PEER-REVIEWED PAPERS

52.    D. Höhler, W. Pfeiffer, V. Ioannidis, H. Stockinger, and A. Stamatakis, “RAxML Grove: an empirical phylogenetic tree database,” Bioinformatics 38, 1741 (2022).
51.    C. Witte, J.H. Fowler, W. Pfeiffer, LL.Hungerford, J. Braun, J. Burchell, et al., “Social network analysis and whole-genome sequencing to evaluate disease transmission in a large, dynamic population: A study of avian mycobacteriosis in zoo birds,” PLoS ONE (2021).
50.    Z. Han, P.S. Thuy-Boun, W. Pfeiffer, V.F. Vartabedian, A. Torkamani, J.R. Teijaro, and D.W. Wolan, “Identification of an N-aceacetylneuraminic acid-presenting bacteria isolated from a human microbiome,” Scientific Reports (2021).
49.   Q. Zhu, U. Mai, W. Pfeiffer, S. Janssen, F. Asnicar, J.G. Sanders, et al., “Phylogenomics of 10,575 genomes reveals evolutionary proximity between domains Bacteria and Archaea,” Nature Communications (2019).
48.    S.M. Strande, H.Cai, T. Cooper, K. Flammer, C. Irving, G. von Laszewski, et al., “Comet: Tales from the Long Tail: Two Years In and 10,000 Users Later,” Proc. PEARC17, New Orleans LA (2017).
47.    W. Pfeiffer, J. Braun, J. Burchell, C.L. Witte, and B.A. Rideout, “Whole-genome analysis of mycobacteria from birds at the San Diego Zoo,” PLoS ONE (2017).
46.    M.A. Miller, T. Schwartz, and W. Pfeiffer, The CIPRES Science Gateway after seven years: Lessons learned and best practices. Proc. Gateways 2016, San Diego, CA (2016).
45.    M.A. Miller, T. Schwartz, and W. Pfeiffer, “User behavior and usage patterns for a highly accessed science gateway,” Proc. XSEDE16, Miami FL (2016).
44.    K.A. Standish, T.M. Carland, G.K. Lockwood, W. Pfeiffer, M. Tatineni, C. Huang, et al., “Group-based variant calling leveraging next-generation supercomputing for large-scale whole-genome sequencing studies,” BMC Bioinfomatics, 16:304 (2015)
43.    R.L. Moore, C. Baru, D. Baxter, G. Fox, A. Majumdar, P. Papadopoulos, et al., “Gateways to Discovery: Cyberinfrastructure for the Long Tail of Science,” Proc. XSEDE14, Atlanta GA (2014).
42.    H. Holstege, W. Pfeiffer, D. Sie, M. Hulsman, T.J. Nicholas, C.C. Lee, et al., “Somatic mutations found in the healthy blood compartment of a 115-year-old woman demonstrate oligoclonal hematopoiesis,” Genome Res. 24, 733-742 (2014).
41.    M.A. Miller, T. Schwartz, and W. Pfeiffer, (2013). “Embedding CIPRES Science Gateway Capabilities in Phylogenetics Software Environments,” Proc. XSEDE13, San Diego CA (2013).
40.    M.A. Miller, W. Pfeiffer, and T. Schwartz, “The CIPRES Science Gateway: Enabling High-Impact Science for Phylogenetics Researchers with Limited Resources,” Proc. XSEDE12, Chicago IL (2012).
39.    R.L. Moore, D.L. Hart, W. Pfeiffer, M. Tatineni, K. Yoshimoto, and W.S. Young, “Trestles: A High-Productivity HPC System Targeted to Modest-Scale and Gateway Users,” Proc. TeraGrid ‘11, Salt Lake City UT (2011).
38.    M.A. Miller, W. Pfeiffer, and T. Schwartz, “The CIPRES Science Gateway: A Community Resource for Phylogenetic Analyses,” Proc. TeraGrid ’11, Salt Lake City UT (2011).
37.    M.A. Miller, W. Pfeiffer, and T. Schwartz, “Creating the CIPRES Science Gateway for Inference of Large Phylogenetic Trees,” Proc. Gateway Computing Environments Workshop (GCE) 2010, New Orleans LA (2010).
36.    W. Pfeiffer and A. Stamatakis, “Hybrid MPI/Pthreads Parallelization of the RAxML Phylogenetics Code,” Proc. HiCOMB 2010, Atlanta GA (2010).
35.    N.J. Wright, W. Pfeiffer, and A. Snavely, “Characterizing Parallel Scaling of Scientific Applications using IPM,” Proc. 10th LCI Intl. Conf. On High-Performance Clustered Computing, Boulder CO (2009).
