Joint PIs

August 2017 - , Institute of Science and Technology for Brain-lnspired Intelligence, Fudan University,  Professor

September 2012 - July 2017, Department of Computer Science, Tongji University, Professor

June 2010 - December 2011, European Molecular Biology Laboratory (EMBL), Research fellow  

May 2008 - September 2012, Institute of Systems Biology, Shanghai University, Associate Professor  

May 2006 - May 2008, ERATO Aihara Project, The University of Tokyo, Researcher  

August 2004 - August 2005, Department of Computer Science, Hong Kong Baptist University,  Research Assistant

Machine Learning and Optimization;  Neuroinformatics;  Bioinformatics;  Systems Biology;

1.J Zhu, C Sun, M Li, G Hu, XM Zhao*, WH Chen*. Compared to histamine-2 receptor  antagonist, proton pump inhibitor induces stronger oral-to-gut microbial transmission and gut microbiome alterations: a randomised controlled trial. Gut. 2023, doi: 10.1136/gutjnl-2023-330168.

2.L Jia, Y Wu, Y Dong, J Chen, WH Chen*, XM Zhao*. A survey on computational strategies  for genome-resolved gut metagenomics. Briefings in Bioinformatics. 2023, 24(3):bbad162.

3. S Lai, Y Yan, Y Pu, S Lin, JG Qiu, BH Jiang, MI Keller, M Wang, P Bork*, WH Chen*, Y  Zheng*, XM Zhao*. Enterotypes of the human gut mycobiome. Microbiome. 2023, 11(1):179.

4. S Pan, XM Zhao*, LP Coelho*. SemiBin2: self-supervised contrastive learning leads to better  MAGs for short- and long-read sequencing. Bioinformatics. 2023, 39: i21-i29.

5. C Sun, J Chen, M Jin, X Zhao, Y Li, Y Dong, N Gao, Z Liu*, P Bork*, XM Zhao*, WH  Chen*. Long-Read Sequencing Reveals Extensive DNA Methylations in Human Gut  Phagenome Contributed by Prevalently Phage-Encoded Methyltransferases. Advanced Science.  2023, 10(25):e2302159.

6.S Lai, S Pan, C Sun, Coelho LP*, WH Chen*, XM Zhao*. metaMIC: reference-free Misassembly Identification and Correction of de novo metagenomic assemblies. Genome Biology, 2022, 23(1):242.

8.LP Coelho*, R Alves, ÁR Del Río, PN Myers, CP Cantalapiedra, J Giner-Lamia, TS Schmidt,  DR Mende, A Orakov, I Letunic, F Hildebrand, T Van Rossum, SK Forslund, S Khedkar, OM Maistrenko, S Pan, L Jia, P Ferretti, S Sunagawa, XM Zhao, HB Nielsen, J Huerta-Cepas*, P Bork*. Towards the biogeography of prokaryotic genes. Nature, 2022, 601(7892):252-256.

9. D Dai, J Zhu, C Sun, M Li, J Liu, S Wu, K Ning, LJ He*, XM Zhao*, WH Chen*. GMrepo v2: a curated human gut microbiome database with special focus on disease markers and crossdataset comparison. Nucleic Acids Research, 2022, 50(D1): D777-D784.

10.S Wu, P Jiang, XM Zhao*; WH Chen*. Treatment regimens may compromise gutmicrobiome-derived signatures for liver cirrhosis. Cell Metabolism, 2021, 33(3): 455-456.

11.S Wu, C Sun, Y Li, T Wang, L Jia, S Lai, Y Yang, P Luo, D Dai, YQ Yang, Q Luo, NL Gao,  K Ning, LJ He, XM Zhao*, WH Chen. GMrepo: a database of curated and consistently annotated human gut metagenomes. Nucleic Acids Research, 2020, 48 (D1): D545-D553.