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Publications of Author

1. Ben Wun, Jeremy Buhler, Patrick Crowley
   Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. [Citation Graph (0, 0)][DBLP]
   IEEE PACT, 2005, pp:173-184 [Conf]
   
2. Praveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Joseph M. Lancaster
   Biosequence Similarity Search on the Mercury System. [Citation Graph (0, 0)][DBLP]
   ASAP, 2004, pp:365-375 [Conf]
   
3. Arpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger D. Chamberlain, Young H. Cho
   Scalable Softcore Vector Processor for Biosequence Applications. [Citation Graph (0, 0)][DBLP]
   FCCM, 2006, pp:295-296 [Conf]
   
4. Rahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris
   Accelerator design for protein sequence HMM search. [Citation Graph (0, 0)][DBLP]
   ICS, 2006, pp:288-296 [Conf]
   
5. Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover
   Detecting protein sequence conservation via metric embeddings. [Citation Graph (0, 0)][DBLP]
   ISMB (Supplement of Bioinformatics), 2003, pp:122-129 [Conf]
   
6. Jeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra
   Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. [Citation Graph (0, 0)][DBLP]
   Pacific Symposium on Biocomputing, 2004, pp:5-16 [Conf]
   
7. Can Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler
   RNA Secondary Structure Prediction Via Energy Density Minimization. [Citation Graph (0, 0)][DBLP]
   RECOMB, 2006, pp:130-142 [Conf]
   
8. Jeremy Buhler
   Provably sensitive Indexing strategies for biosequence similarity search. [Citation Graph (0, 0)][DBLP]
   RECOMB, 2002, pp:90-99 [Conf]
   
9. Jeremy Buhler, Uri Keich, Yanni Sun
   Designing seeds for similarity search in genomic DNA. [Citation Graph (0, 0)][DBLP]
   RECOMB, 2003, pp:67-75 [Conf]
   
10. Jeremy Buhler, Rachel Nordgren
    Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. [Citation Graph (0, 0)][DBLP]
    Comparative Genomics, 2004, pp:15-29 [Conf]
    
11. Jeremy Buhler, Martin Tompa
    Finding motifs using random projections. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2001, pp:69-76 [Conf]
    
12. Yanni Sun, Jeremy Buhler
    Designing multiple simultaneous seeds for DNA similarity search. [Citation Graph (0, 0)][DBLP]
    RECOMB, 2004, pp:76-84 [Conf]
    
13. Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang
    Selecting Degenerate Multiplex PCR Primers. [Citation Graph (0, 0)][DBLP]
    WABI, 2003, pp:512-526 [Conf]
    
14. Jeremy Buhler
    Efficient large-scale sequence comparison by locality-sensitive hashing. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2001, v:17, n:5, pp:419-428 [Journal]
    
15. Yanni Sun, Jeremy Buhler
    Designing patterns for profile HMM search. [Citation Graph (0, 0)][DBLP]
    Bioinformatics, 2007, v:23, n:2, pp:42-43 [Journal]
    
16. Yanni Sun, Jeremy Buhler
    Choosing the best heuristic for seeded alignment of DNA sequences. [Citation Graph (0, 0)][DBLP]
    BMC Bioinformatics, 2006, v:7, n:, pp:133- [Journal]
    
17. Jeremy Buhler
    Provably Sensitive Indexing Strategies for Biosequence Similarity Search. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2003, v:10, n:3/4, pp:399-417 [Journal]
    
18. Jeremy Buhler, Martin Tompa
    Finding Motifs Using Random Projections. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2002, v:9, n:2, pp:225-242 [Journal]
    
19. Yanni Sun, Jeremy Buhler
    Designing Multiple Simultaneous Seeds for DNA Similarity Search. [Citation Graph (0, 0)][DBLP]
    Journal of Computational Biology, 2005, v:12, n:6, pp:847-861 [Journal]
    
20. Jeremy Buhler, Uri Keich, Yanni Sun
    Designing seeds for similarity search in genomic DNA. [Citation Graph (0, 0)][DBLP]
    J. Comput. Syst. Sci., 2005, v:70, n:3, pp:342-363 [Journal]
    
21. 
    Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. [Citation Graph (, )][DBLP]
    
    
22. 
    FPGA-accelerated seed generation in Mercury BLASTP. [Citation Graph (, )][DBLP]
    
    
23. 
    A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP. [Citation Graph (, )][DBLP]
    
    
24. 
    Application-guided tool development for architecturally diverse computation. [Citation Graph (, )][DBLP]
    
    
25. 
    Application development on hybrid systems. [Citation Graph (, )][DBLP]
    
    
26. 
    Deadlock avoidance for streaming computations with filtering. [Citation Graph (, )][DBLP]
    
    
27. 
    Auto-Pipe: Streaming Applications on Architecturally Diverse Systems. [Citation Graph (, )][DBLP]