34.    W. Pfeiffer and N.J. Wright, “Modeling and Predicting Application Performance on Parallel Computers Using HPC Challenge Benchmarks,” Proc. IPDPS 2008, Miami FL (2008).
33.    G. Almasi, et al., “Unlocking the Performance of the BlueGene/L Supercomputer,” Proc. SC2004, Pittsburgh PA (2004).
32.    W. Pfeiffer, “Memory Performance Model for Loops and Kernels on Power3 Processors,” Proc. PMEO-PDS ’04, Santa Fe NM (2004).
31.    P. Messina, D. Culler, W. Pfeiffer, W. Martin, J.T. Oden, and G. Smith, “Architecture,” Communications of the ACM 41, 36 (1998).
30.    W. Pfeiffer and J. Kim, “Autotasking Performance on the CRAY Y-MP,” in Cray User Group 1991 Fall Proceedings, Santa Fe NM, 292 (1991).
29.    W.A. Houlberg, et al., “Modeling Transport in Toroidal Plasmas: Status and Issues,” Phys. Fluids B 2, 2913 (1990).
28.    P. Messina, et al., “Benchmarking Advanced Architecture Computers,” Concurrency: Practice and Experience 2, 195 (1990).
27.    W. Pfeiffer, A. Alagar, A. Kamrath, R.H. Leary, and J. Rogers, “Benchmarking and Optimization of Scientific Codes on the CRAY X-MP, CRAY-2, and SCS-40 Vector Computers,” The J. of Supercomputing 4, 131 (1990).
26.    R.J. Groebner, W. Pfeiffer, et al., “Experimentally Inferred Ion Thermal Diffusivity Profiles in the Doublet III Tokamak:  Comparison With Neoclassical Theory,” Nucl. Fusion 26, 543 (1986).
25.    W. Pfeiffer, ” Computing at the San Diego Supercomputer Center, University of California at San Diego,” IEEE Software 2(6), 60 (November 1985).
24.    J.C. DeBoo, et al, “Beta and Confinement Experiments on Doublet III With High Power Neutral Beam Heating,” Sov. J. Plasma Phys. 11, 40 (1985).
23.    L.L. Lao, H. St. John, R.D. Stambaugh, A.G. Kellman, and W. Pfeiffer, “Reconstruction of Current Profile Parameters and Plasma Shapes in Tokamaks,” Nucl. Fusion 25, 1611 (1985).
22.    L.L. Lao, H. St. John, R.D. Stambaugh, and W. Pfeiffer, “Separation of p and ℓi in Tokamaks of Non-Circular Cross-Section,” Nucl. Fusion 25, 1421 (1985).
21.    W. Pfeiffer, “Double Sawtooth Oscillations in the Doublet III Tokamak,” Nucl. Fusion 25, 673 (1985).
20.    W. Pfeiffer, F.B. Marcus, C.J. Armentrout, G.L. Jahns, T.W. Petrie, and R.E. Stockdale, “Giant Sawtooth Oscillations in the Doublet III Tokamak,” Nucl. Fusion 25, 655 (1985).
19.    N. Ohyabu, et al., “A Regime of Improved Energy Confinement in Beam-Heated Expanded-Boundary Discharges in Doublet III,” Nucl. Fusion 25, 49 (1985).
18.    M. Nagami, et al., “High-Beta Injection Experiments With Shaped Plasmas in Doublet-III,” in Plasma Physics and Controlled Nuclear Fusion Research (Proc. 9th Int. Conf., Baltimore MD, 1982), IAEA, Vienna, Vol. 1, 27 (1983).
17.    P.C. Liewer, W. Pfeiffer, and R.E. Waltz, “Determination of Electron and Ion Thermal Conductivities by Analysis of Alcator-A Profile Data,” Phys. Fluids 26, 563 (1983).
16.    K.H. Burrell, et al., “Attainment of Reactor Level Volume-Averaged Toroidal Beta in Doublet III,” Nucl. Fusion 23, 535 (1983).
15.    S. Ejima, et al., “Scaling of Energy Confinement With Minor Radius, Current and Density in Doublet III Ohmically Heated Plasmas,” Nucl. Fusion 22, 1627 (1982).
14.    M. Nagami, et al., “Simplified Poloidal Divertor Experiments in Doublet III,” in Plasma Physics and Controlled Nuclear Fusion Research (Proc. 8th Int. Conf., Brussels, 1980), IAEA, Vienna, Vol. 2, 367 (1981).
