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--------------------------------------------------------------------------------------- COMPUTATIONAL
DEVELOPMENTAL BIOLOGY (MORPHOGENESIS) DISSERTATIONS
AND MISCELLANEOUS --------------------------------------------------------------------------------------- MOST CURRENT PUBLICATIONS (2010/2009) 55. Modeling conformational ensembles of slow functional motions in Pin1-WW.
(HTML) (PDF) Faruck Morcos,
Santanu Chatterjee, Christopher
L. McClendon, Paul R. Brenner, Roberto Lopez-Rendon,
John Zintsmaster, Maria Ercsey-Ravasz,
Chris R. Sweet, Matthew P. Jacobson, Jeffrey W. Peng,
and Jesús A. Izaguirre. PLoS Comput Biol 6(12):
e1001015. (2010) doi:10.1371/journal.pcbi.1001015 54. Inferring protein-protein interactions from multiple protein
domain combinations. (PDF) Kanaan SP, Huang C, Wuchty S, Chen DZ, Izaguirre JA. Methods Mol Biol. (2009) 541:43-59. 53. MDLab: A Molecular Dynamics
Simulation Prototyping Environment. (PDF) Cickovski T, Chatterjee S, Wenger J, Sweet CR, Izaguirre JA. J
Comput Chem (2010) 31:1345-1356. 52. String Method with Collective Variables from Normal Modes:
Application to Alanine Dipeptide.
(PDF) Santanu Chatterjee,
Christopher R. Sweet, and Jesús A. Izaguirre. Submitted. 51. Belief
Propagation Estimation of Protein and Domain Interactions using the
Sum-Product Algorithm (PDF). Faruck Morcos,
Marcin Sikora, Mark Alber, Dale Kaiser, and Jesús
A. Izaguirre. IEEE T. Inform. Theory,
Special Issue on Neuroscience and Molecular Biology (2010) 56:742–755. 46. A separable shadow hybrid Monte Carlo method. (PDF) C.
R. Sweet, S. S. Hampton, R. D. Skeel, and J. A.
Izaguirre, J. Chem. Phys. (2009) 131,
174106. 28. Multiscale dynamics of
macromolecules using Normal Mode Langevin (PDF) Jesús A. Izaguirre, Chris R. Sweet,
and Vijay S. Pande. Pac Symp Biocomput.
(2010) 15:240-51. 27. Estimation of Protein and Domain Interactions in the
Switching Motility System of Myxococcus xanthus (PDF) Faruck Morcos,
Marcin Sikora, Mark Alber, Dale Kaiser, and Jesús
A. Izaguirre. Pac Symp
Biocomput. (2010) 15:157-65. 26. Determination of Specificity Residues in Two Component
Systems using Graphlets (PDF) Faruck Morcos,
Charles Lamanna, Nitesh
V. Chawla, and Jesús A.
Izaguirre. Proc. International
Conference on Bioinformatics & Computational Biology BIOCOMP’ 09 25. Adaptive dimensionality reduction of stochastic differential
equations for protein dynamics (PDF). Jesus
A. Izaguirre and Christopher R. Sweet. Proc.
Second International Workshop on Model Reduction in Reacting Flows, April
2009, Notre Dame, IN. MOLECULAR DYNAMICS 49. Biomolecular committor
probability calculation enabled by processing in network storage. (PDF) Paul Brenner, Justin M.
Wozniak, Douglas Thain, Aaron Striegel,
Jeff W. Peng, and
Jesus A. Izaguirre. Parallel Computing, 34:652–660,
2008. 48. Normal Mode
Partitioning of Langevin Dynamics for Biomolecules. (PDF) C.R. Sweet, P. Petrone, V.S. Pande, J.A.
Izaguirre, J. Chem. Phys. 128:
145101, 2008. S48. Supplementary
Information for Normal Mode Partitioning of Langevin
Dynamics for Biomolecules. (PDF) 47.
Accelerating the Replica Exchange Method Through an Efficient All-Pairs
Exchange. (PDF) P. Brenner, C. R. Sweet, D. VonHandorf, J. A. Izaguirre, J. Chem. Phys. 126(7):074103,
2007. 22.
MDL, A Domain-Specific Language for Molecular Dynamics (PDF) T. Cickovski,
C. Sweet, and J. A. Izaguirre, Proc. 40th Annual Simulation
Symposium, March 2007, Norfolk, VA.
20.
