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 techniquesActive tension and membrane friction mediate cortical flows and blebbing in a model actomyosin cortex
Sakamoto R, Murrell M. Active tension and membrane friction mediate cortical flows and blebbing in a model actomyosin cortex. Physical Review Research 2024, 6: 033024. DOI: 10.1103/physrevresearch.6.033024.Peer-Reviewed Original ResearchActomyosin cortexCell membraneActin cytoskeletonCortical flowMembrane blebbingCell divisionCell migrationCytoskeletonActomyosinBiological phenomenaMembrane bulgesBlebsCellsMembraneViscoelastic fluidMechanical responseElastic stressesStress yieldActinUbiquitous structuresApoptosisMechanical stressMembrane elasticityPhysical behavior
2022
The hierarchical basis of serial homology and evolutionary novelty
DiFrisco J, Love A, Wagner G. The hierarchical basis of serial homology and evolutionary novelty. Journal Of Morphology 2022, 284: e21531. PMID: 36317664, DOI: 10.1002/jmor.21531.Peer-Reviewed Original ResearchConceptsSerial homologyWing serial homologsTree of lifeExtent of homologyParalogous genesEvolutionary noveltyPhylogenetic historyPhylogenetic conceptsGene sequencesSerial homologsEvolutionary precursorPhylogenetic interpretationMost biologistsHomologyCell typesBiological phenomenaGenetic contributionEpidermal appendagesWidespread overlapGenesNew charactersHomologLineagesAppendagesFecundityCounting fluorescently labeled proteins in tissues in the spinning–disk microscope using single–molecule calibrations
Liao M, Kuo Y, Howard J. Counting fluorescently labeled proteins in tissues in the spinning–disk microscope using single–molecule calibrations. Molecular Biology Of The Cell 2022, 33: ar48. PMID: 35323029, PMCID: PMC9265152, DOI: 10.1091/mbc.e21-12-0618.Peer-Reviewed Original ResearchConceptsEnd-binding protein 1Spinning-disk confocal microscopyConfocal microscopySingle-molecule imagingComplex biological phenomenaFly larvaeLiving cellsCell surfaceMicrotubule endsBiological phenomenaProtein 1Brightness of fluorophoresCytoplasmic concentrationEpifluorescence microscopeBiological systemsSensory neuronsCellsSingle moleculesAbsolute numberMolecular numberTissueLarvaeMicrotubulesEGFPProtein
2018
CellCycleTRACER accounts for cell cycle and volume in mass cytometry data
Rapsomaniki M, Lun X, Woerner S, Laumanns M, Bodenmiller B, Martínez M. CellCycleTRACER accounts for cell cycle and volume in mass cytometry data. Nature Communications 2018, 9: 632. PMID: 29434325, PMCID: PMC5809393, DOI: 10.1038/s41467-018-03005-5.Peer-Reviewed Original Research
2013
Photonic crystal enhanced microscopy for imaging of live cell adhesion
Chen W, Long K, Lu M, Chaudhery V, Yu H, Choi J, Polans J, Zhuo Y, Harley B, Cunningham B. Photonic crystal enhanced microscopy for imaging of live cell adhesion. Analyst 2013, 138: 5886-5894. PMID: 23971078, DOI: 10.1039/c3an01541f.Peer-Reviewed Original ResearchConceptsTime-resolved imagingPhotonic crystalsRelevant time-scalesTime-scalesDrug-induced apoptosisSubmicron resolutionSpatial resolutionMorphological signaturesStem cell differentiationCell-surface interactionsFilopodial extensionsPhotonsCell adhesionCell differentiationDynamic informationCell attachmentLiving cell adhesionMonitor cell behaviorCell behaviorBiological phenomenaResolutionApoptosisEvolutionChemotaxisLabel-free
2012
SPLOOCE
Kroll J, Galante P, Ohara D, Navarro F, Ohno-Machado L, de Souza S. SPLOOCE. RNA Biology 2012, 9: 1339-1343. PMID: 23064119, PMCID: PMC3597574, DOI: 10.4161/rna.22182.Peer-Reviewed Original ResearchIncorporating auxiliary information for improved prediction in high-dimensional datasets: an ensemble of shrinkage approaches
Boonstra P, Taylor J, Mukherjee B. Incorporating auxiliary information for improved prediction in high-dimensional datasets: an ensemble of shrinkage approaches. Biostatistics 2012, 14: 259-272. PMID: 23087411, PMCID: PMC3590922, DOI: 10.1093/biostatistics/kxs036.Peer-Reviewed Original ResearchConceptsHigh-dimensional datasetsAuxiliary informationRidge estimatorBayesian alternativeOutcome YSimulation studyEstimates of BShrinkage approachBiological processesRidge regressionGene expression datasetsDatasetGenomic technologiesMicroarray technologyOptimal choiceBalance efficiencyX.EstimationPrediction errorPolymerase chain reactionBiological phenomenaInformationTechnologyQuantitative real-time polymerase chain reaction
2011
Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions
Bhattacharyya M, Vishveshwara S. Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein – ligand interactions. Molecular Omics 2011, 7: 2320-2330. PMID: 21617814, DOI: 10.1039/c1mb05038a.Peer-Reviewed Original ResearchConceptsConformational ensemblesPyrrolysyl-tRNA synthetaseProtein conformational ensemblesImportant biological phenomenaRNA/DNA complexesProtein-ligand interactionsProtein foldingLigand induced variationsConformational populationsDifferent ligandsMD simulation trajectoriesDNA complexesAmino acidsBiological phenomenaSuch subtle changesD. hafnienseSimulation trajectoriesEnzyme catalysisBackbone levelProteinAtomistic detailsNetwork analysisMD snapshotsMolecular dynamics simulationsObjective clustering
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