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Jeremy Buhler

Jeremy D. Buhler

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2008
28EEArpith C. Jacob, Jeremy Buhler, Roger D. Chamberlain: Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. ASAP 2008: 191-196
27EEArpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Brandon Harris, Roger D. Chamberlain: Mercury BLASTP: Accelerating Protein Sequence Alignment. TRETS 1(2): (2008)
2007
26EEArpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain: FPGA-accelerated seed generation in Mercury BLASTP. FCCM 2007: 95-106
25EEBrandon Harris, Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain: A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP. FPL 2007: 765-769
24EEArpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain: Preliminary results in accelerating profile HMM search on FPGAs. IPDPS 2007: 1-8
23EERoger D. Chamberlain, Mark A. Franklin, Eric J. Tyson, Jeremy Buhler, Saurabh Gayen, Patrick Crowley, James H. Buckley: Application development on hybrid systems. SC 2007: 50
22EEYanni Sun, Jeremy Buhler: Designing patterns for profile HMM search. Bioinformatics 23(2): 42-43 (2007)
21EEPraveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Arpith C. Jacob, Joseph M. Lancaster: Biosequence Similarity Search on the Mercury System. VLSI Signal Processing 49(1): 101-121 (2007)
2006
20EEArpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger D. Chamberlain, Young H. Cho: Scalable Softcore Vector Processor for Biosequence Applications. FCCM 2006: 295-296
19EERahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris: Accelerator design for protein sequence HMM search. ICS 2006: 288-296
18EECan Alkan, Emre Karakoç, Süleyman Cenk Sahinalp, Peter J. Unrau, H. Alexander Ebhardt, Kaizhong Zhang, Jeremy Buhler: RNA Secondary Structure Prediction Via Energy Density Minimization. RECOMB 2006: 130-142
17EEYanni Sun, Jeremy Buhler: Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinformatics 7: 133 (2006)
2005
16EEBen Wun, Jeremy Buhler, Patrick Crowley: Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. IEEE PACT 2005: 173-184
15EEBenjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon: Operon prediction without a training set. Bioinformatics 21(7): 880-888 (2005)
14EEJeremy Buhler, Uri Keich, Yanni Sun: Designing seeds for similarity search in genomic DNA. J. Comput. Syst. Sci. 70(3): 342-363 (2005)
13EEYanni Sun, Jeremy Buhler: Designing Multiple Simultaneous Seeds for DNA Similarity Search. Journal of Computational Biology 12(6): 847-861 (2005)
2004
12EEPraveen Krishnamurthy, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Kwame Gyang, Joseph M. Lancaster: Biosequence Similarity Search on the Mercury System. ASAP 2004: 365-375
11EEJeremy Buhler, Rachel Nordgren: Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. Comparative Genomics 2004: 15-29
10EEJeremy Buhler, Richard Souvenir, Weixiong Zhang, Rob Mitra: Design of a High-Throughput Assay for Alternative Splicing Using Polymerase Colonies. Pacific Symposium on Biocomputing 2004: 5-16
9EEYanni Sun, Jeremy Buhler: Designing multiple simultaneous seeds for DNA similarity search. RECOMB 2004: 76-84
2003
8EEEran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover: Detecting protein sequence conservation via metric embeddings. ISMB (Supplement of Bioinformatics) 2003: 122-129
7EEJeremy Buhler, Uri Keich, Yanni Sun: Designing seeds for similarity search in genomic DNA. RECOMB 2003: 67-75
6EERichard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang: Selecting Degenerate Multiplex PCR Primers. WABI 2003: 512-526
5EEJeremy Buhler: Provably Sensitive Indexing Strategies for Biosequence Similarity Search. Journal of Computational Biology 10(3/4): 399-417 (2003)
2002
4EEJeremy Buhler: Provably sensitive Indexing strategies for biosequence similarity search. RECOMB 2002: 90-99
3 Jeremy Buhler, Martin Tompa: Finding Motifs Using Random Projections. Journal of Computational Biology 9(2): 225-242 (2002)
2001
2EEJeremy Buhler, Martin Tompa: Finding motifs using random projections. RECOMB 2001: 69-76
1 Jeremy Buhler: Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics 17(5): 419-428 (2001)

Coauthor Index

1Can Alkan [18]
2James H. Buckley [23]
3Roger D. Chamberlain [12] [19] [20] [21] [23] [24] [25] [26] [27] [28]
4Young H. Cho [20]
5Patrick Crowley [16] [23]
6H. Alexander Ebhardt [18]
7Mark A. Franklin [12] [19] [21] [23]
8Saurabh Gayen [23]
9Jeffrey I. Gordon [15]
10Kwame Gyang [12] [21]
11Eran Halperin [8]
12Brandon Harris [19] [20] [25] [27]
13Arpith C. Jacob [20] [21] [24] [25] [26] [27] [28]
14Emre Karakoç [18]
15Richard M. Karp [8]
16Uri Keich [7] [14]
17Robert Krauthgamer [8]
18Praveen Krishnamurthy [12] [21]
19Joseph M. Lancaster [12] [21] [24] [25] [26] [27]
20Rahul P. Maddimsetty [19]
21Rob Mitra [10]
22Rachel Nordgren [11]
23Süleyman Cenk Sahinalp [18]
24Justin L. Sonnenburg [15]
25Richard Souvenir [6] [10]
26Gary D. Stormo [6]
27Yanni Sun [7] [9] [13] [14] [17] [22]
28Martin Tompa [2] [3]
29Eric J. Tyson [23]
30Peter J. Unrau [18]
31Ben Westover [8]
32Benjamin P. Westover [15]
33Ben Wun [16]
34Kaizhong Zhang [18]
35Weixiong Zhang [6] [10]

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Copyright © Sun May 17 03:24:02 2009 by Michael Ley (ley@uni-trier.de)