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Jeremy Buhler - Publications

Affiliations: 
Computer Science Washington University, Saint Louis, St. Louis, MO 
Area:
Computer Science, Computer Engineering, Bioinformatics Biology
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30 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2014 Lopatto D, Hauser C, Jones CJ, Paetkau D, Chandrasekaran V, Dunbar D, MacKinnon C, Stamm J, Alvarez C, Barnard D, Bedard JE, Bednarski AE, Bhalla S, Braverman JM, Burg M, ... ... Buhler J, et al. A central support system can facilitate implementation and sustainability of a Classroom-based Undergraduate Research Experience (CURE) in Genomics. Cbe Life Sciences Education. 13: 711-23. PMID 25452493 DOI: 10.1187/Cbe.13-10-0200  0.315
2014 Cole SV, Gardner JR, Buhler JD. WOODSTOCC: Extracting latent parallelism from a DNA sequence aligner on a GPU Proceedings - Ieee 13th International Symposium On Parallel and Distributed Computing, Ispdc 2014. 197-204. DOI: 10.1109/ISPDC.2014.30  0.359
2012 Ihuegbu NE, Stormo GD, Buhler J. Fast, sensitive discovery of conserved genome-wide motifs. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 19: 139-47. PMID 22300316 DOI: 10.1089/Cmb.2011.0249  0.374
2012 Sun Y, Buhler J, Yuan C. Designing filters for fast-known NcRNA identification. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 9: 774-87. PMID 22084145 DOI: 10.1109/Tcbb.2011.149  0.646
2011 Ganesan N, Chamberlain RD, Buhler J, Taufer M. Rolling partial prefix-sums to speedup evaluation of uniform and affine recurrence equations Proceedings of Spie - the International Society For Optical Engineering. 8060. DOI: 10.1117/12.884896  0.37
2010 Shaffer CD, Alvarez C, Bailey C, Barnard D, Bhalla S, Chandrasekaran C, Chandrasekaran V, Chung HM, Dorer DR, Du C, Eckdahl TT, Poet JL, Frohlich D, Goodman AL, Gosser Y, ... ... Buhler J, et al. The genomics education partnership: successful integration of research into laboratory classes at a diverse group of undergraduate institutions. Cbe Life Sciences Education. 9: 55-69. PMID 20194808 DOI: 10.1187/09-11-0087  0.31
2010 Ganesan N, Chamberlain RD, Buhler J, Taufer M. Accelerating HMMER on GPUs by implementing hybrid data and task parallelism 2010 Acm International Conference On Bioinformatics and Computational Biology, Acm-Bcb 2010. 418-421. DOI: 10.1145/1854776.1854844  0.324
2010 Chamberlain RD, Franklin MA, Tyson EJ, Buckley JH, Buhler J, Galloway G, Gayen S, Hall M, Shands EFB, Singla N. Auto-pipe: Streaming applications on architecturally diverse systems Computer. 43: 42-49. DOI: 10.1109/Mc.2010.62  0.354
2010 Jacob AC, Buhler JD, Chamberlain RD. Rapid RNA folding: Analysis and acceleration of the Zuker recurrence Proceedings - Ieee Symposium On Field-Programmable Custom Computing Machines, Fccm 2010. 87-94. DOI: 10.1109/FCCM.2010.22  0.667
2010 Jacob AC, Buhler JD, Chamberlain RD. Design of throughput-optimized arrays from recurrence abstractions Proceedings of the International Conference On Application-Specific Systems, Architectures and Processors. 133-140. DOI: 10.1109/ASAP.2010.5540753  0.661
2009 Lancaster J, Buhler J, Chamberlain RD. Acceleration of Ungapped Extension in Mercury BLAST. Microprocessors and Microsystems. 33: 281-289. PMID 20160873 DOI: 10.1016/J.Micpro.2009.02.007  0.391
2009 Sun Y, Buhler J. Designing patterns and profiles for faster HMM search. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 6: 232-43. PMID 19407348 DOI: 10.1109/Tcbb.2008.14  0.606
2009 Jacob AC, Buhler JD, Chamberlain RD. Optimal runtime reconfiguration strategies for systolic arrays Fpl 09: 19th International Conference On Field Programmable Logic and Applications. 162-167. DOI: 10.1109/FPL.2009.5272515  0.675
