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Page 1
Genome sequence and analysis of the Irish potato famine pathogen Phytophthora infestans.
Haas BJ, Kamoun S, Zody MC, Jiang RH, Handsaker RE, Cano LM, Grabherr M, Kodira CD, Raffaele S, Torto-Alalibo T, Bozkurt TO, Ah-Fong AM, Alvarado L, Anderson VL, Armstrong MR, Avrova A, Baxter L, Beynon J, Boevink PC, Bollmann SR, Bos JI, Bulone V, Cai G, Cakir C, Carrington JC, Chawner M, Conti L, Costanzo S, Ewan R, Fahlgren N, Fischbach MA, Fugelstad J, Gilroy EM, Gnerre S, Green PJ, Grenville-Briggs LJ, Griffith J, Grünwald NJ, Horn K, Horner NR, Hu CH, Huitema E, Jeong DH, Jones AM, Jones JD, Jones RW, Karlsson EK, Kunjeti SG, Lamour K, Liu Z, Ma L, Maclean D, Chibucos MC, McDonald H, McWalters J, Meijer HJ, Morgan W, Morris PF, Munro CA, O'Neill K, Ospina-Giraldo M, Pinzón A, Pritchard L, Ramsahoye B, Ren Q, Restrepo S, Roy S, Sadanandom A, Savidor A, Schornack S, Schwartz DC, Schumann UD, Schwessinger B, Seyer L, Sharpe T, Silvar C, Song J, Studholme DJ, Sykes S, Thines M, van de Vondervoort PJ, Phuntumart V, Wawra S, Weide R, Win J, Young C, Zhou S, Fry W, Meyers BC, van West P, Ristaino J, Govers F, Birch PR, Whisson SC, Judelson HS, Nusbaum C. Haas BJ, et al. Among authors: handsaker re. Nature. 2009 Sep 17;461(7262):393-8. doi: 10.1038/nature08358. Epub 2009 Sep 9. Nature. 2009. PMID: 19741609 Free article.
Concerted neuron-astrocyte gene expression declines in aging and schizophrenia.
Ling E, Nemesh J, Goldman M, Kamitaki N, Reed N, Handsaker RE, Genovese G, Vogelgsang JS, Gerges S, Kashin S, Ghosh S, Esposito JM, French K, Meyer D, Lutservitz A, Mullally CD, Wysoker A, Spina L, Neumann A, Hogan M, Ichihara K, Berretta S, McCarroll SA. Ling E, et al. Among authors: handsaker re. bioRxiv [Preprint]. 2024 Jan 8:2024.01.07.574148. doi: 10.1101/2024.01.07.574148. bioRxiv. 2024. PMID: 38260461 Free PMC article. Updated. Preprint.
Integrated detection and population-genetic analysis of SNPs and copy number variation.
McCarroll SA, Kuruvilla FG, Korn JM, Cawley S, Nemesh J, Wysoker A, Shapero MH, de Bakker PI, Maller JB, Kirby A, Elliott AL, Parkin M, Hubbell E, Webster T, Mei R, Veitch J, Collins PJ, Handsaker R, Lincoln S, Nizzari M, Blume J, Jones KW, Rava R, Daly MJ, Gabriel SB, Altshuler D. McCarroll SA, et al. Nat Genet. 2008 Oct;40(10):1166-74. doi: 10.1038/ng.238. Epub 2008 Sep 7. Nat Genet. 2008. PMID: 18776908
Mapping copy number variation by population-scale genome sequencing.
Mills RE, Walter K, Stewart C, Handsaker RE, Chen K, Alkan C, Abyzov A, Yoon SC, Ye K, Cheetham RK, Chinwalla A, Conrad DF, Fu Y, Grubert F, Hajirasouliha I, Hormozdiari F, Iakoucheva LM, Iqbal Z, Kang S, Kidd JM, Konkel MK, Korn J, Khurana E, Kural D, Lam HY, Leng J, Li R, Li Y, Lin CY, Luo R, Mu XJ, Nemesh J, Peckham HE, Rausch T, Scally A, Shi X, Stromberg MP, Stütz AM, Urban AE, Walker JA, Wu J, Zhang Y, Zhang ZD, Batzer MA, Ding L, Marth GT, McVean G, Sebat J, Snyder M, Wang J, Ye K, Eichler EE, Gerstein MB, Hurles ME, Lee C, McCarroll SA, Korbel JO; 1000 Genomes Project. Mills RE, et al. Among authors: handsaker re. Nature. 2011 Feb 3;470(7332):59-65. doi: 10.1038/nature09708. Nature. 2011. PMID: 21293372 Free PMC article.
