Bryan, JG, and Hoff, PD. “Smaller \(p\)-values in genomics studies using distilled historical information.” Biostatistics, (July 16, 2021). https://doi.org/10.1093/biostatistics/kxaa053
Sheffer, M, Lowry, E, Beelen, N, Borah, M, Amara, SN, Mader, CC, Roth, JA, Tsherniak, A, Freeman, SS, Dashevsky, O, Gandolfi, S, Bender, S, Bryan, JG, Zhu, C, Wang, L, Tariq, I, Kamath, GM, Simoes, RD, Dhimolea, E, Yu, C, Hu, Y, Dufva, O, Giannakis, M, Syrgkanis, V, Fraenkel, E, Golub, T, Romee, R, Mustjoki, S, Culhane, AC, Wieten, L, Mitsiades, CS. “Genome-scale screens identify factors regulating tumor cell responses to natural killer cells.” Nature Genetics, (July, 12, 2021). https://doi.org/10.1038/s41588-021-00889-w
Bryan, J, Mandan, A, Kamat, G, Gottschalk, WK, Badea, A, Adams, KJ, Thompson, JW, Colton, CA, Mukherjee, S, Lutz, MW. “Likelihood ratio statistics for gene set enrichment in Alzheimer’s disease pathways.” Alzheimer’s & Dementia, (January 21, 2021). https://doi.org/10.1002/alz.12223
Dhimolea, E, Simoes, RDM, Kansara, D, Al-Khafaji, A, Bouyssou, J, Weng, X, Sharma, S, Raja, J, Awate, P, Shirasaki, R, Tang, H, Glassner, BJ, Liu, Z, Gao, D, Bryan, J, Bender, S, Roth, J, Scheffer, M, Jeselsohn, R, Gray, NS, Georgakoudi, I, Vazquez, F, Tsherniak, A, Chen, Y, Welm, A, Cihangir, D, Melnick, A, Bartholdy, B, Brown, M, Culhane, AC, Mitsiades, CS. “An Embryonic Diapause-like Adaptation with Suppressed Myc Activity Enables Tumor Treatment Persistence.” Cancer Cell, (January 07, 2021). https://doi.org/10.1016/j.ccell.2020.12.002
Wu, J, Bryan, J, Rubinstein, SM, Wang, L, Lenoue-Newton, M, Zuhour, R, Levy, M, Micheel, C, Xu, Y, Bhavnani, SK, Mackey, L, and Warner, JL. “Opportunities and Challenges for Analyzing Cancer Data at the Inter- and Intra-Institutional Levels.” JCO Precision Oncology, (June 25, 2020): 743-756
Corsello, SM, Nagari, RT, Spangler, RD, Rossen, J, Kocak, M, Bryan, JG, Humeidi, R, Peck, D, Wu, X, Tang, AA, Wang, VM, Bender, SA, Lemire, E, Narayan, R, Montgomery, P, Ben-David, U, Garvie, CW, Chen, Y, Rees, MG, Lyons, NJ, McFarland, JM, Wong, BT, Wang, L, Dumont, N, O’Hearn, PJ, Stefan, E, Doench, JG, Greulich, H, Meyerson, M, Vazquez, F, Subramanian, A, Roth, JA, Bittker, JA, Boehm, JS, Mader, CC, Tsherniak, A and Golub, TR. “Discovering the anticancer potential of non-oncology drugs by systematic viability profiling.” Nature Cancer, (January 2020) doi:10.1038/s43018-019-0018-6
McFarland, JM, Ho, ZV, Kugener, G, Dempster, JM, Montgomery, PG, Bryan, JG, Krill-Burger, JM, Green, TM, Vazquez, F, Boehm, JS, Golub, TR, Hahn, WC, Root, DE and Tsherniak, A. “Improved Estimation of Cancer Dependencies from Large-Scale RNAi Screens Using Model-Based Normalization and Data Integration.” Nature Communications 9, no. 1 (December 2018). https://doi.org/10.1038/s41467-018-06916-5.
Gray, SW, Gagan, J, Cerami, E, Cronin, AM, Uno, H, Oliver, N, Lowenstein, C, Lederman, R, Revette, A, Suarez, A, Lee, C, Bryan, J, Sholl, L, and Van Allen, EM. “Interactive or static reports to guide clinical interpretation of cancer genomics.” Journal of the American Medical Informatics Association 25.5 (May 1, 2018): 458-464.
Meyers, RM, Bryan, JG, McFarland, JM, Weir, BA, Sizemore, AE, Xu, H, Dharia, NV, Montgomery, PG, Cowley, GS, Pantel, S, Goodale, A, Lee, Y, Ali, LD, Jiang, G, Lubonja, R, Harrington, WF, Strickland, M, Wu, T, Hawes, DC, Zhivich, VA, Wyatt, MR, Kalani, Z, Chang, JJ, Okamoto, M, Stegmaier, K, Golub, TR, Boehm, JS, Vazquez, F, Root, DE, Hahn, WC, and Tsherniak, A. “Computational correction of copy number effect improves specificity of CRISPR–Cas9 essentiality screens in cancer cells.” Nature Genetics 49.12 (October 30, 2017): 1779-1784.
Mackey, L, Bryan, J, and Mo, MY. “Weighted Classification Cascades for Optimizing Discovery Significance in the HiggsML Challenge.” Ed. Cowan, G, Germain, C, Guyon, I, Kégl, B and Rousseau, D. Proceedings of the Nips 2014 Workshop on High Energy Physics and Machine Learning 42 (December 13, 2015): 129-134.
BTF: R package for Bayesian inference in a low-rank tensor factorization model
ceres: R package for correction of copy-number effect in CRISPR-Cas9 essentiality screens in cancer cell lines
Nonparametric empirical Bayes estimation using entropic optimal transport. Speed session talk at Joint Statistical Meetings, Online, August 12th, 2021
Smaller \(p\)-Values in Genomics Studies Using Distilled Auxilliary Information. Contributed talk at the World Meeting of the International Society for Bayesian Analysis, Online, June 28th, 2021
Smaller \(p\)-Values in Genomics Studies Using Distilled Historical Information. Contributed talk at Joint Statistical Meetings, Online, August 3rd, 2020
Incompleteness and the Underground. Paper presented at the 2nd Annual Duke-Stanford Graduate Conference, Durham, NC. April 6, 2019
Incompleteness and the Underground. Paper presented at the 57th Annual Southern Conference on Slavic Studies, Mobile, AL. March 15, 2019
CERES: A New Approach to Correct for Copy Number in CRISPR-Cas9 Screens. CTD^2 D-HIP Webinar Series. CTD^2 Network. July 12, 2018
CERES—A model for inferring genetic dependencies in cancer cell lines from CRISPR knockout screens. Meeting on Biological Data Science. Cold Spring Harbor Laboratory. October 26, 2016