2011
Power of Data Mining Methods to Detect Genetic Associations and Interactions
Molinaro AM, Carriero N, Bjornson R, Hartge P, Rothman N, Chatterjee N. Power of Data Mining Methods to Detect Genetic Associations and Interactions. Human Heredity 2011, 72: 85-97. PMID: 21934324, PMCID: PMC3222116, DOI: 10.1159/000330579.Peer-Reviewed Original ResearchConceptsMonte Carlo logic regressionRandom forestVariable importance measuresRF variable importance measuresData mining methodsComplex variable interactionsMining methodsTree-based methodsDimensionality reductionPrediction modelSuch methodsImportance measuresLogic regressionSimulation modelMultifactor dimensionality reductionData analysisVariable interactionsAlgorithmSimulation study
2009
RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes
Abyzov A, Bjornson R, Felipe M, Gerstein M. RigidFinder: A fast and sensitive method to detect rigid blocks in large macromolecular complexes. Proteins Structure Function And Bioinformatics 2009, 78: 309-324. PMID: 19705487, DOI: 10.1002/prot.22544.Peer-Reviewed Original ResearchConceptsLarge macromolecular complexesMacromolecular complexesLarge-scale conformational changesRNA polymerase IIT7 RNA polymeraseMultiple polypeptide chainsPolymerase IIRNA polymeraseDistance conservationPhosphate dikinaseDifferent conformationsInter-residue distancesLarge complexesConformational changesPolypeptide chainDomain motionPartial refoldingFurther distinguishing featureConformationStructure determinationComplexesDikinaseSensitive identificationGroELIdentificationIntegrating 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 goalToolboxSimulations