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Page 1
An integrative TAD catalog in lymphoblastoid cell lines discloses the functional impact of deletions and insertions in human genomes.
Li C, Bonder MJ, Syed S, Jensen M; Human Genome Structural Variation Consortium (HGSVC); HGSVC Functional Analysis Working Group; Gerstein MB, Zody MC, Chaisson MJP, Talkowski ME, Marschall T, Korbel JO, Eichler EE, Lee C, Shi X. Li C, et al. Among authors: chaisson mjp. Genome Res. 2024 Dec 23;34(12):2304-2318. doi: 10.1101/gr.279419.124. Genome Res. 2024. PMID: 39638559
Multi-platform discovery of haplotype-resolved structural variation in human genomes.
Chaisson MJP, Sanders AD, Zhao X, Malhotra A, Porubsky D, Rausch T, Gardner EJ, Rodriguez OL, Guo L, Collins RL, Fan X, Wen J, Handsaker RE, Fairley S, Kronenberg ZN, Kong X, Hormozdiari F, Lee D, Wenger AM, Hastie AR, Antaki D, Anantharaman T, Audano PA, Brand H, Cantsilieris S, Cao H, Cerveira E, Chen C, Chen X, Chin CS, Chong Z, Chuang NT, Lambert CC, Church DM, Clarke L, Farrell A, Flores J, Galeev T, Gorkin DU, Gujral M, Guryev V, Heaton WH, Korlach J, Kumar S, Kwon JY, Lam ET, Lee JE, Lee J, Lee WP, Lee SP, Li S, Marks P, Viaud-Martinez K, Meiers S, Munson KM, Navarro FCP, Nelson BJ, Nodzak C, Noor A, Kyriazopoulou-Panagiotopoulou S, Pang AWC, Qiu Y, Rosanio G, Ryan M, Stütz A, Spierings DCJ, Ward A, Welch AE, Xiao M, Xu W, Zhang C, Zhu Q, Zheng-Bradley X, Lowy E, Yakneen S, McCarroll S, Jun G, Ding L, Koh CL, Ren B, Flicek P, Chen K, Gerstein MB, Kwok PY, Lansdorp PM, Marth GT, Sebat J, Shi X, Bashir A, Ye K, Devine SE, Talkowski ME, Mills RE, Marschall T, Korbel JO, Eichler EE, Lee C. Chaisson MJP, et al. Nat Commun. 2019 Apr 16;10(1):1784. doi: 10.1038/s41467-018-08148-z. Nat Commun. 2019. PMID: 30992455 Free PMC article.
Haplotype-resolved diverse human genomes and integrated analysis of structural variation.
Ebert P, Audano PA, Zhu Q, Rodriguez-Martin B, Porubsky D, Bonder MJ, Sulovari A, Ebler J, Zhou W, Serra Mari R, Yilmaz F, Zhao X, Hsieh P, Lee J, Kumar S, Lin J, Rausch T, Chen Y, Ren J, Santamarina M, Höps W, Ashraf H, Chuang NT, Yang X, Munson KM, Lewis AP, Fairley S, Tallon LJ, Clarke WE, Basile AO, Byrska-Bishop M, Corvelo A, Evani US, Lu TY, Chaisson MJP, Chen J, Li C, Brand H, Wenger AM, Ghareghani M, Harvey WT, Raeder B, Hasenfeld P, Regier AA, Abel HJ, Hall IM, Flicek P, Stegle O, Gerstein MB, Tubio JMC, Mu Z, Li YI, Shi X, Hastie AR, Ye K, Chong Z, Sanders AD, Zody MC, Talkowski ME, Mills RE, Devine SE, Lee C, Korbel JO, Marschall T, Eichler EE. Ebert P, et al. Among authors: chaisson mjp. Science. 2021 Apr 2;372(6537):eabf7117. doi: 10.1126/science.abf7117. Epub 2021 Feb 25. Science. 2021. PMID: 33632895 Free PMC article.
Gaps and complex structurally variant loci in phased genome assemblies.
Porubsky D, Vollger MR, Harvey WT, Rozanski AN, Ebert P, Hickey G, Hasenfeld P, Sanders AD, Stober C; Human Pangenome Reference Consortium; Korbel JO, Paten B, Marschall T, Eichler EE. Porubsky D, et al. Genome Res. 2023 Apr;33(4):496-510. doi: 10.1101/gr.277334.122. Epub 2023 May 10. Genome Res. 2023. PMID: 37164484 Free PMC article.
Complex genetic variation in nearly complete human genomes.
