Eric Jakobsson

Description

Address

  • 3261 Beckman Institute
  • 405 North Mathews Avenue
  • Urbana, Illinois 61801

Biography

Eric Jakobsson's home department is Molecular and Integrative Physiology. He also has appointments in the Center for Biophysics and Computational Biology, the Biochemistry Department, the Bioengineering Department, the Neuroscience Program, and the National Center for Supercomputing Applications. He is currently on leave from the University of Illinois for teaching and administrative purposes in order to serve as the Director of the Center for Bioinformatics and Computational Biology at the National Institute of General Medical Sciences and the Chair of the Biomedical Information Science and Technology Initiative Consortium at the National Institutes of Health, in Bethesda, Maryland. However, he is maintaining his research laboratory in the Beckman Institute through weekly commuting.

Honors

Elected Fellow of the American Physical Society (1994); U of I Advising Award; Tau Beta Pi Engineering Academic Honorary Society.

Research

Jakobsson's Beckman Institute research areas include: Computer-aided design of components for nanodevices, structure of biological membranes, structure-function relationships in biological and synthetic ion channels, computer-aided drug research, comparative genomics of microbes, use of technology to introduce quantitative approaches to biology education.

Publications

  • 2016
    • Barati-Farimani, A.; Tajkhorshid, E.; Aluru, N.; Jakobsson, E., Behavior of Water in 3-D Confinement: Implications for Macromolecular Function. Biophysical Journal 2016, 110, (3), 341a-341a.
    • Farimani, A. B.; Aluru, N. R.; Tajkhorshid, E.; Jakobsson, E., Computational Approach to Designing Antibody for Ebola Virus. Biophysical Journal 2016, 110, (3), 537a-537a.
  • 2015
    • Sun, J.; Jakobsson, E.; Wang, Y.; Jeffrey Brinker, C. J., Nanoporous Silica-Based Protocells at Multiple Scales for Designs of Life and Nanomedicine. Life 2015, 5, (1), 214-229.

    • Kim, T. J.; Joo, C.; Seong, J.; Vafabakhsh, R.; Botvinick, E. L.; Berns, M. W.; Palmer, A. E.; Wang, N.; Ha, T.; Jakobsson, E.; Sun, J.; Wang, Y., Distinct Mechanisms Regulating Mechanical Force-Induced Ca2+ Signals at the Plasma Membrane and the ER in Human MSCs. Elife 2015, 4, DOI:ARTN e04876 DOI:10.7554/eLife.04876.

  • 2014
    • Fogarty, J. C.; Chiu, S. W.; Kirby, P.; Jakobsson, E.; Pandit, S. A., Automated Optimization of Water-Water Interaction Parameters for a Coarse-Grained Model. Journal of Physical Chemistry B 2014, 118, (6), 1603-1611, DOI: 10.1021/jp409545x.

  • 2013
    • Li, Y. H.; Liu, H.; Rata, I.; Jakobsson, E., Building a Knowledge-Based Statistical Potential by Capturing High-Order Inter-Residue Interactions and Its Applications in Protein Secondary Structure Assessment. Journal of Chemical Information and Modeling 2013, 53, (2), 500-508.

    • Zhou, H.; Jakobsson, E., Predicting Protein-Protein Interaction by the Mirrortree Method: Possibilities and Limitations. Plos One 2013, 8, (12), DOI: 10.1371/journal.pone.0081100.

  • 2011
    • Zhao, G. J.; Subbaiah, P. V.; Chiu, S. W.; Jakobsson, E.; Scott, H. L., Conjugated double bonds in lipid bilayers: A molecular dynamics simulation study. Chemistry and Physics of Lipids 2011, 164, (3), 251-257. 

    • Li, Y. H.; Rata, I.; Jakobsson, E., Sampling Multiple Scoring Functions Can Improve Protein Loop Structure Prediction Accuracy. Journal of Chemical Information and Modeling 2011, 51, (7), 1656-1666.

