Xijin
Ge 
Assistant
Professor of Bioinformatics
Department
of Mathematics and Statistics
Harding
Hall 124
Tel.
605-688-6879
Office hour Monday
11-11:50am
Wednesday 3-3:50pm
Providing bioinformatics
& statistics consulting to SDSU researchers. Send me an email or just
walk in.
Courses 2009 SP: Math 492/592 Tp: Data Mining
2008 Fall: Math
459/559 Bioinformatics
2008 SP: Stat/Math381 Introduction to Probability
& Statistics
2007 Fall: Math 459/559 Bioinformatics
Links
My
software usage How-To
Statistics at UCLA (Introductions to
various statistics software, examples, videos etc)
Education
PhD
in Engineering,
MS
in
BS
in Applied Physics,
Research
Modern biotechnologies often produce
thousands or even millions of data points in a single experiment. Proper
interpretation of such data is a big challenge. While this might be the source
of headache for traditional bench scientists, it means opportunity for
computational scientists. We are in the era of big science.
Dr. Ge conducts research in the general
field of bioinformatics, focusing on the development and application of
statistical and computational methods to analyze massive data sets generated by
modern genomics technologies. Teamed up with a large network of collaborators,
his research strives to better the accuracy of cancer (especially breast
cancer) diagnosis, discover novel human genes in the human genome, and
understand the molecular logic underling plant physiological processes, etc.
Dr. Ge’s own research often involves applying new strategies to re-analyze and
interpret large-scale genomic databases to make specific discoveries about the
biology of the cell.
Current collaborators in:
- Northshore
University Healthsystem Research Institute (breast cancer and psychiatric
genetics)
- SDSU (plant
genomics and physiology)
Current team members
·
Tyler
Wilson (PhD student)
·
Greg
Geiszler(PhD student; co-advising with Prof. Jose Gonzalez)
·
Li
Cai (Statistics Masters student)
·
Him
Acharya (Masters student, RA from computer science)
Funding
Dr
Ge’s research activity has been supported by the NIH, USDA, Susan G. Komen for
the Cure Foundation, and the SDSU Agricultural Experiment Station.
Selected Publications:
(Full
list: Google
Scholar and PubMed)
1. F Sutton, DG Chen, XJ Ge and D Kenefick, Cbf genes of the
Fr-A2 allele are differentially regulated between long-term cold acclimated
crown tissue of freeze- resistant and - susceptible, winter wheat mutant lines,
BMC Plant Biology (accepted, 2009).
2. H Dong, XJ Ge, Y Shen, L Chen, Y Kong, H Zhang,
X Man, L Tang, H Yuan, H Wang, G Zhao, W Jin. Gene expression profile analysis
of human hepatocellular carcinoma using SAGE and LongSAGE, BMC Med Genomics 2:5, 2009. Full text
3. XJ Ge, WS Rubinstein, Y-C Jung, QF Wu, Genome-wide analysis of antisense transcription with Affymetrix
exon array, BMC Genomics, 9:27, 2008.
Full text (BMC Highly accessed)
4. XJ Ge, QF Wu, and SM Wang. SAGE detects microRNA precursors, BMC Genomics 7:285, 2006. (BMC Highly accessed)
5. XJ Ge, Q Wu, Y-C Jung, J Chen, and SM Wang. A large quantity
of novel human antisense transcripts detected by LongSAGE, Bioinformatics 22:2475-2479, 2006. (Thomson
Scientific “New Hot Paper”)
6. Y Guo, Y Chen, H
Itoh, A Watanabe, XJ Ge, T Kodama
and H Aburatani. Identification and characterization of lin-28 homolog B
(LIN28B) in human hepatocellular carcinoma, Gene
384: 51-61, 2006.