Backward error analysis of multiscale symplectic integrators and propagators (PDF) C. R. Sweet and J. A. Izaguirre,
Proc. Third International Conference Multiscale Materials Modeling MMM2006, Freiburg,
Germany, September 2006. 41.
Parallel Multigrid Summation for the N-body Problem
(PDF), Jesús A. Izaguirre, Scott S.
Hampton, and Thierry Matthey, Journal
of Parallel and Distributed Computing, 65:949-962, 2005. 40. MDSimAid: Automatic Parameter Optimization in Fast
Electrostatic Algorithms (PDF), Michael S. Crocker, Scott S. Hampton, Thierry
Matthey, and Jesús A. Izaguirre, Journal of Computational Chemistry,
Vol. 26, pp. 1021-1031, 2005. 38.
Shadow Hybrid Monte Carlo: An Efficient Propagator in Phase Space of
Macromolecules (PDF),
Jesús A. Izaguirre and Scott S.
Hampton, Journal of Computational
Physics, Vol. 200, No. 2, pp. 581-604, 2004. 37. ProtoMol, an Object-Oriented Framework for Prototyping
Novel Algorithms for Molecular Dynamics (PDF), Thierry Matthey, Trevor Cickovski, Scott Hampton, Alice Ko,
Qun Ma, Matthew Nyerges,
Troy Raeder, Thomas Slabach and Jesús
A. Izaguirre, ACM Transactions on
Mathematical Software, Vol. 20, No. 3, pp. 237-265, 2004. 12.
Improved Sampling for Biological Molecules Using Shadow Hybrid Monte Carlo (PDF), Scott S. Hampton and Jesús A. Izaguirre, In M. Bubak,
G. D. von Albada, and P. M. A. Sloot;
J. J. Dongarra, editors, 4th International Conference on Computational Science, Kraków, Poland, volume 3037 of Lecture Notes in Computer Science, pp. 268-274. Springer-Verlag, New York, 2004. 35.
Targeted mollified impulse - a multiscale
stochastic integrator for long molecular dynamics simulations (PDF), Q. Ma
and J. A. Izaguirre, Multiscale Modeling and Simulation, Vol. 2, No.
1, pp. 1-21, 2003. 34. Verlet-I/r-RESPA is limited by nonlinear instability (PDF), Qun Ma, Jesús A. Izaguirre and
Robert D. Skeel, SIAM Journal on Scientific Computing, Vol. 24, No. 6, pp.
1951-1973, May 6, 2003. 10. ProtoMol: A Molecular Dynamics Research Framework for
Algorithmic Development (PDF), Thierry Matthey, Alice N. Ko and Jesús A. Izaguirre,
Springer Verlag LNCS 2659, Computational Science-
ICCS 2003, International conference Melbourne, Australia and St. Petersburg,
Russia, June 2003, Part III, pp 50-59. 9. Long
time step molecular dynamics using targeted Langevin
stabilization (PDF), Qun Ma and Jesús
A. Izaguirre, Proceedings of the ACM
Symposium on Applied Computing SAC 03, pp. 178-182, 2003. 8.
Nonlinear instability in multiple time stepping molecular dynamics (PDF), Qun
Ma, Jesús A. Izaguirre and Robert D. Skeel, Proceedings
of the ACM Symposium on Applied Computing SAC 03, pp. 167-171, 2003. 33. An Impulse
Integrator for Langevin Dynamics (PS) (PDF), R.D. Skeel and J. A. Izaguirre, Molecular Physics, Vol. 100, No. 24,
3885-3891, 2002. 7.
