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 ResearchConceptsTopologically 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
2016
Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education
Noble DB, Mochrie SG, O'Hern CS, Pollard TD, Regan L. Promoting convergence: The integrated graduate program in physical and engineering biology at Yale University, a new model for graduate education. Biochemistry And Molecular Biology Education 2016, 44: 537-549. PMID: 27292366, PMCID: PMC5132113, DOI: 10.1002/bmb.20977.Peer-Reviewed Original ResearchConceptsGraduate programsStudent peer learningDiversity of studentsVariety of careersNew graduate programCurricular requirementsPeer learningTransferable skillsPh.D.sEnrichment activitiesScience outreachGraduate schoolCommunication skillsOwn institutionSimilar programsTraining programNovel handQuantitative methodologyStudentsRecruiting activitySophisticated understandingSkillsProgram cohortSeamless blendingProgram
2015
Protein design: Past, present, and future
Regan L, Caballero D, Hinrichsen MR, Virrueta A, Williams DM, O'Hern CS. Protein design: Past, present, and future. Biopolymers 2015, 104: 334-350. PMID: 25784145, PMCID: PMC4856012, DOI: 10.1002/bip.22639.Peer-Reviewed Original Research
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
2013
Which Biomarkers Reveal Neonatal Sepsis?
Wang K, Bhandari V, Chepustanova S, Huber G, O'Hara S, O'Hern CS, Shattuck MD, Kirby M. Which Biomarkers Reveal Neonatal Sepsis? PLOS ONE 2013, 8: e82700. PMID: 24367543, PMCID: PMC3867385, DOI: 10.1371/journal.pone.0082700.Peer-Reviewed Original ResearchConceptsNeonatal intensive care unitNeonatal sepsisHospital Neonatal Intensive Care UnitIntensive care unitWhite blood cellsEssential diagnostic informationNeutrophil CD64Care unitSet of biomarkersOptimal biomarkerSepsisHematological dataScoring systemIndividual biomarkersLogistic regressionRapid diagnosisBlood cellsBiomarkersDiagnostic performanceLASSO logistic regressionDiagnostic informationDiagnostic classifierCD64InfantsInfection