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1

Mercury BLASTP

Jacob, Arpith, Lancaster, Joseph, Buhler, Jeremy, Harris, Brandon, Chamberlain, Roger D.

Journal:

ACM Transactions on Reconfigurable Technology and Systems

Year:

2008

Language:

english

File:

PDF, 761 KB

english, 2008

2

Acceleration of ungapped extension in Mercury BLAST

Joseph Lancaster, Jeremy Buhler, Roger D. Chamberlain

Journal:

Microprocessors and Microsystems

Year:

2009

Language:

english

File:

PDF, 782 KB

english, 2009

3

Designing seeds for similarity search in genomic DNA

Jeremy Buhler, Uri Keich, Yanni Sun

Journal:

Journal of Computer and System Sciences

Year:

2005

Language:

english

File:

PDF, 326 KB

english, 2005

4

Biosequence Similarity Search on theMercurySystem

Praveen Krishnamurthy, Jeremy Buhler, Roger Chamberlain, Mark Franklin, Kwame Gyang, Arpith Jacob, Joseph Lancaster

Journal:

Journal of Signal Processing Systems

Year:

2007

Language:

english

File:

PDF, 538 KB

english, 2007

5

Finding Motifs Using Random Projections

Buhler, Jeremy, Tompa, Martin

Journal:

Journal of Computational Biology

Year:

2002

Language:

english

File:

PDF, 309 KB

english, 2002

6

Choosing the best heuristic for seeded alignment of DNA sequences

Yanni Sun, Jeremy Buhler

Journal:

BMC Bioinformatics

Year:

2006

Language:

english

File:

PDF, 342 KB

english, 2006

7

[IEEE 2011 International Conference on Parallel Processing (ICPP) - Taipei, Taiwan (2011.09.13-2011.09.16)] 2011 International Conference on Parallel Processing - Bloom Filter Performance on Graphics Engines

Ma, Lin, Chamberlain, Roger D., Buhler, Jeremy D., Franklin, Mark A.

Year:

2011

Language:

english

File:

PDF, 1.03 MB

english, 2011

8

[IEEE 2010 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines - Charlotte, NC, USA (2010.05.2-2010.05.4)] 2010 18th IEEE Annual International Symposium on Field-Programmable Custom Computing Machines - Rapid RNA Folding: Analysis and Acceleration of the Zuker Recurrence

Jacob, Arpith C., Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2010

Language:

english

File:

PDF, 410 KB

english, 2010

9

[IEEE 2013 Data-Flow Execution Models for Extreme Scale Computing (DFM) - Edinburgh, Scotland, UK (2013.9.8-2013.9.8)] 2013 Data-Flow Execution Models for Extreme Scale Computing - Polyhedral Constraints for Bounded-Memory Execution of Synchronized Filtering Dataflow

Li, Peng, Buhler, Jeremy

Year:

2013

Language:

english

File:

PDF, 187 KB

english, 2013

10

[IEEE 2014 IEEE 13th International Symposium on Parallel and Distributed Computing (ISPDC) - France (2014.6.24-2014.6.27)] 2014 IEEE 13th International Symposium on Parallel and Distributed Computing - WOODSTOCC: Extracting Latent Parallelism from a DNA Sequence Aligner on a GPU

Cole, Stephen V., Gardner, Jacob R., Buhler, Jeremy D.

Year:

2014

Language:

english

File:

PDF, 268 KB

english, 2014

11

[IEEE 2009 IEEE International SOC Conference (SOCC) - Belfast, Northern Ireland (2009.09.9-2009.09.11)] 2009 IEEE International SOC Conference (SOCC) - Efficient runtime performance monitoring of FPGA-based applications

Lancaster, Joseph M., Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2009

Language:

english

File:

PDF, 277 KB

english, 2009

12

[IEEE 2010 21st IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP) - Rennes, France (2010.07.7-2010.07.9)] ASAP 2010 - 21st IEEE International Conference on Application-specific Systems, Architectures and Processors - Deadlock-avoidance for streaming applications with split-join structure: Two case studies

Li, Peng, Agrawal, Kunal, Buhler, Jeremy, Chamberlain, Roger D., Lancaster, Joseph M.

