Addy, Nathan J. and Steven S. Andrews "Libmoleculizer: a library for generating biochemical species and reactions from protein interaction rules" Bioinformatics, submitted, 2010.
Andrews, Steven S. "Spatial and stochastic cellular modeling with the Smoldyn simulator" Methods for Molecular Biology, in press, 2010.
Andrews, Steven S., Nathan J. Addy, Roger Brent, and Adam P. Arkin "Detailed simulations of cell biology with Smoldyn 2.1" PLoS Comp. Biol. 6:e1000705, 2010. pdf SuppA SuppB SuppC SuppD
Andrews, Steven S. "Accurate particle-based simulation of adsorption, desorption, and partial transmission" Phys. Biol. 6:046015, 2009. pdf SuppA SuppB SuppC SuppD
Andrews, Steven S., Tuan Dinh, and Adam P. Arkin. "Stochastic models of biological processes" Encyclopedia of Complexity and System Science, Meyers, Robert (Ed.) Volume 9:8730-8749. Springer, NY, 2009. pdf
Yu, Richard C., Orna Resnekov, Pia Abola, Steven S. Andrews, Kirsten R. Benjamin, Jehoshua Bruck, Ian Burbulis, Alejandro Colman-Lerner, Drew Endy, Andrew Gordon, Mark Holl, Larry Lok, Robert Maxwell, Gustavo Pesce, Eduard Serra, Richard D. Smith, Ty Thomson, Annie Tsong, and Roger Brent. "The Alpha project, a model system for systems biology research" IEEE Sys. Biol. 2:222-233, 2008. pdf
Andrews, Steven S. and Adam P. Arkin. "A mechanical explanation for cytoskeletal rings and helices in bacteria." Biophys. J. 93:1872-1884, 2007. pdf Supp correction
Andrews, Steven S. and Adam P. Arkin. "Systems biology: A switch for sex." Curr. Biol. 17:R410, 2007. pdf (Dispatch about Ingolia and Murray, Curr. Biol. 17:668, 2007.)
Andrews, Steven S. and Adam P. Arkin. "Simulating cell biology." Curr. Biol. 16:R523, 2006. pdf
Andrews, Steven S. and Adam P. Arkin. "Simulated niche partitioning by bacteria." Proc. Intl. Conf. on Complex Systems, 2005. pdf
Andrews, Steven S. "Serial rebinding of ligands to clustered receptors as exemplified by bacterial chemotaxis." Phys. Biol. 2:111-122, 2005. pdf
Lipkow, Karen, Steven S. Andrews, and Dennis Bray. "Simulated diffusion of phosphorylated CheY through the cytoplasm of Escherichia coli." J. Bact., 187:45-53, 2005. pdf commentary
Adelman, Joshua L. and Steven S. Andrews. "Intracellular pattern formation: A spatial stochastic model of bacterial division site selection proteins MinCDE." Proc. Santa Fe Inst. Summer School, 2004. pdf
Goldman, Jacki, Steven S. Andrews, and Dennis Bray "Size and composition of membrane protein clusters predicted by Monte Carlo analysis" Eur. Biophys. J. 33:506-512, 2004. pdf
Andrews, Steven S. and Dennis Bray. "Stochastic simulation of chemical reactions with spatial resolution and single molecule detail." Phys. Biol., 1:137-151, 2004. pdf Supp1 Supp2 Chosen as one of six Physical Biology highlights of 2004-2005. Single most cited paper in Physical Biology between 2004 (journal inception) and 2008.
Andrews, Steven S. Review of System Modeling in Cellular Biology: From Concepts to Nuts and Bolts, edited by Zoltan Szallasi, Jörg Stelling, and Vipul Periwal. The Quarterly Review of Biology, 82:145, 2007. pdf
Andrews, Steven S. "Using rotational averaging to calculate the bulk response of isotropic and anisotropic samples from molecular parameters" J. Chem. Ed. 81:877-885, 2004. pdf
Treynor, Thomas P., Steven S. Andrews, and Steven G. Boxer. "Intervalence band Stark effect of the special pair radical cation in bacterial photosynthetic reaction centers." J. Phys. Chem. B 107:11230-11239, 2003. pdf
Andrews, Steven S. and Steven G. Boxer. "Vibrational Stark effects of nitriles. II. Physical origins of effects from experiment and perturbation models." J. Phys. Chem. A 106:469-477, 2002. pdf
Andrews, Steven S. and Steven G. Boxer. "Analysis of noise for rapid-scan and step-scan FTIR difference spectroscopy." Appl. Spectrosc. 55:1161-1165, 2001. pdf
Andrews, Steven S. and Steven G. Boxer "Vibrational Stark effects of nitriles. I. Methods and experimental results" J. Phys. Chem. A 104:11853-11863, 2000. pdf
Andrews, Steven S. and Steven G. Boxer "A liquid nitrogen immersion cryostat for optical measurements" Rev. Sci. Instrum. 71:3567-3569, 2000. pdf
Park, Eun Sun, Steven S. Andrews, Robert B. Hu, and Steven G. Boxer "Vibrational Stark spectroscopy in proteins: A probe and calibration for electrostatic fields" J. Phys. Chem. B 103:9813-9817, 1999. pdf
Zafiriou, Oliver C., Steven S. Andrews, and Wei Wang "Concordant estimates of oceanic carbon monoxide source and sink processes in the Pacific yield a balanced global ‘blue-water’ CO budget" Global Biogeochem. Cycles 17:1015, 2003. pdf
Xie, Huixiang, Steven S. Andrews, William R. Martin, Jared Miller, Lori Ziolkowski, Craig D. Taylor, and Oliver C. Zafiriou "Validated methods for sampling and headspace analysis of carbon monoxide in seawater" Mar. Chem. 77:93-108, 2002. pdf
Andrews, Steven S., Sigalit Caron, and Oliver C. Zafiriou "Photochemical oxygen consumption in marine waters: A major sink for colored dissolved organic matter?" Limnol. Oceanog. 45:267-277, 2000. pdf
Weiss, Peter S., Steven S. Andrews, James E. Johnson, and Oliver C. Zafiriou "Photoproduction of carbonyl sulfide in South Pacific Ocean waters as a function of irradiation wavelength" Geophys. Res. Lett. 22:215-218, 1995. pdf
Lipson, J.E.G. and S.S. Andrews "A Born-Green-Yvon integral equation treatment of a compressible fluid" J. Chem. Phys. 96:1426-1434, 1992. pdf
Andrews, Steven S. and Karen Lipkow "Smoldyn: a Simulator for Cellular Systems Biology" Presented at the Institute for Mathematics and its Applications Conference, Minneapolis, MN, May 2008, and at Apple's Worldwide Developers Conference, San Francisco, CA, June 2008. pdf
Andrews, Steven S., Adeleh Moghaddam, and Jay T. Groves "Quantification of reaction rates in the E. coli Min system" Presented at the American Chemical Society Conference, San Francisco, CA, September 2006. pdf
Andrews, Steven S. and Adam P. Arkin "Mechanics explains coiled protein polymers in bacteria" Presented at the Keystone Symposium on Computational Biology, Taos, NM, March 2006. pdf