Email: jtilson@renci.org
Phone: 919-445-9657
More Info: http://www.renci.org/~jtilson/profile.html
Area of Expertise: parallel processing, parallel algorithms, computational chemistry, computational biology
Area of expertise
Parallel processing, development of parallel algorithms and performance models
Computational Chemistry: Development of chemistry algorithms and methods.
Computational Biology: Development of biological and multi-domain workflows.
Projects
Biophysics: Development of biological workflows
performance evaluation: Analysis of application scalability on large HPC systems
Select MotifNetwork computed domain maps from the MotifNetwork project are available here
Older and less maintained MotifNetwork information may be found here
Background
Computational Scientist: Center For Computational Research (SUNY-Buffalo)(1999-2005)
Argonne National Laboratory, HPC and parallel processing (1992-1999).
Michigan State University. Ph.D. Physical Chemistry (1992).
Recent Awards
Best Application Research Paper Award, MotifNetwork: A Grid-Enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for study of phylogeny, protein interactions, and intraspecies variation, Jeffrey L. Tilson, Gloria Rendon, Mao-Feng Ger, and Eric Jakobsson. IEEE BIBE at Harvard Medical. Boston, MA, Oct 15, 2007.
Team member on the work receiving the GRIDtoday Readers Choice Award for the RENCI Bioportal (2006)
Tutorials/Education
“Nanotechnologies and High Performance Computing in Education and Research”, CeNAT and the SC08 Education program. Hosted by Earth University, Gu á cimo, Lim ó n, Costa Rica.
“RENCI Summer Institute 2007,” S. McLean, J. Shelton-Murphy, J. L. Tilson, N. Nicely, E. Scott, D. Bedard, T. Ford, (RENCI) and B. Gotwals, G. Gabrielli, G. A. Stefan (NCSSM).
“Gateway to the TeraGrid for Bio-Scientists: A Tutorial. What does it do?” How is it used in course curricula? How was it constructed?, J. McGee, J. L. Tilson, S. McLean, TeraGrid 2007, Madison, WI, June, 2007.
“Bridging Teaching, Learning, and Education in Grid-enabled Bioinformatics,” G. Rendon, S. McLean, J. R. Mashl, M. A. Miller, N. Nicely, B. Southey, J. Tenegra, J. L. Tilson, and E. Jakobsson, TeraGrid 2007, Madison, WI, June, 2007.
“RENCI: Biology and Biomedical Science Gateway,” S. McLean, M. Rynge, J. L. Tilson, TeraGrid 2006, Indianapolis, IN, June, 2006.
Posters
Shreedhar Natarajan, Gloria Rendon, Jeffrey Tilson, Mao-Feng Ger, Eric Jakobsson, “Domain-centric characterization and analysis of protein sequences,” International Society for Computational Biology, ISMB, 2008, Toronto, ON, CA July 19-23.
Xiaojun Guan, Jeffrey Tilson, Dennis Simpson, Gloria Rendon, Eric Jakobsson, Jefferson Heard, Dave Bowman, William Kaufman, “Merging protein interaction networks with protein motif analyses for biological discovery,” International Society for Computational Biology, ISMB, 2008, Toronto, ON, CA July 19-23.
Jeffrey L. Tilson, Walter C. Ermler, Paul S. Julienne, “Electronic Structure Calculations using a Parallel Spin-Orbit Configuration Interation Code,” Teragrid’08, Las Vegas, NV, June 9-13, 2008.
Gloria Rendon, Jeffrey L. Tilson, Mao-Feng Ger, Eric Jakobsson, “Finding prokaryotic ion channels,” American Chemical Society (ACS’07), Annual Meeting, Boston, MA 2007.
Jeffrey L. Tilson, Gloria Rendon, and Eric Jakobsson, “MotifNetwork: A Grid-enabled Workflow for High-throughput Domain-centered Analysis of Biological Sequences”, Pacific Rim Application and Grid Middleware Assembly (PRAGMA13) Workshop. NCSA, Sept, 2007.
