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
2019
Organization of Embryonic Morphogenesis via Mechanical Information
Das D, Jülich D, Schwendinger-Schreck J, Guillon E, Lawton AK, Dray N, Emonet T, O'Hern CS, Shattuck MD, Holley SA. Organization of Embryonic Morphogenesis via Mechanical Information. Developmental Cell 2019, 49: 829-839.e5. PMID: 31178400, PMCID: PMC6590525, DOI: 10.1016/j.devcel.2019.05.014.Peer-Reviewed Original ResearchConceptsEmbryonic organizerCell motionCell polarityTransgenic perturbationsEmbryonic morphogenesisMorphogen signalingTail organizerZebrafish embryosCell movementMechanical informationCell adhesionCell contractilityNeighboring cellsLocal biochemicalEmbryosMorphogenesisSecondary consequenceAdditional mechanismCellsMorphogensTranscriptionSignalingSystematic analysisOrganizersComputational modeling
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