Topology of viral evolution

By Joseph Chan, Gunnar E. Carlsson, Raul Rabadan. Proceedings of the National Academy of Sciences of the United States of America, 2013

300 citations recorded by the source corpus.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/225340cdc517405831bb91ed9da9ab38e8549c31

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Citations in the corpus

Random Walks on Simplicial Complexes and the normalized Hodge Laplacian (2018, background): “Simplicial complex models have been successful in developing new insights into biological data [32, 92], structural and functional connectivity in the brain [57,58,104], coverage of sensor networks [42,56,90,121], signal processing [8,115], mobility analysis [54], and robotics [105].”
A roadmap for the computation of persistent homology (2015, methodology): “coverage in sensor networks [37], protein structure [56,77,126], stability of fullerene molecules [125], robotics [10, 105, 119], signals in images [29, 65], periodicity in time series [102], breast-cancer classification [41, 99], viral evolution [25], natural images [23], contagion spread on networ”
Cliques and cavities in the human connectome (2016, background): “Cycle representatives have previously been considered in biology (Chan et al. 2013; Petri et al. 2014; Lord et al. 2016; Kim et al. 2014; Emmett et al. 2016; Mamuye et al. 2016), but to our knowledge this is a first attempt to compare topological features in multiple brains.”
Clique topology reveals intrinsic geometric structure in neural correlations (2015, methodology): “Comparison to prior applications in biology Topological data analysis has previously been used in biological applications to identify individual persistent cycles that may have meaningful interpretation [3, 4, 5, 6, 7, 8].”
Two’s company, three (or more) is a simplex (2016, background): “…for breast cancer survival (Nicolau et al, 2011), measurement of structure and stability of biomolecules (Gameiro et al, 2013; Xia et al, 2015), new frameworks for understanding viral evolution (Chan et al, 2013), and characterization of dynamics in gene regulatory networks (Boczko et al, 2005).”
What are higher-order networks? (2021, background): “Higher-order networks have also proven useful in genomics and evolutionary biology [59, 234], structural biology [289], as well as for the analysis of structures such as vascular networks [25,49,267].”