Logsdon GA, Ebert P, Audano PA, Loftus M, Porubsky D, Ebler J, Yilmaz F, Hallast P, Prodanov T, Yoo D, Paisie CA, Harvey WT, Zhao X, Martino GV, Henglin M, Munson KM, Rabbani K, Chin CS, Gu B, Ashraf H, Austine-Orimoloye O, Balachandran P, Bonder MJ, Cheng H, Chong Z, Crabtree J, Gerstein M, Guethlein LA, Hasenfeld P, Hickey G, Hoekzema K, Hunt SE, Jensen M, Jiang Y, Koren S, Kwon Y, Li C, Li H, Li J, Norman PJ, Oshima KK, Paten B, Phillippy AM, Pollock NR, Rausch T, Rautiainen M, Scholz S, Song Y, Söylev A, Sulovari A, Surapaneni L, Tsapalou V, Zhou W, Zhou Y, Zhu Q, Zody MC, Mills RE, Devine SE, Shi X, Talkowski ME, Chaisson MJP, Dilthey AT, Konkel MK, Korbel JO, Lee C, Beck CR, Eichler EE, Marschall T. Logsdon GA, et al. Among authors: chaisson mjp. bioRxiv [Preprint]. 2024 Sep 25:2024.09.24.614721. doi: 10.1101/2024.09.24.614721. bioRxiv. 2024. PMID: 39372794 Free PMC article. Preprint.
Reconstructing complex regions of genomes using long-read sequencing technology.
Huddleston J, Ranade S, Malig M, Antonacci F, Chaisson M, Hon L, Sudmant PH, Graves TA, Alkan C, Dennis MY, Wilson RK, Turner SW, Korlach J, Eichler EE. Huddleston J, et al. Genome Res. 2014 Apr;24(4):688-96. doi: 10.1101/gr.168450.113. Epub 2014 Jan 13. Genome Res. 2014. PMID: 24418700 Free PMC article.
An integrated map of structural variation in 2,504 human genomes.
Sudmant PH, Rausch T, Gardner EJ, Handsaker RE, Abyzov A, Huddleston J, Zhang Y, Ye K, Jun G, Fritz MH, Konkel MK, Malhotra A, Stütz AM, Shi X, Casale FP, Chen J, Hormozdiari F, Dayama G, Chen K, Malig M, Chaisson MJP, Walter K, Meiers S, Kashin S, Garrison E, Auton A, Lam HYK, Mu XJ, Alkan C, Antaki D, Bae T, Cerveira E, Chines P, Chong Z, Clarke L, Dal E, Ding L, Emery S, Fan X, Gujral M, Kahveci F, Kidd JM, Kong Y, Lameijer EW, McCarthy S, Flicek P, Gibbs RA, Marth G, Mason CE, Menelaou A, Muzny DM, Nelson BJ, Noor A, Parrish NF, Pendleton M, Quitadamo A, Raeder B, Schadt EE, Romanovitch M, Schlattl A, Sebra R, Shabalin AA, Untergasser A, Walker JA, Wang M, Yu F, Zhang C, Zhang J, Zheng-Bradley X, Zhou W, Zichner T, Sebat J, Batzer MA, McCarroll SA; 1000 Genomes Project Consortium; Mills RE, Gerstein MB, Bashir A, Stegle O, Devine SE, Lee C, Eichler EE, Korbel JO. Sudmant PH, et al. Among authors: chaisson mjp. Nature. 2015 Oct 1;526(7571):75-81. doi: 10.1038/nature15394. Nature. 2015. PMID: 26432246 Free PMC article.
Discovery and genotyping of structural variation from long-read haploid genome sequence data.
Huddleston J, Chaisson MJP, Steinberg KM, Warren W, Hoekzema K, Gordon D, Graves-Lindsay TA, Munson KM, Kronenberg ZN, Vives L, Peluso P, Boitano M, Chin CS, Korlach J, Wilson RK, Eichler EE. Huddleston J, et al. Among authors: chaisson mjp. Genome Res. 2017 May;27(5):677-685. doi: 10.1101/gr.214007.116. Epub 2016 Nov 28. Genome Res. 2017. PMID: 27895111 Free PMC article.
Expectations and blind spots for structural variation detection from long-read assemblies and short-read genome sequencing technologies.
Zhao X, Collins RL, Lee WP, Weber AM, Jun Y, Zhu Q, Weisburd B, Huang Y, Audano PA, Wang H, Walker M, Lowther C, Fu J; Human Genome Structural Variation Consortium; Gerstein MB, Devine SE, Marschall T, Korbel JO, Eichler EE, Chaisson MJP, Lee C, Mills RE, Brand H, Talkowski ME. Zhao X, et al. Among authors: chaisson mjp. Am J Hum Genet. 2021 May 6;108(5):919-928. doi: 10.1016/j.ajhg.2021.03.014. Epub 2021 Mar 30. Am J Hum Genet. 2021. PMID: 33789087 Free PMC article.
60 results