**P.M. Mira, J.C. Meza, A. Nandipati, and M. Barlow**, *Molecular Biology and Evolution* (2015). doi: 10.1093/molbev/msv146.

# Research: Publications

# Rational Design of Antibiotic Treatment Plans: A Treatment Plan for Managing Evolution and Reversing Resistance→

/**P.M. Mira, K. Crona, D. Greene, J.C. Meza, B. Sturmfels, and M. Barlow,** *PLoS ONE*, 10(5) (2015). doi:10.1371/journal.pone.0122283.

# Rational Design of Antibiotic Treatment Plans→

/**P.M. Mira, K. Crona, D. Greene, J.C. Meza, and B. Sturmfels**, *arXiv*:1406.1564 (2014).

# Fast Solution of Load Shedding Problems via a Sequence of Linear Programs→

/**H.S. Bhat, G.J. Vaz, and J.C. Meza**, 2013 IEEE International Conference on Big Data, 1-6, (2013).

# Minimizing the Kohn-Sham Total Energy for Periodic Systems→

/**C. Yang and J.C. Meza,** *Linear Algebra and its Applications* 436 (8), 2764-2779 (2012).

# Algorithms and Tools for High-Throughput Geometry-Based Analysis of Crystalline Porous Materials→

/**T.F. Willems, C.H. Rycroft, M. Kazi, J.C. Meza, and M. Haranczyk**, *Microporous and Mesoporous Materials*, 149, 1 (2012).

# SYNAPPS: Data-Driven Analysis for Supernova Spectroscopy→

/**R.C. Thomas, P.E. Nugent, and J.C. Meza**, Publications of the Astronomical Society of the Pacific, 123(900), 237-248 (2011), The University of Chicago Press. doi:10.1086/658673.

# Dimension Reduction Using Rule Ensemble Machine Learning Methods: A Numerical Study of Three Ensemble Methods→

/**O. DeMasi, J. Meza, and D.H. Bailey**, *arXiv*:1108.6094 (2011).

# SelInv—An Algorithm for Selected Inversion of a Sparse Symmetric Matrix→

/**L. Lin, C. Yang, J.C. Meza, J. Lu, L. Ying, and E.W. Weinan,** *ACM Transactions on Mathematical Software*, 37, 4 (2011).

# Steepest Descent→

/**J.C. Meza**, *Wiley Interdisciplinary Reviews: Computational Statistics* (2011). doi: 10.1002/wics.117.

# Optimization Strategies for the Vulnerability Analysis of the Electric Power Grid→

/**A. Pinar, J. Meza, V. Donde, and B. Lesieutre**, *SIAM Journal on Optimization*, Vol. 20, No. 4, 1786-1810 (2010).

# Newton's Method (PDF)→

/**J.C. Meza**, Lawrence Berkeley National Laboratory Technical Report, LBNL-3311E (2010).

# Steepest Descent (PDF)→

/**J.C. Meza**, Lawrence Berkeley National Laboratory (February 2010).

# Tuning an Electronic Structure Code→

/**D.H. Bailey, L.W. Wang, Z. Zhao, J. Meza, E. Strohmaier, and B. Lee**, in *Performance Tuning of Scientific Applications*, D.H. Bailey, R. Lucas, and S. Williams (Eds.) (2010).

# A Numerical Comparison of Rule Ensemble Methods and Support Vector Machines (PDF)→

/**J.C. Meza and M. Woods**, Lawrence Berkeley National Laboratory Technical Report, LBNL-2971E (2009).

# Solving a Class of Nonlinear Eigenvalue Problems by Newton's Method (PDF)→

/**W. Gao, C. Yang, and J.C. Meza**, Lawrence Berkeley National Laboratory Technical Report, LBNL-2187E (2009).

# The Linearly Scaling 3D Fragment Method for Large Scale Electronic Structure Calculations (PDF)→

/**Z. Zhao, J.C. Meza, B. Lee, H. Shan, E. Strohmaier, D. Bailey, and L.-W. Wang**, *Journal of Physics: Conference Series*, LBNL-2162E (June 2009).

# KSSOLV - a MATLAB Toolbox for Solving the Kohn-Sham Equations (PDF)→

/**C. Yang, J.C. Meza, B. Lee, and L.-W. Wang**, *ACM Transactions on Mathematical Software*, Vol. 36, 1-35 (2009).

# Mathematical and Statistical Opportunities in Cyber Security (PDF)→

/**J.C. Meza, S. Campbell, and D. Bailey**, Lawrence Berkeley National Laboratory Technical Report, LBNL-1667E (2009).

# Optimization Strategies for the Vulnerability Analysis of the Electric Power Grid (PDF)→

/**A. Pinar, J. Meza, V. Donde, and B. Lesieutre**, *SIAM Journal on Optimization*, Vol. 20, No. 4, 1786-1810, LBNL-63473 (2009).