Publication

• Bo Xia#, Weimin Zhang, Guisheng Zhao, Xinru Zhang, Jiangshan Bai, Ran Brosh, Aleksandra Wudzinska, Emily Huang, Hannah Ashe, Gwen Ellis, Maayan Pour, Yu Zhao, Camila Coelho, Yinan Zhu, Alexander Miller, Jeremy S Dasen, Matthew T Maurano, Sang Y Kim, Jef D Boeke#, Itai Yanai#. On the genetic basis of tail-loss evolution in humans and apes. Nature (2024), 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.

• Wanqing Pan*, Weimin Zhang*, Binghan Zheng*, Brendan R Camellato, Jeffrey Stern, Ziyan Lin, Alireza Khodadadi-Jamayran, Jacqueline Kim, Philip Sommer, Karen Khalil, Elaina Weldon, Jiangshan Bai, Yinan Zhu, Peter Meyn; Adriana Heguy, Massimo Mangiola, Adam Griesemer, Brendan J Keating#, Robert A Montgomery#, Bo Xia#,  Jef D Boeke#. Cellular dynamics in pig-to-human kidney xenotransplantation. Med (2024), (online, co-corresponding author). URL

• Jimin Tan, Nina Shenker-Tauris, Javier Rodriguez-Hernaez, Eric Wang, Theodore Sakellaropoulos, Francesco Boccalatte, Palaniraja Thandapani, Jane Skok, Iannis Aifantis, David Fenyö, Bo Xia#, Aristotelis Tsirigos#. Cell type-specific prediction of 3D chromatin organization enables high-throughput in silico genetic screening. Nature Biotechnology (2023), 41(8), 1140-1150. URL (co-corresponding author) 

• Bo Xia, Yun Yan, Maayan Baron, Florian Wagner, Dalia Barkley, Marta Chiodin, Sang Y Kim, David L Keefe, Joseph P Alukal, Jef D Boeke, and Itai Yanai. Widespread transcriptional scanning in the testis modulates gene evolution rates. Cell (2020), 180 (2), 248-262. (Cover) URL

Cell Preview: Sperm Go to (Transcription) Extremes

Media coverage: EurekaAlert!, ScienceDaily, Phys.org

• Bo Xia and Itai Yanai. A periodic table of cell types. Development (2019), 146(12): dev169854. URL

• Chenxu Zhu*, Yun Gao*, Hongshan Guo*, Bo Xia*, Jinghui Song, Xinglong Wu, Hu Zeng, Kehkooi Kee, Fuchou Tang#, Chengqi Yi #. Single-cell 5-formylcytosine landscapes of mammalian early embryos and ESCs at single-base resolution. Cell Stem Cell (2017), 20(5), 720-731. URL

• Bo Xia*, Dali Han*, Xingyu Lu*, Zhaozhu Sun, Ankun Zhou, Qiangzong Yin, Hu Zeng, Menghao Liu, Xiang Jiang, Wei Xie, Chuan He#, Chengqi Yi#. Bisulfite-free, base-resolution analysis of 5-formylcytosine at the genome scale. Nature Methods (2015), 12(11), 1047–1050. URL

• Eloi Schmauch*, Brian Piening*, Maedeh Mohebnasab*, Bo Xia*, Chenchen Zhu*, Jeffrey Stern*, Weimin Zhang*, Alexa K. Dowdell, Jacqueline I. Kim, David Andrijevic, Karen Khalil, Ian S. Jaffe, Bao-Li Loza, Loren Gragert, Brendan R Camellato, ... , Harvey Pass, Ramin S Herati, Adam Griesemer, Manolis Kellis#, Michael P Snyder#, Robert A Montgomery#, Jef D Boeke# & Brendan J Keating#. Integrative multi-omics profiling in human decedents receiving pig heart xenografts. Nature Medicine (2024), 30, 1448–1460.

• Dalia Barkley, Reuben Moncada, Maayan Pour, Deborah A Liberman, Ian Dryg, Gregor Werba, Wei Wang, Maayan Baron, Anjali Rao, Bo Xia, Gustavo S França, Alejandro Weil, Deborah F Delair, Cristina Hajdu, Amanda W Lund, Iman Osman, and Itai Yanai. Recurrence of cancer cell states across diverse tumors and their interactions with the microenvironment. Nature Genetics (2022), 54(8):1192-1201.

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

• Hu Zeng, Manas Mondal, Ruyi Song, Jun Zhang, Bo Xia, Menghao Liu, Chenxu Zhu, Bo He, Yi Qin Gao#, Chengqi Yi#. Unnatural cytosine bases recognized as thymines by DNA polymerases via a tautomerization-dependent mechanism. Angewandte Chemie (2019), 131(1), 136-139.

• Hu Zeng*, Bo He*, Bo Xia, Dongsheng Bai, Xingyu Lu, Jiabin Cai, Lei Chen, Ankun Zhou, Chenxu Zhu, Haowei Meng, Yun Gao, Hongshan Guo, Chuan He#, Qing Dai#, Chengqi Yi#. Bisulfite-free, nano-scale analysis of 5-hydroxymethylcytosine at single base resolution. Journal of the American Chemical Society (2018), 140(41), 13190–13194.

• Luisa Cimmino, Igor Dolgalev, Yubao Wang, Akihide Yoshimi, Gaëlle H Martin, Jingjing Wang, Victor Ng, Bo Xia, Matthew T Witkowski, Marisa Mitchell-Flack, Isabella Grillo, Sofia Bakogianni, Delphine Ndiaye-Lobry, Miguel Torres Martín, Maria Guillamot, Robert S Banh, Mingjiang Xu, Maria E Figueroa, Ross A Dickins, Omar Abdel-Wahab, Christopher Y Park, Aristotelis Tsirigos, Benjamin G Neel#, Iannis Aifantis#. Restoration of TET2 function blocks aberrant self-renewal and leukemia progression. Cell (2017), 170(6), 1079-1095.

• Jinying Peng, Bo Xia, and Chengqi Yi. Single-base resolution analysis of DNA epigenome via high-throughput sequencing. Science China Life Sciences (2016), 59(3), 219–226.

• Lining Lu, Chenxu Zhu, Bo Xia, and Chengqi Yi. Oxidative demethylation of DNA and RNA mediated by non-heme iron-dependent dioxygenases. Chemistry–An Asian Journal (2014), 9(8): 2018–2029.

• Chengqi Yi, Bo Xia, Ankun Zhou. 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).

• Chengqi Yi, Chenxu Zhu, Bo Xia. 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).

• Aristotelis Tsirigos, Bo Xia, Jimin Tan. Cell type-specific prediction of 3d chromatin architecture. PCT/US2023/014501 (2023); WO2023168079A2 (2023). 

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

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