lu Z, Chan C, Turaga K, Au J. Surgical management of peritoneal metastasis: Opportunities for pharmaceutical research. Journal Of Controlled Release 2023, 361: 717-726. PMID: 37574051, PMCID: PMC10560040, DOI: 10.1016/j.jconrel.2023.08.017.Peer-Reviewed Original ResearchConceptsCytoreductive surgeryIntraperitoneal chemotherapyPatient ascitesPeritoneal metastasisPM patientsTreatment of peritoneal metastasesPresence of ascitesAccumulation of ascitesProtein bindingTumor locationTumor sizeSystemic treatmentAscites samplesAscitesClinical advancesAAG concentrationPatient managementTreatment outcomesPaclitaxelVariable efficacyPatientsProteomic analysisFree fractionAscites proteinsHyperthermic temperatures
2022
Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways
Kasher M, Williams F, Freidin M, Malkin I, Cherny S, Benjamin E, Chasman D, Dehghan A, Ahluwalia T, Meigs J, Tracy R, Alizadeh B, Ligthart S, Bis J, Eiriksdottir G, Pankratz N, Gross M, Rainer A, Snieder H, Wilson J, Psaty B, Dupuis J, Prins B, Vaso U, Stathopoulou M, Franke L, Lehtimaki T, Koenig W, Jamshidi Y, Siest S, Abbasi A, Uitterlinden A, Abdollahi M, Schnabel R, Schick U, Nolte I, Kraja A, Hsu Y, Tylee D, Zwicker A, Uher R, Davey-Smith G, Morrison A, Hicks A, van Duijn C, Ward-Caviness C, Boerwinkle E, Rotter J, Rice K, Lange L, Perola M, de Geus E, Morris A, Makela K, Stacey D, Eriksson J, Frayling T, Slagboom E, Livshits G. Understanding the complex genetic architecture connecting rheumatoid arthritis, osteoporosis and inflammation: discovering causal pathways. Human Molecular Genetics 2022, 31: 2623-2632. PMID: 35349660, PMCID: PMC9402243, DOI: 10.1093/hmg/ddac061.Peer-Reviewed Original ResearchConceptsCausal single nucleotide polymorphismsSingle nucleotide polymorphismsGenetic architectureColocalization analysisSame molecular functionAnalysis of pleiotropyComplex genetic architectureGenome-wide association study summary statisticsOp phenotypeMolecular functionsGenomic regionsPleiotropyOsteoporosis ConsortiumGenetic relationshipsGenetic backgroundGenetic variantsNucleotide polymorphismsMendelian randomizationGenesTraitsPhenotypeGenetic factorsProtein bindingUK BiobankHorizontal pleiotropy
2021
Chemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates
Hsiang M, Chobrutskiy BI, Diaz M, Huda TI, Creadore S, Zaman S, Cios KJ, Gozlan EC, Blanck G. Chemical complementarity between immune receptors and cancer mutants, independent of antigen presentation protein binding, is associated with increased survival rates. Translational Oncology 2021, 14: 101069. PMID: 33780706, PMCID: PMC8039726, DOI: 10.1016/j.tranon.2021.101069.Peer-Reviewed Original ResearchT cell receptor alpha geneAmino acidsT cell receptorChemical complementarityV-J recombinationMutant amino acidsThe Cancer Genome Atlas (TCGA) databaseCancer Genome Atlas (TCGA) databaseCancer mutantsBioinformatics approachAlpha geneReceptor alpha geneImmune receptorsComplement genesAtlas databaseMutantsPeptide sequencesSpecific interactionsGenesII bindingLRP2Region 3 sequencesUterine cancerProtein bindingBinding
2020
Identification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene
Yao GQ, Zhu M, Walker J, Insogna K. Identification of a 22 bp DNA cis Element that Plays a Critical Role in Colony Stimulating Factor 1-Dependent Transcriptional Activation of the SPHK1 Gene. Calcified Tissue International 2020, 107: 52-59. PMID: 32246175, PMCID: PMC7274855, DOI: 10.1007/s00223-020-00685-4.Peer-Reviewed Original ResearchConceptsColony stimulating factor 1Sphingosine kinase 1Bp fragmentSPHK1 promoterBp sequenceSphK1 geneDNA cis elementsProtein binding regionsSPHK1 gene expressionBp DNA fragmentStimulating factor 1Dual-luciferase reporterPutative DNATranscriptional activationTranscription factorsNuclear proteinsDNA sequencesCis elementsDNA bindingGene expressionPromoter activityDNA fragmentsKinase 1EMSAsProtein binding
2019
Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome
