2020
Data Sanitization to Reduce Private Information Leakage from Functional Genomics
Gürsoy G, Emani P, Brannon CM, Jolanki OA, Harmanci A, Strattan JS, Cherry JM, Miranker AD, Gerstein M. Data Sanitization to Reduce Private Information Leakage from Functional Genomics. Cell 2020, 183: 905-917.e16. PMID: 33186529, PMCID: PMC7672785, DOI: 10.1016/j.cell.2020.09.036.Peer-Reviewed Original ResearchConceptsFunctional genomicsSingle-cell RNA sequencingAccurate reference genomesFunctional genomics datasetsFunctional genomics experimentsOrganismal phenotypesGene regulationReference genomeNext-generation sequencingRaw readsGenomics experimentsRNA sequencingGenomic datasetsGenetic variantsGenomicsKnown individualsSequencingReadsEnvironmental samplesGenomeIlluminaPhenotypeGood statistical powerRegulationStatistical power
2018
Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species
Kim J, Lim H, Shin S, Cha H, Seo J, Kim S, Park S, Son G. Comprehensive transcriptome analysis of Sarcophaga peregrina, a forensically important fly species. Scientific Data 2018, 5: 180220. PMID: 30398471, PMCID: PMC6219405, DOI: 10.1038/sdata.2018.220.Peer-Reviewed Original ResearchConceptsGenome informationSarcophaga peregrinaFly speciesSequence informationS. peregrinaComprehensive transcriptome analysisPrecise sequence informationDe novo assemblyMinimal postmortem intervalImportant fly speciesPrimary sequence informationGene expression datasetsFunctional annotationGenome databaseNovo assemblyTranscriptome analysisGene OntologyKyoto EncyclopediaRaw readsRNA sequencingRNA transcriptsIllumina MiSeqExpression datasetsForensic importanceUnigenes
2015
BitMapper: an efficient all-mapper based on bit-vector computing
Cheng H, Jiang H, Yang J, Xu Y, Shang Y. BitMapper: an efficient all-mapper based on bit-vector computing. BMC Bioinformatics 2015, 16: 192. PMID: 26063651, PMCID: PMC4462005, DOI: 10.1186/s12859-015-0626-9.Peer-Reviewed Original ResearchConceptsNext-generation sequencingMapping next-generation sequencingState-of-the-art all-mappersState-of-the-artReference genomeRaw readsBit-vector algorithmMap locationBit-vectorGPL licenseEdit distanceVerification timeGenomeRunning timeData setsComputational challengesExperimental resultsIndelsHttp://homeVerificationSequenceAlgorithmMultiple locations
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