Home      Publications      Teaching      Software      Hardware      Dissertation

List of Publications

Please see my Google scholar profile here.

Page contents

Systems biology

Singh, Dilawar and Steven S. Andrews, "Python interfaces for the Smoldyn simulator" Bioinformatics submitted and BioRxiv, 2020.12.15.422958v2, 2020. pdf

Steven S. Andrews and Roger Brent, "Individual yeast cells signal at different levels but each with good precision" Science submitted and BioRxiv, 2020.01.15.906867, 2020. pdf

Steven S. Andrews, "Effects of surfaces and macromolecular crowding on bimolecular reaction rates" Physical Biology, 17:045001, 2020. pdf

Johnston, Stuart T., Christopher N. Angstmann, Satya N.V. Arjunan, Casper H.L. Beentjes, Adrien Coulier, Samuel A. Isaacson, Ash A. Khan, Karen Lipkow, and Steven S. Andrews, "Accurate particle-based reaction algorithms for fixed timestep simulators" 2018 MATRIX Annals, MATRIX Book Series 3:149-164 2020. pdf

Steven S. Andrews, "Rule-based modeling using wildcards in the Smoldyn simulator" Methods in Molecular Biology, 1945:179-202, 2019. pdf

Steven S. Andrews, Roger Brent, and Gabor Balazsi, "Transferring information without distortion" eLife, 2018. pdf

Steven S. Andrews, "Particle-based stochastic simulators" Encyclopedia of Computational Neuroscience, 2018. pdf

Steven S. Andrews, "Smoldyn: particle-based simulation with rule-based modeling, improved molecular interaction, and a library interface" Bioinformatics, 33:710-717, 2017. pdf

Steven S. Andrews, William J. Peria, Richard C. Yu, Alejandro Colman-Lerner, and Roger Brent, "Push-pull and feedback mechanisms can align signaling system outputs with inputs" Cell Systems, 3:444-455, 2016. pdf Supp Press release Commentary

Akintunde Emiola, Steven S. Andrews, Carolin Heller, and John George, "Crosstalk between the lipopolysaccharide and phospholipid pathways during outer membrane biogenesis in Escherichia coli" Proc. Natl. Acad. Sci. USA 113:3108-3113, 2016. pdf Supp1 Excel file

Steven S. Andrews and Suzannah Rutherford, "A method and on-line tool for maximum likelihood calibration of immunoblots and other measurements that are quantified in batches" PLoS ONE 11:e0149575, 2016. pdf

Akintunde Emiola, John George, and Steven S. Andrews, "A Complete Pathway Model for Lipid A Biosynthesis in Escherichia coli" PLoS ONE 10:e0121216, 2015. pdf

Martin Robinson, Steven S. Andrews, and Radek Erban, "Multiscale reaction-diffusion simulations with Smoldyn" Bioinformatics 31:2406-2408, 2015. pdf Supp1 Supp2

Steven S. Andrews, Satya N. V. Arjunan, Gianfranco Balbo, Arne T. Bittig, Jerome Feret, Kazunari Kaizu, and Fei Liu "Simulating macromolecular crowding with particle and lattice-based methods (Team 3)" In David Gilbert, Monika Heiner, Koichi Takahashi, and Adelinde M. Uhrmacher, eds. Multiscale Spatial Computational Systems Biology, pp. 170-187, 2015. pdf

Schmidt Hugo G., Sven Sewitz, Steven S. Andrews, and Karen Lipkow, "An Integrated Model of Transcription Factor Diffusion Shows the Importance of Intersegmental Transfer and Quaternary Protein Structure for Target Site Finding." PLoS ONE 9:e108575, 2014. pdf Supp1 Supp2 Supp3 Supp4

Claeys Bouuaert, Corentin, Karen Lipkow, Steven S. Andrews, Danxu Liu, and Ronald Chalmers, "The autoregulation of a eukaryotic DNA transposon" eLife, 2:e00668, 2013. pdf

Andrews, Steven S. "Spatial and stochastic cellular modeling with the Smoldyn simulator" In Bacterial Molecular Networks: Methods and Protocols, van Helden et al. (eds.) Methods for Molecular Biology 804:519-542, 2012. pdf

Gladkov, Denis V., Samuel Alberts, Roshan M. D'Souza, and Steven Andrews "Accelerating the Smoldyn spatial stochastic biochemical reaction network simulator using GPUs" Proceedings of the 19th High Performance Computing Symposia 2011. pdf

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. and Adam P. Arkin. "Simulated niche partitioning by bacteria." in Unifying Themes in Complex Systems Volume V, Proc. 5th Intl. Conf. on Complex Systems, Ali Minai, Dan Braha, and Yaneer Bar-Yam (Eds.) pp. 10-22, 2010. pdf

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. "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.


Steven S. Andrews and James Tretton, "The physical principles of circular dichroism" Journal of Chemical Education, 97:4370-4376, 2020. 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

Polymer Theory

Andrews, Steven S. "Physical models and computational methods for modeling cytoskeletal and DNA filaments" Physical Biology 11:011001, 2014. pdf Chosen as one of twelve Physical Biology highlights of 2014.

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

Book review

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

Selected posters

Andrews, Steven S. "Rule-based modeling using wildcards", 2017 pdf

Andrews, Steven S., Alejandro Colman-Lerner, and Roger Brent "Mechanisms for High Fidelity Cell Signaling", 2016 pdf

Andrews, Steven S. "Smoldyn: cell biology simulation with spatial detail", 2016 pdf

Andrews, Steven S., Richard Yu, Gustavo Pesce, and Roger Brent "Signaling mechanisms that can yield Dose-Response Alignment", 2012 pdf

Andrews, Steven S. and Karen Lipkow "Smoldyn: a Simulator for Cellular Systems Biology", 2008 pdf

Andrews, Steven S., Adeleh Moghaddam, and Jay T. Groves "Quantification of reaction rates in the E. coli Min system", 2006 pdf

Andrews, Steven S. and Adam P. Arkin "Mechanics explains coiled protein polymers in bacteria", 2006 pdf