Faculty
SELF-INTRODUCTION：
Ying Xu is Professor of School of Medicine, Cheungkong Scholars Chair Professor, 1000 Scholars Chair Professor, Computational Systems Biology and Bioinformatics Scholar, Southern University of Science and Technology. He joined the School of Medicine of Southern University of Science and Technology in January 2023. Previously, he was "Board Professor" and "Georgia Science Association Distinguished Scholar Chair" in the Department of Biochemistry, University of Georgia (2003-2022), and the first Director of the Institute of Bioinformatics, University of Georgia (2003-2011). He is an AAAS Fellow and an IEEE Fellow. He received his Ph.D. in Computer Science (Combinatorics and Algorithms) from the University of Colorado in 1991. He joined Oak Ridge National Laboratory in 1993 and worked for ten years as an assistant researcher, researcher, senior staff scientist and group leader. At the beginning, he participated in the Human Genome sequencing project, engaged in the computational methods and software implementation of searching protein-coding genes in the genome. He has also developed computational methods for protein tertiary structure prediction, statistical analysis of microbial genomes, modeling of metabolic systems, and functional prediction. In 2003, his research team joined the University of Georgia to establish the Institute of Bioinformatics, and at the same time joined the Department of Biochemistry at the University of Georgia. Since 2008, we began to study the driving force and mechanism of tumor occurrence, development and metastasis through tumor omics data. He has published nearly 400 academic papers and five books, including the world's first "tumor informatics" monograph, with more than 20000 citations and H index of 71. Since 1995, the UNIVERSITY has trained 38 postdocs and more than 20 doctors, 19 of whom are teaching in American research universities, and more than 20 are teaching in European, Korean and domestic universities. Since 2003, he has hosted the International Symposium on Bioinformatics (2003-2013) and the International Symposium on Systems Biology of Cancer (2011-) in China every year, and lectured on summer courses on Bioinformatics or cancer informatics every year, attracting more than 20,000 participants.
EDUCATION:
1978-1982, Bachelor degree, Department of Computer Science, Jilin University;
1982-1985, Master degree, Department of Computer Science, Jilin University;
1986-1991, He received his PhD in Computer Science from the University of Colorado.
WOKRING EXPERIENCE:
1986-1991, Research Assistant, Department of Computer Science, University of Colorado, USA;
1991-1993, Assistant Professor, Department of Mathematics, Colorado School of Mines, USA;
1993-1997, Assistant Researcher, Department of Computer Science and Mathematics, Oak Ridge National Laboratory, USA;
1997-2003, Senior Researcher and project leader, Oak Ridge National Laboratory, USA;
2003-2022, "Board of Trustees Professor" and "Georgia Science Association Distinguished Scholar" Chair Professor, Department of Biochemistry, University of Georgia, USA;
2003-2011, he was the first Director of the Bioinformatics Institute at the University of Georgia;
In January 2023, Professor of the Department of Medicine, Southern University of Science and Technology.
Over the past 25 years, he has been an adjunct professor in the following units
1997-present: Adjunct Professor, School of Computer Science and Technology, Jilin University;
In 2002, Adjunct Professor, Institute of Bioinformatics, Zhejiang University;
In 2005, Adjunct Professor, Peking University School of Life Sciences;
In 2006, Adjunct Professor, Department of Statistics, Chenggong University, Taiwan Province;
In 2007, Adjunct Professor, Institute of Systems Biology, Central University, Taiwan Province;
In 2007, Adjunct Professor, Department of Electrical Engineering, Georgia Institute of Technology, USA;
In 2018, the Jilin Provincial Scientist Studio was established in the Third Clinical Hospital of Jilin University.
HONORS AND AWARDS:
In 2001, he received the R&D100 award, which is given by the US R&D magazine to the 100 most important inventions each year;
In 2003, he was awarded the title of Outstanding Scholar by the Georgia Cancer Society;
In 2003, he was awarded the title of Distinguished Scholar by the Georgia Science Association;
In 2007, he was elected as Fellow of the American Association for the Advancement of Science;
In 2008, Changjiang Scholar Chair Professor, Ministry of Education (Department of Computer Science, Jilin University);
In 2012, Chair Professor of the Thousand Talents Program of the Organization Department of the Central Committee (Department of Computer Science, Jilin University);
In 2016, he won the Changbai Mountain Friendship Award of Jilin Province;
In 2018, Jilin Provincial International Science and Technology Cooperation Award;
In 2021, he was elected as an IEEE Fellow.
RESEARCH:
1993-1995: Using mathematical statistics and computational methods to search for protein-coding genes in human genome. GRAIL-II, a computer program developed by the author, became an important tool for human genomics scholars from the mid-1990s to the mid-2000s, and for a considerable period of time, this program was the gold standard in the related field, with more than 1000 citations.
From 1995 to 1999, using biostatistical and computational methods, he developed the 3D protein structure prediction programs PROSPECT and RAPTOR. Both of them were widely used in the 1990s and the following 15 years, with more than 2000 citations.
