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 626, 1042–1048. (Cover; # co-corresponding author). Also see BioRxiv.
Nature News & Views: A mobile DNA sequence could explain tail loss in humans and ape
Media coverage: New York Times, CNN, Reuters, Scientific American, Nature, Science, Science News, The Scientist, Smithsonian Magazine, BBC News, Associated Press(AP), etc.
Credit: Aman Raghuwanshi Edit: Bailey Tischer, Bo Xia
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
Credit: Oksana Smyshliaeva, via iStock
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
Cell Preview: Sperm Go to (Transcription) Extremes
Media coverage: 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 626, 1042–1048. (Cover; co-corresponding author) URL
Nature News & Views: A mobile DNA sequence could explain tail loss in humans and ape
Media coverage: New York Times, CNN, Reuters, Scientific American, Nature, Science, Science News, The Scientist, Smithsonian Magazine, BBC News, Associated Press(AP), etc.
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
Cell Preview: Sperm Go to (Transcription) Extremes
Media coverage: 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).