Transformer architecture and attention mechanisms in genome data analysis: a comprehensive review

SR Choi, M Lee - Biology, 2023 - mdpi.com
Simple Summary The rapidly advancing field of deep learning, specifically transformer-
based architectures and attention mechanisms, has found substantial applicability in …

Precise integration of large DNA sequences in plant genomes using PrimeRoot editors

C Sun, Y Lei, B Li, Q Gao, Y Li, W Cao, C Yang… - Nature …, 2024 - nature.com
A technique for chromosomal insertion of large DNA segments is much needed in plant
breeding and synthetic biology to facilitate the introduction of desired agronomic traits and …

[HTML][HTML] Natural Language Processing in Medicine and Ophthalmology: A Review for the 21st-century clinician

W Rojas-Carabali, R Agrawal… - Asia-Pacific Journal of …, 2024 - Elsevier
ABSTRACT Natural Language Processing (NLP) is a subfield of artificial intelligence that
focuses on the interaction between computers and human language, enabling computers to …

Large language models in plant biology

HYI Lam, XE Ong, M Mutwil - Trends in Plant Science, 2024 - cell.com
Large language models (LLMs), such as ChatGPT, have taken the world by storm. However,
LLMs are not limited to human language and can be used to analyze sequential data, such …

HEAP: a task adaptive-based explainable deep learning framework for enhancer activity prediction

Y Liu, Z Wang, H Yuan, G Zhu… - Briefings in …, 2023 - academic.oup.com
Enhancers are crucial cis-regulatory elements that control gene expression in a cell-type-
specific manner. Despite extensive genetic and computational studies, accurately predicting …

Comprehensive Assessment of BERT-Based Methods for Predicting Antimicrobial Peptides

W Gao, J Zhao, J Gui, Z Wang, J Chen… - Journal of Chemical …, 2024 - ACS Publications
In recent years, the prediction of antimicrobial peptides (AMPs) has gained prominence due
to their high antibacterial activity and reduced susceptibility to drug resistance, making them …

iEnhancer-DLRA: identification of enhancers and their strengths by a self-attention fusion strategy for local and global features

L Zeng, Y Liu, ZG Yu, Y Liu - Briefings in Functional Genomics, 2022 - academic.oup.com
Identification and classification of enhancers are highly significant because they play crucial
roles in controlling gene transcription. Recently, several deep learning-based methods for …

deep-AMPpred: A Deep Learning Method for Identifying Antimicrobial Peptides and Their Functional Activities

J Zhao, H Liu, L Kang, W Gao, Q Lu… - Journal of Chemical …, 2025 - ACS Publications
Antimicrobial peptides (AMPs) are small peptides that play an important role in disease
defense. As the problem of pathogen resistance caused by the misuse of antibiotics …

RiceSNP-ABST: a deep learning approach to identify abiotic stress-associated single nucleotide polymorphisms in rice

Q Lu, J Xu, R Zhang, H Liu, M Wang, X Liu… - Briefings in …, 2025 - academic.oup.com
Given the adverse effects faced by rice due to abiotic stresses, the precise and rapid
identification of single nucleotide polymorphisms (SNPs) associated with abiotic stress traits …

Predmoter—cross-species prediction of plant promoter and enhancer regions

F Kindel, S Triesch, U Schlüter… - Bioinformatics …, 2024 - academic.oup.com
Motivation Identifying cis-regulatory elements (CREs) is crucial for analyzing gene
regulatory networks. Next generation sequencing methods were developed to identify CREs …