| Year |
Citation |
Score |
| 2023 |
Jones MS, McDargh ZA, Wiewiora RP, Izaguirre JA, Xu H, Ferguson AL. Molecular Latent Space Simulators for Distributed and Multimolecular Trajectories. The Journal of Physical Chemistry. A. PMID 37314375 DOI: 10.1021/acs.jpca.3c01362 |
0.351 |
|
| 2016 |
Kastner KW, Izaguirre JA. Accelerated Molecular Dynamics Simulations of the Octopamine Receptor using GPUs: Discovery of an Alternate Agonist-Binding Position. Proteins. PMID 27318014 DOI: 10.1002/Prot.25091 |
0.426 |
|
| 2015 |
Feng H, Costaouec R, Darve E, Izaguirre JA. A comparison of weighted ensemble and Markov state model methodologies. The Journal of Chemical Physics. 142: 214113. PMID 26049485 DOI: 10.1063/1.4921890 |
0.399 |
|
| 2015 |
Feng H, Siwo G, Izaguirre JA, Thain D, Abdul-Wahid B. Greedy Algorithms for Fast Discovery of Macrostates from Molecular Dynamics Simulations Lecture Notes On Information Theory. 2. DOI: 10.12720/lnit.2.4.302-309 |
0.307 |
|
| 2014 |
Abdul-Wahid B, Feng H, Rajan D, Costaouec R, Darve E, Thain D, Izaguirre JA. AWE-WQ: fast-forwarding molecular dynamics using the accelerated weighted ensemble. Journal of Chemical Information and Modeling. 54: 3033-43. PMID 25207854 DOI: 10.1021/Ci500321G |
0.466 |
|
| 2013 |
Sweet JC, Nowling RJ, Cickovski T, Sweet CR, Pande VS, Izaguirre JA. Long Timestep Molecular Dynamics on the Graphical Processing Unit. Journal of Chemical Theory and Computation. 9: 3267-3281. PMID 24436689 DOI: 10.1021/Ct400331R |
0.756 |
|
| 2012 |
Abdul-Wahid B, Yu L, Rajan D, Feng H, Darve E, Thain D, Izaguirre JA. Folding Proteins at 500 ns/hour with Work Queue. Proceedings ... Ieee International Conference On Escience. Ieee International Conference On Escience. 2012: 1-8. PMID 25540799 DOI: 10.1109/eScience.2012.6404429 |
0.345 |
|
| 2010 |
Morcos F, Chatterjee S, McClendon CL, Brenner PR, López-Rendón R, Zintsmaster J, Ercsey-Ravasz M, Sweet CR, Jacobson MP, Peng JW, Izaguirre JA. Modeling conformational ensembles of slow functional motions in Pin1-WW. Plos Computational Biology. 6: e1001015. PMID 21152000 DOI: 10.1371/Journal.Pcbi.1001015 |
0.687 |
|
| 2010 |
Cickovski T, Chatterjee S, Wenger J, Sweet CR, Izaguirre JA. MDLab: a molecular dynamics simulation prototyping environment. Journal of Computational Chemistry. 31: 1345-56. PMID 19882726 DOI: 10.1002/Jcc.21418 |
0.768 |
|
| 2010 |
Morcos F, Sikora M, Alber MS, Kaiser D, Izaguirre JA. Belief propagation estimation of protein and domain interactions using the sum-product algorithm Ieee Transactions On Information Theory. 56: 742-755. DOI: 10.1109/Tit.2009.2037051 |
0.341 |
|
| 2009 |
Sweet CR, Hampton SS, Skeel RD, Izaguirre JA. A separable shadow Hamiltonian hybrid Monte Carlo method. The Journal of Chemical Physics. 131: 174106. PMID 19894997 DOI: 10.1063/1.3253687 |
0.409 |
|
| 2009 |
Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA. Inferring protein-protein interactions from multiple protein domain combinations. Methods in Molecular Biology (Clifton, N.J.). 541: 43-59. PMID 19381530 DOI: 10.1007/978-1-59745-243-4_3 |
0.564 |
|
| 2008 |
