Machine learning for antimicrobial resistance prediction: current practice, limitations, and clinical perspective

JI Kim, F Maguire, KK Tsang, T Gouliouris… - Clinical microbiology …, 2022 - Am Soc Microbiol
Antimicrobial resistance (AMR) is a global health crisis that poses a great threat to modern
medicine. Effective prevention strategies are urgently required to slow the emergence and …

Diffusion models in bioinformatics and computational biology

Z Guo, J Liu, Y Wang, M Chen, D Wang, D Xu… - Nature reviews …, 2024 - nature.com
Denoising diffusion models embody a type of generative artificial intelligence that can be
applied in computer vision, natural language processing and bioinformatics. In this Review …

Deep learning-based kcat prediction enables improved enzyme-constrained model reconstruction

F Li, L Yuan, H Lu, G Li, Y Chen, MKM Engqvist… - Nature Catalysis, 2022 - nature.com
Enzyme turnover numbers (k cat) are key to understanding cellular metabolism, proteome
allocation and physiological diversity, but experimentally measured k cat data are sparse …

Controlling gene expression with deep generative design of regulatory DNA

J Zrimec, X Fu, AS Muhammad, C Skrekas… - Nature …, 2022 - nature.com
Abstract Design of de novo synthetic regulatory DNA is a promising avenue to control gene
expression in biotechnology and medicine. Using mutagenesis typically requires screening …

A review of deep learning applications in human genomics using next-generation sequencing data

WS Alharbi, M Rashid - Human Genomics, 2022 - Springer
Genomics is advancing towards data-driven science. Through the advent of high-throughput
data generating technologies in human genomics, we are overwhelmed with the heap of …

Computational scoring and experimental evaluation of enzymes generated by neural networks

SR Johnson, X Fu, S Viknander, C Goldin… - Nature …, 2024 - nature.com
In recent years, generative protein sequence models have been developed to sample novel
sequences. However, predicting whether generated proteins will fold and function remains …

Enabling technology and core theory of synthetic biology

XE Zhang, C Liu, J Dai, Y Yuan, C Gao, Y Feng… - Science China Life …, 2023 - Springer
Synthetic biology provides a new paradigm for life science research (“build to learn”) and
opens the future journey of biotechnology (“build to use”). Here, we discuss advances of …

[HTML][HTML] Machine learning in clinical decision making

L Adlung, Y Cohen, U Mor, E Elinav - Med, 2021 - cell.com
Machine learning is increasingly integrated into clinical practice, with applications ranging
from pre-clinical data processing, bedside diagnosis assistance, patient stratification …

A foundational large language model for edible plant genomes

J Mendoza-Revilla, E Trop, L Gonzalez… - Communications …, 2024 - nature.com
Significant progress has been made in the field of plant genomics, as demonstrated by the
increased use of high-throughput methodologies that enable the characterization of multiple …

Designing artificial synthetic promoters for accurate, smart, and versatile gene expression in plants

E Yasmeen, J Wang, M Riaz, L Zhang, K Zuo - Plant Communications, 2023 - cell.com
With the development of high-throughput biology techniques and artificial intelligence, it has
become increasingly feasible to design and construct artificial biological parts, modules …