Publications & Talks



  • Journal Articles

  • cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on CPU+GPU.
    Jing Zhang, Hao Wang, Wu-chun Feng.
    In IEEE/ACM Transactions on Computational Biology and Bioinformatics (TCBB), PP (99): October 2015.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • OpenDwarfs: Characterization of Dwarf-Based Benchmarks on Fixed and Reconfigurable Architectures.
    Konstantinos Krommydas, Wu-chun Feng, Christos D. Antonopoulos, Nikolaos Bellas.
    In Journal of Signal Processing Systems, 1--20, October 2015.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • MPI-ACC: Accelerator-Aware MPI for Scientific Applications.
    Ashwin M. Aji, Lokendra Panwar, Feng Ji, Karthik Murthy, Milind Chabbi, Pavan Balaji, Keith Bisset, James Dinan, Wuchun Feng, John Mellor-Crummey, Xiaosong Ma, Rajeev Thakur.
    In IEEE Transactions on Parallel and Distributed Systems, PP (99): June 2015.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • SDAFT: A Novel Scalable Data Access Framework for Parallel BLAST.
    Jiangling Yin, Junyao Zhang, Jun Wang, Wu-chun Feng.
    In Parallel Computing, 40 (10): 697–709, August 2014.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • High-Performance Biocomputing for Simulating the Spread of Contagion over Large Contact Networks.
    Keith R. Bisset, Ashwin M. Aji, Madhav V. Marathe, Wu-chun Feng.
    In BMC Genomics, 13 (S2): S3, April 2012.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Multi-Dimensional Characterization of Electrostatic Surface Potential Computation on Graphics Processors.
    Mayank Daga, Wu-chun Feng.
    In BMC Bioinformatics, 13 (S5): S4, April 2012.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Communication and Data-Intensive Science in the Beginning of the 21st Century.
    Jack Faris, Evelyne Kolker, Alex Szalay, Leon Bradlow, Ewa Deelman, Wu-chun Feng, Judy Qiu, Donna Russell, Elizabeth Stewart, Eugene Kolker.
    In OMICS A Journal of Integrative Biology, 15 (4): 213--215, April 2011.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • The Terabase Metagenomics Workshop and the Vision of an Earth Microbiome Project.
    Jack Gilbert, Folker Meyer, Dion Antonopoulos, Pavan Balaji, C. Titus Brown, Christopher T. Brown, Narayan Desai, Jonathan A. Eisen, Dirk Evers, Dawn Field, Wu-chun Feng, Daniel Huson, Janet Jansson, Rob Knight, James Knight, Eugene Kolker, Kostas Konstantindis, Joel Kostka, Nikos Kyrpides, Rachel Mackelprang, Alice McHardy, Christopher Quince, Jeroen Raes, Alexander Sczyrba, Ashley Shade, Rick Stevens.
    In Standards in Genomic Sciences, 3 (3): 243-248, December 2010.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Global-Scale Distributed I/O with ParaMEDIC.
    Pavan Balaji, Wu-chun Feng, Heshan Lin, Jeremy Archuleta, S. Matsuoka, A. Warren, J. Setubal, E. Lusk, R. Thakur, Ian Foster, D. Katz, S. Jha, K. Shinpaugh, S. Coghlan, D. Reed.
    In Concurrency and Computation: Practice and Experience, 22 (16): 2266-2281, November 2010.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Coordinating Computation and I/O in Massively Parallel Sequence Search.
    Heshan Lin, Xiaosong Ma, Wu-chun Feng, Nagiza Samatova.
    In IEEE Transactions on Parallel and Distributed Systems, PP (99): 1-14, May 2010.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Accelerating Electrostatic Surface Potential Calculation with Multi-Scale Approximation on Graphics Processing Units.
    Ramu Anandakrishnan, Tom R.W. Scogland, Andrew T. Fenley, John C. Gordon, Wu-chun Feng, Alexey V. Onufriev.
    In Journal of Molecular Graphics and Modelling, 28 904-910, April 2010.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Missing Genes in the Annotation of Prokaryotic Genomes.
    Andrew S. Warren, Jeremy Archuleta, Wu-chun Feng, Joao Carlos Setubal.
    In BMC Bioinformatics 2010, 11 (131): 1-12, March 2010.
      Preprint (PDF)               Citations:  [ BibTeX    XML    PlainText ]   

