Publications

You can also find our articles on Google Scholar.

Journal Articles

Genetics and Environment Distinctively Shape the Human Immune Cell Epigenome

Published in Nature Genetics, 2026

We used single-nucleus methylation sequencing and ATAC-seq to systematically explore how pathogen/chemical exposures and genetic variation shape the immune cell epigenome, revealing that exposure-associated DMRs are enriched in regulatory regions while genotype-associated DMRs preferentially locate in gene body marks.

Recommended citation: Wang W^*, Hariharan M^*, Ding W^*, Bartlett A, Barragan C, Castanon R, Wang R, Rothenberg V, Song H, Nery JR, Altshul J, Kenworthy M, Liu H, Tian W, Zhou J, Zeng Q, Chen H, Aldridge A, Gündüz IB, Müller F, Norell T, Broderick TJ, McClain MT, Satterwhite LL, Burke TW, Petzold EA, Woods CW, Fowler VG Jr, Ruffin F, Ecker JR. (2026). "Genetics and environment distinctively shape the human immune cell epigenome." Nature Genetics. 58:392–403. doi:10.1038/s41588-025-02479-6
Download Paper

Brain Region-Specific Epigenomic Reorganization and Altered Cell States in Alzheimer’s Disease

Published in bioRxiv, 2025

A large-scale single-cell multi-omic atlas (>230,000 cells) integrating DNA methylation and 3D genome architecture from AD patients and controls across three brain regions, revealing widespread AD-associated epigenomic changes and marked reorganization of 3D genome structure.

Recommended citation: Wang W, Berube P, Yang B, Castanon R, Bartlett A, Komandur K, Nery JR, Barragan C, Kenworthy M, Valadon C, Altshul J, Petrella A, Chan D, Chen C, Saldaña Acerbo A, Luo J, Jain M, Soma E, Chen H, Liem M, Marrin M, O'Connor C, Zemke N, Oakley D, Ren B, Hyman BT^#, Ecker JR^#. (2025). "Brain region-specific epigenomic reorganization and altered cell states in Alzheimer's disease." bioRxiv. doi:10.1101/2025.09.29.678849
Download Paper

TCF-1 Promotes Chromatin Interactions across Topologically Associating Domains in T Cell Progenitors

Published in Nature Immunology, 2022

Co-occupancy of TCF-1 and CTCF alters the structure of topologically associating domains in T cell progenitors, leading to interactions between previously insulated regulatory elements and target genes, linked to H3K27ac deposition and NIPBL recruitment at active enhancers.

Recommended citation: Wang W^*, Chandra A^*, Goldman N^*, Yoon S^*, Ferrari EK^*, Nguyen SC, Joyce EF, Vahedi G. (2022). "TCF-1 promotes chromatin interactions across topologically associating domains in T cell progenitors." Nature Immunology. 23(7):1052–1062. doi:10.1038/s41590-022-01232-z
Download Paper

Joint Profiling of Chromatin Accessibility and CAR-T Integration Site Analysis at Population and Single-Cell Levels

Published in Proceedings of the National Academy of Sciences, 2020

Development of EpiVIA, a method for joint profiling of chromatin accessibility and lentiviral integration sites at single-cell resolution, enabling single-cell deconstruction of gene regulation during CAR-T therapy.

Recommended citation: Wang W, Fasolino M, Cattau B, Goldman N, Kong W, Frederick MA, McCright SJ, Kiani K, Fraietta JA, Vahedi G. (2020). "Joint profiling of chromatin accessibility and CAR-T integration site analysis at population and single-cell levels." Proceedings of the National Academy of Sciences. 117(10):5442–5452. doi:10.1073/pnas.1919259117
Download Paper

Chromosome Level Comparative Analysis of Brassica Genomes

Published in Plant Molecular Biology, 2019

Chromosome-level comparative genomic analysis of Brassica species revealing patterns of gene synteny, polyploidization dynamics, and asymmetric gene retention across the Brassicaceae family.

Recommended citation: Wang W, Guan R, Liu X, Zhang H, Song B, Xu Q, Fan G, Chen W, Wu X, Yin Y, Xu X. (2019). "Chromosome level comparative analysis of Brassica genomes." Plant Molecular Biology. 99(3):237–249. doi:10.1007/s11103-019-00833-x
Download Paper

Bridge-AD Lab