Dr Jiyuan An
Position:
- Senior Research Fellow, Australian Prostate Cancer Research Centre - Queensland
Websites:
Biography:
Dr An received his PhD and Masters degree in computer science from University of Tsukuba and Kyushu Institute of Technology, Japan. In his current role, he is engaged in discovering significant non-coding genes from microarray and sequencing data. He also creates mathematical models for biological data, and finds the most suitable parameters for the models.
Dr An and his colleagues recently focussed on the high rate of false positive rates in current miRNA target prediction tools. This renders identification of co-regulating groups of miRNAs and target genes unreliable. They devised a procedure to identify highly probable co-regulating miRNAs, and the corresponding co-regulated gene groups, using a sequence of statistical tests to: (1) identify genes that are highly probable miRNA targets; (2) determine for each gene, the minimum number of miRNAs that co-regulate it with high probability; (3) find, for each gene, the combination of the determined minimum size of miRNAs that co-regulate it with the lowest p-value; and (4) discover for each such combination of miRNAs, the group of genes that are co-regulated by these miRNAs with the lowest p-value computed based on GO term annotations of the genes.
Best publications:
- Jiyuan An, John Lai, Melanie L. Lehman, Colleen C Nelson (2012) MiRDeep*: An Integrated Application Tool For MiRNA Identification From RNA Sequencing Data, Nucleic Acids Research 2012; doi: 10.1093/nar/gks1187. web page
- Jiyuan An, Liew AW-C, Nelson CC (2012) Seed-Based Biclustering of Gene Expression Data. PLoS ONE 7(8): e42431. doi:10.1371/journal.pone.0042431
- Jiyuan An, KP. CHOI, CA. WELLS and YP CHEN, "Identifying co-regulating microRNA" Journal of Bioinformatics and Computational Biology, 7(1) 99-115, 2010. Source Code
- Jiyuan An, CHEN YPP, “Finding rule groups to classify high dimensional gene expression datasets”,Computational Biology and Chemistry 33(1):108-113. (2009) (ERA2010 rank B)
- Jiyuan An, CHEN YPP, “Finding Coverage Using Incremental Attribute Combinations”, International Journal of Innovative Computing, Information and Control, 5(5): 1419-1428,2009 (ERA2010 rank B)
- Jiyuan An, Chen YPP, “Finding edging genes from microarray data", Journal of Biotechnology, 135(3):233-240, 2008. (ERA2010 rank A)
- Jiyuan An, Y.-P. P. Chen, H. Chen. “DDR: An Index Method for Large Time Series Datasets", Information Systems(IS), 30(5): 333-348 2005. (ERA2010 rank A*)
MiRDeep*: An Integrated Application Tool For MiRNA Identification From RNA Sequencing Data
micro RNA, microarray, normal functioning.
