2023
An integrated platform for high-throughput nanoscopy
Barentine A, Lin Y, Courvan E, Kidd P, Liu M, Balduf L, Phan T, Rivera-Molina F, Grace M, Marin Z, Lessard M, Rios Chen J, Wang S, Neugebauer K, Bewersdorf J, Baddeley D. An integrated platform for high-throughput nanoscopy. Nature Biotechnology 2023, 41: 1549-1556. PMID: 36914886, PMCID: PMC10497732, DOI: 10.1038/s41587-023-01702-1.Peer-Reviewed Original ResearchConceptsLarge data volumesUser-defined extensionsPlugin frameworkData compressionData volumeCamera frameFrame rateAnalysis platformAcquisition taskPlatformIntegrated acquisitionThroughputSingle-molecule localization microscopyTypical throughputHundreds of cellsThree-dimensional fluorescenceFrameworkTens of cellsLocalization microscopyWorkflow
2016
A generic, cost-effective, and scalable cell lineage analysis platform
Biezuner T, Spiro A, Raz O, Amir S, Milo L, Adar R, Chapal-Ilani N, Berman V, Fried Y, Ainbinder E, Cohen G, Barr H, Halaban R, Shapiro E. A generic, cost-effective, and scalable cell lineage analysis platform. Genome Research 2016, 26: 1588-1599. PMID: 27558250, PMCID: PMC5088600, DOI: 10.1101/gr.202903.115.Peer-Reviewed Original ResearchConceptsLineage analysisSingle cell lineage analysisSingle-cell sequencing dataSingle-cell genomicsCurrent sequencing-based methodsIndividual cellsCell lineage analysisSingle-cell sequencingSequencing-based methodsLineage treesSequencing dataLineage relationsCellsTreesGenomicsAnalysis platformInput cellsSequencingBulk analysisVivoDiscoveryLandscape
2015
Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle
Alves TC, Pongratz RL, Zhao X, Yarborough O, Sereda S, Shirihai O, Cline GW, Mason G, Kibbey RG. Integrated, Step-Wise, Mass-Isotopomeric Flux Analysis of the TCA Cycle. Cell Metabolism 2015, 22: 936-947. PMID: 26411341, PMCID: PMC4635072, DOI: 10.1016/j.cmet.2015.08.021.Peer-Reviewed Original Research
2012
The screening and ranking algorithm to detect DNA copy number variations
Niu Y, Zhang H. The screening and ranking algorithm to detect DNA copy number variations. The Annals Of Applied Statistics 2012, 6: 1306-1326. DOI: 10.1214/12-aoas539.Peer-Reviewed Original ResearchDNA copy number variationsSource of genetic variationGenome analysis platformHigh-throughput dataCopy number variationsRanking algorithmGenetic variationNumber variationsPhenotypic differencesTheoretical propertiesThroughput dataAnalysis platformAlgorithmCharacterization algorithmGenomeComputational methods
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