Xijin Ge

Title

Professor

Office Building

Chicoine Architecture, Mathematics and Engineering Hall

Office

258

Mailing Address

Chicoine Architecture, Math & Engineering Building 258
Math and Statistics-Box 2225
University Station
Brookings, SD 57007

Social Media Links

• X
• LinkedIn

Education

• Ph.D. in engineering | University of Tokyo, Japan | 2000
• M.S. in condensed matter physics | Beijing University of Science and Technology, China | 1997
• B.S. in applied physics | Beijing University of Science and Technology, China | 1994

Academic Interests

• Data science
• AI
• Bioinformatics
• Genomics

Academic Responsibilities

• STAT 435/535 Applied Bioinformatics, spring semesters for students with biological background.
• STAT 736 Bioinformatics, fall semester for students in statistics, computer science departments or others with programming skills.
• STAT 414/514 Basic R programming,  spring semester, one credit online course.
• STAT 492 Data visualization using R.
• STAT 442 Exploratory and Cloud-based Data Analysis. A project-based course where students analyze real datasets and present and discuss every week.

Grants

• An interactive tool for in-depth and reproducible analysis of RNA-seq data. National Institutes of Health, SDSU, Sept. 2020, $869,378.
• The Immune regulation of macrophage antibody dependent cellular phagocytosis. National Institutes of Health, SDSU, July 2020, $1,500,000.
• BioSystems Networks and Translational Research - Insights into Inflammation (BioSNTR-II). National Institutes of Health, March 2022, $12,000,000.
• Adventures in Drug Discovery: Integrating Data Science into the Science Curriculum, National Institutes of Health, July 2023, $1,000,000.
• The Biochemical Spatiotemporal NeTwork Resource (BioSNTR): Building a bio-Economy in South Dakota. National Science Foundation and the State of South Dakota, July 2013, $25,000,000.
• Large-scale expression analysis of natural antisense transcripts, National Institutes of Health, SDSU, April 2009, $835,586.

Areas of Research

• Development of tools (iDep and ShinyGo) and resources (pathway databases) for the interpretation of large genomic data.
• Using AI, especially Large Language Models like ChatGPT, to help analyze and visualize data.

Publications

• Ge X., D. Jung, ShinyGO: a graphical enrichment tool for animals and plants, Bioinformatics, 36:2628-2629, 2020.
• Ge S.X., Son E.W., Yao R.N.: iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data, BMC Bioinformatics  19:124, 2018.
• Ge S.X. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics. 18(1):200, 2017.
• Ling M.H., Ban Y., Wen H., Wang S.M., Ge S.X. Conserved expression of natural antisense transcripts in mammals. BMC Genomics. 14:243, 2013.
• Shi L., et al. The MicroArray Quality Control (MAQC)-II study of common practices for the development and validation of microarray-based predictive models. Nature Biotechnology, 28(8):827-38, 2010.
• Ge X., Iwata S. Learning the parts of objects by auto-association. Neural Network.15(2):285-95, 2002.