In this talk I will present some recent work on gene classification and assembly. In the first part of the talk, I'll present a new alignment-free algorithm for gene classification. This method transforms DNA sequences into feature vectors which contain the occurrence, location and order relation of k-tuples in the DNA sequence, and uses a hierarchical procedure to cluster DNA sequences based on the feature vectors. In the second part of the talk, I will present a de bruijn graph based parallel gene assembler, called SWAP (small world asynchronous parallel model), that my group has developed. Unlike existing approaches, SWAP uses algorithmic techniques to guarantee localized communication where each process communicates with at most 8 other processes irrespective of the total number of processes in the system. This makes our approach scalable to large supercomputers and large assembly datasets. Nevertheless, like with most applications doing fine-grained data accesses, there is still room for improvement. In the last part of the talk, I'll describe some possible future directions we are investigating to utilize MPI-3 RMA and active messages to improve the efficiency of our computation.

About Professor Yanjie Wei: Professor Wei received his BS in Applied Physics from Sichuan University, China in Jul. 2004 and PhD in Computational Biophysics from Michigan Technological University in Dec. 2007. He is currently an associate professor in the Center for High Performance Computing at Shenzhen Institutes of Advanced Technology (SIAT), Chinese Academy of Sciences. Before joining SIAT, he worked as a postdoctoral research associate in the Department of Chemical and Biological Engineering at Princeton University. Specifically, his research interests include protein folding, protein structure prediction, gene assembly and classification. By developing advanced computational algorithms and optimization techniques, he aims at solving biologically important problems in the above mentioned areas. Dr. Wei has published more than 10 papers in peer-reviewed journals, such as Proteins, Journal of Chemical Physics, Journal of Physical Chemistry B, Chemical Engineering Sci., etc. He has presented his works at various conferences and workshops, including an invited talk at ACS 2010 annual conference. He also serves as a reviewer for several journals and conferences, including Journal of Chem. Phy., ICIC 2012, 3PGCIC, and ICPADS 2012.