Below are papers on “algorithms in nature” that I have read and enjoyed. I tried to restrict the papers to only those that study a detailed biological mechanism. I am more forgiving in the other direction; i.e., I included papers that did not propose an algorithm but that make a biological observation that seems to me ripe for algorithmic translation.
Reviews and perspectives
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- Information processing and distributed computation in plant organs. G. Bassel. Trends in Plant Science, 2018.
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- Distributed information processing in biological and computational systems. S. Navlakha and Z. Bar-Joseph. Commun. ACM, 2015.
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- Design principles of regulatory networks: searching for the molecular algorithms of the cell. W.A. Lim et al. Cell 2013.
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- Algorithms in nature: the convergence of systems biology and computational thinking. S. Navlakha and Z. Bar-Joseph. Mol. Sys. Biol., 2011.
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- Algorithmic systems biology. C. Priami. Commun. ACM, 2009.
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- Executable cell biology. J. Fisher and T.A. Henzinger. Nat. Biotechnol., 2007.
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- Protein molecules as computational elements in living cells. D. Bray. Nature, 1995.
Molecular biology
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- Optimal regulatory circuit topologies for fold-change detection. Adler et al., Cell. Syst., 2017
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- Parallel computation with molecular-motor-propelled agents in nanofabricated networks. Nicolau et al. Proc. Natl. Acad. Sci. U.S.A., 2016.
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- Robustness and compensation of information transmission of signaling pathways. Uda et al. Science, 2013.
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- Evidence of non-random mutation rates suggests an evolutionary risk management strategy. Martincorena et al. Nature, 2012.
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- The cell cycle switch computes approximate majority. L. Cardelli and A. Csikasz-Nagy. Sci. Rep., 2012.
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- A biological solution to a fundamental distributed computing problem. Y. Afek et al. Science, 2011.
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- Evolution of a modular software network. M. Fortuna et al. Proc. Natl. Acad. Sci. U.S.A., 2011.
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- Information transduction capacity of noisy biochemical signaling networks. R. Cheong et al. Science, 2011.
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- Comparing genomes to computer operating systems in terms of the topology and evolution of their regulatory control networks. K-K. Yan et al. Proc. Natl. Acad. Sci. U.S.A., 2010.
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- Defining network topologies that can achieve biochemical adaptation. Ma et al. Cell, 2009.
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- Spontaneous evolution of modularity and network motifs. N. Kashtan and U. Alon. Proc. Natl. Acad. Sci. U.S.A., 2005.
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- Intracellular signaling as a parallel distributed process. D. Bray. J. Theor. Biol., 1990.
Cellular biology
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- A living mesoscopic cellular automaton made of skin scales. L. Manukyan et al. Nature, 2017.
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- Decision-making without a brain: how an amoeboid organism solves the two-armed bandit Reid et al., J. Roy. Soc. Interface, 2016
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- Greedy scheduling of cellular self-replication leads to optimal doubling times with a log-Frechet distribution. R. Pugatch. Proc. Natl. Acad. Sci. U.S.A., 2015.
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- Universal distribution of component frequencies in biological and technological systems. T. Pang and S. Maslov. Proc. Natl. Acad. Sci. U.S.A., 2013.
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- Slime mold uses an externalized spatial “memory” to navigate in complex environments. Reid et al. Proc. Natl. Acad. Sci. U.S.A., 2012.
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- Energetic costs of cellular computation. Mehta and Schwab. Proc. Natl. Acad. Sci. U.S.A., 2012.
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- Smart swarms of bacteria-inspired agents with performance adaptable interactions. A. Shklarsh et al. PLoS Comput. Biol., 2011.
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- Rules for biologically inspired adaptive network design. A. Tero et al. Science, 2010.
Neuroscience
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- A neural data structure for novelty detection. S. Dasgupta et al. Proc. Natl. Acad. Sci. U.S.A., 2018.
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- A neural algorithm for a fundamental computing problem. S. Dasgupta et al. Science, 2017.
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- Decreasing-rate pruning optimizes the construction of efficient and robust distributed networks. Navlakha et al. PLoS Comput. Biol., 2015.
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- A visual motion detection circuit suggested by Drosophila connectomics. Takemura et al., Nature, 2013
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- Efficient physical embedding of topologically complex information processing networks in brains and computer circuits. Bassett et al. PLoS Comput. Biol., 2010.
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- A neuromorphic approach to computer vision. T. Serre and T. Poggio. Commun. ACM, 2010.
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- One rule to grow them all: a general theory of neuronal branching and its practical application. Cuntz et al. PLoS Comput. Biol., 2010.
Plant biology
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- High-resolution laser scanning reveals plant architectures that reflect universal network design principles. A. Conn et al. Cell Syst., 2017.
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- Rumor has it…: Relay communication of stress cues in plants. Falik et al. PLoS One, 2012.
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- Heliostat field optimization: A new computationally efficient model and biomimetic layout. Noone et al. Solar Energy, 2012
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- Hydraulic integration and shrub growth form linked across continental aridity gradients. H. J. Schenk et al. Proc. Natl. Acad. Sci. U.S.A., 2008.
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- Evidence for complex, collective dynamics and emergent, distributed computation in plants. D. Peak et al. Proc. Natl. Acad. Sci. U.S.A., 2004.
Insects & other organisms (e.g., fish, bats)
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- A distributed algorithm to maintain and repair the trail networks of arboreal ants. A. Chandrasekhar et al. Nature Sci. Rep., 2018.
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- How regulation based on a common stomach leads to economic optimization of honeybee foraging. Schmickl and Karsai. J. Theor. Biol., 2015.
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- Designing collective behavior in a termite-inspired robot construction team. Werfel et al. Science, 2014.
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- Space partitioning without territoriality in gannets. E. D. Wakefield et al. Science, 2013.
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- A universal strategy for visually guided landing. Baird et al. Proc. Natl. Acad. Sci. U.S.A., 2013.
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- The regulation of ant colony foraging activity without spatial information. Prabhakar et al. PLoS Comput. Biol., 2012.
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- Predatory fish select for coordinated collective motion in virtual prey. Ioannou et al. Science, 2012.
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- Fast and accurate decisions through collective vigilance in fish shoals. Ward et al. Proc. Natl. Acad. Sci. U.S.A., 2011.
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- Optimal localization by pointing off axis. Yovel et al. Science, 2010.
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- On optimal decision-making in brains and social insect colonies. J.A. Marshall et al. J. Roy. Soc. Interface, 2009.
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- Infotaxis as a strategy for searching without gradients. Vergassola et al. Nature, 2007.