  • Conference Papers

  • new  PaPar: A Parallel Data Partitioning Framework for Big Data Applications.
    Hao Wang, Jing Zhang, Da Zhang, Sarunya Pumma, Wu-chun Feng.
    In Proceedings of the IEEE International Parallel and Distributed Processing Symposium, Orlando, Florida, May 2017.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • new  Eliminating Irregularities of Protein Sequence Search on Multicore Architectures.
    Jing Zhang, Sanchit Misra, Hao Wang, Wu-chun Feng.
    In Proceedings of the IEEE International Parallel and Distributed Processing Symposium, Orlando, Florida, May 2017.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • AAlign: A SIMD Framework for Pairwise Sequence Alignment on x86-based Multi- and Many-core Processors.
    Kaixi Hou, Hao Wang, Wu-chun Feng.
    In Proceedings of the IEEE International Parallel and Distributed Processing Symposium (IPDPS), Chicago, IL, USA, May 2016.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • pDindel: Accelerating InDel Detection on a Multicore CPU Architecture with SIMD.
    Da Zhang, Hao Wang, Kaixi Hou, Jing Zhang, Wu-chun Feng.
    In Proceedings of the 5th IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Miami, FL, USA, October 2015.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • GLAF: A Visual Programming and Auto-Tuning Framework for Parallel Computing.
    Konstantinos Krommydas, Ruchira Sasanka, Wu-chun Feng.
    In Proceedings of the International Conference on Parallel Processing, Beijing, China, September 2015.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • CentroidBLAST: Accelerating Sequence Search via Clustering.
    Wu-chun Feng, Konstantinos Krommydas, Liqing Zhang.
    In Proceedings of the 7th International Conference on Bioinformatics and Computational Biology, Honolulu, Hawaii, March 2015.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Aeromancer: A Workflow Manager for Large-Scale MapReduce-Based Scientific Workflows.
    Nabeel Mohamed, Nabanita Maji, Jing Zhang, Nataliya Timoshevskaya, Wu-chun Feng.
    In Proceedings of the 3rd IEEE International Conference on Big Data Science and Engineering (BDSE), Beijing, China, September 2014.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • SAIS-OPT: On the Characterization and Optimization of the SA-IS Algorithm for Suffix Array Construction.
    Nataliya Timoshevskaya, Wu-chun Feng.
    In Proceedings of the 4th IEEE International Conference on Computational Advanced in Bio and Medical Sciences, Miami Beach, Florida, June 2014.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • On the Programmability and Performance of Heterogeneous Platforms.
    Konstantinos Krommydas, Thomas R.W. Scogland, Wu-chun Feng.
    In Proceedings of the 19th IEEE International Conference on Parallel and Distributed Systems (ICPADS 2013), Seoul, Korea, December 2013.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Optimizing Burrows-Wheeler Transform-Based Sequence Alignment on Multicore Architectures.
    Jing Zhang, Heshan Lin, Pavan Balaji, Wu-chun Feng.
    In Proceedings of the 13th IEEE/ACM International Symposium on Cluster, Cloud and Grid Computing (CCGrid), Delft, Netherlands, May 2013.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Accelerating Data-Intensive Genome Analysis in the Cloud.
    Nabeel M. Mohamed, Heshan Lin, Wu-chun Feng.
    In Proceedings of the 5th International Conference on Bioinformatics and Computational Biology (BICoB), Honolulu, Hawaii, USA, March 2013.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Architecture-Aware Mapping and Optimization on a 1600-Core GPU.
    Mayank Daga, Tom Scogland, Wu-chun Feng.
    In Proceedings of the 17th IEEE International Conference on Parallel and Distributed Systems, Tainan, Taiwan, December 2011.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Accelerating Protein Sequence Search in a Heterogeneous Computing System.
