Publication

Publications:

• X. Peng, J. W. Smith, M. K. Callahan, K. S. Panageas, R. Shen. (2023+) “SpaTopic: Topic Inference of Tissue Microenvironments with Multiplexed Imaging Data”. (Available upon request)

• A.S. Rolig*, X. Peng*, E.R. Sturgill, C. Mick, G.H. Mcgee, M. Kasiewicz, W. Miller, Y. Koguchi, M. Adamow, J. Lee, J. Kaufmann, N. Yanamandra, S. Griffin, J. Smothers, C. Garnet-Benson, I. Jarchem, R. Shen, M. K. Callahan, W. L. Redmond. (2023+) “Response to anti-PD-1 + anti-LAG-3 checkpoint blockade is associated with T regulatory cell functional reprogramming and instability” (under revision)

• X. Peng, K. S. Dorman. (2023+) “Constrained mixture of factor analyzers model enables joint dimension reduction and clustering on omics data”. (Available upon request)

• X. Peng, J. Lee, M. Adamow, C. Maher, M. A. Postow, M. K. Callahan, K. S. Panageas, R. Shen (2023). “A topic modeling approach reveals the dynamic T cell composition of peripheral blood during cancer immunotherapy”. Cell Reports Methods, 3(8). 100546. doi: 10.1016/j.crmeth.2023.100546.

• X. Peng, K. S. Dorman. (2023). Accurate estimation of molecular counts from amplicon sequence data with unique molecular identifiers. Bioinformatics. 39(1), btad002. doi: 10.1093/bioinformatics/btad002.

• R. S. Vanguri, J. W. Smithy, Y. Li, M. Zhuang, C. Maher, N. Aleynick, X. Peng, H. Al-Ahmadie, S. A. Funt, J. E. Rosenberg, G. Iyer, D. Bajorin, J. C. Mathews, S. Nadeem, K. S. Panageas, R. Shen, M. K. Callahan, T. J. Hollmann. (2023), Integration of peripheral blood- and tissue-based biomarkers of response to immune checkpoint blockade in urothelial carcinoma. The Journal of Pathology. doi: 10.1002/path.6197

• K. S. Dorman, X. Peng, Y. Zhang. (2021). Denoising Methods for Inferring Microbiome Community Content and Abundance. Book chapter for “Statistical Analysis of Microbiome Data” in the Frontiers in Probability and the Statistical Sciences series by Springer. doi.org/10.1007/978-3-030-73351-3_1

• X. Peng, K. S. Dorman. (2020). AmpliCI: A High-resolution Model-Based Approach for Denoising Illumina Amplicon Data. Bioinformatics. doi.org/10.1093/bioinformatics/btaa648

• Q. Y. Li, X. Peng, E. R. Burrough, O. Sahin, S. A. Gould, N. K. Gabler, C. L. Loving, K. S. Dorman, and J. F. Patience. (2020). Dietary soluble and insoluble fiber with or without enzymes altered the intestinal microbiota in weaned pigs challenged with Enterotoxigenic E. coli F18. Frontiers in Microbiology. 11, 1110. doi: 10.3389/fmicb.2020.01110

Presentations:

• Talk in Microbiome COSI, Intelligent Systems for Molecular Biology (ISMB), July 2018, Chicago

• Talk in Contributed Session, Joint Statistical Meeting (JSM), August 2019, Denver

• Poster in  HitSeq COSI, Intelligent Systems for Molecular Biology (ISMB), July 2020, Virtual

• Talk in Contributed Session (Best student paper award), Joint Statistical Meeting (JSM), August 2020, Virtual

• Talk in Contributed Session, Eastern North American Region (ENAR) Spring Meeting, March 2021, Virtual

• Poster in  HitSeq COSI, Intelligent Systems for Molecular Biology (ISMB), July 2022, Madison

• Poster in Society for Immunotherapy of Cancer (SITC) 37th Annual Meeting, November 2022, Boston

• Poster in Statistical Methods in Imaging Conference, May 2023, Minneapolis

• Poster in NYC Epidemiology Forum, June 2023, New York

• Talk in Contributed Session, Joint Statistical Meeting (JSM), August 2023, Toronto

• Poster in Society for Immunotherapy of Cancer (SITC) 38th Annual Meeting, November 2023, San Diego