Xiaojun Guan, Dave Bowman, Jeffrey L. Tilson, Dennis Simpson, Gloria Rendon, Eric Jakobsson, William Kaufman, “Merging protein interaction networks with protein motif analysis for biological discovery”, Determinants of genome stability in human disease, Chapel Hill, NC, October 2007.
Publications
M-F Ger, G. Rendon, J.L. Tilson, E. Jakobsson, “Domain-Based Identification and Analysis of Glutamate Receptor Ion Channels and their relatives in Prokaryotes” (submitted)
G. Rendon, J.L. Tilson, R.J. Mashl, E. Jakobsson, “Identifying prokaryotic counterparts of HCN and CNG channels by use of an evolutionary domain network”(submitted)
G. Rendon, J.L. Tilson, R. Kantorovitz, E. Jakobsson, “40 likely prokaryotic homologues of the cys-loop ligand ion channel family. On using a combination of computational tools and data mining techniques to improve the efficacy of the search” (submitted)
Jeffrey L. Tilson, Gloria Rendon, and Eric Jakobsson. Algorithms and Performance measurements for MotifNetwork analysis programs, Technical Report TR-09-02, RENCI, North Carolina, July 2009.
J.L. Tilson, G. Rendon, E. Jakobsson, “MotifNetwork: High throughput determination of Evolutionary Domain Network” Proceedings of the 2009 International Conference on Bioinformatics and Computational Biology (BIOCOMP’09), July 13-16, 2009.
Jeffrey L. Tilson, Mark S.C. Reed, and Robert J. Fowler, “Workflows for Performance Evaluation and Tuning,” Proceedings of the 7th IEEE International Conference on Cluster Computing, 2008, CLUSTER 2008, Tsukuba, Japan, pg. 8.
Jeffrey L. Tilson, Alan Blatecky, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson, “MotifNetwork: Genome-Wide Domain Analysis using Grid-enabled Workflows,” Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on 14-17 Oct. 2007 Page(s):872-879.
Jeffrey L. Tilson, Gloria Rendon, Mao-Feng Ger, Eric Jakobsson, “MotifNetwork: A Grid-enabled Workflow for High-throughput Domain Analysis of Biological Sequences: Implications for annotation and study of phylogeny, protein interactions, and intraspecies variation,” Bioinformatics and Bioengineering, 2007. BIBE 2007. Proceedings of the 7th IEEE International Conference on 14-17 Oct. 2007 Page(s):620-627.
L. Ramakrishnan, M. S.C Reed, J. L. Tilson, D. A. Reed, “Grid Portals for Bioinformatics,” Second International Workshop on Grid Computing Environments (GCE), Workshop at SC|06, Tampa, Florida (2006).
S. J. Wierzchowski, Z. H. Fang, D. A. Kofke and J. L. Tilson, “Three-body effects in hydrogen fluoride: survey of potential energy surfaces,” Mol Phys 104, 503, (2006)
E. Ruckenstein, E. Shulgin, J. L. Tilson, “Treatment of Dilute Clusters of Methanol and Water by ab Initio Quantum Mechanical Calculations,” J. Phys. Chem. A. 109(5); 807-815. (2005)
J. L. Tilson, C. Naleway, M. Seth, R. Shepard, A. F. Wagner, and W. C. Ermler, “Ab initio study of AmCl+: f-f spectroscopy and chemical binding,” J. Chem. Phys. 121, 5661 (2004)
E. Ruckenstein, I. L. Shulgin, J. L. Tilson, “The Structure of Dilute Clusters of Methane and Water by ab Initio Quantum Mechanical Calculations,” J. Phys. Chem. A. 107(13); 2289-2295. (2003)
J. L. Tilson, C. Naleway, M. Seth, R. Shepard, A. F. Wagner, and W. C. Ermler, “An ab initio study of the f-f spectroscopy of americium +3,” J. Chem. Phys. 116, 5494 (2002)
C. Naleway, M. Seth, R. Shepard, A. F. Wagner, J. L. Tilson, W. C. Ermler, and S. R. Brozell, “An ab initio study of the ionization potentials and f-f spectroscopy of europium atoms and ions,” 116, 5481 (2002)
R. Shepard, A. F. Wagner, M. Minkoff, and J. L. Tilson, “The Subspace Projected Approximate Matrix (SPAM) Modification of the Davidson Method,” J. Comp. Phys. 172, 472-514 (2001)
J. L. Tilson, R. Shepard, C. Naleway, A. F. Wagner, and W. C. Ermler, “Ab initio determination of americium ionization potentials,” J. Chem. Phys. 112, 2292 (2000).
