Office BuildingChicoine Architecture, Mathematics and Engineering Hall
Mailing AddressChicoine Architecture, Math & Engineering Building 258
Math & Statistics-Box 2225
Brookings, SD 57007
BiographyDr. Ge's teaching and research focus on bioinformatics, artificial intelligence (AI), and data science. Bioinformatics is a discipline that combines statistics, computer science, and biological context to analyze large genomics datasets.
We develop easy to use tools such as iDEP and ShinyGO that can translate massive genomic data into actionable insights.
Neural networks decomposes complex patterns into building blocks.
Exploratory bioinformatics investigation reveals the importance of “junk” DNA in early embryo development. It also identified key regulators that are later confirmed experimentally.
Education2000 PhD in Engineering, University of Tokyo, Japan
1997 MS in Condensed Matter Physics, Beijing University of Science and Technology, China
1994 BS in Applied Physics, Beijing University of Science and Technology, China
Academic InterestsData Science, AI, Bioinformatics, Genomics
Academic ResponsibilitiesSTAT 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.
GrantsNational Institutes of Health (NIH): An interactive tool for in-depth and reproducible analysis of RNA-seq data; Award Number:R01HG010805; Principal Investigator (PI): Xijin Ge; Organization: SDSU; Start Date: 09/2020; Award Amount: $869,378
NIH: The Immune regulation of macrophage antibody dependent cellular phagocytosis, Award Number: U01AI148153; PI: Adam Hoppe; Role: Consultant; Organization: SDSU; Start Date: 07/2020; Award Amount: ~$1,500,000
NIH: BioSystems Networks and Translational Research - Insights into Inflammation (BioSNTR-II), Award Number: P20GM135008; PI: Adam Hoppe; Role: Core co-director; Start Date: 03/2022; Total award amount: ~$12,000,000
NIH: Adventures in Drug Discovery: Integrating Data Science into the Science Curriculum, Award Number: R25GM150143; PI: Charles Xie; Role: Consultant; Organization: Institute for Future Intelligence; Start Date: 07/2023; Total award amount: ~$1,000,000
National Science Foundation & the State of South Dakota: The Biochemical Spatiotemporal NeTwork Resource (BioSNTR): Building a bio-Economy in South Dakota, PI: James Rice, Start Date: 07/2013; Role: Participant; Organization: SD EPSCoR; Total award amount: ~25,000,000.
NIH: Large-scale expression analysis of natural antisense transcripts, Award number: R01GM083226, PI: Xijin Ge; Role: PI, Organization: SDSU; Start Date: 04/2009; Award amount: $835,586
Creative ActivitiesSelected publications:
Ge X, D Jung, ShinyGO: a graphical enrichment tool for animals and plants, Bioinformatics, 36:2628-2629, 2020.
Ge S.X., Son EW, Yao RN, iDEP: an integrated web application for differential expression and pathway analysis of RNA-Seq data, BMC Bioinformatics 19:124, 2018.
Ge SX. Exploratory bioinformatics investigation reveals importance of "junk" DNA in early embryo development. BMC Genomics. 18(1):200, 2017.
Ling MH, Ban Y, Wen H, Wang SM, Ge SX. 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.
Free online Book:
Learn R through Examples, https://gexijin.github.io/learnR/