Bioinformatics

  • Assembly algorithms for next-generation sequencing data. Miller, Jason R., Sergey Koren, and Granger Sutton. Genomics 95.6 (2010): 315-327.
  • Genome assembly reborn: recent computational challenges. Pop, Mihai. Briefings in bioinformatics 10.4 (2009): 354-366.
  • How to apply de Bruijn graphs to genome assembly. Compeau, Phillip EC, Pavel A. Pevzner, and Glenn Tesler. Nature biotechnology 29.11 (2011): 987-991.
  • Meraculous: De Novo Genome Assembly with Short Paired-End Reads.Chapman, Jarrod A., et al. PloS one 6.8 (2011): e23501.
  • Velvet: Algorithms for de novo short read assembly using de Bruijn graphs. Zerbino, Daniel R., and Ewan Birney. Genome research 18.5 (2008): 821-829.
  • A New Approach to Fragment Assembly in DNA Sequencing. Pevzner, Pavel A., Haixu Tang, and Michael S. Waterman. Proceedings of the fifth annual international conference on Computational biology. ACM, 2001.
  • Fragment assembly with double-barreled data. Pevzner, Pavel A., and Haixu Tang. Bioinformatics 17.suppl 1 (2001): S225-S233.
  • Myers, Eugene W. "The fragment assembly string graph." Bioinformatics 21.suppl 2 (2005): ii79-ii85.
  • A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Marçais, Guillaume, and Carl Kingsford. Bioinformatics 27.6 (2011): 764-770.

    Parallel Computing

  • Parallel De Bruijn Graph Construction and Traversal for De Novo Genome Assembly. Georganas, Evangelos, et al. Proceedings of the International Conference for High Performance Computing, Networking, Storage and Analysis. IEEE Press, 2014.
  • Parallel graph processing on graphics processors made easy. Zhong, Jianlong, and Bingsheng He. Proceedings of the VLDB Endowment 6.12 (2013): 1270-1273.
  • Memory Efficient Minimum Substring Partitioning. Li, Yang, et al. Proceedings of the VLDB Endowment 6.3 (2013): 169-180.
  • The Euler Tour Technique and Parallel Rooted Spanning Tree. Cong, Guojing, and David A. Bader. Parallel Processing, 2004. ICPP 2004. International Conference on. IEEE, 2004.
  • Exploring the Limits of GPUs With Parallel Graph Algorithms. Yogaratnam, Kumanan. Diss. Carleton University, 2010.
  • GPU-Accelerated Bidirected De Bruijn Graph Construction for Genome Assembly. Lu, Mian, et al. Web Technologies and Applications. Springer Berlin Heidelberg, 2013. 51-62.
  • Gpu-euler: Sequence assembly using gpgpu. Mahmood, Syed Faraz, and Huzefa Rangwala. High Performance Computing and Communications (HPCC), 2011 IEEE 13th International Conference on. IEEE, 2011.
  • Scalable GPU Graph Traversal. Merrill, Duane, Michael Garland, and Andrew Grimshaw. ACM SIGPLAN Notices. Vol. 47. No. 8. ACM, 2012.
  • Fast and Scalable List Ranking on the GPU. Rehman, M. Suhail, Kishore Kothapalli, and P. J. Narayanan. Proceedings of the 23rd international conference on supercomputing. ACM, 2009.
  • MapGraph: A High Level API for Fast Development of High Performance Graph Analytics on GPUs. Fu, Zhisong, Michael Personick, and Bryan Thompson. Proceedings of Workshop on GRAph Data management Experiences and Systems. ACM, 2014.
  • Efficient parallel graph exploration on multi-core CPU and GPU. Hong, Sungpack, Tayo Oguntebi, and Kunle Olukotun. Parallel Architectures and Compilation Techniques (PACT), 2011 International Conference on. IEEE, 2011.
  • Real-time parallel hashing on the GPU. Dan A., et al. ACM Transactions on Graphics (TOG). Vol. 28. No. 5. ACM, 2009.
  • Efficient gather and scatter operations on graphics processors. He, BingSHeng, et al. Proceedings of the 2007 ACM/IEEE conference on Supercomputing. ACM, 2007.

    Books on Algorithms and Programming

  • Efficient parallel algorithms. Gibbons, Alan, and Wojciech Rytter. Cambridge University Press, 1989.
  • An introduction to parallel algorithms. JáJá, Joseph. Vol. 17. Reading: Addison-Wesley, 1992.
  • CUDA C programming guide. NVIDIA Documentation. Version 4.2, 2012.
  • Professional CUDA C programming. John Cheng, Max Grossman and Ty McKercher. John Wiley & Sons, 2014.