Please see my Google scholar profile here.
Andrews, Steven S. Light and Waves: A Conceptual Introduction to Physics Springer: Switzerland, 2023. ISBN: 978-3-031-24096-6. DOI: 10.1007/978-3-031-24097-3. website
Andrews, Steven S., H. Steven Wiley, and Herbert M. Sauro, "Design patterns of biological cells" BioEssays 2024. pdf video
Bilal Shaikh, Lucian P. Smith, Dan Vasilescu, Gnaneswara Marupilla, Michael Wilson, Eran Agmon, Henry Agnew, Steven S. Andrews, Azraf Anwar, Moritz E. Beber, Frank T. Bergmann, David Brooks, Lutz Brusch, Laurence Calzone, Kiri Choi, Joshua Cooper, John Detloff, Brian Drawert, Michel Dumontier, G. Bard Ermentrout, James R. Faeder, Andrew P. Freiburger, Fabian Frohlich, Akira Funahashi, Alan Garny, John H. Gennari, Padraig Gleeson, Anne Goelzer, Zachary Haiman, Jan Hasenauer, Joseph L. Hellerstein, Henning Hermjakob, Stefan Hoops, Jon C. Ison, Diego Jahn, Henry V. Jakubowski, Ryann Jordan, Matus Kalas, Matthias Konig, Wolfram Liebermeister, Rahuman S. Malik Sheriff, Synchon Mandal, Robert McDougal, J. Kyle Medley, Pedro Mendes, Robert Muller, Chris J. Myers, Aurelien Naldi, Tung V.N. Nguyen, David P. Nickerson, Brett G. Olivier, Drashti Patoliya, Loic Pauleve, Linda R. Petzold, Ankita Priya, Anand K. Rampadarath, Johann M. Rohwer, Ali S. Saglam, Dilawar Singh, Ankur Sinha 43, Jacky Snoep, Hugh Sorby, Ryan Spangler, Jorn Starruss, Payton J. Thomas, David van Niekerk, Daniel Weindl, Fengkai Zhang, Anna Zhukova, Arthur P. Goldberg, James C. Schaff, Michael L. Blinov, Herbert M. Sauro, Ion I. Moraru, and Jonathan R. Karr, "BioSimulators: a central registry of simulation engines and services for recommending specific tools" Nucleic Acids Research 50:W108-W114, 2022. pdf
Kochen, Michael A., Steven S. Andrews, H. Steven Wiley, Song Feng, and Herbert M. Sauro, "Dynamics and sensitivity of signaling pathways" Current Pathobiology Reports 10:11-22, 2022. pdf
Singh, Dilawar and Steven S. Andrews, "Python interfaces for the Smoldyn simulator" Bioinformatics 38:291-293, 2022. pdf
Steven S. Andrews and Roger Brent, "Individual yeast cells signal at different levels but each with good precision" 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
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
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. "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