    Shucai Xiao, Heshan Lin, Wu-chun Feng.
    In Proceedings of the 25th International Parallel and Distributed Processing Symposium, Anchorage, Alaska, USA, May 2011.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Towards Accelerating Molecular Modeling via Multi-Scale Approximation on a GPU.
    Mayank Daga, Wu-chun Feng, Thomas Scogland.
    In Proceedings of the 1st IEEE International Conference on Computational Advances in Bio and Medical Sciences (ICCABS), Orlando, Florida, USA, February 2011.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • GPU-RMAP: Accelerating Short-Read Mapping on Graphics Processors.
    Ashwin M. Aji, Liqing Zhang, Wu-chun Feng.
    In Proceedings of the 13th IEEE International Conference on Computational Science and Engineering, Hong Kong, China, December 2010.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Towards Chip-on-Chip Neuroscience: Fast Mining of Neuronal Spike Streams Using Graphics Hardware.
    Yong Cao, Debprakash Patnaik, Sean Ponce, Jeremy Archuleta, Patrick Butler, Wu-chun Feng, Naren Ramakrishnan.
    In Proceedings of the 7th ACM International Conference on Computing Frontiers, Bertinoro, Italy, pp. 1--10, May 2010.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Inter-Block GPU Communication via Fast Barrier Synchronization.
    Shucai Xiao, Wu-chun Feng.
    In Proceedings of the 24th IEEE International Parallel and Distributed Processing Symposium (IPDPS), Atlanta, Georgia, USA, April 2010.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • On the Robust Mapping of Dynamic Programming onto a Graphics Processing Unit.
    Shucai Xiao, Ashwin M. Aji, Wu-chun Feng.
    In Proceedings of the 15th International Conference on Parallel and Distributed Systems (ICPADS), Shenzhen, China, December 2009.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Multi-Dimensional Characterization of Temporal Data Mining on Graphics Processors.
    Jeremy Archuleta, Yong Cao, Tom Scogland, Wu-chun Feng.
    In Proceedings of the 23rd IEEE International Parallel and Distributed Processing Symposium (IPDPS), Rome, Italy, May 2009.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Massively Parallel Genomic Sequence Search on the Blue Gene/P Architecture.
    Heshan Lin, Pavan Balaji, Ruth Poole, Carlos Sosa, Xiaosong Ma, Wu-chun Feng.
    In Proceedings of the ACM/IEEE SC|08: The International Conference on High-Performance Computing, Networking, Storage, and Analysis, Austin, Texas, November 2008.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Optimizing Performance, Cost, and Sensitivity in Pairwise Sequence Search on a Cluster of PlayStations.
    Ashwin M. Aji, Wu-chun Feng.
    In Proceedings of the IEEE International Conference on BioInformatics and BioEngineering, Athens, Greece, October 2008.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Distributed I/O with ParaMEDIC: Experiences with a Worldwide Supercomputer.
    P. Balaji, W. Feng, H. Lin, J. Archuleta, S. Matsuoka, A. Warren, J. Setubal, E. Lusk, R. Thakur, I. Foster, D. S. Katz, S. Jha, K. Shinpaugh, S. Coghlan, D. Reed.
    In Proceedings of the International Supercomputing Conference, Dresden, Germany, June 2008. Distinguished Paper Award
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Semantic-based Distributed I/O with the ParaMEDIC Framework.
    Pavan Balaji, Wu-chun Feng, Heshan Lin.
    In Proceedings of the 17th ACM/IEEE International Symposium on High-Performance Distributed Computing, Boston, Massachusetts, USA, June 2008.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Cell-SWat: Modeling and Scheduling Wavefront Computations on the Cell Broadband Engine.
    Ashwin M. Aji, Wu-chun Feng, Filip Blagojevic, Dimitrios S. Nikolopoulos.
    In Proceedings of the 5th ACM International Conference on Computing Frontiers, Ischia, Italy, May 2008.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Semantics-based Distributed I/O for mpiBLAST (Short Paper).
