Publications

  1. Packaging Biocomputing Software to Maximize Distribution and Reuse.
    Bush, WS, Wheeler, N, Beaulieu-Jones, B, Darabos, C.
    Pac Symp Biocomput. 2020;25 :739-742. .
    PubMed PMID:31797644 .
  2. Hadoop and PySpark for reproducibility and scalability of genomic sequencing studies.
    Wheeler, NR, Benchek, P, Kunkle, BW, Hamilton-Nelson, KL, Warfe, M, Fondran, JR, Haines, JL, Bush, WS.
    Pac Symp Biocomput. 2020;25 :523-534. .
    PubMed PMID:31797624 PubMed Central PMC6956992.
  3. Inferring the Molecular Mechanisms of Noncoding Alzheimer's Disease-Associated Genetic Variants.
    Amlie-Wolf, A, Tang, M, Way, J, Dombroski, B, Jiang, M, Vrettos, N, Chou, YF, Zhao, Y, Kuzma, A, Mlynarski, EE et al..
    J. Alzheimers Dis. 2019;72 (1):301-318. doi: 10.3233/JAD-190568.
    PubMed PMID:31561366 .
  4. Systematic analysis of dark and camouflaged genes reveals disease-relevant genes hiding in plain sight.
    Ebbert, MTW, Jensen, TD, Jansen-West, K, Sens, JP, Reddy, JS, Ridge, PG, Kauwe, JSK, Belzil, V, Pregent, L, Carrasquillo, MM et al..
    Genome Biol. 2019;20 (1):97. doi: 10.1186/s13059-019-1707-2.
    PubMed PMID:31104630 PubMed Central PMC6526621.
  5. PTCD1 Is Required for Mitochondrial Oxidative-Phosphorylation: Possible Genetic Association with Alzheimer's Disease.
    Fleck, D, Phu, L, Verschueren, E, Hinkle, T, Reichelt, M, Bhangale, T, Haley, B, Wang, Y, Graham, R, Kirkpatrick, DS et al..
    J. Neurosci. 2019;39 (24):4636-4656. doi: 10.1523/JNEUROSCI.0116-19.2019.
    PubMed PMID:30948477 PubMed Central PMC6561697.
  6. Association of Rare Coding Mutations With Alzheimer Disease and Other Dementias Among Adults of European Ancestry.
    Patel, D, Mez, J, Vardarajan, BN, Staley, L, Chung, J, Zhang, X, Farrell, JJ, Rynkiewicz, MJ, Cannon-Albright, LA, Teerlink, CC et al..
    JAMA Netw Open. 2019;2 (3):e191350. doi: 10.1001/jamanetworkopen.2019.1350.
    PubMed PMID:30924900 PubMed Central PMC6450321.
  7. DASHR 2.0: integrated database of human small non-coding RNA genes and mature products.
    Kuksa, PP, Amlie-Wolf, A, Katanić, Ž, Valladares, O, Wang, LS, Leung, YY.
    Bioinformatics. 2019;35 (6):1033-1039. doi: 10.1093/bioinformatics/bty709.
    PubMed PMID:30668832 PubMed Central PMC6419920.
  8. Rare genetic variation implicated in non-Hispanic white families with Alzheimer disease.
    Beecham, GW, Vardarajan, B, Blue, E, Bush, W, Jaworski, J, Barral, S, DeStefano, A, Hamilton-Nelson, K, Kunkle, B, Martin, ER et al..
    Neurol Genet. 2018;4 (6):e286. doi: 10.1212/NXG.0000000000000286.
    PubMed PMID:30569016 PubMed Central PMC6278241.
  9. A rare missense variant of CASP7 is associated with familial late-onset Alzheimer's disease.
    Zhang, X, Zhu, C, Beecham, G, Vardarajan, BN, Ma, Y, Lancour, D, Farrell, JJ, Chung, J, Alzheimer's Disease Sequencing Project, Mayeux, R et al..
    Alzheimers Dement. 2019;15 (3):441-452. doi: 10.1016/j.jalz.2018.10.005.
    PubMed PMID:30503768 PubMed Central PMC6408965.
  10. Translating Alzheimer's disease-associated polymorphisms into functional candidates: a survey of IGAP genes and SNPs.
    Katsumata, Y, Nelson, PT, Estus, S, Alzheimer's Disease Neuroimaging Initiative (ADNI), Fardo, DW.
