2024
Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition
Zhang Y, Wang Z, Jiang Y, Littler D, Gerstein M, Purcell A, Rossjohn J, Ou H, Song J. Epitope-anchored contrastive transfer learning for paired CD8+ T cell receptor–antigen recognition. Nature Machine Intelligence 2024, 6: 1344-1358. DOI: 10.1038/s42256-024-00913-8.Peer-Reviewed Original ResearchPeptide-major histocompatibility complexT cellsEpitope-specific T cellsImmune responseResidue-level interactionsPredicted binding strengthSpike-specific immune responsesTCR-based immunotherapyTumor-associated antigensT cell antigen recognitionPredicted binding specificityAdaptive immune responsesTCR cross-reactivityTCR repertoireCross-reactivityBinding specificityAutoimmune diseasesImmunodominant epitopesContact residuesAntigen recognitionHistocompatibility complexTCRImmunotherapyDistance matrixT-cell receptor-antigen recognitionT-cell receptor binding prediction: A machine learning revolution
Weber A, Pélissier A, Martínez M. T-cell receptor binding prediction: A machine learning revolution. ImmunoInformatics 2024, 15: 100040. DOI: 10.1016/j.immuno.2024.100040.Peer-Reviewed Original ResearchProtein language modelsT cell receptorExtract biological insightsUnlabeled protein sequencesProtein sequencesBinding specificityBiological insightsProtein modelsRepertoire dataDeep learning modelsSequenceBlack-box modelsUnsupervised clustering approachDataset biasEvolution of computational modelsLack of generalityLanguage modelImmunizing sequencesMachine learning effortsCompetitive performanceOpaque modelsBiological propertiesLearning modelsClustering approachSupervised modelsCharacterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq
Guo L, Grinko A, Olson S, Leipold A, Graveley B, Saliba A, Pyle A. Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-Seq. RNA 2024, 30: rna.080032.124. PMID: 39174298, PMCID: PMC11482623, DOI: 10.1261/rna.080032.124.Peer-Reviewed Original ResearchNontemplated additionRNA-seqRNA sequencingGroup II self-splicing intronsTemplate-switching oligonucleotidesLong-read sequencingRNA-seq technologySelf-splicing intronsTemplate-switching reactionsLong RNA transcriptsRNA sequencing methodsWell-characterized enzymesPoly(A)-enriched RNART enzymeRNA identityNucleotide specificityEnzymatic specificityRNA librariesRNA transcriptsLong RNAsHuman RNARNA moleculesRNA referenceAccurate sequencingBinding specificity
2023
Efficient evolution of human antibodies from general protein language models
Hie B, Shanker V, Xu D, Bruun T, Weidenbacher P, Tang S, Wu W, Pak J, Kim P. Efficient evolution of human antibodies from general protein language models. Nature Biotechnology 2023, 42: 275-283. PMID: 37095349, PMCID: PMC10869273, DOI: 10.1038/s41587-023-01763-2.Peer-Reviewed Original ResearchConceptsProtein language modelsDiverse protein familiesLaboratory evolutionProtein familyProtein structureBinding specificityRare mutationsSelection pressureAntibiotic resistanceNatural evolutionary strategyEnzyme activityHuman antibodiesMature antibodiesAffinity maturationProteinAntibody bindingBinding affinityMutationsBindingEvolutionary strategyAffinityAntibodiesSevere acute respiratory syndrome coronavirus 2Acute respiratory syndrome coronavirus 2Respiratory syndrome coronavirus 2
2022
Diversity and distribution of MHC class I and II alleles in chicken populations worldwide
Martin R, Tregaskes C, Kaufman J. Diversity and distribution of MHC class I and II alleles in chicken populations worldwide. Molecular Immunology 2022, 150: 27. DOI: 10.1016/j.molimm.2022.05.092.Peer-Reviewed Original ResearchMinimal essential MHCClass II lociPeptide binding specificityPopulation bottlenecksClass II genesFancy breedsIllumina MiSeqPopulation geneticsLinkage disequilibriumCommercial flocksLow diversityChicken populationsArtificial selectionBinding specificityFree-range local chickensExon 2Genetic associationII lociHaplotypesResponse to infectionTapasin geneII genesTranslocation specificityExpress class II genesMHC allelesA positron emission tomography imaging probe selectively targeting the BD1 bromodomain and extra-terminal domain
Bai P, Yan L, Bagdasarian F, Wilks M, Wey H, Wang C. A positron emission tomography imaging probe selectively targeting the BD1 bromodomain and extra-terminal domain. Chemical Communications 2022, 58: 9654-9657. PMID: 35943085, PMCID: PMC9618257, DOI: 10.1039/d2cc03785h.Peer-Reviewed Original ResearchConceptsPositron emission tomography imaging studiesPositron emission tomographyNon-human primatesModerate brain uptakeImaging studiesBrain uptakePositron emission tomography imaging probeEmission tomographyBrain permeabilityBrainBromodomains of BRD2Clinical translationExtra-terminal domainTranslational potentialInhibitor developmentNeurological diseasesBinding specificity
2021
Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites
Pratt H, Andrews G, Phalke N, Huey J, Purcaro M, van der Velde A, Moore J, Weng Z. Factorbook: an updated catalog of transcription factor motifs and candidate regulatory motif sites. Nucleic Acids Research 2021, 50: d141-d149. PMID: 34755879, PMCID: PMC8728199, DOI: 10.1093/nar/gkab1039.Peer-Reviewed Original ResearchConceptsChIP-seqHT-SELEXTranscription factorsDNA-binding transcription factorsHT-SELEX experimentsChIP-seq dataChIP-seq experimentsAnnotation of variantsTF binding sitesCis-regulatory elementsTranscriptional regulatory proteinsDatabase of annotationsIntegrated analysisENCODE projectHuman genomeMotif modelsTrait heritabilityRegulatory proteinsBinding specificityGene expressionMotifBinding sitesCell typesRegulatory effectsComprehensive collectionThe Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partners
De Kumar B, Darland D. The Hox protein conundrum: The “specifics” of DNA binding for Hox proteins and their partners. Developmental Biology 2021, 477: 284-292. PMID: 34102167, PMCID: PMC8846413, DOI: 10.1016/j.ydbio.2021.06.002.Peer-Reviewed Original ResearchConceptsProtein binding specificityHox proteinsAnterior-posterior body axisTranscription factor-DNA interactionsBinding specificityHox protein functionMulti-protein interactionsHomeodomain transcription factorHomeotic genesSegmental identityUnique target specificityProtein functionTranscription factorsCooperative binding modelGene expressionBody axisMolecular characterizationTarget specificityProteinDNAMouse systemRecent studiesSubsequent alterationDrosophilaGenes
2011
Finding subtypes of transcription factor motif pairs with distinct regulatory roles
Bais AS, Kaminski N, Benos PV. Finding subtypes of transcription factor motif pairs with distinct regulatory roles. Nucleic Acids Research 2011, 39: e76-e76. PMID: 21486752, PMCID: PMC3113591, DOI: 10.1093/nar/gkr205.Peer-Reviewed Original ResearchConceptsTF binding sitesTranscription factorsDownstream regulationMotif pairsTF-DNA binding specificityBinding preferencesDNA binding specificityDNA binding preferencesDistinct regulatory rolesDownstream regulatory effectsMultiple regulatory pathwaysDifferent binding preferencesDyad motifDNA sequencesSequence elementsRegulatory pathwaysBinding specificityRegulatory roleDifferential recruitmentBinding sitesMotif discoveryRegulationCofactorMotifDistinct modes
2005
Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity
Raviscioni M, Gu P, Sattar M, Cooney AJ, Lichtarge O. Correlated Evolutionary Pressure at Interacting Transcription Factors and DNA Response Elements Can Guide the Rational Engineering of DNA Binding Specificity. Journal Of Molecular Biology 2005, 350: 402-415. PMID: 15946684, DOI: 10.1016/j.jmb.2005.04.054.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBiological EvolutionComputational BiologyDNADNA Mutational AnalysisDNA-Binding ProteinsEntropyEvolution, MolecularGenomicsHumansModels, GeneticModels, StatisticalMutationNucleic Acid ConformationPhylogenyProtein BindingProtein EngineeringReceptors, Cytoplasmic and NuclearReceptors, EstrogenResponse ElementsSoftwareThermodynamicsTranscription FactorsConceptsDNA binding specificityTranscription factorsBinding specificityEvolutionary importanceEvolutionary pressureResponse elementInteracting Transcription FactorsRational engineeringRelative evolutionary importanceProtein-DNA interfaceProtein-DNA interactionsTranscription factor proteinsDNA response elementsAmino acid residuesNuclear hormone receptorsTranscriptional regulatorsEvolutionary traceImportant residuesGene expressionRecognition codeMolecular mechanismsAcid residuesFactor proteinProtein residuesLRH-1
1999
Proteasome inhibition by the natural products epoxomicin and dihydroeponemycin: Insights into specificity and potency
Kim K, Myung J, Sin N, Crews C. Proteasome inhibition by the natural products epoxomicin and dihydroeponemycin: Insights into specificity and potency. Bioorganic & Medicinal Chemistry Letters 1999, 9: 3335-3340. PMID: 10612595, DOI: 10.1016/s0960-894x(99)00612-5.Peer-Reviewed Original Research
1988
Biosynthesis and turnover of a 34‐kDa protein growth factor in human cytotrophoblasts
ROY‐CHOUDHURY S, SEN‐MAJUMDAR A, MURTHY U, MISHRA V, KLIMAN H, NESTLER J, STRAUSS J, Manjusri D. Biosynthesis and turnover of a 34‐kDa protein growth factor in human cytotrophoblasts. The FEBS Journal 1988, 172: 777-783. PMID: 3350024, DOI: 10.1111/j.1432-1033.1988.tb13957.x.Peer-Reviewed Original ResearchConceptsProtein growth factorsWestern blot analysisMolecular massPolypeptide molecular massPartial amino acid sequenceAmino acid sequenceBlot analysisGrowth factorMetabolic labeling experimentsPulse-chase experimentsCellular mRNAsVitro translationAcid sequenceReceptor binding specificityBinding specificityIntact cellsLow molecular massBiosynthesisCultured cytotrophoblastsProteinMultinuclear syncytiotrophoblastHuman placentaLabeling experimentsHuman cytotrophoblastsCells
This site is protected by hCaptcha and its Privacy Policy and Terms of Service apply