Brown AL, de Smith AJ, Gant VU, Yang W, Scheurer ME, Walsh KM, Chernus JM, Kallsen NA, Peyton SA, Davies GE, Ehli EA, Winick N, Heerema NA, Carroll AJ, Borowitz MJ, Wood BL, Carroll WL, Raetz EA, Feingold E, Devidas M, Barcellos LF, Hansen HM, Morimoto L, Kang AY, Smirnov I, Healy J, Laverdière C, Sinnett D, Taub JW, Birch JM, Thompson P, Spector LG, Pombo-de-Oliveira MS, DeWan AT, Mullighan CG, Hunger SP, Pui CH, Loh ML, Zwick ME, Metayer C, Ma X, Mueller BA, Sherman SL, Wiemels JL, Relling MV, Yang JJ, Lupo PJ, Rabin KR. Inherited genetic susceptibility to acute lymphoblastic leukemia in Down syndrome. Blood 2019, 134: 1227-1237. PMID: 31350265, PMCID: PMC6788009, DOI: 10.1182/blood.2018890764.Peer-Reviewed Original ResearchMeSH KeywordsChildCyclin-Dependent Kinase Inhibitor p16DNA-Binding ProteinsDown SyndromeGATA3 Transcription FactorGene FrequencyGenetic Predisposition to DiseaseGenome-Wide Association StudyHumansIkaros Transcription FactorPolymorphism, Single NucleotidePrecursor Cell Lymphoblastic Leukemia-LymphomaTranscription FactorsConceptsFirst genome-wide association studySusceptibility lociGenome-wide association studiesGenome-wide significanceFurther biological insightsGenetic variationEnhancer activityRisk lociBiological insightsLymphoblastoid cell linesAssociation studiesDifferential protein bindingFunctional significanceLociRisk allele frequenciesCell linesAllele frequenciesHigh penetranceRisk allelesProtein bindingCDKN2AGenetic susceptibilityHigher proliferationPenetranceAllele associations
2018
Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins
Kisley L, Miller K, Davis CM, Guin D, Murphy EA, Gruebele M, Leckband DE. Soluble Zwitterionic Poly(sulfobetaine) Destabilizes Proteins. Biomacromolecules 2018, 19: 3894-3901. PMID: 30064224, DOI: 10.1021/acs.biomac.8b01120.Peer-Reviewed Original ResearchConceptsProtein melting temperatureBiotechnological applicationsSpecific proteinsProtein conformationTryptophan fluorescenceProteinTryptophan residuesThermal denaturation studiesDenaturation studiesCooperativity increasesProtein bindingPSBLocal polarityInteractsResiduesPEG solutionBindingCooperativityConformationFluorescence
2011
GroEL/GroES‐mediated protein folding
Horwich A, Tyagi N, Clare D, Saibil H. GroEL/GroES‐mediated protein folding. The FASEB Journal 2011, 25: 319.3-319.3. DOI: 10.1096/fasebj.25.1_supplement.319.3.Peer-Reviewed Original ResearchProtein foldingGroEL/GroES chaperonin systemGroE chaperonin systemSubstrate protein bindingNon-native speciesChaperonin systemGroEL ringApical domainConformational trajectoryDomain movementsGroES bindingGroESHydrophobic contactsGroELFoldingInitial associationBindingProtein bindingOpen ringCryoEMSpeciesATPDomainNumber of approaches
2006
The Unique-5 and -6 Motifs of ZO-1 Regulate Tight Junction Strand Localization and Scaffolding Properties
Fanning AS, Little BP, Rahner C, Utepbergenov D, Walther Z, Anderson JM. The Unique-5 and -6 Motifs of ZO-1 Regulate Tight Junction Strand Localization and Scaffolding Properties. Molecular Biology Of The Cell 2006, 18: 721-731. PMID: 17182847, PMCID: PMC1805089, DOI: 10.1091/mbc.e06-08-0764.Peer-Reviewed Original ResearchConceptsProper cellular locationMAGUK protein familyZO-1Tight junction transmembrane proteinsGUK domainTight junctionsMAGUK proteinsProtein familyScaffolding functionsTransmembrane proteinComplex protein bindingCellular locationLateral cell membranesRegulatory functionsC-terminalCultured cellsCell membraneJunction strandsVariable regionsMotifProteinBindingU5Protein bindingMAGUKs
1998
Binding of the 60-kDa Ro autoantigen to Y RNAs: evidence for recognition in the major groove of a conserved helix.
Green C, Long K, Shi H, Wolin S. Binding of the 60-kDa Ro autoantigen to Y RNAs: evidence for recognition in the major groove of a conserved helix. RNA 1998, 4: 750-65. PMID: 9671049, PMCID: PMC1369656, DOI: 10.1017/s1355838298971667.Peer-Reviewed Original ResearchConceptsY RNAsSpecific base pairsRo proteinRRNA precursorConserved helixMajor grooveBase pairsSmall cytoplasmic RNAThree-nucleotide bulgeProtein side chainsProtein bindsCytoplasmic RNARNA sequencesProtein recognitionRNAXenopus oocytesProteinHelixRo autoantigenDistinct classesDiethyl pyrocarbonateProtein bindingStructural alterationsSide chainsDimethyl sulfate
1967
The physiological disposition of the carcinostatic 1,3‐bis(2‐chloroethyU‐l‐nitrosourea (BCNU) in man and animals
DeVita V, Denham C, Davidson J, Oliverio V. The physiological disposition of the carcinostatic 1,3‐bis(2‐chloroethyU‐l‐nitrosourea (BCNU) in man and animals. Clinical Pharmacology & Therapeutics 1967, 8: 566-577. PMID: 4951973, DOI: 10.1002/cpt196784566.Peer-Reviewed Original Research
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