PArallel SeQUence AssembLer, a Parallel de Novo Genome Sequence Assembler, is designed for shared memory parallelism, using OpenMP due to its good tradeoff between performance and programmer productivity.
Xing Liu, Pushkar R. Pande, Henning Meyerhenke, and David A. Bader, ''PASQUAL: Parallel Techniques for Next Generation Genome Sequence Assembly,'' IEEE Transactions on Parallel and Distributed Systems, vol. 24, no. 5, pp. 977-986, May, 2013.
A parallel SpMV code for Intel Xeon Phi using the ELLPACK Sparse Block (ESB) Format. The ESB format has been used in the Intel MKL SpMV Format Prototype Package.
Xing Liu, Mikhail Smelyanskiy, Edmond Chow, and Pradeep Dubey, ''Efficient Sparse Matrix-Vector Multiplication on x86-based Many-core Processors,'' In 27th International Conference on Supercomputing (ICS), Eugene, Oregon, June 10-14, 2013.
StokesDT is a parallel toolkit for performing large-scale Brownian and Stokesian dynamics simulations on UNIX/LINUX platforms. StokesDT is written in C++ and is optimized for x86-based multicore and Intel MIC-based manycore architectures.
Xing Liu and Edmond Chow, ''Large-scale Hydrodynamic Brownian Simulations on Multicore and Manycore Architectures,'' In 28th IEEE International Parallel & Distributed Processing Symposium (IPDPS), Phoenix, AZ, May 19-23, 2014.
GTFock is a distributed framework for Fock matrix construction. It uses a new scalable parallel algorithm for Fock matrix construction, which significantly reduces communication and has better load balance than other current codes..
Xing Liu, Aftab Patel and Edmond Chow, '' A New Scalable Parallel Algorithm for Fock Matrix Construction,'' In 28th IEEE International Parallel & Distributed Processing Symposium (IPDPS), Phoenix, AZ, May 19-23, 2014.