Publications

  1. Identification of putative causal loci in whole-genome sequencing data via knockoff statistics.
    He, Z, Liu, L, Wang, C, Le Guen, Y, Lee, J, Gogarten, S, Lu, F, Montgomery, S, Tang, H, Silverman, EK et al..
    Nat Commun. 2021;12 (1):3152. doi: 10.1038/s41467-021-22889-4.
    PubMed PMID:34035245 PubMed Central PMC8149672.
  2. Reconcile the debate over protective effects of BCG vaccine against COVID-19.
    Fu, W, Ho, PC, Liu, CL, Tzeng, KT, Nayeem, N, Moore, JS, Wang, LS, Chou, SY.
    Sci Rep. 2021;11 (1):8356. doi: 10.1038/s41598-021-87731-9.
    PubMed PMID:33863950 PubMed Central PMC8052320.
  3. Tailor: Targeting heavy tails in flow cytometry data with fast, interpretable mixture modeling.
    Ionita, M, Schretzenmair, R, Jones, D, Moore, J, Wang, LS, Rogers, W.
    Cytometry A. 2021;99 (2):133-144. doi: 10.1002/cyto.a.24307.
    PubMed PMID:33476090 .
  4. Using INFERNO to Infer the Molecular Mechanisms Underlying Noncoding Genetic Associations.
    Amlie-Wolf, A, Kuksa, PP, Lee, CY, Mlynarski, E, Leung, YY, Wang, LS.
    Methods Mol Biol. 2021;2254 :73-91. doi: 10.1007/978-1-0716-1158-6_6.
    PubMed PMID:33326071 .
  5. An integrated multi-omics approach identifies epigenetic alterations associated with Alzheimer's disease.
    Nativio, R, Lan, Y, Donahue, G, Sidoli, S, Berson, A, Srinivasan, AR, Shcherbakova, O, Amlie-Wolf, A, Nie, J, Cui, X et al..
    Nat Genet. 2020;52 (10):1024-1035. doi: 10.1038/s41588-020-0696-0.
    PubMed PMID:32989324 PubMed Central PMC8098004.
  6. Examination of the Effect of Rare Variants in TREM2, ABI3, and PLCG2 in LOAD Through Multiple Phenotypes.
    Olive, C, Ibanez, L, Farias, FHG, Wang, F, Budde, JP, Norton, JB, Gentsch, J, Morris, JC, Li, Z, Dube, U et al..
    J Alzheimers Dis. 2020;77 (4):1469-1482. doi: 10.3233/JAD-200019.
    PubMed PMID:32894242 PubMed Central PMC7927150.
  7. Reply: CYLD variants in frontotemporal dementia associated with severe memory impairment in a Portuguese cohort.
    Oyston, LJ, Chatterton, Z, Hallupp, M, Rajan, N, Kwok, JB, Dobson-Stone, C.
    Brain. 2020;143 (8):e68. doi: 10.1093/brain/awaa184.
    PubMed PMID:32666099 PubMed Central PMC7447510.
  8. Whole-Exome Sequencing Analysis of Alzheimer's Disease in Non-APOE*4 Carriers.
    Fan, KH, Feingold, E, Rosenthal, SL, Demirci, FY, Ganguli, M, Lopez, OL, Kamboh, MI.
    J Alzheimers Dis. 2020;76 (4):1553-1565. doi: 10.3233/JAD-200037.
    PubMed PMID:32651314 PubMed Central PMC7484092.
  9. SparkINFERNO: a scalable high-throughput pipeline for inferring molecular mechanisms of non-coding genetic variants.
    Kuksa, PP, Lee, CY, Amlie-Wolf, A, Gangadharan, P, Mlynarski, EE, Chou, YF, Lin, HJ, Issen, H, Greenfest-Allen, E, Valladares, O et al..
    Bioinformatics. 2020;36 (12):3879-3881. doi: 10.1093/bioinformatics/btaa246.
    PubMed PMID:32330239 PubMed Central PMC7320617.
  10. 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 .
  11. 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.
  12. Alzheimer Disease Pathology-Associated Polymorphism in a Complex Variable Number of Tandem Repeat Region Within the MUC6 Gene, Near the AP2A2 Gene.
    Katsumata, Y, Fardo, DW, Bachstetter, AD, Artiushin, SC, Wang, WX, Wei, A, Brzezinski, LJ, Nelson, BG, Huang, Q, Abner, EL et al..
    J Neuropathol Exp Neurol. 2020;79 (1):3-21. doi: 10.1093/jnen/nlz116.
    PubMed PMID:31748784 PubMed Central PMC8204704.
  13. 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 PubMed Central PMC7316086.
  14. 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.
  15. 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.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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. 2020;25 (8):1859-1875. doi: 10.1038/s41380-018-0112-7.
    PubMed PMID:30108311 PubMed Central PMC6375806.
  24. 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.
  25. 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.
  26. 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.
  27. Whole genome sequencing of Caribbean Hispanic families with late-onset Alzheimer's disease.
    Vardarajan, BN, Barral, S, Jaworski, J, Beecham, GW, Blue, E, Tosto, G, Reyes-Dumeyer, D, Medrano, M, Lantigua, R, Naj, A et al..
    Ann Clin Transl Neurol. 2018;5 (4):406-417. doi: 10.1002/acn3.537.
    PubMed PMID:29688227 PubMed Central PMC5899906.
  28. 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.
  29. 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.
  30. 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.
  31. Analysis of neurodegenerative Mendelian genes in clinically diagnosed Alzheimer Disease.
    Fernández, MV, Kim, JH, Budde, JP, Black, K, Medvedeva, A, Saef, B, Deming, Y, Del-Aguila, J, Ibañez, L, Dube, U et al..
    PLoS Genet. 2017;13 (11):e1007045. doi: 10.1371/journal.pgen.1007045.
    PubMed PMID:29091718 PubMed Central PMC5683650.
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