Artificial intelligence-based multi-omics analysis fuels cancer precision medicine

X He, X Liu, F Zuo, H Shi, J Jing - Seminars in Cancer Biology, 2023 - Elsevier
With biotechnological advancements, innovative omics technologies are constantly
emerging that have enabled researchers to access multi-layer information from the genome …

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 …

[HTML][HTML] SCENIC+: single-cell multiomic inference of enhancers and gene regulatory networks

C Bravo González-Blas, S De Winter, G Hulselmans… - Nature …, 2023 - nature.com
Joint profiling of chromatin accessibility and gene expression in individual cells provides an
opportunity to decipher enhancer-driven gene regulatory networks (GRNs). Here we present …

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 …

[PDF][PDF] Chromatin accessibility in the Drosophila embryo is determined by transcription factor pioneering and enhancer activation

KJ Brennan, M Weilert, S Krueger, A Pampari, H Liu… - Developmental cell, 2023 - cell.com
Chromatin accessibility is integral to the process by which transcription factors (TFs) read out
cis-regulatory DNA sequences, but it is difficult to differentiate between TFs that drive …

[HTML][HTML] Interpreting biologically informed neural networks for enhanced proteomic biomarker discovery and pathway analysis

E Hartman, AM Scott, C Karlsson, T Mohanty… - Nature …, 2023 - nature.com
The incorporation of machine learning methods into proteomics workflows improves the
identification of disease-relevant biomarkers and biological pathways. However, machine …

Emotion recognition in EEG signals using deep learning methods: A review

M Jafari, A Shoeibi, M Khodatars… - Computers in Biology …, 2023 - Elsevier
Emotions are a critical aspect of daily life and serve a crucial role in human decision-making,
planning, reasoning, and other mental states. As a result, they are considered a significant …

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 …

Sequence basis of transcription initiation in the human genome

K Dudnyk, D Cai, C Shi, J Xu, J Zhou - Science, 2024 - science.org
Transcription initiation is a process that is essential to ensuring the proper function of any
gene, yet we still lack a unified understanding of sequence patterns and rules that explain …

Artificial intelligence-based risk stratification, accurate diagnosis and treatment prediction in gynecologic oncology

Y Jiang, C Wang, S Zhou - Seminars in Cancer Biology, 2023 - Elsevier
As data-driven science, artificial intelligence (AI) has paved a promising path toward an
evolving health system teeming with thrilling opportunities for precision oncology …