Mutations causing medullary cystic kidney disease type 1 lie in a large VNTR in MUC1 missed by massively parallel sequencing.
Kirby A, Gnirke A, Jaffe DB, Barešová V, Pochet N, Blumenstiel B, Ye C, Aird D, Stevens C, Robinson JT, Cabili MN, Gat-Viks I, Kelliher E, Daza R, DeFelice M, Hůlková H, Sovová J, Vylet'al P, Antignac C, Guttman M, Handsaker RE, Perrin D, Steelman S, Sigurdsson S, Scheinman SJ, Sougnez C, Cibulskis K, Parkin M, Green T, Rossin E, Zody MC, Xavier RJ, Pollak MR, Alper SL, Lindblad-Toh K, Gabriel S, Hart PS, Regev A, Nusbaum C, Kmoch S, Bleyer AJ, Lander ES, Daly MJ. Kirby A, et al. Among authors: handsaker re. Nat Genet. 2013 Mar;45(3):299-303. doi: 10.1038/ng.2543. Epub 2013 Feb 10. Nat Genet. 2013. PMID: 23396133 Free PMC article.
Using population admixture to help complete maps of the human genome.
Genovese G, Handsaker RE, Li H, Altemose N, Lindgren AM, Chambert K, Pasaniuc B, Price AL, Reich D, Morton CC, Pollak MR, Wilson JG, McCarroll SA. Genovese G, et al. Among authors: handsaker re. Nat Genet. 2013 Apr;45(4):406-14, 414e1-2. doi: 10.1038/ng.2565. Epub 2013 Feb 24. Nat Genet. 2013. PMID: 23435088 Free PMC article.
Large multiallelic copy number variations in humans.
Handsaker RE, Van Doren V, Berman JR, Genovese G, Kashin S, Boettger LM, McCarroll SA. Handsaker RE, et al. Nat Genet. 2015 Mar;47(3):296-303. doi: 10.1038/ng.3200. Epub 2015 Jan 26. Nat Genet. 2015. PMID: 25621458 Free PMC article.
Genome of The Netherlands population-specific imputations identify an ABCA6 variant associated with cholesterol levels.
van Leeuwen EM, Karssen LC, Deelen J, Isaacs A, Medina-Gomez C, Mbarek H, Kanterakis A, Trompet S, Postmus I, Verweij N, van Enckevort DJ, Huffman JE, White CC, Feitosa MF, Bartz TM, Manichaikul A, Joshi PK, Peloso GM, Deelen P, van Dijk F, Willemsen G, de Geus EJ, Milaneschi Y, Penninx BW, Francioli LC, Menelaou A, Pulit SL, Rivadeneira F, Hofman A, Oostra BA, Franco OH, Mateo Leach I, Beekman M, de Craen AJ, Uh HW, Trochet H, Hocking LJ, Porteous DJ, Sattar N, Packard CJ, Buckley BM, Brody JA, Bis JC, Rotter JI, Mychaleckyj JC, Campbell H, Duan Q, Lange LA, Wilson JF, Hayward C, Polasek O, Vitart V, Rudan I, Wright AF, Rich SS, Psaty BM, Borecki IB, Kearney PM, Stott DJ, Adrienne Cupples L; Genome of The Netherlands Consortium; Jukema JW, van der Harst P, Sijbrands EJ, Hottenga JJ, Uitterlinden AG, Swertz MA, van Ommen GJ, de Bakker PI, Eline Slagboom P, Boomsma DI, Wijmenga C, van Duijn CM. van Leeuwen EM, et al. Nat Commun. 2015 Mar 9;6:6065. doi: 10.1038/ncomms7065. Nat Commun. 2015. PMID: 25751400 Free PMC article.
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