2024
Identifying topologically associating domains using differential kernels
Maisuradze L, King M, Surovtsev I, Mochrie S, Shattuck M, O’Hern C. Identifying topologically associating domains using differential kernels. PLOS Computational Biology 2024, 20: e1012221. PMID: 39008525, PMCID: PMC11249266, DOI: 10.1371/journal.pcbi.1012221.Peer-Reviewed Original ResearchMeSH KeywordsAlgorithmsAnimalsChromatinComputational BiologyHumansImage Processing, Computer-AssistedConceptsTopologically associating domainsHi-C mapsFalse discovery rateChromatin conformation capture techniquesEnhancer-promoter interactionsLow false discovery rateSelf-interacting regionsStructure of chromatinRegulate gene expressionAverage contact probabilitiesHi-CLocus IDNA transcriptionGene expressionChromatinDiscovery rateContact probabilityBiological phenomenaState-of-the-artKernel-based techniqueComputer visionReplicationCorrelated changesDisease statesCapture techniques
2020
Using physical features of protein core packing to distinguish real proteins from decoys
Grigas AT, Mei Z, Treado JD, Levine ZA, Regan L, O'Hern CS. Using physical features of protein core packing to distinguish real proteins from decoys. Protein Science 2020, 29: 1931-1944. PMID: 32710566, PMCID: PMC7454528, DOI: 10.1002/pro.3914.Peer-Reviewed Original ResearchConceptsProtein structureReal protein structuresProtein coreReal proteinsAmino acid sequenceProtein core packingProtein structure predictionBiennial Critical AssessmentSet of decoysAcid sequenceProtein packingHydrophobic residuesCore packingStructure Prediction competitionTarget sequenceStructure predictionDecoy structuresProteinHydrophobic coreDecoysResiduesProtein Structure Prediction competitionsKey physical featuresSequenceImportant physical features
2014
Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models
Zhou AQ, O'Hern CS, Regan L. Predicting the side‐chain dihedral angle distributions of nonpolar, aromatic, and polar amino acids using hard sphere models. Proteins Structure Function And Bioinformatics 2014, 82: 2574-2584. PMID: 24912976, DOI: 10.1002/prot.24621.Peer-Reviewed Original Research