Comparative analyses of gene co-expression networks: Implementations and applications in the study of evolution

K Ovens, BF Eames, I McQuillan - Frontiers in Genetics, 2021 - frontiersin.org
Similarities and differences in the associations of biological entities among species can
provide us with a better understanding of evolutionary relationships. Often the evolution of …

Protein ensembles link genotype to phenotype

R Nussinov, CJ Tsai, H Jang - PLoS computational biology, 2019 - journals.plos.org
Classically, phenotype is what is observed, and genotype is the genetic makeup. Statistical
studies aim to project phenotypic likelihoods of genotypic patterns. The traditional genotype …

[HTML][HTML] Transcriptome-derived networks reconstruct distinct immune strategies to counteract fungal infection under different iron availability between Arabidopsis and …

A Garcia-Molina, H Martín-Cardoso, M Ribaya… - Plant Stress, 2025 - Elsevier
Fe, an essential element for plants to sustain central biological functions, recently emerged
as a modulator of immunity. However, our understanding of the crosstalk between Fe and …

Link prediction based on community information and its parallelization

J Wang, Y Ma, M Liu, W Shen - IEEE Access, 2019 - ieeexplore.ieee.org
Link prediction refers to predicting the likelihood of the existence of an unknown link or a
future link based on the observed information. It plays an important role in complex network …

An effective community-based link prediction model for improving accuracy in social networks

MM Iqbal, K Latha - Journal of Intelligent & Fuzzy Systems, 2022 - content.iospress.com
Link prediction plays a predominant role in complex network analysis. It indicates to
determine the probability of the presence of future links that depends on available …

Experimental and In Silico Analysis of TEM β-Lactamase Adaptive Evolution

M Standley, V Blay, V Beleva Guthrie, J Kim… - ACS infectious …, 2022 - ACS Publications
Multiple mutations often have non-additive (epistatic) phenotypic effects. Epistasis is of
fundamental biological relevance but is not well understood mechanistically. Adaptive …

Quantification of the resilience and vulnerability of HIV-1 native glycan shield at atomistic detail

S Chakraborty, ZT Berndsen, NW Hengartner… - IScience, 2020 - cell.com
Dense surface glycosylation on the HIV-1 envelope (Env) protein acts as a shield from the
adaptive immune system. However, the molecular complexity and flexibility of glycans make …

Strong selection of the TLR2 coding region among the Lagomorpha suggests an evolutionary history that differs from other mammals

F Neves, A Águeda-Pinto, A Pinheiro, J Abrantes… - Immunogenetics, 2019 - Springer
Toll-like receptors (TLRs) are one of the first lines of defense against pathogens and are
crucial for triggering an appropriate immune response. Among TLRs, TLR2 is functional in …

Evolutionary rewiring of the dynamic network underpinning allosteric epistasis in NS1 of influenza A virus

J Gonzales, I Kim, W Hwang, JH Cho - bioRxiv, 2024 - biorxiv.org
Viral proteins frequently mutate to evade or antagonize host innate immune responses, yet
the impact of these mutations on the molecular energy landscape remains unclear …

Transcriptome-derived networks reconstruct distinct immune strategies under different iron availability between Arabidopsis and rice

A Garcia-Molina, H Martín-Cardoso, M Ribaya… - 2024 - researchsquare.com
Fe, an essential element for plants to sustain central biological functions, recently emerged
as a modulator of immunity. However, our understanding of the crosstalk between Fe and …