Ye Ding, Ph.D.

Ye Ding, Ph.D.

RNA Bioinformatics
Research Professor, Department of Biomedical Sciences, University at Albany
Ph.D., Carnegie Mellon University (1990)
(518) 486-1719
Fax: (518) 474-3181

Research Interests

Our RNA Bioinformatics laboratory has been engaged in algorithms and software tool development for prediction of RNA secondary structure and their applications, with a recent major focus on computational prediction and validation for functional elucidation of regulatory non-coding RNAs (ncRNAs), particularly animal microRNAs (miRNAs) and small bacterial RNAs (sRNAs).

Other research interests include potential interaction between miRNAs and N6-methyladenosine modification (m6A), interaction between miRNAs and single-nucleotide polymorphisms (SNPs) with human disease association, regulatory functions of miRNAs for stem cell pluripotency and cell differentiation.

A long-term service obligation to the scientific community is the continuing development and maintenance of the Sfold web server for making our software and database tools freely available to scientists around the world. 

Select Publications
Rennie W, Kanoria S, Liu C, Mallick B, Long D, Wolenc A, Carmack CS, Lu J, Ding Y. STarMirDB: A database of microRNA binding sites. RNA Biol. 2016; 13 (6): 554-560.
Rennie W, Liu C, Carmack CS, Wolenc A, Kanoria S, Lu J, Long D, Ding Y. STarMir: a web server for prediction of microRNA binding sites. Nucleic Acids Res. 2014; Jul (42): W114-8.
Long DD, Lee R, Williams P, Chan CY, Ambros V, Ding Y. Potent role of target structure in microRNA function. Nature Structural & Molecular Biology. 2007; 14 (4): 287-294.
Shao Y, Wu S, Chan CY, Klapper JR, Schneider E, Ding Y. A structural analysis of in vitro catalytic activities of hammerhead ribozymes. BMC Bioinformatics. 2007; 8 469-480.
Ding Y, Chan CY, Lawrence CE. RNA secondary structure prediction by centroids in a Boltzmann weighted ensemble. RNA. 2005; 11 (8): 1157-1166.
Ding Y, Chan CY, Lawrence CE. Sfold web server for statistical folding and rational design of nucleic acids. Nucleic Acids Research. 2004; 32 (Webserver issue): W135-141.
Ding Y, Lawrence CE. A statistical sampling algorithm for RNA secondary structure prediction. Nucleic Acids Research. 2003; 31 (24): 7280-7301.
Full publication listing