From 1998 to 2012, he worked in microbial systems biology, focusing on (1) the role of microorganisms in carbon cycling in nature; And (2) the role of microorganisms in cellulose degradation. The objectives are to: (1) substantially enhance carbon recovery capacity by studying the metabolic networks of relevant microorganisms through large-scale computational simulations and analyzing the metabolic patterns of these microorganisms through genetic engineering; And (2) the possibility of bioenergy generation, and the possible target genes or metabolic pathways. A total of more than 100 articles have been published, and the highest single article has been cited more than 1000 times.
2007-present: Engaged in tumor systems biology research. Through big data analysis and mathematical modeling of tumor tissues, the main driving force and important mechanism of tumor occurrence, development and metastasis are studied. Since 2012, a new theory of tumor evolution has been gradually established, that is, metabolic reprogramming in tumor cells is to produce enough H(+) to balance OH(-) produced by the Fenton reaction, thereby maintaining cellular pH stability and cell survival. The basic hypothesis of Xu's group is that all clinical manifestations of a tumor are the result of its metabolic programming for survival. This new and improving theory of tumor evolution will provide new ideas for the prevention, early diagnosis and treatment of tumors.
2020 - present, Research on the pathogenesis of Alzheimer's disease.
MANUSCRIPT REVIEWER AND EDITOR：
Since 1998, he has served as editor, associate editor, and editorial board member of more than a dozen professional journals, including:
2009-present, Associate Editor, Journal of Computer Science and Technology;
He was editor-in-chief of IEEE/ACM Transaction on Computational Biology and Bioinformatics from January 2013 to December 2016;
And the editorial board of Frontiers in Oncology, Journal of Molecular Cell Biology, Genes and Diseases, Mathematical Biosciences.
RECENTLY PUBLICATIONS：
1. Sha Cao, Xiwen Zhu, Chi Zhang, Hong Qian, Heinz-Bernd Schuttler, Jianping Gong, Ying Xu; Competition between DNA Methylation, Nucleotide Synthesis, and Antioxidation in Cancer versus Normal Tissues. Cancer Res 1 August 2017; 77 (15): 4185–4195. https://doi.org/10.1158/0008-5472.CAN-17-0262
2. Han Zhang, Tanner Yohe, Le Huang, Sarah Entwistle, Peizhi Wu, Zhenglu Yang, Peter K Busk, Ying Xu, Yanbin Yin, dbCAN2: a meta server for automated carbohydrate-active enzyme annotation, Nucleic Acids Research, Volume 46, Issue W1, 2 July 2018, Pages W95–W101, https://doi.org/10.1093/nar/gky418
3. Huiyan Sun, Yi Zhou, Michael Francis Skaro, Yiran Wu, Zexing Qu, Fenglou Mao, Suwen Zhao, Ying Xu; Metabolic Reprogramming in Cancer Is Induced to Increase Proton Production. Cancer Res 1 March 2020; 80 (5): 1143–1155. https://doi.org/10.1158/0008-5472.CAN-19-3392
4. Yi Zhou, Huiyan Sun, Ying Xu, Metabolic reprogramming in cancer: the bridge that connects intracellular stresses and cancer behaviors, National Science Review, Volume 7, Issue 8, August 2020, Pages 1270–1273, https://doi.org/10.1093/nsr/nwaa082
5. Yi Zhou, Wennan Chang, Xiaoyu Lu, Jin Wang, Chi Zhang, Ying Xu, Acid-base homeostasis and implications to the phenotypic behaviors of cancer, Genomics, Proteomics & Bioinformatics, 2022, ISSN 1672-0229, https://doi.org/10.1016/j.gpb.2022.06.003.
6. Renbo Tan, Yi Zhou, Zheng An, Ying Xu, WITHDRAWN: Understanding cancer as a survival process under persistent stresses, Medicine in Omics, 2021, 100009, ISSN 2590-1249, https://doi.org/10.1016/j.meomic.2021.100009.
7. Dingyun Liu, Feiyang Xing, Yueying Wang, Jun Xiao, Zheng An, Ying Xu, Molecular bases of morphologically diffused tumors across multiple cancer types, National Science Review, Volume 9, Issue 11, November 2022, nwac177, https://doi.org/10.1093/nsr/nwac177
8. Renbo Tan, Yi Zhou, Zheng An, Ying Xu, Cancer is a survival process under persistent microenvironmental and cellular stresses, Genomics, Proteomics & Bioinformatics, 2022, ISSN 1672-0229, https://doi.org/10.1016/j.gpb.2022.03.002.
9. Jun Bai, Renbo Tan, Zheng An, Ying Xu, Quantitative estimation of intracellular oxidative stress in human tissues, Briefings in Bioinformatics, Volume 23, Issue 4, July 2022, bbac206, https://doi.org/10.1093/bib/bbac206
10. Liu Dingyun, Bai Jun, Chen Qian, Tan Renbo, An Zheng, Xiao Jun, Qu Yingwei, Xu Ying. Brain metastases: It takes two factors for a primary cancer to metastasize to brain, Frontiers in Oncology, December 2022, https://www.frontiersin.org/articles/10.3389/fonc.2022.1003715.