Year:

2010

Language:

english

File:

PDF, 109 KB

english, 2010

13

[IEEE 2009 International Conference on Field Programmable Logic and Applications (FPL) - Prague, Czech Republic (2009.08.31-2009.09.2)] 2009 International Conference on Field Programmable Logic and Applications - Optimal runtime reconfiguration strategies for systolic arrays

Jacob, Arpith C., Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2009

Language:

english

File:

PDF, 580 KB

english, 2009

14

[IEEE 2011 IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP) - Santa Monica, CA, USA (2011.09.11-2011.09.14)] ASAP 2011 - 22nd IEEE International Conference on Application-specific Systems, Architectures and Processors - TimeTrial: A low-impact performance profiler for streaming data applications

Lancaster, Joseph M., Shands, E. F. Berkley, Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2011

Language:

english

File:

PDF, 665 KB

english, 2011

15

[IEEE 2010 21st IEEE International Conference on Application-specific Systems, Architectures and Processors (ASAP) - Rennes, France (2010.07.7-2010.07.9)] ASAP 2010 - 21st IEEE International Conference on Application-specific Systems, Architectures and Processors - Design of throughput-optimized arrays from recurrence abstractions

Jacob, Arpith C., Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2010

Language:

english

File:

PDF, 574 KB

english, 2010

16

[IEEE 2013 20th International Conference on High Performance Computing (HiPC) - Bengaluru (Bangalore), Karnataka, India (2013.12.18-2013.12.21)] 20th Annual International Conference on High Performance Computing - Adding data parallelism to streaming pipelines for throughput optimization

Li, Peng, Agrawal, Kunal, Buhler, Jeremy, Chamberlain, Roger D.

Year:

2013

Language:

english

File:

PDF, 1.09 MB

english, 2013

17

Provably Sensitive Indexing Strategies for Biosequence Similarity Search

Journal:

Journal of Computational Biology

Year:

2003

Language:

english

File:

PDF, 302 KB

english, 2003

18

[IEEE 2008 International Conference on Application-Specific Systems, Architectures and Processors (ASAP) - Leuven, Belgium (2008.07.2-2008.07.4)] 2008 International Conference on Application-Specific Systems, Architectures and Processors - Accelerating Nussinov RNA secondary structure prediction with systolic arrays on FPGAs

Jacob, Arpith, Buhler, Jeremy, Chamberlain, Roger D.

Year:

2008

Language:

english

File:

PDF, 404 KB

english, 2008

19

[IEEE 2007 IEEE International Parallel and Distributed Processing Symposium - Long Beach, CA, USA (2007.03.26-2007.03.30)] 2007 IEEE International Parallel and Distributed Processing Symposium - Preliminary results in accelerating profile HMM search on FPGAs

Jacob, Arpith C., Lancaster, Joseph M., Buhler, Jeremy D., Chamberlain, Roger D.

Year:

2007

Language:

english

File:

PDF, 466 KB

english, 2007

20

[IEEE 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007) - Napa, CA, USA (2007.04.23-2007.04.25)] 15th Annual IEEE Symposium on Field-Programmable Custom Computing Machines (FCCM 2007) - FPGA-accelerated seed generation in Mercury BLASTP

Jacob, Arpith, Lancaster, Joseph, Buhler, Jeremy, Chamberlain, Roger D.

Year:

2007

Language:

english

File:

PDF, 381 KB

english, 2007

21

[IEEE 2007 International Conference on Field Programmable Logic and Applications - Amsterdam, Netherlands (2007.08.27-2007.08.29)] 2007 International Conference on Field Programmable Logic and Applications - A Banded Smith-Waterman FPGA Accelerator for Mercury BLASTP

Harris, Brandon, Jacob, Arpith C., Lancaster, Joseph M., Buhler, Jeremy, Chamberlain, Roger D.

Year:

2007

Language:

english

File:

PDF, 196 KB

english, 2007

22

[IEEE 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines - Napa, CA (2006.4.24-2006.4.24)] 2006 14th Annual IEEE Symposium on Field-Programmable Custom Computing Machines - Scalable Softcore Vector Processor for Biosequence Applications

Jacob, Arpith, Harris, Brandon, Buhler, Jeremy, Chamberlain, Roger, Cho, Young

Year:

2006

Language:

english

File:

PDF, 122 KB

english, 2006

23

Designing Multiple Simultaneous Seeds for DNA Similarity Search

Sun, Yanni, Buhler, Jeremy

Journal:

Journal of Computational Biology

Year:

2005

Language:

english

File:

PDF, 133 KB

english, 2005

24

Fast, Sensitive Discovery of Conserved Genome-Wide Motifs

Ihuegbu, Nnamdi E., Stormo, Gary D., Buhler, Jeremy

Journal:

Journal of Computational Biology

Year:

2012

Language:

english

File:

PDF, 246 KB

english, 2012

25

Microencapsulated human mesenchymal stem cells decrease liver fibrosis in mice

Meier, Raphael P.H., Mahou, Redouan, Morel, Philippe, Meyer, Jeremy, Montanari, Elisa, Muller, Yannick D., Christofilopoulos, Panayiotis, Wandrey, Christine, Gonelle-Gispert, Carmen, Bühler, Leo H.

Journal:

Journal of Hepatology

Year:

2015

Language:

english

File:

PDF, 1.17 MB

english, 2015

26

A focus on the role of platelets in liver regeneration: do platelet-endothelial cell interactions initiate the regenerative process?

