2023
A draft human pangenome reference
Liao W, Asri M, Ebler J, Doerr D, Haukness M, Hickey G, Lu S, Lucas J, Monlong J, Abel H, Buonaiuto S, Chang X, Cheng H, Chu J, Colonna V, Eizenga J, Feng X, Fischer C, Fulton R, Garg S, Groza C, Guarracino A, Harvey W, Heumos S, Howe K, Jain M, Lu T, Markello C, Martin F, Mitchell M, Munson K, Mwaniki M, Novak A, Olsen H, Pesout T, Porubsky D, Prins P, Sibbesen J, Sirén J, Tomlinson C, Villani F, Vollger M, Antonacci-Fulton L, Baid G, Baker C, Belyaeva A, Billis K, Carroll A, Chang P, Cody S, Cook D, Cook-Deegan R, Cornejo O, Diekhans M, Ebert P, Fairley S, Fedrigo O, Felsenfeld A, Formenti G, Frankish A, Gao Y, Garrison N, Giron C, Green R, Haggerty L, Hoekzema K, Hourlier T, Ji H, Kenny E, Koenig B, Kolesnikov A, Korbel J, Kordosky J, Koren S, Lee H, Lewis A, Magalhães H, Marco-Sola S, Marijon P, McCartney A, McDaniel J, Mountcastle J, Nattestad M, Nurk S, Olson N, Popejoy A, Puiu D, Rautiainen M, Regier A, Rhie A, Sacco S, Sanders A, Schneider V, Schultz B, Shafin K, Smith M, Sofia H, Abou Tayoun A, Thibaud-Nissen F, Tricomi F, Wagner J, Walenz B, Wood J, Zimin A, Bourque G, Chaisson M, Flicek P, Phillippy A, Zook J, Eichler E, Haussler D, Wang T, Jarvis E, Miga K, Garrison E, Marschall T, Hall I, Li H, Paten B. A draft human pangenome reference. Nature 2023, 617: 312-324. PMID: 37165242, PMCID: PMC10172123, DOI: 10.1038/s41586-023-05896-x.Peer-Reviewed Original Research
2022
Semi-automated assembly of high-quality diploid human reference genomes
Jarvis E, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger M, Porubsky D, Cheng H, Asri M, Logsdon G, Carnevali P, Chaisson M, Chin C, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton R, Fulton L, Garg S, Gerton J, Ghurye J, Granat A, Green R, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger E, Jain M, Kirsche M, Kolmogorov M, Korbel J, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell M, McDaniel J, Nie F, Olsen H, Olson N, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg S, Sanders A, Schatz M, Schmitt A, Schneider V, Selvaraj S, Shafin K, Shumate A, Stitziel N, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin A, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook J, Eichler E, Phillippy A, Paten B, Howe K, Miga K. Semi-automated assembly of high-quality diploid human reference genomes. Nature 2022, 611: 519-531. PMID: 36261518, PMCID: PMC9668749, DOI: 10.1038/s41586-022-05325-5.Peer-Reviewed Original ResearchConceptsDiploid genome assemblyGenome assemblyProtein-coding genesGlobal genetic variationCurrent human reference genomeDiploid human genomeHigh-quality assemblyAccurate long readsNon-synonymous amino acid changesHuman reference genomeAmino acid changesMost chromosomesReference assemblyReference genomeHuman genomeCentromeric regionsGenetic variationHigh diversityGenome sequencingLong readsSingle nucleotideGenomeAcid changesManual curationBiological genomes
2021
Fast alignment and preprocessing of chromatin profiles with Chromap
Zhang H, Song L, Wang X, Cheng H, Wang C, Meyer C, Liu T, Tang M, Aluru S, Yue F, Liu X, Li H. Fast alignment and preprocessing of chromatin profiles with Chromap. Nature Communications 2021, 12: 6566. PMID: 34772935, PMCID: PMC8589834, DOI: 10.1038/s41467-021-26865-w.Peer-Reviewed Original Research
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
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