J. L. Tilson, W. C. Ermler, R. Pitzer, “Parallel Spin-Orbit Configuration Interaction,” Computer Physics Communications, 128, 128-138. (2000).
J. L. Tilson, M. Minkoff, A. F. Wagner, R. Shepard, P. Sutton, R. J. Harrison, R. A. Kendall, A. T. Wong, “High-Performance Computational Chemistry: Hartree-Fock Electronic Structure Calculations on Massively Parallel Processors,” Int. J. High Perf. Comp. App. 13, 291 (1999).
M. Celino, F. Cleri, L. Columbo, M. Rosati, J. Tilson, “Large Scale Atomistic Simulations using the Tight Binding Approach,” Mat. Res. Soc. Symp. Proc. 491, 481-488 (1998)
R. L. Asher, E. H. Appelman, J. L. Tilson, M. Litorja, J. Berkowitz, and B. Ruscic, “A photoionization study of trifluoromethanol, CF3OH, trifluoromethyl hypofluorite, CF3OF, and trifluoromethyl hypochlorite, CF3OCl,” J. Chem. Phys. 106, 9111 (1997)
I. T. Foster, J. L. Tilson, A. F. Wagner, R. Shepard, R. J. Harrison, R. A. Kendall, R. J. Littlefield, “Toward High-Performance Computational Chemistry: I. Scalable Fock Matrix Construction Algorithms,” J. Comp. Chem. 17, 109-123 (1996).
R. J. Harrison, M. F. Guest, R. A. Kendall, D. E. Bernholdt, A. T. Wong, M. Stave, J. L. Ancell, A. C. Hess, R. J. Littlefield, G. L. Fann, J. Nieplocha, G. S. Thomas, D. Elwood, J. L. Tilson, R. L. Shepard, A. F. Wagner, I. T. Foster, E. Lusk, R. Stevens, “Toward High-Performance Computational Chemistry: II. A Scalable Self-Consistent Field Program,” J. Comp. Chem. 17, 124-132 (1996).
S. Kumaran, K. P. Lee, J. V. Michael, J. L. Tilson, A. Suslensky, A. Lifshitz, “Isomerization and Decomposition of Chloromethylacetylene,” Isreal J. Chem, 36, 223-232 (1996).
J. L. Tilson, “Massively Parallel SCF Calculations,” I&EC Research, 34 4161-4165 (1995).
I. T. Foster, J. L. Tilson, A. F. Wagner, R. Shepard, R. J. Harrison, R. A. Kendall, R. J. Littlefield, “Scalable Algorithms for Computational Chemistry,” Parallel Computing Newsletter, CRPC, 2(4) (1994).
J. L. Tilson, J. F. Harrison, “Electronic and Geometric Structures of ScSe+ and ScSeH,” J. Phys. Chem, 98 6474-6480 (1994).
J. L. Tilson, J. F. Harrison, “Electronic and Geometric Structures of various products of the scandium+ + hydrogen sulfide reaction,” J. Phys. Chem, 96 1667-1674 (1992).
J. L. Tilson, J. F. Harrison, “Electronic and Geometric Structures of various products of the scandium+ + water reaction,” J. Phys. Chem, 95 5097-5103 (1991).
RENCI Technical Reports (TR series began in 2008)
Jeffrey L. Tilson, Mark S.C. Reed, and Robert J. Fowler, “Workflows for Performance Evaluation and Tuning.” Technical Report TR-08-03, RENCI, North Carolina, May 2008.
