2014
HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads
Li P, Jiang X, Wang S, Kim J, Xiong H, Ohno-Machado L. HUGO: Hierarchical mUlti-reference Genome cOmpression for aligned reads. Journal Of The American Medical Informatics Association 2014, 21: 363-373. PMID: 24368726, PMCID: PMC3932469, DOI: 10.1136/amiajnl-2013-002147.Peer-Reviewed Original ResearchConceptsBase quality valuesCompression algorithmStorage savingsGenome compressionSequence Alignment/Map (SAM) formatCompression ratioNovel compression algorithmComparable compression ratioCompression mechanismK-means clusteringDifferent reference genomesQuality valuesDecompression qualityLossless compressionExecution timeCompression rateAligned readsMap formatAlgorithmBiomedical communityDifferent quality valuesExperimental datasetsAdaptive schemeStorage capabilityArchiving
2013
Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP)
Lin K, Tharp M, Conway M, Hsieh A, Ross M, Kim J, Kim H. Feasibility of Using Clinical Element Models (CEM) to Standardize Phenotype Variables in the Database of Genotypes and Phenotypes (dbGaP). PLOS ONE 2013, 8: e76384. PMID: 24058713, PMCID: PMC3776754, DOI: 10.1371/journal.pone.0076384.Peer-Reviewed Original Research
2012
Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration
Jiang X, Menon A, Wang S, Kim J, Ohno-Machado L. Doubly Optimized Calibrated Support Vector Machine (DOC-SVM): An Algorithm for Joint Optimization of Discrimination and Calibration. PLOS ONE 2012, 7: e48823. PMID: 23139819, PMCID: PMC3490990, DOI: 10.1371/journal.pone.0048823.Peer-Reviewed Original Research
2009
Towards large-scale sample annotation in gene expression repositories
Pitzer E, Lacson R, Hinske C, Kim J, Galante P, Ohno-Machado L. Towards large-scale sample annotation in gene expression repositories. BMC Bioinformatics 2009, 10: s9. PMID: 19761579, PMCID: PMC2745696, DOI: 10.1186/1471-2105-10-s9-s9.Peer-Reviewed Original Research