Jesús A. Izaguirre

39 papers A 3B 1C 1Misc 7Journal 18Unranked 7

Year	Rank	Type	Title / Venue / Authors
2014	J	`jnl`	AWE-WQ: Fast-Forwarding Molecular Dynamics Using the Accelerated Weighted Ensemble. J. Chem. Inf. Model. Badi Abdul-Wahid, Haoyun Feng, Dinesh Rajan, Ronan Costaouec, Eric Darve, Douglas Thain, Jesús A. Izaguirre
2013	B	`conf`	Case Studies in Designing Elastic Applications. CCGRID Dinesh Rajan, Andrew Thrasher, Badi Abdul-Wahid, Jesús A. Izaguirre, Scott J. Emrich, Douglas Thain
2012	—	`conf`	Folding proteins at 500 ns/hour with Work Queue. eScience Badi Abdul-Wahid, Li Yu, Dinesh Rajan, Haoyun Feng, Eric Darve, Douglas Thain, Jesús A. Izaguirre
2011	C	`conf`	Converting a High Performance Application to an Elastic Cloud Application. CloudCom Dinesh Rajan, Anthony Canino, Jesús A. Izaguirre, Douglas Thain
2010	J	`jnl`	Belief propagation estimation of protein and domain interactions using the sum-product algorithm. IEEE Trans. Inf. Theory Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre
2010	Misc	`conf`	Estimation of Protein and Domain Interactions in the Switching Motility System of Myxococcus Xanthus. Pacific Symposium on Biocomputing Faruck Morcos, Marcin Sikora, Mark S. Alber, Dale Kaiser, Jesús A. Izaguirre
2010	J	`jnl`	MDLab: A molecular dynamics simulation prototyping environment. J. Comput. Chem. Trevor M. Cickovski, Santanu Chatterjee, Jacob Wenger, Christopher R. Sweet, Jesús A. Izaguirre
2010	J	`jnl`	Modeling Conformational Ensembles of Slow Functional Motions in Pin1-WW. PLoS Comput. Biol. 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
2010	Misc	`conf`	Multiscale Dynamics of Macromolecules Using Normal Mode Langevin. Pacific Symposium on Biocomputing Jesús A. Izaguirre, Christopher R. Sweet, Vijay S. Pande
2009	—	`conf`	Determination of Specificity Residues in Two Component Systems using Graphlets. BIOCOMP Faruck Morcos, Charles Lamanna, Nitesh V. Chawla, Jesús A. Izaguirre
2008	J	`jnl`	Addendum. Cytoprophet: a Bioinform. Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre
2008	J	`jnl`	Biomolecular committor probability calculation enabled by processing in network storage. Parallel Comput. Paul R. Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeffrey W. Peng, Jesús A. Izaguirre
2008	J	`jnl`	Cytoprophet: a Bioinform. Faruck Morcos, Charles Lamanna, Marcin Sikora, Jesús A. Izaguirre
2008	J	`jnl`	Making the best of a bad situation: Prioritized storage management in GEMS. Future Gener. Comput. Syst. Justin M. Wozniak, Paul R. Brenner, Douglas Thain, Aaron Striegel, Jesús A. Izaguirre
2007	J	`jnl`	A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Comput. Phys. Commun. Nan Chen, James A. Glazier, Jesús A. Izaguirre, Mark S. Alber
2007	A	`conf`	Biomolecular Path Sampling Enabled by Processing in Network Storage. IPDPS Paul R. Brenner, Justin M. Wozniak, Douglas Thain, Aaron Striegel, Jeffrey W. Peng, Jesús A. Izaguirre
2007	J	`jnl`	From Genes to Organisms Via the Cell: A Problem-Solving Environment for Multicellular Development. Comput. Sci. Eng. 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
2007	—	`conf`	MDL, A Domain-Specific Language for Molecular Dynamics. Annual Simulation Symposium Trevor M. Cickovski, Chris Sweet, Jesús A. Izaguirre
