2011
Influence of Host Phylogeographic Patterns and Incomplete Lineage Sorting on Within-Species Genetic Variability in Wigglesworthia Species, Obligate Symbionts of Tsetse Flies
Symula RE, Marpuri I, Bjornson RD, Okedi L, Beadell J, Alam U, Aksoy S, Caccone A. Influence of Host Phylogeographic Patterns and Incomplete Lineage Sorting on Within-Species Genetic Variability in Wigglesworthia Species, Obligate Symbionts of Tsetse Flies. Applied And Environmental Microbiology 2011, 77: 8400-8408. PMID: 21948847, PMCID: PMC3233068, DOI: 10.1128/aem.05688-11.Peer-Reviewed Original ResearchConceptsObligate symbiontsHost speciesGenetic variationMultiple host populationsIncongruence length difference testIncomplete lineage sortingHost-symbiont combinationsSingle host speciesPopulation-level processesIncomplete lineageLineage sortingPhylogeographic patternsSouthern lineagesSymbiont lineagesHost mtDNAWigglesworthia glossinidiaMolecular varianceBacterial symbiontsEvolutionary associationEvolutionary historySouthern populationsMitochondrial DNA haplogroupsVariable lociSymbiontsGenetic variability
2010
Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families
Patel PV, Gianoulis TA, Bjornson RD, Yip KY, Engelman DM, Gerstein MB. Analysis of membrane proteins in metagenomics: Networks of correlated environmental features and protein families. Genome Research 2010, 20: 960-971. PMID: 20430783, PMCID: PMC2892097, DOI: 10.1101/gr.102814.109.Peer-Reviewed Original ResearchConceptsProtein familyMembrane proteinsMembrane protein familyRecent metagenomic studiesMembrane protein contentAdditional environmental featuresProtein diversityDisparate habitatsGenomic diversityPhosphate transporterProtein variationMetagenomic sequencesMetagenomic studiesEnvironmental featuresIron transporterHuman impactProteinOceanographic variablesMarine sitesEcological analysisTransportersDiversityProtein contentFamilyClimate change
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 goalToolboxSimulationsPeakSeq 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