2007
Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data
Galante P, Trimarchi J, Cepko C, de Souza S, Ohno-Machado L, Kuo W. Automatic correspondence of tags and genes (ACTG): a tool for the analysis of SAGE, MPSS and SBS data. Bioinformatics 2007, 23: 903-905. PMID: 17277333, DOI: 10.1093/bioinformatics/btm023.Peer-Reviewed Original Research
2006
A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies
Kuo W, Liu F, Trimarchi J, Punzo C, Lombardi M, Sarang J, Whipple M, Maysuria M, Serikawa K, Lee S, McCrann D, Kang J, Shearstone J, Burke J, Park D, Wang X, Rector T, Ricciardi-Castagnoli P, Perrin S, Choi S, Bumgarner R, Kim J, Short G, Freeman M, Seed B, Jensen R, Church G, Hovig E, Cepko C, Park P, Ohno-Machado L, Jenssen T. A sequence-oriented comparison of gene expression measurements across different hybridization-based technologies. Nature Biotechnology 2006, 24: 832-840. PMID: 16823376, DOI: 10.1038/nbt1217.Peer-Reviewed Original ResearchApproximation properties of haplotype tagging
Vinterbo S, Dreiseitl S, Ohno-Machado L. Approximation properties of haplotype tagging. BMC Bioinformatics 2006, 7: 8. PMID: 16401341, PMCID: PMC1395335, DOI: 10.1186/1471-2105-7-8.Peer-Reviewed Original ResearchConceptsApproximation propertiesCombinatorial optimization problemsOptimization problemImplementable algorithmComputational effortSolution qualityTerms of complexitySimple algorithmSize m.Population membersSingle processor machineAlgorithmProblemAsymptoticsApproximationProcessor machineHaplotype taggingNPsUnique identification
2005
Representation in stochastic search for phylogenetic tree reconstruction
Weber G, Ohno-Machado L, Shieber S. Representation in stochastic search for phylogenetic tree reconstruction. Journal Of Biomedical Informatics 2005, 39: 43-50. PMID: 16359929, DOI: 10.1016/j.jbi.2005.11.001.Peer-Reviewed Original Research
2004
Genomic Analysis of Mouse Retinal Development
Blackshaw S, Harpavat S, Trimarchi J, Cai L, Huang H, Kuo W, Weber G, Lee K, Fraioli R, Cho S, Yung R, Asch E, Ohno-Machado L, Wong W, Cepko C. Genomic Analysis of Mouse Retinal Development. PLOS Biology 2004, 2: e247. PMID: 15226823, PMCID: PMC439783, DOI: 10.1371/journal.pbio.0020247.Peer-Reviewed Original ResearchMeSH KeywordsAnimalsBromodeoxyuridineCell LineageChromosome MappingCluster AnalysisComputational BiologyDatabases, GeneticExpressed Sequence TagsGene Expression RegulationGene Expression Regulation, DevelopmentalGene LibraryGenomeIn Situ HybridizationInterneuronsMiceMitosisMolecular Sequence DataNeurogliaOpen Reading FramesRetinaRNA, MessengerStem CellsTime FactorsConceptsMitotic progenitor cellsRetinal cell typesGene expressionCell typesExpression patternsRetinal developmentDevelopmental gene expression patternsGene expression patternsMajor retinal cell typesOpen reading frameProgenitor cellsMüller gliaPhotoreceptor-enriched genesGene expression profilesMouse retinal developmentMajor cell typesRetinal disease genesGenomic analysisMultiple retinal cell typesChromosomal intervalMolecular atlasMultiple transcriptsReading frameTaxonomic classificationDisease genes