40 citations · 143 across the 8 of their papers we have counts for
8 papers
Bézier interpolation improves the inference of dynamical models from data
Kai Shimagaki, John P. Barton
Many dynamical systems, from quantum many-body systems to evolving populations to financial markets, are described by stochastic processes. Parameters characterizing such processes…
Pathogenesis, Symptomatology, and Transmission of SARS-CoV-2 through Analysis of Viral Genomics and Structure
Halie M. Rando, Adam L. MacLean, Alexandra J. Lee +31
The novel coronavirus SARS-CoV-2, which emerged in late 2019, has since spread around the world and infected hundreds of millions of people with coronavirus disease 2019 (COVID-19)…
Studying viral populations with tools from quantum spin chains
Saumya Shivam, Christopher L. Baldwin, John Barton +2
We study Eigen's model of quasi-species, characterized by sequences that replicate with a specified fitness and mutate independently at single sites. The evolution of the populatio…
Inference of compressed Potts graphical models
Francesca Rizzato, Alice Coucke, Eleonora de Leonardis +4
We consider the problem of inferring a graphical Potts model on a population of variables, with a non-uniform number of Potts colors (symbols) across variables. This inverse Potts…
On the entropy of protein families
John Barton, Arup Chakraborty, Simona Cocco +2
Proteins are essential components of living systems, capable of performing a huge variety of tasks at the molecular level, such as recognition, signalling, copy, transport, ... The…
Identification of drug resistance mutations in HIV from constraints on natural evolution
Thomas C. Butler, John P. Barton, Mehran Kardar +1
Human immunodeficiency virus (HIV) evolves with extraordinary rapidity. However, its evolution is constrained by interactions between mutations in its fitness landscape. Here we sh…
Large Pseudo-Counts and -Norm Penalties Are Necessary for the Mean-Field Inference of Ising and Potts Models
J. P. Barton, S. Cocco, E. De Leonardis +1
Mean field (MF) approximation offers a simple, fast way to infer direct interactions between elements in a network of correlated variables, a common, computationally challenging pr…
Spin models inferred from patient data faithfully describe HIV fitness landscapes and enable rational vaccine design
Karthik Shekhar, Claire F. Ruberman, Andrew L. Ferguson +3
Mutational escape from vaccine induced immune responses has thwarted the development of a successful vaccine against AIDS, whose causative agent is HIV, a highly mutable virus. Kno…