7. S Lee, J Chen, G
Zhou, RZ Shi, G Bouffard, M Kocherginsky, XJ
Ge, M Sun, N Jayathilaka, YC Kim, N Emmanuel, S Bohlander, M Minden, J
Kline, O Ozer, R Larson, M LeBeau, E Green, J Trent, T Karrison, P Liu, SM
Wang, and JD Rowley, Gene expression profiles in acute myeloid leukemia with
common translocations using SAGE, Proc.
Nat. Acad. Sci. U.S.A. 103, 1030-1035, 2006.
8. Y Chen, Y Guo, XJ Ge, H Itoh, A Watanabe, T Fujiwara,
T Kodama and H Aburatani. Elevated expression and potential roles of human Sp5,
a member of Sp transcription factor family, in human cancers, Biochem. Biophys. Res. Commun. 340,
758-766, 2006.
9. XJ Ge, YC Jung, QF
10. S Lee , D Johnson, K
Dunbar, H Dong, XJ Ge, YC Kim, C
Wing, N Jayathilaka, N Emmanuel, CQ Zhou, HL Gerber, CC Tseng, and SM Wang.
2.45GHz radiofrequency fields alter gene expression in cultured human cells. FEBS Lett., 579, 4829-4836, 2005.
11. XJ Ge, S Yamamoto, S Tsutsumi, Y Midorikawa, S Ihara, SM Wang,
and H Aburatani. Interpreting expression profiles of cancers by genome-wide
survey of breadth of expression in normal tissues, Genomics, 86,127-141, 2005. (Recommended by Faculty
of 1000 and Genome
Biology, ScienceDirect
Top25) Full
text
12. T Minami, K Horiuchi,
M Miura, MR Abid, W Takabe, N Noguchi, T Kohro, XJ Ge, H Aburatani, T Hamakubo, T Kodama, WC Aird. Vascular
endothelial growth factor- and thrombin-induced termination factor, Down
syndrome critical region-1, attenuates endothelial cell proliferation and
angiogenesis. J. Biol.
Chem., 279, 50537-50554, 2004. (JBC “Paper of the
Week”)
13. A Mukasa, K Ueki, XJ Ge, T Ide, T Fujimaki, R Nishikawa, A
Asai, M Nakafuku, T Kirino & H Aburatani, Selective Expression of a Subset
of Neuronal Genes in Oligodendroglioma with Chromosome 1p Loss, Brain Pathology, 14,34-42, 2004.
14. XJ Ge,
15. S Tsutsumi, T Taketani, K Nishimura, XJ Ge, T Taki, K Sugita, E
Ishii, R Hanada, M Ohki, H Aburatani & Y Hayashi. Two distinct gene
expression signatures in pediatric acute lymphoblastic leukemia with MLL
rearrangements. Cancer Res., 63,
4882-4887, 2003.
16. XJ Ge, and
17. XJ Ge, S Yonamine, YM Mi, S Tsutsumi, Y Kobune, H Aburatani, and S Iwata, A
physics-inspired algorithm for information visualization with application to
gene expression analysis, Journal of The School of Engineering, The University
of Tokyo, XLVII, 89-103, 2000.
18. XJ Ge, NX Chen, WQ Zhang and FW Zhu, Selective field evaporation in field-ion
microscopy for ordered alloys, J. of
Applied Physics, 85, 3488-3493, 1999.
19. NX Chen, XJ Ge, WQ Zhang and FW Zhu, Atomistic analysis of the
field-ion microscopy image of Fe3Al, Physical
Review B-Condensed Matter, 57, 14203-14208, 1998.
20. XJ Ge, NX Chen, and ZD Chen, Efficient algorithms for 2D arithmetic Fourier
transform, IEEE Trans. on Signal
Processing, 45, 2136-2140, 1997.
Professional
Activities
Member:
International Society for Computational
Biology
Journal Reviewer: Bioinformatics, BMC Bioinformatics,
Evolutionary Bioinformatics, BMC Genomics, IEEE Trans. Information Technologies
in BioMedicine, etc.
Other
Manager
of the mailing list for Brookings
Chinese Community
Last
Update: 2/24/09