Meyer, Jeremy, Lejmi, Esma, Fontana, Pierre, Morel, Philippe, Gonelle-Gispert, Carmen, Bühler, Léo

Journal:

Journal of Hepatology

Year:

2015

Language:

english

File:

PDF, 2.16 MB

english, 2015

27

[ACM Press the 23rd international conference - Edmonton, AB, Canada (2014.08.24-2014.08.27)] Proceedings of the 23rd international conference on Parallel architectures and compilation - PACT '14 - Improving Performance of Streaming Applications with Filtering and Control Messages

Li, Peng, Buhler, Jeremy

Year:

2014

Language:

english

File:

PDF, 300 KB

english, 2014

28

[ACM Press the 20th annual international conference - Cairns, Queensland, Australia (2006.06.28-2006.07.01)] Proceedings of the 20th annual international conference on Supercomputing - ICS '06 - Accelerator design for protein sequence HMM search

Maddimsetty, Rahul P., Buhler, Jeremy, Chamberlain, Roger D., Franklin, Mark A., Harris, Brandon

Year:

2006

Language:

english

File:

PDF, 500 KB

english, 2006

29

[ACM Press the 22nd ACM symposium - Thira, Santorini, Greece (2010.06.13-2010.06.15)] Proceedings of the 22nd ACM symposium on Parallelism in algorithms and architectures - SPAA '10 - Deadlock avoidance for streaming computations with filtering

Li, Peng, Agrawal, Kunal, Buhler, Jeremy, Chamberlain, Roger D.

Year:

2010

Language:

english

File:

PDF, 408 KB

english, 2010

30

[ACM Press the 17th ACM SIGPLAN symposium - New Orleans, Louisiana, USA (2012.02.25-2012.02.29)] Proceedings of the 17th ACM SIGPLAN symposium on Principles and Practice of Parallel Programming - PPoPP '12 - Efficient deadlock avoidance for streaming computation with filtering

Buhler, Jeremy D., Agrawal, Kunal, Li, Peng, Chamberlain, Roger D.

Year:

2012

Language:

english

File:

PDF, 689 KB

english, 2012

31

[ACM Press the Sixth International Workshop - San Francisco, California (2015.02.07-2015.02.08)] Proceedings of the Sixth International Workshop on Programming Models and Applications for Multicores and Manycores - PMAM '15 - Deadlock-free buffer configuration for stream computing

Li, Peng, Beard, Jonathan, Buhler, Jeremy

Year:

2015

Language:

english

File:

PDF, 569 KB

english, 2015

32

[ACM Press the sixth annual international conference - Washington, DC, USA (2002.04.18-2002.04.21)] Proceedings of the sixth annual international conference on Computational biology - RECOMB '02 - Provably sensitive Indexing strategies for biosequence similarity search

Year:

2002

Language:

english

File:

PDF, 1.73 MB

english, 2002

33

[ACM Press the fifth annual international conference - Montreal, Quebec, Canada (2001.04.22-2001.04.25)] Proceedings of the fifth annual international conference on Computational biology - RECOMB '01 - Finding motifs using random projections

Buhler, Jeremy, Tompa, Martin

Year:

2001

Language:

english

File:

PDF, 144 KB

english, 2001

34

[ACM Press the First ACM International Conference - Niagara Falls, New York (2010.08.02-2010.08.04)] Proceedings of the First ACM International Conference on Bioinformatics and Computational Biology - BCB '10 - Accelerating HMMER on GPUs by implementing hybrid data and task parallelism

Ganesan, Narayan, Chamberlain, Roger D., Buhler, Jeremy, Taufer, Michela

Year:

2010

Language:

english

File:

PDF, 305 KB

english, 2010

35

[ACM Press the 2007 ACM/IEEE conference - Reno, Nevada (2007.11.10-2007.11.16)] Proceedings of the 2007 ACM/IEEE conference on Supercomputing - SC '07 - Application development on hybrid systems

Chamberlain, Roger D., Franklin, Mark A., Tyson, Eric J., Buhler, Jeremy, Gayen, Saurabh, Crowley, Patrick, Buckley, James H.

Year:

2007

Language:

english

File:

PDF, 556 KB

english, 2007

36

A meta‐analysis of extended versus standard lymphadenectomy in patients undergoing pancreatoduodenectomy for pancreatic adenocarcinoma

Orci, Lorenzo A., Meyer, Jeremy, Combescure, Christophe, Bühler, Leo, Berney, Thierry, Morel, Philippe, Toso, Christian

Journal:

Year:

2015

Language:

english

File:

PDF, 406 KB

english, 2015

37

[IEEE 2014 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS) - Hsinchu, Taiwan (2014.12.16-2014.12.19)] 2014 20th IEEE International Conference on Parallel and Distributed Systems (ICPADS) - Orchestrating safe streaming computations with precise control

Li, Peng, Agrawal, Kunal, Buhler, Jeremy, Chamberlain, Roger D.