    • Rendon, G.; Kantorovitz, M. 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 2011, 5, (4), 325-344.

    • Zhao, G. J.; Subbaiah, P. V.; Mintzer, E.; Chiu, S. W.; Jakobsson, E.; Scott, H. L., Molecular Dynamic Simulation Study of Cholesterol and Conjugated Double Bonds in Lipid Bilayers. Chemistry and Physics of Lipids 2011, 164, (8), 811-818.

  • 2010
    • Rendon, G.; Ger, M. F.; Kantorovitz, R.; Natarajan, S.; Tilson, J.; Jakobsson, E., Understanding the "Horizontal Dimension" of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains. Journal of Computer Science and Technology 2010, 25, (1), 82-94.

    • Rata, I. A.; Li, Y. H.; Jakobsson, E., Backbone Statistical Potential from Local Sequence-Structure Interactions in Protein Loops. Journal of Physical Chemistry B 2010, 114, (5), 1859-1869.

    • Ger, M. F.; Rendon, G.; Tilson, J. L.; Jakobsson, E., Domain-Based Identification and Analysis of Glutamate Receptor Ion Channels and Their Relatives in Prokaryotes. PLOS One 2010, 5, (10).

    • Lee, K. I.; Toghraee, R.; Jakobsson, E.; Ravaioli, U., A Study of Brownian Dynamics Simulation for Ion Transport Through a Transmembrane Pore with a Molecular Adapter. Journal of Computational and Theoretical Nanoscience 2010, 7, (12), 2547-2554.

    • Li, Y. H.; Rata, I.; Chiu, S. W.; Jakobsson, E., Improving predicted protein loop structure ranking using a Pareto-optimality consensus method. BMC Structural Biology 2010, 10.

    • Natarajan, S.; Mashl, J.; Jakobsson, E., Evolutionary coupling in the K(V)1.2-beta(2) complex. Channels 2010, 4, (5), 355-374.

    • Toghraee, R.; Lee, K. I.; Papke, D.; Chiu, S. W.; Jakobsson, E.; Ravaioli, U., Simulation of Ion Conduction in alpha-Hemolysin Nanopores with Covalently Attached beta-Cyclodextrin Based on Boltzmann Transport Monte Carlo Model. Journal of Computational and Theoretical Nanoscience 2010, 7, (12), 2555-2567. 

    • Chiu, S. W.; Scott, H. L.; Jakobsson, E., A Coarse-Grained Model Based on Morse Potential for Water and n-Alkanes. Journal of Chemical Theory and Computation 2010, 6, (3), 851-863.

    • Falkenberg, C. V.; Jakobsson, E., A Biophysical Model for Integration of Electrical, Osmotic, and pH Regulation in the Human Bronchial Epithelium. Biophysical Journal 2010, 98, (8), 1476-1485.

  • 2009
    • Jakobsson, E., Biology: Using a Ubiquitous Knowledge Environment to Integrate Teaching, Learning, and Research in Biology and Chemistry. In Ubiquitous Learning, Cope, B.; Kalantzis, M., Eds. University of Illinois Press: Champaign, IL, 2009; pp 216-229

    • Jakobsson, E., Biology: Using a Ubiquitous Knowledge Environment to Integrate Teaching, Learning, and Research in Biology and Chemistry. In Ubiquitous Learning, Cope, B.; Kalantzis, M., Eds. University of Illinois Press: Champaign, IL, 2009; pp 216-229

    • Chiu, S. W.; Pandit, S. A.; Scott, H. L.; Jakobsson, E., An Improved United Atom Force Field for Simulation of Mixed Lipid Bilayers. Journal of Physical Chemistry B 2009, 113, (9), 2748-2763.

    • Natarajan, S.; Jakobsson, E., Functional equivalency inferred from "authoritative sources" in networks of homologous proteins. Public Library of Science 2009, 4, (6), e5898.

