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Application of Aligned-UMAP to longitudinal biomedical studies.
Dadu A, Satone VK, Kaur R, Koretsky MJ, Iwaki H, Qi YA, Ramos DM, Avants B, Hesterman J, Gunn R, Cookson MR, Ward ME, Singleton AB, Campbell RH, Nalls MA, Faghri F. Dadu A, et al. Among authors: qi ya. Patterns (N Y). 2023 May 8;4(6):100741. doi: 10.1016/j.patter.2023.100741. eCollection 2023 Jun 9. Patterns (N Y). 2023. PMID: 37409055 Free PMC article.
A fully automated FAIMS-DIA mass spectrometry-based proteomic pipeline.
Reilly L, Lara E, Ramos D, Li Z, Pantazis CB, Stadler J, Santiana M, Roberts J, Faghri F, Hao Y, Nalls MA, Narayan P, Liu Y, Singleton AB, Cookson MR, Ward ME, Qi YA. Reilly L, et al. Among authors: qi ya. Cell Rep Methods. 2023 Oct 23;3(10):100593. doi: 10.1016/j.crmeth.2023.100593. Epub 2023 Sep 19. Cell Rep Methods. 2023. PMID: 37729920 Free PMC article.
TDP-43 and other hnRNPs regulate cryptic exon inclusion of a key ALS/FTD risk gene, UNC13A.
Koike Y, Pickles S, Estades Ayuso V, Jansen-West K, Qi YA, Li Z, Daughrity LM, Yue M, Zhang YJ, Cook CN, Dickson DW, Ward M, Petrucelli L, Prudencio M. Koike Y, et al. Among authors: qi ya. PLoS Biol. 2023 Mar 17;21(3):e3002028. doi: 10.1371/journal.pbio.3002028. eCollection 2023 Mar. PLoS Biol. 2023. PMID: 36930682 Free PMC article.
African ancestry neurodegeneration risk variant disrupts an intronic branchpoint in GBA1.
Álvarez Jerez P, Wild Crea P, Ramos DM, Gustavsson EK, Radefeldt M, Damianov A, Makarious MB, Ojo OO, Billingsley KJ, Malik L, Daida K, Bromberek S, Hu F, Schneider Z, Surapaneni AL, Stadler J, Rizig M, Morris HR, Pantazis CB, Leonard HL, Screven L, Qi YA, Nalls MA, Bandres-Ciga S, Hardy J, Houlden H, Eng C, Burchard EG, Kachuri L, Lin CH, Black DL; Global Parkinson’s Genetics Program (GP2); Singleton AB, Fischer S, Bauer P, Reed X, Ryten M, Beetz C, Ward M, Okubadejo NU, Blauwendraat C. Álvarez Jerez P, et al. Among authors: qi ya. Nat Struct Mol Biol. 2024 Dec;31(12):1955-1963. doi: 10.1038/s41594-024-01423-2. Epub 2024 Dec 12. Nat Struct Mol Biol. 2024. PMID: 39668204 Free PMC article.
ProtPipe: A Multifunctional Data Analysis Pipeline for Proteomics and Peptidomics.
Li Z, Weller CA, Shah S, Johnson NL, Hao Y, Jarreau PB, Roberts J, Guha D, Bereda C, Klaisner S, Machado P, Zanovello M, Prudencio M, Oskarsson B, Staff NP, Dickson DW, Fratta P, Petrucelli L, Narayan P, Cookson MR, Ward ME, Singleton AB, Nalls MA, Qi YA. Li Z, et al. Among authors: qi ya. Genomics Proteomics Bioinformatics. 2024 Nov 22:qzae083. doi: 10.1093/gpbjnl/qzae083. Online ahead of print. Genomics Proteomics Bioinformatics. 2024. PMID: 39576693 Free article.
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