Miscellany
Chromium Chloride Density Difference Contours, A. Alvarado-Swaisgood, K. Baumruck, D. Washecheck, Amoco Corporation, J. Tilson, J. Harrison, Michigan State University, M. Krogh and J. Thingvold, NCSA, University of Illinois at Urbana-Champaign. “Science in Depth,” IEEE Computer Graphics and Applications, vol.11, no.2, pp. 10-12, Mar/Apr, 1991.
- Exhibition: Virtual Photography PHSColograms, Gahlberg Gallery: The Arts Center, College of DuPage, DuPage, IL, November 25, 1994-December 20, 1994 Sony Gallery, Chicago, IL, February 4, 1993 – May 28, 1993 IMAGES DU FUTUR ’92, Montréal, Canada, May 15, 1992 – September 20, 1992 Science in Depth traveling show: ACM SIGGRAPH, Chicago, IL, July 1992 – August 1992 NASA Ames Research Center, Moffett Field, CA, December 1991-July 1992 Computer Museum, Boston, MA, February-September 1991 Museum of Science and Industry, Chicago, IL, November 1990-January 1991 Feature, New York, NY, December 4, 1990
- Literature:Virtual Photography PHSColograms, Gahlberg Gallery: The Arts Center, College of DuPage catalogue Henderson, Harold, “Art or Science?” (article), Chicago Reader, August 16, 1991, pp. 1-21 Beyond 2000, international syndication, Sydney, Australia, Summer 1991 (video) Csuri, Charles A., “Science in Depth” (article), IEEE Computer Graphics and applications, March 1991, pp. 10-12 Science in Depth catalogue, NASA Ames, Computer Musuem & Museum of Science and Industry NASA Ames Science in Depth video documentary CNN, Cable Network News, “Science and Technology” international syndication, 1990 (video) Wild Chicago, local syndication 1990 (video)
Data Sonification and Sound Visualization, H. G. Kaper, E. Wiebel, S. Tipei, Computing in Science and Engineering, 1(4), 48-58 (1999). Example of the sonification of chemistry data.
Density Difference Contours of the Uranium Atom, J. L. Tilson, D. Borland, E. Knisley, J. Shelton. Renaissance Computing Institute, 2008.
- Description: This image is from an animation being created for the RENCI hemispherical dome. It shows the changes in electronic structure when incorporating approximations to relativity into the calculation. Inclusion of relativity shifts some of the electronic density from the Blue regions to the Red.
David Borland, Eric Knisley, and Jeffrey L. Tilson, “A Visual Depiction of the Influence of Relativistic Effects on the Electronic Structure of Uranium,” Teragrid’08, Visualization Gallery, Las Vegas, NV, June 9-13, 2008.
Presentations (this section is under development)
Electronic Structure Calculations: The Heavy Elements, Jeffrey L. Tilson, Walter C. Ermler, and Paul Julienne, Supercomputing 2008 conference, RENCI booth presentation, 2008, Austin, TX.
J.L. Tilson, G. Rendon, E. Jakobsson, “MotifNetwork: High throughput determination of Evolutionary Domain Network” 2009 International Conference on Bioinformatics and Computational Biology, July 13-16, 2009
MotifNetwork: An Environment For High-Throughout Domain Analysis, Jeffrey L. Tilson, Gloria Rendon, Eric Jakobsson, Supercomputing 2008 conference, RENCI booth presentation, 2008, Austin, TX.
High-throughput sialylmotif network analysis in the glycosyltransferase protein family Arun K. Datta, Jeffrey L. Tilson, Gloria Rendon, Eric Jakobsson, Annual Meeting of the Society for Glycobiology, Nov 12-15, 2008 Fort Worth, TX.
Computational Science at the Renaissance Computing Center (RENCI), J.L. Tilson, to the Virtual Lung Project (VLP). April 22, 2008. VLP information may be found here. A PDF version of the presentation ishere.