Morcos F, Lamanna C, Sikora M, Izaguirre J. Cytoprophet: a Cytoscape plug-in for protein and domain interaction networks inference. Bioinformatics (Oxford, England). 24: 2265-6. PMID 18653520 DOI: 10.1093/Bioinformatics/Btn380 |
0.346 |
|
| 2008 |
Sweet CR, Petrone P, Pande VS, Izaguirre JA. Normal mode partitioning of Langevin dynamics for biomolecules. The Journal of Chemical Physics. 128: 145101. PMID 18412479 DOI: 10.1063/1.2883966 |
0.328 |
|
| 2008 |
Brenner P, Wozniak JM, Thain D, Striegel A, Peng JW, Izaguirre JA. Biomolecular committor probability calculation enabled by processing in network storage Parallel Computing. DOI: 10.1016/j.parco.2008.08.001 |
0.702 |
|
| 2008 |
Wozniak JM, Brenner P, Thain D, Striegel A, Izaguirre JA. Making the best of a bad situation: Prioritized storage management in GEMS Future Generation Computer Systems. 24: 10-16. DOI: 10.1016/J.Future.2007.04.003 |
0.685 |
|
| 2007 |
Cickovski T, Aras K, Alber MS, Izaguirre JA, Swat M, Glazier JA, Merks RM, Glimm T, Hentschel HG, Newman SA. From Genes to Organisms Via the Cell A Problem-Solving Environment for Multicellular Development. Computing in Science & Engineering. 9: 50-60. PMID 19526065 DOI: 10.1109/Mcse.2007.74 |
0.719 |
|
| 2007 |
Chen N, Glazier JA, Izaguirre JA, Alber MS. A parallel implementation of the Cellular Potts Model for simulation of cell-based morphogenesis. Computer Physics Communications. 176: 670-681. PMID 18084624 DOI: 10.1016/J.Cpc.2007.03.007 |
0.412 |
|
| 2007 |
Brenner P, Sweet CR, VonHandorf D, Izaguirre JA. Accelerating the replica exchange method through an efficient all-pairs exchange. The Journal of Chemical Physics. 126: 074103. PMID 17328589 DOI: 10.1063/1.2436872 |
0.676 |
|
| 2007 |
Huang C, Morcos F, Kanaan SP, Wuchty S, Chen DZ, Izaguirre JA. Predicting protein-protein interactions from protein domains using a set cover approach. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 4: 78-87. PMID 17277415 DOI: 10.1109/Tcbb.2007.1001 |
0.596 |
|
| 2007 |
Brenner P, Wozniak JM, Thain D, Striegel A, Peng JW, Izaguirre JA. Biomolecular path sampling enabled by processing in network storage Proceedings - 21st International Parallel and Distributed Processing Symposium, Ipdps 2007; Abstracts and Cd-Rom. DOI: 10.1109/IPDPS.2007.370446 |
0.614 |
|
| 2007 |
Cickovski T, Sweet C, Izaguirre JA. MDL, A domain-specific language for molecular dynamics Proceedings - Simulation Symposium. 256-264. DOI: 10.1109/ANSS.2007.26 |
0.73 |
|
| 2006 |
Hampton SS, Brenner P, Wenger A, Chatterjee S, Izaguirre JA. Biomolecular Sampling: Algorithms, Test Molecules, and Metrics Lecture Notes in Computational Science and Engineering. 49: 103-123. |
0.689 |
|
| 2005 |
Cickovski TM, Huang C, Chaturvedi R, Glimm T, Hentschel HG, Alber MS, Glazier JA, Newman SA, Izaguirre JA. A framework for three-dimensional simulation of morphogenesis. Ieee/Acm Transactions On Computational Biology and Bioinformatics / Ieee, Acm. 2: 273-88. PMID 17044166 DOI: 10.1109/Tcbb.2005.46 |
0.768 |
|
| 2005 |
Chaturvedi R, Huang C, Kazmierczak B, Schneider T, Izaguirre JA, Glimm T, Hentschel HG, Glazier JA, Newman SA, Alber MS. On multiscale approaches to three-dimensional modelling of morphogenesis. Journal of the Royal Society, Interface / the Royal Society. 2: 237-53. PMID 16849182 DOI: 10.1098/Rsif.2005.0033 |
