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ORCIDJesús A. Izaguirre
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2010 – 2019
- 2014
[j18]Badi Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain
, Jesús A. Izaguirre:
AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble. J. Chem. Inf. Model. 54(10): 3033-3043 (2014)- 2013
- [c19]Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesús A. Izaguirre, Scott J. Emrich, Douglas Thain:
Case Studies in Designing Elastic Applications. CCGRID 2013: 466-473 - 2012
- [c18]Badi Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesús A. Izaguirre:
Folding proteins at 500 ns/hour with Work Queue. eScience 2012: 1-8 - 2011
- [c17]Dinesh Rajan, Anthony Canino, Jesús A. Izaguirre, Douglas Thain:
Converting a High Performance Application to an Elastic Cloud Application. CloudCom 2011: 383-390 - 2010
- [j17]Trevor M. Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre:
MDLab: A molecular dynamics simulation prototyping environment. J. Comput. Chem. 31(7): 1345-1356 (2010) - [j16]Faruck Morcos, Santanu Chatterjee, Christopher L. McClendon, Paul R. Brenner, Roberto López-Rendón, John Zintsmaster, Mária Ercsey-Ravasz, Christopher R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng, Jesús A. Izaguirre:
Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW. PLoS Comput. Biol. 6(12) (2010) - [j15]Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre:
Belief propagation estimation of protein and domain interactions using the sum-product algorithm. IEEE Trans. Inf. Theory 56(2): 742-755 (2010) - [c16]Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre:
Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus. Pacific Symposium on Biocomputing 2010: 157-165 - [c15]Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande:
Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. Pacific Symposium on Biocomputing 2010: 240-251
2000 – 2009
- 2009
- [c14]Faruck Morcos, Charles Lamanna, Nitesh V. Chawla, Jesús A. Izaguirre:
Determination of Specificity Residues in Two Component Systems using Graphlets. BIOCOMP 2009: 860-866 - 2008
- [j14]Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. Bioinform. 24(19): 2265-2266 (2008) - [j13]Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre:
Addendum. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. Bioinform. 24(23): 2805 (2008) - [j12]Justin M. Wozniak, Paul R. Brenner, Douglas Thain, Aaron Striegel, Jesús A. Izaguirre:
Making the best of a bad situation: Prioritized storage management in GEMS. Future Gener. Comput. Syst. 24(1): 10-16 (2008) - [j11]Paul R. Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeffrey W. Peng, Jesús A. Izaguirre:
Biomolecular committor probability calculation enabled by processing in network storage. Parallel Comput. 34(11): 652-660 (2008) - 2007
- [j10]Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber:
A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Comput. Phys. Commun. 176(11-12): 670-681 (2007) - [j9]Trevor M. Cickovski, Kedar Aras, Maciej Swat, Roeland Merks, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre:
From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Comput. Sci. Eng. 9(4): 50-60 (2007) - [j8]Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre:
Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. IEEE ACM Trans. Comput. Biol. Bioinform. 4(1): 78-87 (2007) - [c13]Trevor M. Cickovski, Chris Sweet, Jesús A. Izaguirre:
MDL, A Domain-Specific Language for Molecular Dynamics. Annual Simulation Symposium 2007: 256-266 - [c12]Paul R. Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeffrey W. Peng, Jesús A. Izaguirre:
Biomolecular Path Sampling Enabled by Processing in Network Storage. IPDPS 2007: 1-6 - 2005
- [j7]Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre:
MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms. J. Comput. Chem. 26(10): 1021-1031 (2005) - [j6]Jesús A. Izaguirre, Scott S. Hampton, Thierry Matthey:
Parallel multigrid summation for the N-body problem. J. Parallel Distributed Comput. 65(8): 949-962 (2005) - [j5]Trevor M. Cickovski, Chengbang Huang, Rajiv Chaturvedi, Tilmann Glimm, H. George E. Hentschel, Mark S. Alber, James A. Glazier, Stuart A. Newman, Jesús A. Izaguirre:
A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE ACM Trans. Comput. Biol. Bioinform. 2(4): 273-288 (2005) - [c11]Justin M. Wozniak, Aaron Striegel, David Salyers, Jesús A. Izaguirre:
GIPSE: Streamlining the Management of Simulation on the Grid. Annual Simulation Symposium 2005: 130-137 - [c10]Justin M. Wozniak, Paul R. Brenner, Douglas Thain, Aaron Striegel, Jesús A. Izaguirre:
Generosity and gluttony in GEMS: grid enabled molecular simulations. HPDC 2005: 191-200 - [c9]Douglas Thain, Sander Klous, Justin M. Wozniak, Paul R. Brenner, Aaron Striegel, Jesús A. Izaguirre:
Separating Abstractions from Resources in a Tactical Storage System. SC 2005: 55 - 2004
- [j4]Jesús A. Izaguirre, Rajiv Chaturvedi, Chengbang Huang, Trevor M. Cickovski, J. Coffland, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier:
COMPUCELL, a multi-model framework for simulation of morphogenesis. Bioinform. 20(7): 1129-1137 (2004) - [j3]Thierry Matthey, Trevor M. Cickovski, Scott S. Hampton, Alice Ko, Qun Ma, Matthew Nyerges, Troy Raeder, Thomas Slabach, Jesús A. Izaguirre:
ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics. ACM Trans. Math. Softw. 30(3): 237-265 (2004) - [c8]Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber:
A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. ACRI 2004: 543-552 - [c7]Scott S. Hampton, Jesús A. Izaguirre:
Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo. International Conference on Computational Science 2004: 268-275 - 2003
- [j2]Qun Ma, Jesús A. Izaguirre:
Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations. Multiscale Model. Simul. 2(1): 1-21 (2003) - [j1]Qun Ma, Jesús A. Izaguirre, Robert D. Skeel:
Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities. SIAM J. Sci. Comput. 24(6): 1951-1973 (2003) - [c6]Rajiv Chaturvedi, Jesús A. Izaguirre, Chengbang Huang, Trevor M. Cickovski, P. Virtue, Gilberto L. Thomas, Gabor Forgacs, Mark S. Alber, H. George E. Hentschel, Stuart A. Newman, James A. Glazier:
Multi-model Simulations of Chicken Limb Morphogenesis. International Conference on Computational Science 2003: 39-49 - [c5]Thierry Matthey, Alice Ko, Jesús A. Izaguirre:
PROTOMOL: A Molecular Dynamics Research Framework for Algorithmic Development. International Conference on Computational Science 2003: 50-59 - [c4]Qun Ma, Jesús A. Izaguirre, Robert D. Skeel:
Nonlinear Instability in Multiple Time Stepping Molecular Dynamics. SAC 2003: 167-171 - [c3]Qun Ma, Jesús A. Izaguirre:
Long Time Step Molecular Dynamics using Targeted Langevin Stabilization. SAC 2003: 178-182 - 2001
- [c2]Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesús A. Izaguirre, Peter M. Kogge:
Petaflop Computing for Protein Folding. PP 2001 - [c1]Thierry Matthey, Jesús A. Izaguirre:
ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization. PP 2001
1990 – 1999
- 1999
- [b1]Jesús A. Izaguirre:
Longer Time Steps for Molecular Dynamics. University of Illinois Urbana-Champaign, USA, 1999 - [p1]Robert D. Skeel, Jesús A. Izaguirre:
The Five Femtosecond Time Step Barrier. Computational Molecular Dynamics 1999: 318-331
Coauthor Index
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