Overcoming instabilities in Verlet-I/r-RESPA with
the mollified impulse method
(PS)(PDF), Jesús A. Izaguirre, Qun Ma,
Thierry Matthey, Jeremiah Willcock, Thomas Slabach, Branden Moore, and
George Viamontes, Computational Methods for Macromolecules: Challenges and Applications,
Proceedings of the 3rd International Workshop on Algorithms for
Macromolecular Modeling, New York, Oct. 12-14, 2000. Lecture Notes in
Computational Science and Engineering (LNCSE), Vol. 24, pp. 146-174. Springer
Verlag, Berlin, 2002. Editors: T. Schlick and H. H. Gan 32. Langevin Stabilization of Molecular Dynamics, (PS) (PDF), Jesús A. Izaguirre, Justin M. Wozniak, Daniel P. Catarello, and Robert D. Skeel,
J. Chem. Phys., 114(5):2090-2098,
Feb. 1 2001. 6. Petaflop Computing for Protein Folding (PS) (PDF), Shannon
K. Kuntz, Richard C. Murphy, Michael T. Niemier, Jesús A. Izaguirre and Peter M. Kogge,
Proc. 10th SIAM Conference on Parallel
Processing for Scientific Computing, March 2001. 5. ProtoMol: A Molecular Dynamics Framework with Incremental
Parallelization (PS) (PDF), Thierry
Matthey and Jesús A. Izaguirre, Proc. 10th SIAM Conference on Parallel
Processing for Scientific Computing, March 2001. 4. Langevin Stabilization of Multiscale
Mollified Molecular Dynamics
(PS) (PDF), Jesús A. Izaguirre, In A. Brandt, K. Binder, and J. Bernholc, editors, Multiscale Computational Methods in Chemistry and Physics, volume 177 of NATO Science Series: Series III Computer
and Systems Sciences, pp. 34-47, IOS Press, Amsterdam, Jan 2001. 31.
Longer Time Steps for Molecular Dynamics (PDF),
Jesús A. Izaguirre, Sebastian Reich and Robert D. Skeel), J. Chem.
Phys., 110(20), pp. 9853-9864, 22 May 1999. 3. BioCoRE: A collaboratory for
structural biology.
M. Bhandarkar, G. Budescu,
W. F. Humphrey, J. A. Izaguirre, S. Izrailev, L. V.
Kalé, D. Kosztin, F. Molnar, J. C. Phillips, and K. Schulten. In Agostino G. Bruzzone, Adelinde Uchrmacher, and Ernest H. Page, editors, Proceedings of the SCS International
Conference on Web-Based Modeling and Simulation, pages 242-251, San
Francisco, California, 1999. 2. The
Five Femtosecond Time Step Barrier (PS), Robert D. Skeel and Jesús A. Izaguirre,
in Computational Molecular Dynamics:
Challenges, Methods, Ideas, Vol. 4 of Lecture
Notes in Computational Science and Engineering, pp. 303-318, Springer-Verlag, Berlin, 1998. 50. Cytoprophet: A Cytoscape plug-in for protein and domain interaction
networks inference. (PDF) Faruck Morcos, Charles Lamanna, Marcin Sikora, and Jesus Izaguirre. Bioinformatics, 19:2265–2266, 2008 43.
Predicting Protein-Protein Interactions from Protein Domains Using a Set
Cover Approach (PDF), Chengbang Huang, Faruck Morcos, Simon P. Kanaan, Stefan Wuchty, Danny Z.
Chen, and Jesús A. Izaguirre, IEEE/ACM Transactions on Computational Biology and Bioinformatics, Vol. 4, pp. 1-10, 2007. 24.
Bayesian Inference of Protein and Domain Interactions Using the Sum-Product
Algorithm (PDF) Marcin Sikora,
Faruck Morcos, Daniel J.
Costello, Jr., and Jesús
A. Izaguirre, Proc. 2007
Information Theory and Applications Workshop, San Diego, Jan. 29 2007. 19.
Prediction of domain interactions in C.
elegans (PDF). Faruck Morcos,
Mike Boxem, Niels Klitgord, Marc Vidal, and Jesús
A. Izaguirre. Proc. Workshop
Computational Biophysics to Systems Biology CBSB06, Forschungszentrum
Jülich, Germany, June 2006. COMPUTATIONAL DEVELOPMENTAL BIOLOGY (MORPHOGENESIS) 48. A
Parallel Implementation of the Cellular Potts Model for Simulation of
Cell-Based Morphogenesis. (PDF) N. Chen, J. A. Glazier, J. A.
Izaguirre, and M. S. Alber, Computer Physics Communications 176:670 (2007). 45.
From Genes To Organisms Via The Cell: A Problem Solving Environment For Multicellular Development (PDF) T. Cickovski,
K. Aras, M. Swat, R. M. H. Merks, T. Glimm, H. G. E.Hentschel, M. S.
Alber, J. A. Glazier, S. A. Newman, J. A.