    Neurobiol. Aging. 2019;74 :135-146. doi: 10.1016/j.neurobiolaging.2018.10.017.
    PubMed PMID:30448613 PubMed Central PMC6331247.
  11. VCPA: genomic variant calling pipeline and data management tool for Alzheimer's Disease Sequencing Project.
    Leung, YY, Valladares, O, Chou, YF, Lin, HJ, Kuzma, AB, Cantwell, L, Qu, L, Gangadharan, P, Salerno, WJ, Schellenberg, GD et al..
    Bioinformatics. 2019;35 (10):1768-1770. doi: 10.1093/bioinformatics/bty894.
    PubMed PMID:30351394 PubMed Central PMC6513159.
  12. INFERNO: inferring the molecular mechanisms of noncoding genetic variants.
    Amlie-Wolf, A, Tang, M, Mlynarski, EE, Kuksa, PP, Valladares, O, Katanic, Z, Tsuang, D, Brown, CD, Schellenberg, GD, Wang, LS et al..
    Nucleic Acids Res. 2018;46 (17):8740-8753. doi: 10.1093/nar/gky686.
    PubMed PMID:30113658 PubMed Central PMC6158604.
  13. Whole exome sequencing study identifies novel rare and common Alzheimer's-Associated variants involved in immune response and transcriptional regulation.
    Bis, JC, Jian, X, Kunkle, BW, Chen, Y, Hamilton-Nelson, KL, Bush, WS, Salerno, WJ, Lancour, D, Ma, Y, Renton, AE et al..
    Mol. Psychiatry. 2018; :. doi: 10.1038/s41380-018-0112-7.
    PubMed PMID:30108311 PubMed Central PMC6375806.
  14. Whole-exome sequencing in 20,197 persons for rare variants in Alzheimer's disease.
    Raghavan, NS, Brickman, AM, Andrews, H, Manly, JJ, Schupf, N, Lantigua, R, Wolock, CJ, Kamalakaran, S, Petrovski, S, Tosto, G et al..
    Ann Clin Transl Neurol. 2018;5 (7):832-842. doi: 10.1002/acn3.582.
    PubMed PMID:30009200 PubMed Central PMC6043775.
  15. Integrative DNA copy number detection and genotyping from sequencing and array-based platforms.
    Zhou, Z, Wang, W, Wang, LS, Zhang, NR.
    Bioinformatics. 2018;34 (14):2349-2355. doi: 10.1093/bioinformatics/bty104.
    PubMed PMID:29992253 PubMed Central PMC6041760.
  16. Quality control and integration of genotypes from two calling pipelines for whole genome sequence data in the Alzheimer's disease sequencing project.
    Naj, AC, Lin, H, Vardarajan, BN, White, S, Lancour, D, Ma, Y, Schmidt, M, Sun, F, Butkiewicz, M, Bush, WS et al..
    Genomics. 2019;111 (4):808-818. doi: 10.1016/j.ygeno.2018.05.004.
    PubMed PMID:29857119 PubMed Central PMC6397097.
  17. Genetic Variation in Genes Underlying Diverse Dementias May Explain a Small Proportion of Cases in the Alzheimer's Disease Sequencing Project.
    Blue, EE, Bis, JC, Dorschner, MO, Tsuang, DW, Barral, SM, Beecham, G, Below, JE, Bush, WS, Butkiewicz, M, Cruchaga, C et al..
    Dement Geriatr Cogn Disord. 2018;45 (1-2):1-17. doi: 10.1159/000485503.
    PubMed PMID:29486463 PubMed Central PMC5971141.
  18. Comprehensive Analysis of Constraint on the Spatial Distribution of Missense Variants in Human Protein Structures.
    Sivley, RM, Dou, X, Meiler, J, Bush, WS, Capra, JA.
    Am. J. Hum. Genet. 2018;102 (3):415-426. doi: 10.1016/j.ajhg.2018.01.017.
    PubMed PMID:29455857 PubMed Central PMC5985282.
  19. The Alzheimer's Disease Sequencing Project: Study design and sample selection.
    Beecham, GW, Bis, JC, Martin, ER, Choi, SH, DeStefano, AL, van Duijn, CM, Fornage, M, Gabriel, SB, Koboldt, DC, Larson, DE et al..
    Neurol Genet. 2017;3 (5):e194. doi: 10.1212/NXG.0000000000000194.
    PubMed PMID:29184913 PubMed Central PMC5646177.
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