Year:

2014

Language:

english

File:

PDF, 120 KB

english, 2014

38

The Fox Project

Journal:

XRDS Crossroads The ACM Magazine for Students

Year:

1995

Language:

english

File:

PDF, 85 KB

english, 1995

39

SPIE Proceedings [SPIE SPIE Defense, Security, and Sensing - Orlando, Florida, United States (Monday 25 April 2011)] Modeling and Simulation for Defense Systems and Applications VI - Rolling partial prefix-sums to speedup evaluation of uniform and affine recurrence equations

Ganesan, Narayan, Kelmelis, Eric J., Chamberlin, Roger D., Buhler, Jeremy, Taufer, Michela

Year:

2011

Language:

english

File:

PDF, 585 KB

english, 2011

40

An optimized method for mouse liver sinusoidal endothelial cell isolation

Meyer, Jeremy, Lacotte, Stéphanie, Morel, Philippe, Gonelle-Gispert, Carmen, Bühler, Léo

Journal:

Experimental Cell Research

Year:

2016

Language:

english

File:

PDF, 1.52 MB

english, 2016

41

Effective orifice area and hemodynamic performance of the transcatheter Edwards Sapien 3 prosthesis: short-term and 1-year follow-up

Külling, Mischa, Külling, Jeremy, Wyss, Christophe, Hürlimann, David, Reho, Ivano, Salzberg, Sacha, Bühler, Ines, Noll, Georg, Grünenfelder, Jürg, Corti, Roberto, Biaggi, Patric

Journal:

European Heart Journal - Cardiovascular Imaging

Year:

2017

Language:

english

File:

PDF, 743 KB

english, 2017

42

[IEEE 2017 International Conference on High Performance Computing & Simulation (HPCS) - Genoa, Italy (2017.7.17-2017.7.21)] 2017 International Conference on High Performance Computing & Simulation (HPCS) - MERCATOR: A GPGPU Framework for Irregular Streaming Applications

Cole, Stephen V., Buhler, Jeremy

Year:

2017

Language:

english

File:

PDF, 293 KB

english, 2017

43

Deadlock-free buffer configuration for stream computing

Li, Peng, Beard, Jonathan C, Buhler, Jeremy D

Journal:

International Journal of High Performance Computing Applications

Year:

2017

Language:

english

File:

PDF, 462 KB

english, 2017

44

Systematic review and meta-analysis of thrombocytopenia as a predictor of post-hepatectomy liver failure

Meyer, Jeremy, Balaphas, Alexandre, Combescure, Christophe, Morel, Philippe, Gonelle-Gispert, Carmen, Bühler, Léo

Journal:

Year:

2019

File:

PDF, 794 KB

2019

45

Extracellular vesicles: future diagnostic and therapeutic tools for liver disease and regeneration

Balaphas, Alexandre, Meyer, Jeremy, Sadoul, Rémy, Morel, Philippe, Gonelle‐Gispert, Carmen, Bühler, Leo Hans

Journal:

Liver International

Year:

2019

Language:

english

File:

PDF, 1.54 MB

english, 2019

46

Platelets and Platelet‐Derived Extracellular Vesicles in Liver Physiology and Disease

Balaphas, Alexandre, Meyer, Jeremy, Sadoul, Karin, Fontana, Pierre, Morel, Philippe, Gonelle‐Gispert, Carmen, Bühler, Leo H.

Journal:

Hepatology Communications

Year:

2019

Language:

english

File:

PDF, 398 KB

english, 2019

47

Extracellular vesicles: future diagnostic and therapeutic tools for liver disease and regeneration

Balaphas, Alexandre, Meyer, Jeremy, Sadoul, Rémy, Morel, Philippe, Gonelle‐Gispert, Carmen, Bühler, Leo Hans

Journal:

Liver International

Year:

2019

File:

PDF, 1.54 MB

2019

48

Gangrenous gas necrosis of the spleen: a case report

Meyer, Jeremy, Dupuis, Arnaud, Huttner, Benedikt D., Tihy, Matthieu, Bühler, Léo

Journal:

BMC Infectious Diseases

Year:

2019

Language:

english

File:

PDF, 4.33 MB

english, 2019

49

Platelets Stimulate Liver Sinusoidal Endothelial Cells to Secrete Interleukin-6 During the Early Phase of Liver Regeneration in Mice

Meyer, Jeremy, Balaphas, Alexandre, Perroud, Elodie, Fontana, Pierre, Lacotte, Stéphanie, Joubert, Clotilde, Morel, Philippe, Robson, Simon, Sadoul, Karin, Gonelle-Gispert, Carmen, Bühler, Léo

Journal:

Transplantation Journal

Year:

2018

File:

PDF, 61 KB

2018

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