Jeremy Buhler

Jeremy D. Buhler

2008
28	EE	Arpith C. Jacob, Jeremy Buhler, Roger D. Chamberlain: Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs. ASAP 2008: 191-196
27	EE	Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Brandon Harris, Roger D. Chamberlain: Mercury BLASTP: Accelerating Protein Sequence Alignment. TRETS 1(2): (2008)
2007
26	EE	Arpith C. Jacob, Joseph M. Lancaster, Jeremy Buhler, Roger D. Chamberlain: FPGA-accelerated seed generation in Mercury BLASTP. FCCM 2007: 95-106
25	EE	Brandon 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
24	EE	Arpith C. Jacob, Joseph M. Lancaster, Jeremy D. Buhler, Roger D. Chamberlain: Preliminary results in accelerating profile HMM search on FPGAs. IPDPS 2007: 1-8
23	EE	Roger 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
22	EE	Yanni Sun, Jeremy Buhler: Designing patterns for profile HMM search. Bioinformatics 23(2): 42-43 (2007)
21	EE	Praveen 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
20	EE	Arpith C. Jacob, Brandon Harris, Jeremy Buhler, Roger D. Chamberlain, Young H. Cho: Scalable Softcore Vector Processor for Biosequence Applications. FCCM 2006: 295-296
19	EE	Rahul P. Maddimsetty, Jeremy Buhler, Roger D. Chamberlain, Mark A. Franklin, Brandon Harris: Accelerator design for protein sequence HMM search. ICS 2006: 288-296
18	EE	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. RECOMB 2006: 130-142
17	EE	Yanni Sun, Jeremy Buhler: Choosing the best heuristic for seeded alignment of DNA sequences. BMC Bioinformatics 7: 133 (2006)
2005
16	EE	Ben Wun, Jeremy Buhler, Patrick Crowley: Exploiting Coarse-Grained Parallelism to Accelerate Protein Motif Finding with a Network Processor. IEEE PACT 2005: 173-184
15	EE	Benjamin P. Westover, Jeremy D. Buhler, Justin L. Sonnenburg, Jeffrey I. Gordon: Operon prediction without a training set. Bioinformatics 21(7): 880-888 (2005)
14	EE	Jeremy Buhler, Uri Keich, Yanni Sun: Designing seeds for similarity search in genomic DNA. J. Comput. Syst. Sci. 70(3): 342-363 (2005)
13	EE	Yanni Sun, Jeremy Buhler: Designing Multiple Simultaneous Seeds for DNA Similarity Search. Journal of Computational Biology 12(6): 847-861 (2005)
2004
12	EE	Praveen 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
11	EE	Jeremy Buhler, Rachel Nordgren: Toward a Phylogenetically Aware Algorithm for Fast DNA Similarity Search. Comparative Genomics 2004: 15-29
10	EE	Jeremy 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
9	EE	Yanni Sun, Jeremy Buhler: Designing multiple simultaneous seeds for DNA similarity search. RECOMB 2004: 76-84
2003
8	EE	Eran Halperin, Jeremy Buhler, Richard M. Karp, Robert Krauthgamer, Ben Westover: Detecting protein sequence conservation via metric embeddings. ISMB (Supplement of Bioinformatics) 2003: 122-129
7	EE	Jeremy Buhler, Uri Keich, Yanni Sun: Designing seeds for similarity search in genomic DNA. RECOMB 2003: 67-75
6	EE	Richard Souvenir, Jeremy Buhler, Gary D. Stormo, Weixiong Zhang: Selecting Degenerate Multiplex PCR Primers. WABI 2003: 512-526
5	EE	Jeremy Buhler: Provably Sensitive Indexing Strategies for Biosequence Similarity Search. Journal of Computational Biology 10(3/4): 399-417 (2003)
2002
4	EE	Jeremy 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
2	EE	Jeremy 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

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

Colors in the list of coauthors