2008 Sun Y, Buhler J. Designing secondary structure profiles for fast ncRNA identification. Computational Systems Bioinformatics / Life Sciences Society. Computational Systems Bioinformatics Conference. 7: 145-56. PMID 19642276  0.586
2008 Jacob A, Lancaster J, Buhler J, Harris B, Chamberlain RD. Mercury BLASTP: Accelerating Protein Sequence Alignment. Acm Transactions On Reconfigurable Technology and Systems. 1: 9. PMID 19492068 DOI: 10.1145/1371579.1371581  0.702
2007 Krishnamurthy P, Buhler J, Chamberlain R, Franklin M, Gyang K, Jacob A, Lancaster J. Biosequence Similarity Search on the Mercury System. Journal of Vlsi Signal Processing Systems For Signal, Image, and Video Technology. 49: 101-121. PMID 18846267  0.613
2007 Souvenir R, Buhler J, Stormo G, Zhang W. An iterative method for selecting degenerate multiplex PCR primers. Methods in Molecular Biology (Clifton, N.J.). 402: 245-68. PMID 17951799 DOI: 10.1007/978-1-59745-528-2_12  0.346
2007 Sun Y, Buhler J. Designing patterns for profile HMM search. Bioinformatics (Oxford, England). 23: e36-43. PMID 17237102 DOI: 10.1093/Bioinformatics/Btl323  0.619
2007 Jacob AC, Lancaster JM, Buhler JD, Chamberlain RD. Preliminary results in accelerating profile HMM search on FPGAs Proceedings - 21st International Parallel and Distributed Processing Symposium, Ipdps 2007; Abstracts and Cd-Rom. DOI: 10.1109/IPDPS.2007.370447  0.704
2007 Harris B, Jacob AC, Lancaster JM, Buhler J, Chamberlain RD. A banded smith-waterman FPGA accelerator for mercury BLASTP Proceedings - 2007 International Conference On Field Programmable Logic and Applications, Fpl. 765-769. DOI: 10.1109/FPL.2007.4380764  0.684
2006 Sun Y, Buhler J. Choosing the best heuristic for seeded alignment of DNA sequences. Bmc Bioinformatics. 7: 133. PMID 16533404 DOI: 10.1186/1471-2105-7-133  0.603
2006 Maddimsetty RP, Buhler J, Chamberlain RD, Franklin MA, Harris B. Accelerator design for protein sequence HMM search Proceedings of the International Conference On Supercomputing. 288-296. DOI: 10.1145/1183401.1183442  0.373
2006 Jacob AC, Harris B, Buhler J, Chamberlain R, Cho YH. Scalable softcore vector processor for biosequence applications Proceedings - 14th Annual Ieee Symposium On Field-Programmable Custom Computing Machines, Fccm 2006. 295-296. DOI: 10.1109/FCCM.2006.62  0.617
2005 Sun Y, Buhler J. Designing multiple simultaneous seeds for DNA similarity search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 12: 847-61. PMID 16108721 DOI: 10.1089/Cmb.2005.12.847  0.606
2005 Buhler J, Keich U, Sun Y. Designing seeds for similarity search in genomic DNA Journal of Computer and System Sciences. 70: 342-363. DOI: 10.1016/J.Jcss.2004.12.003  0.605
2005 Buhler J, Nordgren R. Toward a phylogenetically aware algorithm for fast DNA similarity search Lecture Notes in Bioinformatics (Subseries of Lecture Notes in Computer Science). 3388: 15-29.  0.333
2003 Buhler J. Provably sensitive indexing strategies for biosequence similarity search. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 10: 399-417. PMID 13677335 DOI: 10.1089/10665270360688093  0.383
2003 Halperin E, Buhler J, Karp R, Krauthgamer R, Westover B. Detecting protein sequence conservation via metric embeddings. Bioinformatics (Oxford, England). 19: i122-9. PMID 12855448 DOI: 10.1093/Bioinformatics/Btg1016  0.332
2002 Buhler J, Tompa M. Finding motifs using random projections. Journal of Computational Biology : a Journal of Computational Molecular Cell Biology. 9: 225-42. PMID 12015879 DOI: 10.1089/10665270252935430  0.661
2001 Buhler J. Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics (Oxford, England). 17: 419-28. PMID 11331236 DOI: 10.1093/Bioinformatics/17.5.419  0.417
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