# indicates equal contribution. * indicates corresponding authors.
15. Yan Feng#, Zhiqiang Zhang#, Yuyang Hong, Yi Ding, Leiqin Liu, Siqi Gao, Hai Fang*, Jiantao Shi* A DNA methylation haplotype block landscape in human tissues and preimplantation embryos reveals regulatory elements defined by comethylation patterns. Genome Research 2023 [Pubmed] [PDF] [Supporting Website]
14. Yuyang Hong#, Leiqin Liu#, Yan Feng#, Zhiqiang Zhang#, Rui Hou, Qiong Xu* and Jiantao Shi* mHapBrowser: a comprehensive database for visualization and analysis of DNA methylation haplotypes. Nucleic Acids Research 2023 [Pubmed] [PDF] [Supporting Website]
13. Shirong Zhang#, Shutao He#, Xin Zhu#, Yunfei Wang, Qionghuan Xie, Xianrang Song， Chunwei Xu, Wenxian Wang, Ligang Xing, Chengqing Xia, Qian Wang, Wenfeng Li, Xiaochen Zhang, Jinming Yu, Shenglin Ma*, Jiantao Shi* and Hongcang Gu* DNA methylation profiling to determine the primary sites of metastatic cancers using formalin-fixed paraffin-embedded tissues. Nature Communications 2023 [Pubmed] [PDF] [Processed data]
12. Siqi Gao#, Hanwen Zhu#, Kangwen Cai, Leiqin Liu, Zhiqiang Zhang, Yi Ding, Yaochen Xu, Xiaoqi Zheng* and Jiantao Shi* TRAmHap: accurate prediction of transcriptional activity from DNA methylation haplotypes in bisulfite-sequencing data. Briefings in Bioinformatics 2023 [Pubmed] [PDF] [Supporting Website]
11. Yi Ding#, Kangwen Cai#, Leiqin Liu, Zhiqiang Zhang, Xiaoqi Zheng* and Jiantao Shi* mHapTk: A comprehensive toolkit for the analysis of DNA methylation haplotypes. Bioinformatics 2022, 38(22):5141-5143. [Pubmed] [PDF] [Supporting Website]
10. Sha Lu#, Jiahao Wang#, Nisile Kakongoma, Wen Hua, Jiahui Xu, Yunfei Wang, Shutao He, Hongcang Gu, Jiantao Shi*, Wensheng Hu* DNA methylation and expression profiles of placenta and umbilical cord blood reveal the characteristics of gestational diabetes mellitus patients and offspring. Clinical Epigenetics 2022, 14(1):69. [Pubmed] [PDF] [Datasets]
9. Qiong Xu, Qiongfang Cha, Hui Qin, Bin Liu, Xueling Wu* and Jiantao Shi* Identification of master regulators driving disease progression, relapse, and drug resistance in lung adenocarcinoma. Frontiers in bioinformatics 2022, 2:813960. [Pubmed] [PDF] [Supporting Website]
8. Zhiqiang Zhang#, Yuhao Dan#, Yaochen Xu, Jiarui Zhang, Xiaoqi Zheng* and Jiantao Shi* The DNA methylation Haplotype (mHap) format and mHapTools. Bioinformatics 37(24):4892-4894. [Pubmed] [PDF] [Supporting Website]
7. Francois E. Mercier *#, Jiantao Shi #, David B. Sykes, Toshihiko Oki, Maja Jankovic, Cheuk Him Man, Youmna Kfoury, Elisabeth Miller, Shutao He, Alex Zhu, Radovan Vasic, John Doench, Alexandre Orthwein, Franziska Michor *, David T. Scadden * Blood advances 2022, 6(17):5072-5084. [Pubmed] [PDF] [Supporting Website]
6. Yujia Shen #, Yuji Mishima #, Jiantao Shi #, Romanos Sklavenitis-Pistofidis #, Robert Allyn Redd, Michele Moschetta, Salomon Manier, Aldo M Roccaro, Antonio Sacco, Yu-Tzu Tai, Francois Emile Mercier, Yawara Kawano, Nang Kham Su, Brianna Berrios, John Doench, David E Root, Franziska Michor, David T Scadden, Irene M Ghobrial *. Progression signature underlies clonal evolution and dissemination of multiple myeloma. Blood 2021, 137(17):2360-2372. [Pubmed] [PDF] [Supporting Website]
5. Zachary D. Smith #, Jiantao Shi #, Hongcang Gu, Julie Donaghey, Kendell Clement, Davide Cacchiarelli, Andreas Gnirke, Franziska Michor *, Alexander Meissner *. Epigenetic restriction of extraembryonic lineages mirrors the somatic transition to cancer. Nature 2017, 549(7673):543-547. [Pubmed] [PDF] [Raw data]
4. Yuji Mishima #, Bruno Paiva #, Jiantao Shi #, Jihye Park #, Salomon Manier, Satoshi Takagi, Mira Massoud, Adriana Perilla-Glen, Yosra Aljawai, Daisy Huynh, Aldo M. Roccaro, Antonio Sacco, Marzia Capelletti, Alexandre Detappe, Diego Alignani, Kenneth C. Anderson, Nikhil C. Munshi, Felipe Prosper, Jens G. Lohr, Gavin Ha, Samuel S. Freeman, Eliezer M. Van Allen, Viktor A. Adalsteinsson, Franziska Michor, Jesus F. San Miguel, Irene M. Ghobrial. The Mutational Landscape of Circulating Tumor Cells in Multiple Myeloma. Cell Rep 2017, 19(1):218-224. [Pubmed] [PDF]
3. Aldo M. Roccaro #, Antonio Sacco #, Jiantao Shi #, Marco Chiarini, Adriana Perilla-Glen, Salomon Manier, Siobhan Glavey, Yosra Aljawai, Yuji Mishima, Yawara Kawano, Michele Moschetta, Mick Correll, Ma. Reina Improgo, Jennifer R. Brown, Luisa Imberti, Giuseppe Rossi, Jorge J. Castillo, Steven P. Treon, Matthew L. Freedman, Eliezer M. Van Allen, Winston Hide, Elaine Hiller, Irene Rainville, Irene M. Ghobrial. Exome sequencing reveals recurrent germline variants in patients with familial Waldenstrom’s macroglobulinemia. Blood 2016, 127(21):2598-2606. [Pubmed] [PDF] [Code
2. Jiantao Shi, Wentao Yang, Mingjie Chen, Yanzhi Du, Ji Zhang, Kankan Wang. PLoS ONE 2011, 6(9):e24576. [PubMed] [PDF]
1. Kankan Wang #, Ping Wang #, Jiantao Shi #, Xuehua Zhu #, Miaomiao He, Xiaohong Jia, Xianwen Yang, Fei Qiu, Wen Jin, Maoxiang Qian, Hai Fang, Jianqing Mi, Xuzhi Yang, Huasheng Xiao, Mark Minden, Yanzhi Du, Zhu Chen, Ji Zhang. PML/RARalpha targets promoter regions containing PU.1 consensus and RARE half sites in acute promyelocytic leukemia. Cancer Cell 2010, 17(2):186-197.[Pubmed] [PDF]