Jeffrey L. Tilson, Ph.D.
Senior Research Scientist
(919) 445-9657 (o)
jtilson at renci.org
Areas of expertise
1) Parallel processing, development of parallel algorithms and performance models
2) Computational Chemistry: Development
of Quantum chemistry algorithms and methods.
3) Computational Genetics/Biology: Development of methods for genomic prediction of complex traits. Association studies pertaining to complex traits especially LOAD. Development of biological and cross-disciplinary computational workflows.
INSTITUTION AND LOCATION
FIELD OF STUDY
W. Connecticut State University
Michigan State University
Argonne National Laboratory
Theoretical Chemistry & Chemical Dynamics
I have a 24 year published history of applying computational techniques to solve problems in the life and physical sciences usually as a multi-disciplinary and collaborative project. IÕve published mathematical, algorithmic, and software enhancements to the analyses of important effects in molecular chemical physics, molecular physical chemistry, and relativistic induced departures from qualitative chemical intuition. Deep computational workflows that consist of software which coordinates many, usually disparate, resources, to solve specific scientific problems is another aspect of my work. Initially, this included integration of parallel processing with web-and grid-service oriented architectures, to solve select classes of problems on genome-scale data sets. That research evolved to building workflows better able to self-correct problems and most recently to GWAS and genetic prediction pipelines specifically applied to Late Onset AlzheimerÕs Disease.
1995-1999 Assistant Computational Scientist, Mathematics and Computer Science Division (MCS) and Chemistry (joint) Argonne National Laboratory, Argonne, Il
1999-2005 Computational Scientist, Center for Computational Research (CCR), University at Buffalo, SUNY. Buffalo, NY.
2005-2009 Research Scientist, Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC.
2009-present Senior Research Scientist, Renaissance Computing Institute, University of North Carolina, Chapel Hill, NC.
Affiliate Staff Scientist, Pacific Northwest National Laboratory (PNNL), Environmental and Molecular Sciences Laboratory (EMSL), Richland, WA (1995-1999).
Adjunct Faculty, Department of Chemistry, University at Buffalo, SUNY. Buffalo, NY.(1999 2005).
SuperComputing Conference (SC07), HPC EditorsÕ Choice award winner, Bioportal, (2007).
IEEE Bioinformatics and Bioengineering, BIBE (Harvard Medical), Best App Research Manuscript. (2007).
Bioinformatics and Bioengineering (BIBE), IEEE Symposium, reviewer (2009).
NSF Strategic Technologies for Cyber Infrastructure (STCI), panel, (2009).
Chemical Physics Letters, reviewer, (2009).
U.S. Department of Energy. High Performance Computational Chemistry proposal reviewer (2013).
Bio- and Medical Informatics and Cybernetics (BMIC), reviewer, (2010- 2013).
Theoretical Chemistry Accounts, reviewer, (2014).
SuperComputing Conference (SC15), Networking and architecture, reviewer, (2015).
"Nanotechnologies and High Performance Computing in Education and Research", CeNAT and the SC08 Education program. Hosted by Earth University, Gu ‡ cimo, Lim — 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.
Barber, R. C.; Phillips, N. R.; Tilson, J. L.; Huebinger, R. M.; Shewale, S. J.; Koenig, J. L.; Mitchel, J. S.; OÕBryant, S. E.; Waring, S. C.; Diaz-Arrastia, R.; Chasse, S.; Wilhelmsen, K. C., Can Genetic Analysis of Putative Blood AlzheimerÕs Disease Biomarkers Lead to Identification of Susceptibility Loci? PLoS One 2015, 10 (12), e0142360
Baldin, I.; Ruth, P.; Xin, Y.; Mandel, A.; Chase, J.; Tilson, J. L.; Prasad, S., Visions of a Future Internet: The ExoGENI Example. University of North Carolina at Chapel Hill, Chapel Hill, NC, USA, 2013; Vol. 1.
Ermler, W. C.; Tilson, J. L., Generally contracted valence–core/valence basis sets for use with relativistic effective core potentials and spin–orbit coupling operators. Comp. Theor. Chem. 2012, 1002 (0), 24-30.
Rendon, G.; Kantorovitz, R.; Tilson, J. L.; Jakobsson, E., Identifying bacterial and archaeal homologs of pentameric ligand-gated ion channel (pLGIC) family using domain-based and alignment-based approaches. Channels (Austin, Tex) 2011, 5 (4), 325-344.
Rendon, G.; Ger, M.-F.; Kantorovitz, R.; Natarjan, S.; Tilson, J.; Jakobsson, E., Understanding the "Horizontal Dimension" of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains. The Journal of Computer Science and Technology 2010, 25 (1), 82-94.
Tilson, J. L.; Rendon, G.; Ger, M.-F.; Jakobsson, E. Algorithms and Performance Measurements for MotifNetwork Analysis Programs; TG-09-02; Renaissance Computing Institute (RENCI): Chapel Hill, NC, 2009.