0.64 |
|
| 2005 |
Crocker MS, Hampton SS, Matthey T, Izaguirre JA. MDSIMAID: automatic parameter optimization in fast electrostatic algorithms. Journal of Computational Chemistry. 26: 1021-31. PMID 15884103 DOI: 10.1002/Jcc.20240 |
0.306 |
|
| 2005 |
Thain D, Klous S, Wozniak J, Brenner P, Striegel A, Izaguirre J. Separating abstractions from resources in a tactical storage system Proceedings of the Acm/Ieee 2005 Supercomputing Conference, Sc'05. 2005. DOI: 10.1109/SC.2005.64 |
0.636 |
|
| 2005 |
Izaguirre JA, Hampton SS, Matthey T. Parallel multigrid summation for the N-body problem Journal of Parallel and Distributed Computing. 65: 949-962. DOI: 10.1016/J.Jpdc.2005.03.006 |
0.405 |
|
| 2005 |
Wozniak JM, Brenner P, Thain D, Striegel A, Izaguirre JA. Generosity and gluttony in GEMS: Grid enabled molecular simulations Proceedings of the Ieee International Symposium On High Performance Distributed Computing. 191-200. |
0.686 |
|
| 2004 |
Izaguirre JA, Chaturvedi R, Huang C, Cickovski T, Coffland J, Thomas G, Forgacs G, Alber M, Hentschel G, Newman SA, Glazier JA. CompuCell, a multi-model framework for simulation of morphogenesis. Bioinformatics (Oxford, England). 20: 1129-37. PMID 14764549 DOI: 10.1093/Bioinformatics/Bth050 |
0.756 |
|
| 2004 |
Matthey T, Cickovski T, Hampton S, Ko A, Ma Q, Nyerges M, Raeder T, Slabach T, Izaguirre JA. ProtoMol, an object-oriented framework for prototyping novel algorithms for molecular dynamics Acm Transactions On Mathematical Software. 30: 237-265. DOI: 10.1145/1024074.1024075 |
0.764 |
|
| 2004 |
Izaguirre JA, Hampton SS. Shadow hybrid Monte Carlo: An efficient propagator in phase space of macromolecules Journal of Computational Physics. 200: 581-604. DOI: 10.1016/J.Jcp.2004.04.016 |
0.367 |
|
| 2004 |
Chaturvedi R, Huang C, Izaguirre JA, Newman SA, Glazier JA, Alber M. A hybrid discrete-continuum model for 3-D skeletogenesis of the vertebrate limb Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 3305: 543-552. |
0.53 |
|
| 2003 |
Ma Q, Izaguirre JA. Targeted Mollified Impulse: A Multiscale Stochastic Integrator for Long Molecular Dynamics Simulations Multiscale Modeling & Simulation. 2: 1-21. DOI: 10.1137/S1540345903423567 |
0.591 |
|
| 2003 |
Ma Q, Izaguirre JA, Skeel RD. Verlet-I/r-RESPA/Impulse is limited by nonlinear instabilities Siam Journal On Scientific Computing. 24: 1951-1973. DOI: 10.1137/S1064827501399833 |
0.546 |
|
| 2003 |
Chaturvedi R, Izaguirre JA, Huang C, Cickovski T, Virtue P, Thomas G, Forgacs G, Alber M, Hentschel G, Newman SA, Glazier JA. Multi-model simulations of chicken limb morphogenesis Lecture Notes in Computer Science (Including Subseries Lecture Notes in Artificial Intelligence and Lecture Notes in Bioinformatics). 2659: 39-49. |
0.76 |
|
| 2002 |
Skeel RD, Izaguirre JA. An impulse integrator for Langevin dynamics Molecular Physics. 100: 3885-3891. DOI: 10.1080/0026897021000018321 |
0.317 |
|
| 1999 |
Izaguirre JA, Reich S, Skeel RD. Longer time steps for molecular dynamics Journal of Chemical Physics. 110: 9853-9864. DOI: 10.1063/1.478995 |
0.402 |
|
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