2007	J	`jnl`	Predicting Protein-Protein Interactions from Protein Domains Using a Set Cover Approach. IEEE ACM Trans. Comput. Biol. Bioinform. Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z. Chen, Jesús A. Izaguirre
2005	J	`jnl`	A Framework for Three-Dimensional Simulation of Morphogenesis. IEEE ACM Trans. Comput. Biol. Bioinform. 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
2005	—	`conf`	GIPSE: Streamlining the Management of Simulation on the Grid. Annual Simulation Symposium Justin M. Wozniak, Aaron Striegel, David Salyers, Jesús A. Izaguirre
2005	A	`conf`	Generosity and gluttony in GEMS: grid enabled molecular simulations. HPDC Justin M. Wozniak, Paul R. Brenner, Douglas Thain, Aaron Striegel, Jesús A. Izaguirre
2005	J	`jnl`	MDSIMAID: Automatic parameter optimization in fast electrostatic algorithms. J. Comput. Chem. Michael S. Crocker, Scott S. Hampton, Thierry Matthey, Jesús A. Izaguirre
2005	J	`jnl`	Parallel multigrid summation for the J. Parallel Distributed Comput. Jesús A. Izaguirre, Scott S. Hampton, Thierry Matthey
2005	A	`conf`	Separating Abstractions from Resources in a Tactical Storage System. SC Douglas Thain, Sander Klous, Justin M. Wozniak, Paul R. Brenner, Aaron Striegel, Jesús A. Izaguirre
2004	—	`conf`	A Hybrid Discrete-Continuum Model for 3-D Skeletogenesis of the Vertebrate Limb. ACRI Rajiv Chaturvedi, Chengbang Huang, Jesús A. Izaguirre, Stuart A. Newman, James A. Glazier, Mark S. Alber
2004	J	`jnl`	COMPUCELL, a multi-model framework for simulation of morphogenesis. Bioinform. 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
2004	Misc	`conf`	Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo. International Conference on Computational Science Scott S. Hampton, Jesús A. Izaguirre
2004	J	`jnl`	ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics. ACM Trans. Math. Softw. Thierry Matthey, Trevor M. Cickovski, Scott S. Hampton, Alice Ko, Qun Ma, Matthew Nyerges, Troy Raeder, Thomas Slabach, Jesús A. Izaguirre
2003	Misc	`conf`	Long Time Step Molecular Dynamics using Targeted Langevin Stabilization. SAC Qun Ma, Jesús A. Izaguirre
2003	Misc	`conf`	Multi-model Simulations of Chicken Limb Morphogenesis. International Conference on Computational Science 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
2003	Misc	`conf`	Nonlinear Instability in Multiple Time Stepping Molecular Dynamics. SAC Qun Ma, Jesús A. Izaguirre, Robert D. Skeel
2003	Misc	`conf`	PROTOMOL: A Molecular Dynamics Research Framework for Algorithmic Development. International Conference on Computational Science Thierry Matthey, Alice Ko, Jesús A. Izaguirre
2003	J	`jnl`	Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations. Multiscale Model. Simul. Qun Ma, Jesús A. Izaguirre
2003	J	`jnl`	Verlet-I/R-RESPA/Impulse is Limited by Nonlinear Instabilities. SIAM J. Sci. Comput. Qun Ma, Jesús A. Izaguirre, Robert D. Skeel
2001	—	`conf`	Petaflop Computing for Protein Folding. PP Shannon K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesús A. Izaguirre, Peter M. Kogge
2001	—	`conf`	ProtoMol: A Molecular Dynamics Framework with Incremental Parallelization. PP Thierry Matthey, Jesús A. Izaguirre
1999	—	`—`	Longer Time Steps for Molecular Dynamics Jesús A. Izaguirre
1999	—	`ch.`	The Five Femtosecond Time Step Barrier. Computational Molecular Dynamics Robert D. Skeel, Jesús A. Izaguirre