Tilson, J. L.; Kandaswamy, G.; Rendon, G.; Jakobsson, E., MotifNetwork: High Throughput Determination of Evolutionary Domain Networks. In International Conference on Bioinformatics & Computational Biology, BIOCOMP 2009, (BIOCOMP), July 13-16, 2009, Las Vegas Nevada, USA, 2 Volumes BIOCOMP, 2009; pp 221-227.
Tilson, J. L.; Reed, M. S. C.; Fowler, R. J., Workflows for performance evaluation and tuning. In IEEE International Conference on Cluster Computing CCGRID 2008, Institute of Electrical and Electronics Engineers Inc: Tsukuba, JP, 2008; pp 79-88.
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.
Tilson, J. L.; Blatecky, A.; Rendon, G.; Ger, M.-F.; Jakobsson, E., MotifNetwork: Genome-Wide Domain Analysis using Grid-enabled Workflows. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, (BIBE07) October 14-17, 2007, Harvard Medical School, Boston, MA, USA, 2007; pp 872-879.
Tilson, J. L.; Rendon, G.; Ger, M.-F.; Jakobsson, E., 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. In Proceedings of the 7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE 2007, (BIBE07) October 14-17, 2007, Harvard Medical School, Boston, MA, USA, 2007; pp 620-627.
Wierzchowski, S. J.; Fang, Z. H.; Kofke, D. A.; Tilson, J. L., Three-body effects in hydrogen fluoride: survey of potential energy surfaces. Mol. Phys. 2006, 104 (4), 503-513.
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.
Ruckenstein, E.; Shulgin, I. L.; Tilson, J. L., Treatment of Dilute Clusters of Methanol and Water by ab Initio Quantum Mechanical Calculations. The Journal of Physical Chemistry A 2005, 109 (5), 807-815.
Ruckenstein, E.; Shulgin, I. L.; Tilson, J. L., The Structure of Dilute Clusters of Methane and Water by ab Initio Quantum Mechanical Calculations. The Journal of Physical Chemistry A 2003, 107 (13), 2289-2295.
Naleway, C.; Seth, M.; Shepard, R.; Wagner, A. F.; Tilson, J. L.; Ermler, W. C.; Brozell, S. R., An ab initio study of the ionization potentials and f--f spectroscopy of europium atoms and ions. J. Chem. Phys. 2002, 116 (13), 5481-5493.
Tilson, J. L.; Shepard, R.; Naleway, C.; Wagner, A. F.; Ermler, W. C., Ab initio determination of americium ionization potentials. J. Chem. Phys. 2000, 112 (5), 2292-2300.
Tilson, J. L.; Minkoff, M.; Wagner, A. F.; Shepard, R.; Sutton, P.; Harrison, R. J.; Kendall, R. A.; Wong, A. T., High-Performance Computational Chemistry: Hartree-Fock Electronic Structure Calculations on Massively Parallel Processors. Int. J. High. Perform. C. 1999, 13 (4), 291-302.
Asher, R. L.; Appelman, E. H.; Tilson, J. L.; Litorja, M.; Berkowitz, J.; Ruscic, B., A photoionization study of trifluoromethanol, CF3OH, trifluoromethyl hypofluorite, CF3OF, and trifluoromethyl hypochlorite, CF3OCl. J. Chem. Phys. 1997, 106 (22), 9111-9121.
Kumaran, S. S.; Lim, K. P.; Michael, J. V.; Tilson, J. L.; Suslensky, A.; Lifshitz, A., Isomerization and Decomposition of Chloromethylacetylene. Isr. J. Chem. 1996, 36 (3), 223-232.
Harrison, R. J.; Guest, M. F.; Kendall, R. A.; Bernholdt, D. E.; Wong, A. T.; Stave, M.; Anchell, J. L.; Hess, A. C.; Littlefield, R. J.; Fann, G. L.; Nieplocha, J.; Thomas, G. S.; Elwood, D.; Tilson, J. L.; Shepard, R. L.; Wagner, A. F.; Foster, I. T.; Lusk, E.; Stevens, R., Toward high-performance computational chemistry: II. A scalable self-consistent field program. J. Comput. Chem. 1996, 17 (1), 124-132.
Foster, I. T.; Tilson, J. L.; Wagner, A. F.; Shepard, R. L.; Harrison, R. J.; Kendall, R. A.; Littlefield, R. J., Toward high-performance computational chemistry: I. Scalable Fock matrix construction algorithms. J. Comput. Chem. 1996, 17 (1), 109-123.
Tilson, J. L.; Harrison, J. F., Electronic and geometric structures of various products of the scandium+ + water reaction. J. Phys. Chem. 1991, 95 (13), 5097-5103.
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.
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.
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.