2024
Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires
Schoelmerich M, Ly L, West-Roberts J, Shi L, Shen C, Malvankar N, Taib N, Gribaldo S, Woodcroft B, Schadt C, Al-Shayeb B, Dai X, Mozsary C, Hickey S, He C, Beaulaurier J, Juul S, Sachdeva R, Banfield J. Borg extrachromosomal elements of methane-oxidizing archaea have conserved and expressed genetic repertoires. Nature Communications 2024, 15: 5414. PMID: 38926353, PMCID: PMC11208441, DOI: 10.1038/s41467-024-49548-8.Peer-Reviewed Original ResearchConceptsExtrachromosomal elementsMethylation motifsPublished complete genomesCell surface proteinsShort readsComplete genomeConserved genesGenetic repertoireLinear genomeNanopore sequencingGenomic backboneStructure predictionGenomic signaturesGenomeMethane-oxidizing archaeaHost cellsSurface proteinsArchaeaGenesActivity in situPeatland soilsGenetic inheritanceMotifMethanoperedensHostA comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline
Du Z, He J, Jiao W. A comprehensive benchmark of graph-based genetic variant genotyping algorithms on plant genomes for creating an accurate ensemble pipeline. Genome Biology 2024, 25: 91. PMID: 38589937, PMCID: PMC11003132, DOI: 10.1186/s13059-024-03239-1.Peer-Reviewed Original ResearchConceptsPlant genomesGenotyping methodsComplexity of plant genomesHeterozygous plant genomesGenotypic algorithmsGenotype millionsShort readsGenomic contextGenomic diversitySequencing technologiesHuman genomeGenomeGenetic variantsExcessive repeatsVariant typeGenotypesStructural variationsEnsemble pipelinePlantsConclusionsOur studyVariant genotypesGenotype performanceVariantsDeletionSequence
2023
A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage
Toy J, Bernardi G. A high-quality reference genome of the kelp surfperch, Brachyistius frenatus (Embiotocidae), a wide-ranging Eastern Pacific reef fish with no pelagic larval stage. Journal Of Heredity 2023, 114: 404-409. PMID: 36790952, PMCID: PMC10287144, DOI: 10.1093/jhered/esad009.Peer-Reviewed Original ResearchConceptsMolecular resourcesLocal adaptationCombination of short-readInvestigations of local adaptationLevel of syntenyStudy of speciationPelagic larval stageDispersive larval stageLarval stageContig N50Short readsGene flowPhylogenetic positionGenomic potentialEmbiotoca jacksoniReef fishesWild populationsSurfperchMarine fishContigsGenomeExcellent modelEmbiotocidaeFamily EmbiotocidaeRecreational fisheries
2020
Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma
Helmsauer K, Valieva M, Ali S, Chamorro González R, Schöpflin R, Röefzaad C, Bei Y, Dorado Garcia H, Rodriguez-Fos E, Puiggròs M, Kasack K, Haase K, Keskeny C, Chen C, Kuschel L, Euskirchen P, Heinrich V, Robson M, Rosswog C, Toedling J, Szymansky A, Hertwig F, Fischer M, Torrents D, Eggert A, Schulte J, Mundlos S, Henssen A, Koche R. Enhancer hijacking determines extrachromosomal circular MYCN amplicon architecture in neuroblastoma. Nature Communications 2020, 11: 5823. PMID: 33199677, PMCID: PMC7669906, DOI: 10.1038/s41467-020-19452-y.Peer-Reviewed Original ResearchConceptsExtrachromosomal circular DNACore regulatory circuitEnhancer hijackingAmplicon structureDistal chromosomal fragmentsGene regulatory elementsMYCN amplificationChIP-seqShort readsHi-C.ATAC-seqChromatin landscapeNanopore sequencingRegulatory elementsRegulatory circuitsChromosome fragmentsMYCN ampliconGene copiesProximal enhancerCo-amplifiedCircular DNAAmpliconsMYCN overexpressionFunctional relevanceMYCN
2016
Full-length transcriptome sequencing on PacBio platform
REN Y, ZHANG J, Yu S, WU Z, RUAN J, HE B, LIU G, Shan G, BU W. Full-length transcriptome sequencing on PacBio platform. Chinese Science Bulletin (Chinese Version) 2016, 61: 1250-1254. DOI: 10.1360/n972015-01384.Peer-Reviewed Original ResearchSingle-molecule real-timePacBio platformNext generation sequencingShort readsSingle-molecule real-time technologyFull-length transcriptome sequencingNGS short readsNGS sequencingFull-length transcriptsInvestigate alternative splicingPlant transcriptomeAlternative polyadenylationIllumina platformTetraploid cottonTranscriptome sequencingAlternative splicingNon-coding RNAsTranscriptome dataGeneration sequencingPacBioPropithecus coquereliTranscriptionTranscriptomeEmbryonic stem cellsFusion transcripts
2010
PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences.
Pitzer E, Kim J, Patel K, Galante P, Ohno-Machado L. PositionMatcher: A Fast Custom-Annotation Tool for Short DNA Sequences. AMIA Joint Summits On Translational Science Proceedings 2010, 2010: 25-9. PMID: 21347141, PMCID: PMC3041550.Peer-Reviewed Original ResearchParallel sequencing technologiesShort DNA sequencesTranscriptome studiesGenomic positionsDNA sequencesSequencing technologiesGenomic tagsExpression technologySequencing readsRapid AnnotationGene levelMicroarray probesShort readsCustom annotationsAbundance valuesAnnotationNovel alignment algorithmReadsBiological referenceTagsIlluminaAffymetrixSequenceMore insightProbe
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