CD8+ T cells in HIV control, cure and prevention

DR Collins, GD Gaiha, BD Walker - Nature Reviews Immunology, 2020 - nature.com
HIV infection can be effectively treated by lifelong administration of combination antiretroviral
therapy, but an effective vaccine will likely be required to end the HIV epidemic. Although the …

Empirical fitness landscapes and the predictability of evolution

JAGM De Visser, J Krug - Nature Reviews Genetics, 2014 - nature.com
The genotype–fitness map (that is, the fitness landscape) is a key determinant of evolution,
yet it has mostly been used as a superficial metaphor because we know little about its …

[HTML][HTML] Preliminary identification of potential vaccine targets for the COVID-19 coronavirus (SARS-CoV-2) based on SARS-CoV immunological studies

SF Ahmed, AA Quadeer, MR McKay - Viruses, 2020 - mdpi.com
The beginning of 2020 has seen the emergence of COVID-19 outbreak caused by a novel
coronavirus, Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2). There is an …

Statistically learning the functional landscape of microbial communities

A Skwara, K Gowda, M Yousef… - Nature ecology & …, 2023 - nature.com
Microbial consortia exhibit complex functional properties in contexts ranging from soils to
bioreactors to human hosts. Understanding how community composition determines …

Inverse statistical problems: from the inverse Ising problem to data science

HC Nguyen, R Zecchina, J Berg - Advances in Physics, 2017 - Taylor & Francis
Inverse problems in statistical physics are motivated by the challenges of 'big data'in
different fields, in particular high-throughput experiments in biology. In inverse problems, the …

Epistatic models predict mutable sites in SARS-CoV-2 proteins and epitopes

J Rodriguez-Rivas, G Croce, M Muscat… - Proceedings of the …, 2022 - pnas.org
The emergence of new variants of severe acute respiratory syndrome coronavirus 2 (SARS-
CoV-2) is a major concern given their potential impact on the transmissibility and …

Coevolutionary landscape inference and the context-dependence of mutations in beta-lactamase TEM-1

M Figliuzzi, H Jacquier, A Schug… - Molecular biology …, 2016 - academic.oup.com
The quantitative characterization of mutational landscapes is a task of outstanding
importance in evolutionary and medical biology: It is, for example, of central importance for …

Turning ecology and evolution against cancer

KS Korolev, JB Xavier, J Gore - Nature Reviews Cancer, 2014 - nature.com
The fight against cancer has drawn researchers from a wide variety of disciplines, ranging
from molecular biology to physics, but the perspective of an ecological theorist has been …

Machine learning and data science in soft materials engineering

AL Ferguson - Journal of Physics: Condensed Matter, 2017 - iopscience.iop.org
In many branches of materials science it is now routine to generate data sets of such large
size and dimensionality that conventional methods of analysis fail. Paradigms and tools from …

Signatures of immune selection in intact and defective proviruses distinguish HIV-1 elite controllers

X Lian, C Gao, X Sun, C Jiang, KB Einkauf… - Science translational …, 2021 - science.org
Increasing evidence suggests that durable drug-free control of HIV-1 replication is enabled
by effective cellular immune responses that may induce an attenuated viral reservoir …