A neutral network connects all genotypes with equivalent phenotypes in a fitness landscape and plays an important role in the mutational robustness and evolvability of biomolecules. In contrast to earlier theoretical works, evidence of large neutral ...
LTR-retrotransposons are the most abundant repeat sequences in plant genomes and play an important role in evolution and biodiversity. Their characterization is of great importance to understand their dynamics. However, the identification and classif...
Recent advances in machine learning have leveraged evolutionary information in multiple sequence alignments to predict protein structure. We demonstrate direct inference of full atomic-level protein structure from primary sequence using a large langu...
In evolutionary models, mutations are exogenously introduced by the modeler, rather than endogenously introduced by the replicator itself. We present a new deep-learning based computational model, the self-replicating artificial neural network (SeRAN...
Journal of computer-aided molecular design
38499823
Computer-aided drug design has advanced rapidly in recent years, and multiple instances of in silico designed molecules advancing to the clinic have demonstrated the contribution of this field to medicine. Properly designed and implemented platforms ...
Journal of chemical information and modeling
38687957
L2 β-lactamases, serine-based class A β-lactamases expressed by , play a pivotal role in antimicrobial resistance (AMR). However, limited studies have been conducted on these important enzymes. To understand the coevolutionary dynamics of L2 β-lactam...
The distinctive nature of cancer as a disease prompts an exploration of the special characteristics the genes implicated in cancer exhibit. The identification of cancer-associated genes and their characteristics is crucial to further our understandin...
IEEE/ACM transactions on computational biology and bioinformatics
38498763
Seasonal influenza vaccines play a crucial role in saving numerous lives annually. However, the constant evolution of the influenza A virus necessitates frequent vaccine updates to ensure its ongoing effectiveness. The decision to develop a new vacci...