Machine learning-guided protein engineering

P Kouba, P Kohout, F Haddadi, A Bushuiev… - ACS …, 2023 - ACS Publications
Recent progress in engineering highly promising biocatalysts has increasingly involved
machine learning methods. These methods leverage existing experimental and simulation …

Variant calling and benchmarking in an era of complete human genome sequences

ND Olson, J Wagner, N Dwarshuis, KH Miga… - Nature Reviews …, 2023 - nature.com
Genetic variant calling from DNA sequencing has enabled understanding of germline
variation in hundreds of thousands of humans. Sequencing technologies and variant-calling …

JASPAR 2024: 20th anniversary of the open-access database of transcription factor binding profiles

I Rauluseviciute, R Riudavets-Puig… - Nucleic acids …, 2024 - academic.oup.com
Abstract JASPAR (https://jaspar. elixir. no/) is a widely-used open-access database
presenting manually curated high-quality and non-redundant DNA-binding profiles for …

Applying interpretable machine learning in computational biology—pitfalls, recommendations and opportunities for new developments

V Chen, M Yang, W Cui, JS Kim, A Talwalkar, J Ma - Nature methods, 2024 - nature.com
Recent advances in machine learning have enabled the development of next-generation
predictive models for complex computational biology problems, thereby spurring the use of …

Signaling pathways involved in colorectal cancer: Pathogenesis and targeted therapy

Q Li, S Geng, H Luo, W Wang, YQ Mo, Q Luo… - … and Targeted Therapy, 2024 - nature.com
Colorectal cancer (CRC) remains one of the leading causes of cancer-related mortality
worldwide. Its complexity is influenced by various signal transduction networks that govern …

[PDF][PDF] Artificial intelligence and machine learning in pharmacological research: bridging the gap between data and drug discovery

S Singh, R Kumar, S Payra, SK Singh - Cureus, 2023 - cureus.com
Artificial intelligence (AI) has transformed pharmacological research through machine
learning, deep learning, and natural language processing. These advancements have …

Gene regulatory network reconstruction: harnessing the power of single-cell multi-omic data

D Kim, A Tran, HJ Kim, Y Lin, JYH Yang… - NPJ Systems Biology and …, 2023 - nature.com
Inferring gene regulatory networks (GRNs) is a fundamental challenge in biology that aims
to unravel the complex relationships between genes and their regulators. Deciphering these …

Emerging applications of machine learning in genomic medicine and healthcare

N Chafai, L Bonizzi, S Botti… - Critical Reviews in Clinical …, 2024 - Taylor & Francis
The integration of artificial intelligence technologies has propelled the progress of clinical
and genomic medicine in recent years. The significant increase in computing power has …

To transformers and beyond: large language models for the genome

ME Consens, C Dufault, M Wainberg, D Forster… - arxiv preprint arxiv …, 2023 - arxiv.org
In the rapidly evolving landscape of genomics, deep learning has emerged as a useful tool
for tackling complex computational challenges. This review focuses on the transformative …

Harnessing deep learning for population genetic inference

X Huang, A Rymbekova, O Dolgova, O Lao… - Nature Reviews …, 2024 - nature.com
In population genetics, the emergence of large-scale genomic data for various species and
populations has provided new opportunities to understand the evolutionary forces that drive …