    Pavan Balaji, Wu-chun Feng, Jeremy Archuleta, Heshan Lin, Rajkumar Kettimuthu, Rajeev Thakur, Xiaosong Ma.
    In Proceedings of the ACM SIGPLAN Symposium on Principles and Practice of Parallel Programming, Salt Lake City, Utah, USA, February 2008.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • A Maintainable Software Architecture for Fast and Modular Bioinformatics Sequence Search.
    Jeremy S. Archuleta, Eli Tilevich, Wu-chun Feng.
    In Proceedings of the 23rd IEEE International Conference on Software Maintenance, Paris, France, October 2007.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Parallel Genomic Sequence-Search on a Massively Parallel System.
    Oystein Thorsen, Brian Smith, Carlos P. Sosa, Karl Jiang, Heshan Lin, Amanda Peters, Wu-chun Feng.
    In Proceedings of the ACM International Conference on Computing Frontiers, Ischia, Italy, May 2007.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Parallel Genomic Sequence-Searching on an Ad-Hoc Grid: Experiences, Lessons Learned, and Implications.
    Mark K. Gardner, Wu-chun Feng, Jeremy S. Archuleta, Heshan Lin, Xiaosong Ma.
    In Proceedings of the ACM/IEEE SC|06: The International Conference on High-Performance Computing, Networking, Storage, and Analysis, Tampa, FL, November 2006.
    Best Paper Nominee
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Exploring I/O Strategies for Parallel Sequence Database Search Tools with S3aSim.
    Avery Ching, Wu-chun Feng, Heshan Lin, Xiaosong Ma, Alok Choudhary.
    In Proceedings of the 15th IEEE International Symposium on High-Performance Distributed Computing (HPDC’06), Paris, France, June 2006.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Whole Genome, Physics-Based Sequence Alignment for Pathogen Signature Design.
    Jason D. Gans, Wu-chun Feng, Murray Wolinsky.
    In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006. (electronic version unavailable)
                 Citations:  [ BibTeX    XML    PlainText ]   
  • Efficient Data Handling in Comparative Genome Analysis Applications.
    Heshan Lin, Xiaosong Ma, Wu-chun Feng, Al Geist, Nagiza Samatova.
    In Proceedings of the 12th SIAM Conference on Parallel Processing for Scientific Computing, San Francisco, California, February 2006. (electronic version unavailable)
                 Citations:  [ BibTeX    XML    PlainText ]   
  • Efficient Data Access for Parallel BLAST.
    Heshan Lin, Xiaosong Ma, Praveen Chandramohan, Al Geist, Nagiza Samatova.
    In Proceedings of the IEEE International Parallel and Distributed Processing Symposium, Denver, Colorado, April 2005.
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • The Design, Implementation, and Evaluation of mpiBLAST.
    Aaron E. Darling, Lucas Carey, Wu-chun Feng.
    In Proceedings of the ClusterWorld Conference, San Jose, California, June 2003.
    LA-UR 03-2862.  
    Best Paper: Applications Track
      Paper (PDF)               Citations:  [ BibTeX    XML    PlainText ]   

  • Posters

  • cuBLASTP: Fine-Grained Parallelization of Protein Sequence Search on a GPU.
    Jing Zhang, Hao Wang, Heshan Lin, Wu-chun Feng.
    In GPU Technology Conference (GTC), San Jose, CA, USA, March 2014.
      Poster (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • Accelerating Molecular Modeling using GPUs.
    Mayank Daga, Wu-chun Feng.
    In GPU Technology Conference, San Jose, California, September 2010.
      Poster (PDF)               Citations:  [ BibTeX    XML    PlainText ]   
  • mpiBLAST: Parallelization of BLAST for Computational Clusters.
    Aaron E. Darling, Wu-chun Feng.
    In SC 2002: High-Performance Networking and Computing Conference (SC2002), Baltimore, Maryland, November 2002.
    LA-UR 02-7222.  
      Poster (PDF)               Citations:  [ BibTeX    XML    PlainText ]   

Our research has been supported by:

Affiliated Sites: Virginia Tech · SEEC · Synergy

Last updated: January 2016