2020
Using blockchain to log genome dataset access: efficient storage and query
Gürsoy G, Bjornson R, Green ME, Gerstein M. Using blockchain to log genome dataset access: efficient storage and query. BMC Medical Genomics 2020, 13: 78. PMID: 32693796, PMCID: PMC7372787, DOI: 10.1186/s12920-020-0716-z.Peer-Reviewed Original ResearchConceptsEfficient queryData streamsMemory requirementsSecure genome analysis competitionAccess log filesSecure data storageProperties of securityMB of memoryAccess logsFast queriesSensitive informationBlockchain platformSecure storageBlockchain technologyUser activityElectronic health recordsLog filesLocal storageRapid queryEfficient storageQueriesData storageDataset accessMore memoryData frames
2011
ACT: aggregation and correlation toolbox for analyses of genome tracks
Jee J, Rozowsky J, Yip KY, Lochovsky L, Bjornson R, Zhong G, Zhang Z, Fu Y, Wang J, Weng Z, Gerstein M. ACT: aggregation and correlation toolbox for analyses of genome tracks. Bioinformatics 2011, 27: 1152-1154. PMID: 21349863, PMCID: PMC3072554, DOI: 10.1093/bioinformatics/btr092.Peer-Reviewed Original ResearchConceptsTranscription start siteInteractive web serverHigh-throughput genomic experimentsModENCODE projectGenome tracksSingle nucleotide polymorphismsRNA-seqStart siteGenomics experimentsGenome ProjectNucleotide polymorphismsEncodesWeb serverAggregationSitesExample datasetPolymorphismACT sitesAggregate profilesToolbox
2009
Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants
Du J, Bjornson RD, Zhang ZD, Kong Y, Snyder M, Gerstein MB. Integrating Sequencing Technologies in Personal Genomics: Optimal Low Cost Reconstruction of Structural Variants. PLOS Computational Biology 2009, 5: e1000432. PMID: 19593373, PMCID: PMC2700963, DOI: 10.1371/journal.pcbi.1000432.Peer-Reviewed Original ResearchConceptsDifferent read lengthsDifferent technologiesSemi-realistic simulationComputational complexityMaximum accuracyAssembly algorithmReconstruction efficiencySimulation toolboxPersonal genomicsAccurate detectionLow costChallenging stepTechnologyCostAlgorithmAccurate assemblyComplexitySmall enough scalesReconstructionGoalIndividual genomesCanonical problemImportant goalToolboxSimulationsQuantifying environmental adaptation of metabolic pathways in metagenomics
Gianoulis TA, Raes J, Patel PV, Bjornson R, Korbel JO, Letunic I, Yamada T, Paccanaro A, Jensen LJ, Snyder M, Bork P, Gerstein MB. Quantifying environmental adaptation of metabolic pathways in metagenomics. Proceedings Of The National Academy Of Sciences Of The United States Of America 2009, 106: 1374-1379. PMID: 19164758, PMCID: PMC2629784, DOI: 10.1073/pnas.0808022106.Peer-Reviewed Original ResearchConceptsMultiple environmental gradientsSpecific biological processesNutrient-limited conditionsDistinct environmental conditionsAmino acid transportMicrobial communitiesAmount of cofactorEnvironmental gradientsEnvironmental adaptationStrongest multivariate correlationsGenetic contentCofactor synthesisBiological processesMicrobial pathwaysMetabolic pathwaysAcid transportMetabolic footprintsAmino acidsParticular pathwayEnvironmental differencesEnvironmental variablesEnvironmental conditionsPathwayMetabolic differencesGeographic sitesPeakSeq enables systematic scoring of ChIP-seq experiments relative to controls
Rozowsky J, Euskirchen G, Auerbach RK, Zhang ZD, Gibson T, Bjornson R, Carriero N, Snyder M, Gerstein MB. PeakSeq enables systematic scoring of ChIP-seq experiments relative to controls. Nature Biotechnology 2009, 27: 66-75. PMID: 19122651, PMCID: PMC2924752, DOI: 10.1038/nbt.1518.Peer-Reviewed Original Research