Publication

On the genetic basis of tail-loss evolution in humans and apes.

Xia, B.#, Zhang, W.*, Zhao, G.*, Zhang, X.*, Bai, J., Brosh, R., Wudzinska, A., Huang, E., Ashe, H., Ellis, G., Pour, M., Zhao, Y., Coelho, C., Zhu, Y., Miller, A., Dasen, J., Maurano, M., Kim, S., Boeke, J.#, and Yanai, I.# (2024) Nature (in press), BioRxiv

News: New York Times, Science, New Scientist, The Scientist, Smithsonian Magazine, BBC News, Mashable

Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening

Tan, J., Shenker-Tauris, N., Rodriguez-Hernaez, J., Wang, E., Sakellaropoulos, T., Boccalatte, F., Thandapani, P., Skok, J., Aifantis, I., Fenyo, D., Xia, B.#, Tsirigos, A.# (2023). Nature Biotechnology. 41(8), 1140-1150. URL


Widespread transcriptional scanning in the testis modulates gene evolution rates.

Xia, B., Yan, Y., Baron, M., Wagner, F., Barkley, D., Chiodin, M., Kim, S., Keefe, D., Alukal, J., Boeke, J. and Yanai, I. (2020) Cell. 180 (2), 248-262. (Cover) URL

Preview: Sperm Go to (Transcription) Extremes

News: EurekaAlert!, ScienceDaily, Phys.org

Credit: Molly Ferguson 

Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale

Xia, B.*, Han, D.*, Lu, X.*, Sun, Z., Zhou, A., Yin, Q., Zeng, H., Liu, M., Jiang, X., Xie, W., He, C.# and Yi, C.# (2015) Nature Methods, 12(11), 1047–1050. URL

Selected publications:

1.   Xia, B.#, Zhang, W.*, Zhao, G.*, Zhang, X.*, Bai, J., Brosh, R., Wudzinska, A., Huang, E., Ashe, H., Ellis, G., Pour, M., Zhao, Y., Coelho, C., Zhu, Y., Miller, A., Dasen, J., Maurano, M., Kim, S., Boeke, J.#, and Yanai, I.# (2024) On the genetic basis of tail-loss evolution in humans and apes. Nature (in press), BioRxiv. (co-corresponding author) URL

News: New York Times, Science, New Scientist, The Scientist, Smithsonian Magazine, BBC News, Mashable

2.   Tan, J., Shenker-Tauris, N., Rodriguez-Hernaez, J., Wang, E., Sakellaropoulos, T., Boccalatte, F., Thandapani, P., Skok, J., Aifantis, I., Fenyo, D., Xia, B.#, Tsirigos, A.# (2023) Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nature Biotechnology, 41(8), 1140-1150. URL (co-corresponding author) 

3.   Xia, B., Yan, Y., Baron, M., Wagner, F., Barkley, D., Chiodin, M., Kim, S., Keefe, D., Alukal, J., Boeke, J. and Yanai, I. (2020) Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell. 180 (2), 248-262. (Cover) URL

Preview: Sperm Go to (Transcription) Extremes

News: EurekaAlert!, ScienceDaily, Phys.org

4.   Xia, B. and Yanai, I. (2019) A periodic table of cell types. Development, 146(12): dev169854. URL

5.   Zhu, C.*, Gao, Y.*, Guo, H.*, Xia, B.*, Song, J., Wu, X., Zeng, H., Kee, K., Tang, F.# and Yi, C. # (2017) Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell, 20(5), 720-731. URL

6.   Xia, B.*, Han, D.*, Lu, X.*, Sun, Z., Zhou, A., Yin, Q., Zeng, H., Liu, M., Jiang, X., Xie, W., He, C.# and Yi, C.# (2015) Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods, 12(11), 1047–1050. URL

More publication:

1.   Barkley, D., Moncada, R., Werba, G., Wang, W., Baron, M., Rao, A., Xia, B., Starvaggi Franca, G., Hajdu, C., Weil, A., Osman, I. Liberman, D., Dryg, I., DeLair, D., Lund, A., and Yanai, I. (2022) Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment. Nature Genetics, 54(8):1192-1201.

2.   Xia, B. and Yanai, I (2022) Gene expression levels tune germline mutation rates through the compound effects of transcription-coupled repair and damage. Human Genetics, 141(6):1211-1222.

3.   Zeng, H.*, Song, R.*, Mondal, M.*, Zhang, J., Xia, B., Liu, M., Zhu, C., He, B., Gao, Y.#, and Yi, C.# (2019) Unnatural cytosine bases recognized as thymines by DNA polymerases via a tautomerization-dependent mechanism. Angewandte Chemie. 131(1), 136-139.

4.   Zeng, H.*, He, B.*, Xia, B., Bai, D., Lu, X., Cai, J., Chen, L., Zhou, A., Zhu, C., Gao, Y., Guo, H., Meng, H., He, C.#, Dai, Q.#, and Yi, C.#. (2018) Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution. Journal of the American Chemical Society, 140(41), 13190–13194.

5.   Cimmino, L., Dolgalev, I., Wang, Y., Yoshimi, A., Martin, G. H., Wang, J., Ng,V., Xia, B., Witkowski, M., Mitchell-Flack, M., Grillo, I., Bakogianni, S., Ndiaye-Lobry, D., Martín. M., Guillamot, M., Banh, R., Xu, M., Figueroa, M., Dickins, R., Abdel-Wahab, O., Park, C., Tsirigos, A., Neel, B. # and Aifantis, I. # (2017). Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell, 170(6), 1079-1095.

6.   Peng, J., Xia, B. and Yi, C. (2016) Single-base resolution analysis of DNA epigenome via high-throughput sequencing. Science China Life Sciences, 59(3), 219–226.

7.   Lu, L., Zhu, C., Xia, B. and Yi, C. (2014) Oxidative demethylation of DNA and RNA mediated by non-heme iron-dependent dioxygenases. Chemistry–An Asian Journal, 9(8): 2018–2029.

Patents:

1.   Yi, C., Xia, B., Zhou, A. 5-formylcytosine specific chemical labeling methods and related applications. Priority date: 2013-09-27.  Granted: WO2015043493A1 (2015); CN104311618B (2015); JP6243013B2 (2017); EP3061764B1 (2019); US10519184B2 (2019).

2.   Yi, C., Zhu, C., Xia, B. Method for marking 5-formylcytosine and use thereof in single base resolution sequencing. Priority date: 2017-02-28. Granted: WO2018157775A1 (2017); CN106957350B (2019); US11293050B2 (2022).

3.   Tsirigos, A., Xia, B., Tan, J.. Cell type-specific prediction of 3d chromatin architecture. PCT/US2023/014501 (2023); WO2023168079A2 (2023). 

Science outreach:

1.   Xia, B. (2020) How to turn a Eureka moment into a research project: from ‘napkin idea’ to published paper. Nature Index. URL

2.   Xia, B. (2018) Eureka! My path to studying the epigenomes. Journal of Stories in Science, #95: 1-3. URL