  • 2008
    • Pandit, S. A.; Chin, S. W.; Jakobsson, E.; Scott, H. L., Atomistic and mean field simulations of lateral organization in membranes. In Computational Modeling of Membrane Bilayers, Elsevier Academic Press Inc: San Diego, 2008; Vol. 60, pp 281-312.

    • Pandit, S. A.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Cholesterol packing around lipids with saturated and unsaturated chains: A simulation study. Langmuir 2008, 24, (13), 6858-6865.

    • Sendlinger, S. C.; DeCoste, D. J.; Dunning, T. H.; Dummitt, D. A.; Jakobsson, E.; Mattson, D. R.; Wiziecki, E. N., Transforming chemistry education through computational science. Computing in Science & Engineering 2008, 10, (5), 34-39.

    • Mashl, R. J.; Jakobsson, E., End-point targeted molecular dynamics: Large-scale conformational changes in potassium channels. Biophysical Journal 2008, 94, (11), 4307-4319.

    • Pandit, S. A.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Cholesterol packing around lipids with saturated and unsaturated chains: A simulation study. Langmuir 2008, 24, 6858-6865.

  • 2007
    • Tilson, J. L.; Rendon, G.; Ger, M. F.; Jakobbson, 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, 2007.

    • Varma, S.; Jakobsson, E., How does the C2 domain "calcium trigger" work? Insights from molecular dynamics simulations. Biophysical Journal 2007, 595A-595A.

    • Varma, S.; Jakobsson, E., The cPLA(2) C2 alpha domain in solution: Structure and dynamics of its Ca2+-activated and cation-free states. Biophysical Journal 2007, 92, (3), 966-976.

    • Pandit, S.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Molecular dynamics simulation of a dioleylphosphatidylserine lipid bilayer. Biophysical Journal 2007, 548A-548A.

    • Pandit, S. A.; Chiu, S. W.; Jakobsson, E.; Grama, A.; Scott, H. L., Cholesterol surrogates: A comparison of cholesterol and 16 : 0 ceramide in POPC Bilayers. Biophysical Journal 2007, 92, (3), 920-927.

    • Pandit, S. A.; Khelashvili, G.; Jakobsson, E.; Grama, A.; Scott, H. L., Lateral organization in lipid-cholesterol mixed bilayers. Biophysical Journal 2007, 92, (2), 440-447.

    • Mashl, R. J.; Jakobsson, E., Protonation states in potassium channels. Biophysical Journal 2007, 267A-267A.

  • 2006
    • Tseng, T. T.; McMahon, A. M.; Zahm, R. J.; Pacold, M. E.; Jakobsson, E., Calcium channel auxiliary subunits. Journal of Molecular Microbiology and Biotechnology 2006, 11, (6), 326-344.

  • 2004
    • Varma S.; Jakobsson E., Ionization States of Residues in OmpF and Mutants: Effects of Dielectric Constant and Interactions Between Residue. Biophysics Journal 2004, 86, (2), 690-704.

  • 2003
    • Chiu S.W., Vasudevan S., Jakobsson E., Mashl R.J., and Scott H.L. (2003), "Structure of Sphingomyelin Bilayers: A Simulation Study," Biophysics Journal 85/6, pp. 3624-3635.

    • Shealy, R.T., Murphy, A.D., Ramarathnam, R., Jakobsson, E., and Subramaniam, S. (2003), "Sequence-function Analysis of the K+-selective Family of Ion Channels Using a Comprehensive Alignment and the KcsA Channel Structure," Biophysics Journal, 84/5, pp. 2929-2942.

    • Joseph, S., Mashl, R.J., Jakobsson, E., and Aluru, N.R. (2003), "Electrolytic Transport in Modified Carbon Nanotubes," Nano Lettters (Communication), 3/10, pp. 1399-1403.

    • Mashl, R.J., Joseph, S., Aluru, N.R., and Jakobsson, E. (2003), "Anomalously Immobilized Water: A New Water Phase Induced by Confinement in Nanotubes," Nano Letters (Communication), 3/5, pp. 589-592.

Press

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