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Featured PhD Student - March 2014


Dong Si
PhD, Old Dominion University
Computer Science Department


Dong Si received his B.S. in Electronic Information Science and Technology with honors from Nanjing University, China. In fall 2009, Dong joined the Computer Science Department of Old Dominion University as a graduate student and then transferred to Ph.D. program in fall 2010. He is currently working with Dr. Jing He as a research assistant.

Dong’s research topic is focused on developing efficient computational methods for the problem of protein secondary structure element (SSE) detection from 3D Cryo-electron microscopy (Cryo-EM) images. The objective is to provide insights into the structure and function of proteins in nature based on image processing, feature detection, pattern recognition, modeling & simulation, machine learning and other computational techniques. Cryo-EM as a cutting edge technology has made itself very successful in studying the protein structures. However, it is still quite challenging to automatically extract the SSE from medium-low resolution cryo-EM images. During his Ph.D. study, a serious of fully automatic detection methods has been developed for solving this challenging problem. The resulting paper “A Machine Learning Approach for the Identification of Protein Secondary Structure Elements from Electron Cryo-Microscopy Density Maps” has been published in the journal of Biopolymers in 2012. Dong has recently developed a novel computational method which can successfully model the beta-strand and beta-barrel structure from medium-low resolution cryo-EM images. To the best of our knowledge, It is the first fully automatic tool that can build the beta-strand and beta-barrel structure from such images. The developed method has been submitted to Structure, Cell Press. As more and more medium-low resolution cryo-EM images being deposited in the EMDB database, it is promising that Dong’s research will make significant contribution for the de novo protein structure prediction from these 3D data.

During his graduate studies, he has been offered the "Modeling and Simulation Research Fellowship" from Virginia Modeling, Analysis and Simulation Center (VMASC) and the Graduate Student Travel Award to present his paper at ACM-BCB 2013 conference. Dong is also a recipient of Outstanding Student Leader for serving as the President of ODU Chinese Students and Scholars Association (CSSA) from 2010 to 2011. He is also the previous member of ODU International Student Advisory Board (ISAB) and Global Student Friendship (GSF). For more information about Dong Si, please visit his personal homepage (http://www.cs.odu.edu/~dsi).