2023
De novo reconstruction of satellite repeat units from sequence data
Zhang Y, Chu J, Cheng H, Li H. De novo reconstruction of satellite repeat units from sequence data. Genome Research 2023, 33: 1994-2001. PMID: 37918962, PMCID: PMC10760446, DOI: 10.1101/gr.278005.123.Peer-Reviewed Original ResearchConceptsSatellite repeat unitSequence dataSatellite repeatsLong tandem repeated sequencesReal sequencing dataSatellite DNA evolutionTandem repeat sequencesDe novo reconstructionRepeat unitsGenomic contentGenome sequenceSatellite DNADNA evolutionModel organismsGenomeComplete assemblySequenceRepeatsCentromereAssemblyDNASpeciesAnnotation
2017
FMtree: a fast locating algorithm of FM-indexes for genomic data
Cheng H, Wu M, Xu Y. FMtree: a fast locating algorithm of FM-indexes for genomic data. Bioinformatics 2017, 34: 416-424. PMID: 28968761, DOI: 10.1093/bioinformatics/btx596.Peer-Reviewed Original ResearchConceptsFull-text indexGenomic dataState-of-the-art algorithmsMultiway treeLocation algorithmLocation operationsState-of-the-artFM-indexTree-based algorithmsPosition of patternsMemory-efficientLong textData localitySupplementary dataOccurrence positionSuffix treeSuffix arrayShort patternsAlgorithmBioinformaticsExperimental resultsTreesTextOperationTask
2015
BitMapper: an efficient all-mapper based on bit-vector computing
Cheng H, Jiang H, Yang J, Xu Y, Shang Y. BitMapper: an efficient all-mapper based on bit-vector computing. BMC Bioinformatics 2015, 16: 192. PMID: 26063651, PMCID: PMC4462005, DOI: 10.1186/s12859-015-0626-9.Peer-Reviewed Original ResearchConceptsNext-generation sequencingMapping next-generation sequencingState-of-the-art all-mappersState-of-the-artReference genomeRaw readsBit-vector algorithmMap locationBit-vectorGPL licenseEdit distanceVerification timeGenomeRunning timeData setsComputational challengesExperimental resultsIndelsHttp://homeVerificationSequenceAlgorithmMultiple locations
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