Izaguirre, Accepted, Computing in
Science and Engineering (2007). 42. A
Framework for Three-Dimensional Simulation of Morphogenesis (PDF), T. Cickovski,
C. Huang, R. Chaturvedi, T. Glimm,
H.G.E. Hentschel, M. Alber,
J. A. Glazier, S. A. Newman, and J. A. Izaguirre, IEEE/ACM Transactions on
Computational Biology and Bioinformatics, Vol. 2, pp. 237-288, 2005. 39. On Multiscale Approaches to Three-Dimensional Modeling of
Morphogenesis (PDF), R. Chaturvedi, C. Huang, B. Kazmierczak, T. Schneider, J. A. Izaguirre, S. A. Newman,
J. A. Glazier, and M. Alber, Journal of the Royal Society, Interface, Vol. 2, pp. 237-253,
2005. 36. CompuCell, a multi-model framework for simulation of
morphogenesis (PDF), Jesús
A. Izaguirre, Rajiv Chaturvedi, Chengbang
Huang, Trevor Cickovski, Joseph Coffland,
Gilberto Thomas, Gabor Forgacs, Mark Alber, Stuart A. Newman, and James A. Glazier, Bioinformatics, Vol. 20, No. 7, pp.
1129-1137, 2004. 13. A
Hybrid Discrete-Continuum Model for 3-D Skeletogenesis
of the Vertebrate Limb (PDF), R. Chaturvedi, C. Huang, J. A. Izaguirre, S. A. Newman, J.
A. Glazier, and M. Alber. In Peter M. A. Sloot, Bastien Chopard, and Alfons G.
Hoekstra, editors, Cellular Automata:
6th International Conference on Cellular Automata for Research and Industry,
ACRI 2004, Amsterdam, The Netherlands, October 25-28, 2004, volume 3305
of Lecture Notes in Computer Science,
pp. 543-552. Springer Verlag, Berlin Heidelberg,
2004. 11.
Multi-model simulations of chicken limb morphogenesis (PDF), Rajiv Chaturvedi,
Jesús A. Izaguirre, Chengbang Huang, Trevor Cickovski,
Patrick Virtue, Gilberto Thomas, Gabor Forgacs,
Mark Alber, Stuart A. Newman, and James A. Glazier,
Springer Verlag LNCS 2659, Computational Science-
ICCS 2003, International conference Melbourne, Australia and St. Petersburg,
Russia, June 2003, Part III, pp 39-49. 44.
Making the Best of a Bad Situation: Prioritized Storage Management in GEMS (PDF) J. M. Wozniak, P. Brenner, D. Thain, A. Striegel and J. A.
Izaguirre, J. of Future Generation Computer Systems 24:10–16 (2008). 23. Biomolecular Path Sampling Enabled by Processing in
Network Storage (PDF)
P. Brenner, J. M.
Wozniak, D. Thain, A. Striegel,
J. W. Peng, and J. A. Izaguirre, The
Sixth IEEE International Workshop on High-Performance Computational Biology
HiCOMB
2007. 21.
Access Control for a Replica Management Database (PDF) J. M. Wozniak, P. Brenner, D. Thain, A. Striegel and J. A.
Izaguirre, Proc. Workshop on
Storage Security and Survivability, October 2006. 18. Biomolecular Sampling: Algorithms, Test Molecules, and
Metrics (PDF). Scott Hampton, Paul Brenner,
Aaron Wenger, Santanu Chatterjee,
and Jesús A. Izaguirre, New Algorithms for Macromolecular Simulation, pp. 103-123, Volume
49 in Lecture Notes in Computational Science and Engineering (LNCSE),
Springer Verlag, Berlin and New York, 2006. 17.
Applying feedback control to a replica management system. (PDF) Justin Wozniak, Paul Brenner,
Doug Thain, Aaron Striegel,
and Jesus A. Izaguirre, Proceedings of 38th
Southeastern Symposium on System Theory, Cookeville, TN, March 2006. 16.
Separating Abstractions from Resources in a Tactical Storage System (PDF) Thain, D.; Klous,
S.; Wozniak, J.; Brenner, P.; Striegel, A. &
Izaguirre, J., Supercomputing, Seattle, WA, Nov.
12-18, 2005. 15.
Generosity and Gluttony in GEMS: Grid Enabled Molecular Simulations (PDF) J. M. Wozniak, P. Brenner, D. Thain, A. Striegel and J. A.
Izaguirre, 14th IEEE International Symposium on High Performance Distributed
Computing (HPDC-14), Research Triangle Park, NC, July 24-27, 2005. 14.
GIPSE: Streamlining the Management of Simulation on the Grid (PDF), J. M. Wozniak, A. Striegel, D. Salyers, and J. A.
