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GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen … See abstract for full author list ➔ Rehm HL, et al. Among authors: beckmann js. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. Cell Genom. 2021. PMID: 35072136 Free PMC article.
The GA4GH Phenopacket schema defines a computable representation of clinical data.
Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium; Haendel MA, Robinson PN. Jacobsen JOB, et al. Among authors: beckmann js. Nat Biotechnol. 2022 Jun;40(6):817-820. doi: 10.1038/s41587-022-01357-4. Nat Biotechnol. 2022. PMID: 35705716 Free PMC article. No abstract available.
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA; Variant Interpretation for Cancer Consortium. Wagner AH, et al. Among authors: beckmann js. Nat Genet. 2020 Apr;52(4):448-457. doi: 10.1038/s41588-020-0603-8. Epub 2020 Apr 3. Nat Genet. 2020. PMID: 32246132 Free PMC article.
Great future or greedy venture: Precision medicine needs philosophy.
Jiao F, Guo R, Beckmann JS, Yan Z, Yang Y, Hu J, Wang X, Xie S. Jiao F, et al. Among authors: beckmann js. Health Sci Rep. 2021 Sep 14;4(3):e376. doi: 10.1002/hsr2.376. eCollection 2021 Sep. Health Sci Rep. 2021. PMID: 34541334 Free PMC article. Review.
COVID19 Disease Map, a computational knowledge repository of virus-host interaction mechanisms.
Ostaszewski M, Niarakis A, Mazein A, Kuperstein I, Phair R, Orta-Resendiz A, Singh V, Aghamiri SS, Acencio ML, Glaab E, Ruepp A, Fobo G, Montrone C, Brauner B, Frishman G, Monraz Gómez LC, Somers J, Hoch M, Kumar Gupta S, Scheel J, Borlinghaus H, Czauderna T, Schreiber F, Montagud A, Ponce de Leon M, Funahashi A, Hiki Y, Hiroi N, Yamada TG, Dräger A, Renz A, Naveez M, Bocskei Z, Messina F, Börnigen D, Fergusson L, Conti M, Rameil M, Nakonecnij V, Vanhoefer J, Schmiester L, Wang M, Ackerman EE, Shoemaker JE, Zucker J, Oxford K, Teuton J, Kocakaya E, Summak GY, Hanspers K, Kutmon M, Coort S, Eijssen L, Ehrhart F, Rex DAB, Slenter D, Martens M, Pham N, Haw R, Jassal B, Matthews L, Orlic-Milacic M, Senff Ribeiro A, Rothfels K, Shamovsky V, Stephan R, Sevilla C, Varusai T, Ravel JM, Fraser R, Ortseifen V, Marchesi S, Gawron P, Smula E, Heirendt L, Satagopam V, Wu G, Riutta A, Golebiewski M, Owen S, Goble C, Hu X, Overall RW, Maier D, Bauch A, Gyori BM, Bachman JA, Vega C, Grouès V, Vazquez M, Porras P, Licata L, Iannuccelli M, Sacco F, Nesterova A, Yuryev A, de Waard A, Turei D, Luna A, Babur O, Soliman S, Valdeolivas A, Esteban-Medina M, Peña-Chilet M, Rian K, Helikar T, Puniya BL, Mo… See abstract for full author list ➔ Ostaszewski M, et al. Among authors: beckmann js. Mol Syst Biol. 2021 Oct;17(10):e10387. doi: 10.15252/msb.202110387. Mol Syst Biol. 2021. PMID: 34664389 Free PMC article.
Genome-wide Association Studies Identify Genetic Loci Associated With Albuminuria in Diabetes.
Teumer A, Tin A, Sorice R, Gorski M, Yeo NC, Chu AY, Li M, Li Y, Mijatovic V, Ko YA, Taliun D, Luciani A, Chen MH, Yang Q, Foster MC, Olden M, Hiraki LT, Tayo BO, Fuchsberger C, Dieffenbach AK, Shuldiner AR, Smith AV, Zappa AM, Lupo A, Kollerits B, Ponte B, Stengel B, Krämer BK, Paulweber B, Mitchell BD, Hayward C, Helmer C, Meisinger C, Gieger C, Shaffer CM, Müller C, Langenberg C, Ackermann D, Siscovick D; DCCT/EDIC; Boerwinkle E, Kronenberg F, Ehret GB, Homuth G, Waeber G, Navis G, Gambaro G, Malerba G, Eiriksdottir G, Li G, Wichmann HE, Grallert H, Wallaschofski H, Völzke H, Brenner H, Kramer H, Mateo Leach I, Rudan I, Hillege HL, Beckmann JS, Lambert JC, Luan J, Zhao JH, Chalmers J, Coresh J, Denny JC, Butterbach K, Launer LJ, Ferrucci L, Kedenko L, Haun M, Metzger M, Woodward M, Hoffman MJ, Nauck M, Waldenberger M, Pruijm M, Bochud M, Rheinberger M, Verweij N, Wareham NJ, Endlich N, Soranzo N, Polasek O, van der Harst P, Pramstaller PP, Vollenweider P, Wild PS, Gansevoort RT, Rettig R, Biffar R, Carroll RJ, Katz R, Loos RJ, Hwang SJ, Coassin S, Bergmann S, Rosas SE, Stracke S, Harris TB, Corre T, Zeller T, Illig T, Aspelund T, Tanaka T, Lendeckel U, Völker U, Gudnason… See abstract for full author list ➔ Teumer A, et al. Among authors: beckmann js. Diabetes. 2016 Mar;65(3):803-17. doi: 10.2337/db15-1313. Epub 2015 Dec 2. Diabetes. 2016. PMID: 26631737 Free PMC article.
404 results