Jeremy Buhler - Publications

Affiliations: 
Computer Science Washington University, Saint Louis, St. Louis, MO 
Area:
Computer Science, Computer Engineering, Bioinformatics Biology

51 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
2015 Li P, Beard J, Buhler J. Deadlock-free buffer configuration for stream computing Proceedings of the 6th International Workshop On Programming Models and Applications For Multicores and Manycores, Pmam 2015. 164-169. DOI: 10.1145/2712386.2712403  1
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  1
2014 Shaffer CD, Alvarez CJ, Bednarski AE, Dunbar D, Goodman AL, Reinke C, Rosenwald AG, Wolyniak MJ, Bailey C, Barnard D, Bazinet C, Beach DL, Bedard JE, Bhalla S, Braverman J, ... ... Buhler J, et al. A course-based research experience: how benefits change with increased investment in instructional time. Cbe Life Sciences Education. 13: 111-30. PMID 24591510 DOI: 10.1187/cbe-13-08-0152  1
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  1
2014 Li P, Buhler J. Polyhedral constraints for bounded-memory execution of synchronized filtering dataflow Proceedings - 2013 3rd Workshop On Data-Flow Execution Models For Extreme Scale Computing, Dfm 2013. 29-37. DOI: 10.1109/DFM.2013.11  1
2012 Sun H, Buhler JD. PhyLAT: a phylogenetic local alignment tool. Bioinformatics (Oxford, England). 28: 1336-44. PMID 22492645 DOI: 10.1093/bioinformatics/bts158  1
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  1
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  1
2012 Dawson RJ, Wang M, Buhler J. Flood incident management for water sensitive urban design Wsud 2012 - 7th International Conference On Water Sensitive Urban Design: Building the Water Sensitive Community, Final Program and Abstract Book 1
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  1
2011 Ma L, Chamberlain RD, Buhler JD, Franklin MA. Bloom filter performance on graphics engines Proceedings of the International Conference On Parallel Processing. 522-531. DOI: 10.1109/ICPP.2011.27  1
2011 Lancaster JM, Shands EFB, Buhler JD, Chamberlain RD. TimeTrial: A low-impact performance profiler for streaming data applications Proceedings of the International Conference On Application-Specific Systems, Architectures and Processors. 69-76. DOI: 10.1109/ASAP.2011.6043238  1
2010 Leung W, Shaffer CD, Cordonnier T, Wong J, Itano MS, Slawson Tempel EE, Kellmann E, Desruisseau DM, Cain C, Carrasquillo R, Chusak TM, Falkowska K, Grim KD, Guan R, Honeybourne J, ... ... Buhler J, et al. Evolution of a distinct genomic domain in Drosophila: comparative analysis of the dot chromosome in Drosophila melanogaster and Drosophila virilis. Genetics. 185: 1519-34. PMID 20479145 DOI: 10.1534/genetics.110.116129  1
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  1
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  1
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  1
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  1
2010 Li P, Agrawal K, Buhler J, Chamberlain RD, Lancaster JM. Deadlock-avoidance for streaming applications with split-join structure: Two case studies Proceedings of the International Conference On Application-Specific Systems, Architectures and Processors. 333-336. DOI: 10.1109/ASAP.2010.5540957  1
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  1
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  1
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  1
2009 Lancaster JM, Buhler JD, Chamberlain RD. Efficient runtime performance monitoring of FPGA-based applications Proceedings - Ieee International Soc Conference, Socc 2009. 23-28. DOI: 10.1109/SOCCON.2009.5398106  1
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  1
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  1
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  0.64
2008 Jacob A, Buhler J, Chamberlain RD. Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs Proceedings of the International Conference On Application-Specific Systems, Architectures and Processors. 191-196. DOI: 10.1109/ASAP.2008.4580177  1
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  1
2007 Sun Y, Buhler J. Designing patterns for profile HMM search. Bioinformatics (Oxford, England). 23: e36-43. PMID 17237102 DOI: 10.1093/bioinformatics/btl323  1
2007 Chamberlain RD, Franklin MA, Tyson EJ, Buhler J, Gayen S, Crowley P, Buckley JH. Application development on hybrid systems Proceedings of the 2007 Acm/Ieee Conference On Supercomputing, Sc'07. DOI: 10.1145/1362622.1362690  1
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  1
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  1
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  1
2006 Slawson EE, Shaffer CD, Malone CD, Leung W, Kellmann E, Shevchek RB, Craig CA, Bloom SM, Bogenpohl J, Dee J, Morimoto ET, Myoung J, Nett AS, Ozsolak F, Tittiger ME, ... ... Buhler J, et al. Comparison of dot chromosome sequences from D. melanogaster and D. virilis reveals an enrichment of DNA transposon sequences in heterochromatic domains. Genome Biology. 7: R15. PMID 16507169 DOI: 10.1186/gb-2006-7-2-r15  1
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  1
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  1
2006 Alkan C, Karakoc E, Cenk Sahinalp S, Unrau P, Alexander Ebhardt H, Zhang K, Buhler J. RNA secondary structure prediction via energy density minimization Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3909: 130-142. DOI: 10.1007/11732990_12  1
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  1
2005 Sonnenburg JL, Xu J, Leip DD, Chen CH, Westover BP, Weatherford J, Buhler JD, Gordon JI. Glycan foraging in vivo by an intestine-adapted bacterial symbiont. Science (New York, N.Y.). 307: 1955-9. PMID 15790854 DOI: 10.1126/science.1109051  1
2005 Westover BP, Buhler JD, Sonnenburg JL, Gordon JI. Operon prediction without a training set. Bioinformatics (Oxford, England). 21: 880-8. PMID 15539453 DOI: 10.1093/bioinformatics/bti123  1
2005 Wun B, Buhler J, Crowley P. Exploiting coarse-grained parallelism to accelerate protein motif finding with a network processor Parallel Architectures and Compilation Techniques - Conference Proceedings, Pact. 2005: 173-184. DOI: 10.1109/PACT.2005.21  1
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  1
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.  1
2004 Buhler JD, Souvenir RM, Zhang W, Mitra RD. Design of a high-throughput assay for alternative splicing using polymerase colonies. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 5-16. PMID 14992488  1
2003 Wang M, Buhler J, Brent MR. The effects of evolutionary distance on TWINSCAN, an algorithm for pair-wise comparative gene prediction. Cold Spring Harbor Symposia On Quantitative Biology. 68: 125-30. PMID 15338610  1
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  1
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  1
2003 Souvenir R, Buhler J, Stormo G, Zhang W. Selecting degenerate multiplex PCR primers Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2812: 512-526.  1
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  1
2001 Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, Eng JK, Bumgarner R, Goodlett DR, Aebersold R, Hood L. Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science (New York, N.Y.). 292: 929-34. PMID 11340206 DOI: 10.1126/science.292.5518.929  1
2001 Buhler J. Efficient large-scale sequence comparison by locality-sensitive hashing. Bioinformatics (Oxford, England). 17: 419-28. PMID 11331236  1
1997 Buhler J, Owerbach D, Schäffer AA, Kimmel M, Gabbay KH. Linkage analyses in type I diabetes mellitus using CASPAR, a software and statistical program for conditional analysis of polygenic diseases. Human Heredity. 47: 211-22. PMID 9239508  1
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