Izaguirre, 38th Annual Simulation Symposium ANSS 05, San Diego, CA, USA, April 2-8, 2005. 1.
Evaluation of Parallel Domain Partitioning Algorithms (PDF), Jesús A. Izaguirre, in Proceedings of the First National Computer Science Encounter, Workshop
of Distributed and Parallel Systems, pp. 44-50, Querétaro, México, Sept.
11-13, 1997. Dissertations and Miscellaneous M17.
Optimal implementation of the shadow hybrid Monte Carlo method. (PDF) C. R. Sweet, S. S. Hampton,
and J. A. Izaguirre. Technical Report TR-2006-09, University of Notre Dame,
2006. M16. On
Being Close to the Data: Executing Code in a Replica Management System. (PDF) J. M. Wozniak, P. Brenner, D. Thain, A. Striegel, J. A.
Izaguirre, 2006. M15. Multiscale Computational Methods for Morphogenesis and
Algorithms for Protein-Protein Interaction Inference, (PDF)
Chengbang Huang, Ph.D. Dissertation,
Dept. of Computer Science and Engineering, University of Notre Dame, July
2005 M14.
Empirical Analysis of Design Patterns - A Case Study in CompuCell3D (PDF),
Kedar Aras, Master’s Thesis, Dept.
of Computer Science & Eng., Univ. of Notre Dame,
Oct. 2005. M13.
Empirical Evaluation of Design Patterns in Scientific Application (PDF) Kedar Aras, Trevor Cickovski, and Jesús A. Izaguirre, Technical Report
TR-2005-08, Dept. of Computer Science & Eng., Univ. of Notre Dame, 2005 M12.
BIOLOGO: A Domain-Specific Language for Morphogenesis (PDF), T. Cickovski,
R. Merks, and J. A. Izaguirre, in preparation, 2005. M10. BioLogo, a
Domain-Specific Language for Morphogenesis (PDF),
Trevor M. Cickovski, M.S. Thesis, Department
of Computer Science and Engineering, University of Notre Dame, December 2004. M9.
Design Patterns for Scientific Software (PDF), T. Cickovski, T. Matthey, and J. A. Izaguirre, Technical
Report TR-2004-29, Department of Computer Science and Engineering, University
of Notre Dame, 2004. M8. Polarizable Force Fields for Flexible Molecules (PDF), Asbjřrn Holt, M.S. Thesis, NTNU and Lunds Univesitet, Norway, July
2004. M7. Improved
Sampling of Configuration Space of Biomolecules
using Shadow Hybrid Monte Carlo (PDF),
Scott S. Hampton, M.S. Thesis, Department of Computer Science and
Engineering, University of Notre Dame, August 2004. M6.
GIPSE: A Toolset for Streamlining the Management Aspects of the Grid for
Simulation-based Research (PDF), A. Striegel, M. Shorts, E. Stuntebeck,
D. Salyers, J. A. Izaguirre M6. MDSimAid :
Automatic Optimization of Fast Electrostatics Algorithms for Molecular
Simulations (PDF),
Alice N. Ko and Jesús A. Izaguirre, International Conference on Computational
Science ICCS 2003. M5. Novel
Multiscale Algorithms for Molecular Dynamics (PDF),
Qun Ma, Ph.D. Thesis, Department of Computer
Science and Engineering, University of Notre Dame, June, 2003. M4. MDSimAid: An Automatic Recommender for Optimization of
Fast Electrostatic Algorithms for Molecular Simulations (PDF), Alice N. Ko.
M.S. Thesis, Department of Computer Science and Engineering, Notre Dame, IN,
Dec. 2002. M3.
Framework Design, Parallelization and Force Computation in Molecular Dynamics
(PDF), Thierry Matthey. Ph.D. Thesis,
Department of Informatics, University of Bergen, Norway, Sept. 2002. M2.
Linearly scalable hybrid Monte Carlo method for conformational sampling of
large biomolecules (PDF), Scott
Hampton and Jesús A. Izaguirre, preprint. M1. A
Tutorial on the Prototyping of Multiple Time Stepping Integrators for
Molecular Dynamics (PS) (PDF), Jesús A. Izaguirre, Thierry Matthey, Jeremiah Willcock, Branden Moore, Qun Ma, Thomas Slabach, and
George Viamontes, 2001. Last modified: 3/8/2010 |
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