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
2017
Genetic effects on gene expression across human tissues
Aguet F, Brown A, Castel S, Davis J, He Y, Jo B, Mohammadi P, Park Y, Parsana P, Segrè A, Strober B, Zappala Z, Cummings B, Gelfand E, Hadley K, Huang K, Lek M, Li X, Nedzel J, Nguyen D, Noble M, Sullivan T, Tukiainen T, MacArthur D, Getz G, Addington A, Guan P, Koester S, Little A, Lockhart N, Moore H, Rao A, Struewing J, Volpi S, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Mash D, Davis D, Sobin L, Barcus M, Branton P, Abell N, Balliu B, Delaneau O, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Han B, He A, Hormozdiari F, Li X, Liu B, Kang E, McDowell I, Ongen H, Palowitch J, Peterson C, Quon G, Ripke S, Saha A, Shabalin A, Shimko T, Sul J, Teran N, Tsang E, Zhang H, Zhou Y, Bustamante C, Cox N, Guigó R, Kellis M, McCarthy M, Conrad D, Eskin E, Li G, Nobel A, Sabatti C, Stranger B, Wen X, Wright F, Ardlie K, Dermitzakis E, Lappalainen T, Aguet F, Ardlie K, Cummings B, Gelfand E, Getz G, Hadley K, Handsaker R, Huang K, Kashin S, Karczewski K, Lek M, Li X, MacArthur D, Nedzel J, Nguyen D, Noble M, Segrè A, Trowbridge C, Tukiainen T, Abell N, Balliu B, Barshir R, Basha O, Battle A, Bogu G, Brown A, Brown C, Castel S, Chen L, Chiang C, Conrad D, Cox N, Damani F, Davis J, Delaneau O, Dermitzakis E, Engelhardt B, Eskin E, Ferreira P, Frésard L, Gamazon E, Garrido-Martín D, Gewirtz A, Gliner G, Gloudemans M, Guigo R, Hall I, Han B, He Y, Hormozdiari F, Howald C, Kyung Im H, Jo B, Yong Kang E, Kim Y, Kim-Hellmuth S, Lappalainen T, Li G, Li X, Liu B, Mangul S, McCarthy M, McDowell I, Mohammadi P, Monlong J, Montgomery S, Muñoz-Aguirre M, Ndungu A, Nicolae D, Nobel A, Oliva M, Ongen H, Palowitch J, Panousis N, Papasaikas P, Park Y, Parsana P, Payne A, Peterson C, Quan J, Reverter F, Sabatti C, Saha A, Sammeth M, Scott A, Shabalin A, Sodaei R, Stephens M, Stranger B, Strober B, Sul J, Tsang E, Urbut S, van de Bunt M, Wang G, Wen X, Wright F, Xi H, Yeger-Lotem E, Zappala Z, Zaugg J, Zhou Y, Akey J, Bates D, Chan J, Chen L, Claussnitzer M, Demanelis K, Diegel M, Doherty J, Feinberg A, Fernando M, Halow J, Hansen K, Haugen E, Hickey P, Hou L, Jasmine F, Jian R, Jiang L, Johnson A, Kaul R, Kellis M, Kibriya M, Lee K, Billy Li J, Li Q, Li X, Lin J, Lin S, Linder S, Linke C, Liu Y, Maurano M, Molinie B, Montgomery S, Nelson J, Neri F, Oliva M, Park Y, Pierce B, Rinaldi N, Rizzardi L, Sandstrom R, Skol A, Smith K, Snyder M, Stamatoyannopoulos J, Stranger B, Tang H, Tsang E, Wang L, Wang M, Van Wittenberghe N, Wu F, Zhang R, Nierras C, Branton P, Carithers L, Guan P, Moore H, Rao A, Vaught J, Gould S, Lockart N, Martin C, Struewing J, Volpi S, Addington A, Koester S, Little A, Brigham L, Hasz R, Hunter M, Johns C, Johnson M, Kopen G, Leinweber W, Lonsdale J, McDonald A, Mestichelli B, Myer K, Roe B, Salvatore M, Shad S, Thomas J, Walters G, Washington M, Wheeler J, Bridge J, Foster B, Gillard B, Karasik E, Kumar R, Miklos M, Moser M, Jewell S, Montroy R, Rohrer D, Valley D, Davis D, Mash D, Undale A, Smith A, Tabor D, Roche N, McLean J, Vatanian N, Robinson K, Sobin L, Barcus M, Valentino K, Qi L, Hunter S, Hariharan P, Singh S, Um K, Matose T, Tomaszewski M, Barker L, Mosavel M, Siminoff L, Traino H, Flicek P, Juettemann T, Ruffier M, Sheppard D, Taylor K, Trevanion S, Zerbino D, Craft B, Goldman M, Haeussler M, Kent W, Lee C, Paten B, Rosenbloom K, Vivian J, Zhu J. Genetic effects on gene expression across human tissues. Nature 2017, 550: 204-213. PMID: 29022597, PMCID: PMC5776756, DOI: 10.1038/nature24277.Peer-Reviewed Original ResearchConceptsGene expression levelsGenetic effectsExpression levelsGenotype-Tissue Expression (GTEx) projectLocal genetic variationMajority of genesHuman genetic traitsDisease-associated variationMolecular functionsGene regulationHuman genomeHuman tissuesExpression projectGenetic variationGenetic basisDiverse tissuesGene expressionTissue specificityGenetic traitsCellular mechanismsGenesFunctional propertiesGenomeTissueLoci
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