13.    R.W. Moore, et al., “Optimization and Control of Plasma Shape and Current Profile in Non-Circular Cross-Section Tokamaks,” in Plasma Physics and Controlled Nuclear Fusion Research (Proc. 8th Int. Conf., Brussels, 1980), IAEA, Vienna, Vol. 1, 283 (1981).
12.    J.C. Wesley, et al., “Shaping and Characteristics of Ohmically Heated Non-Circular Plasmas in Doublet III,” in Plasma Physics and Controlled Nuclear Fusion Research (Proc. 8th Int. Conf., Brussels, 1980), IAEA, Vienna, Vol. 1, 35 (1981).
11.    M.R. Rosenberg, R.R. Dominguez, W. Pfeiffer, and R.E. Waltz, “Linear Kinetic Theory of High-m Tearing Modes,” Phys. Fluids 23, 2022 (1980).
10.    R.E. Waltz, W. Pfeiffer, and R.R. Dominguez, “Convective Amplification of Drift Waves and Thermal Fluctuation Levels in a Stable Plasma,” Phys. Fluids 23, 985 (1980).
9.    R.E. Waltz, W. Pfeiffer, and R.R. Dominguez, “Coupling of Drift Modes in a Torus,” Phys. Fluids 23, 605 (1980).
8.    R.E. Waltz, W. Pfeiffer, and R.R. Dominguez, “Electrostatic Drift Waves in Tokamaks: A Numerical Study of Instability and Transport,” Nucl. Fusion 20, 43 (1980).
7.    W. Pfeiffer, “A Graphical Method for Finding Complex Roots and Its Application to Plasma Physics Problems,” J. Comp. Phys. 33, 387 (1979).
6.    W. Pfeiffer and R.E. Waltz, “Empirical Scaling Laws for Energy Confinement in Ohmically Heated Tokamaks,” Nucl. Fusion 19, 51 (1979).
5.    R.L. Freeman, et al., “Doublet Research at General Atomic Company,” in Plasma Physics and Controlled Nuclear Fusion Research (Proc. 7th Int. Conf., Innsbruck, 1978), IAEA, Vienna, Vol. 1, 157 (1979).
4.    W. Pfeiffer, J.R. Brown, and A.C. Marshall, “Analysis and Results of Pulsed-Neutron Experiments on the Fort St. Vrain High-Temperature Gas-Cooled Reactor,” Nucl. Technol. 27, 352 (1975).
3.   W. Pfeiffer, “Computer Simulation of Pulsed-Neutron Experiments Performed on the Fort St. Vrain High-Temperature Gas-Cooled Reactor,” Nucl. Technol. 27, 337 (1975).
2.   W. Pfeiffer and J.L. Shapiro, “Reflection and Transmission Functions in Reactor Physics,” Nucl. Sci. Eng. 38, 253 (1969).
1.    W.W. Pfeiffer and J.L. Shapiro, “Applications of a Macroscopic Formulation of Transport Theory,” Nucl. Sci. Eng. 34, 336 (1968).

TECHNICAL REPORTS
8.    W. Pfeiffer, et al., “Evaluation of a Multithreaded Architecture for Defense Applications,” SDSC Technical Report SDSC TR-1999-1 (1999).
7.    W. Pfeiffer, S. Hotovy, N.A. Nystrom, D. Rudy, T. Sterling, and M. Straka, “JNNIE: The Joint NSF-NASA Initiative on Evaluation,” SDSC Report GA-A22123 (1995).
6.    W. Pfeiffer, J.L. Luxon, F.B. Marcus, and R.E. Waltz, “Confinement Analysis Procedures for Tokamak Plasmas of Noncircular Cross Section,” General Atomic Report GA-A16388 (1981).
5.    W. Pfeiffer, R.H. Davidson, R.L. Miller, and R.E. Waltz, “ONETWO:  A Computer Code for Modeling Plasma Transport in Tokamaks,” General Atomic Report GA-A16178 (1980).
4.    W. Pfeiffer, R.W. Moore, and R.H. Davidson, “Transport Simulation of Stable, High-Beta Equilibria in a Tokamak,” General Atomic Report GA-A16020 (1980).
3.    W. Pfeiffer, “SIGMA — A Code for Generating Multi-Group, Neutral-Plasma Cross Sections,” General Atomic Report GA-A14159 (1976).
2.    W. Pfeiffer, “Calculation of Neutral Transport in a Plasma Using a Neutron Transport  Method,” General Atomic Report GA-A13995 (1976).
1.    W. Pfeiffer, G. Malek, and K. Lund, “POKE:  A Gas-Cooled Reactor Flow and Thermal Analysis Code,” Gulf General Atomic Report GA-A10226 (1970).