Acquisition and analysis of DIA-based proteomic data: A comprehensive survey in 2023

R Lou, W Shui - Molecular & Cellular Proteomics, 2024 - ASBMB
Data-independent acquisition (DIA) mass spectrometry (MS) has emerged as a powerful
technology for high-throughput, accurate, and reproducible quantitative proteomics. This …

FM-FCN: a neural network with filtering modules for accurate vital signs extraction

F Zhu, Q Niu, X Li, Q Zhao, H Su, J Shuai - Research, 2024 - spj.science.org
Neural networks excel at capturing local spatial patterns through convolutional modules, but
they may struggle to identify and effectively utilize the morphological and amplitude periodic …

oBABC: A one-dimensional binary artificial bee colony algorithm for binary optimization

F Zhu, Z Shuai, Y Lu, H Su, R Yu, X Li, Q Zhao… - Swarm and Evolutionary …, 2024 - Elsevier
Artificial bee colony (ABC) algorithm is a widely utilized swarm intelligence (SI) algorithm for
addressing continuous optimization problems. However, most binary variants of ABC …

Artificial intelligence-based evaluation of prognosis in cirrhosis

Y Zhai, D Hai, L Zeng, C Lin, X Tan, Z Mo, Q Tao… - Journal of Translational …, 2024 - Springer
Cirrhosis represents a significant global health challenge, characterized by high morbidity
and mortality rates that severely impact human health. Timely and precise prognostic …

AttnPep: A Self-Attention-Based Deep Learning Method for Peptide Identification in Shotgun Proteomics

Y Li, Q He, H Guo, SC Shuai, J Cheng… - Journal of proteome …, 2024 - ACS Publications
In shotgun proteomics, the proteome search engine analyzes mass spectra obtained by
experiments, and then a peptide-spectra match (PSM) is reported for each spectrum …

ProPept-MT: A Multi-Task Learning Model for Peptide Feature Prediction

G He, Q He, J Cheng, R Yu, J Shuai, Y Cao - International Journal of …, 2024 - mdpi.com
In the realm of quantitative proteomics, data-independent acquisition (DIA) has emerged as
a promising approach, offering enhanced reproducibility and quantitative accuracy …

LMCD-OR: a large-scale, multilevel categorized diagnostic dataset for oral radiography

J Zhu, L Zeng, Z Mo, L Cao, Y Wu, L Hong… - Journal of Translational …, 2024 - Springer
In recent years, digital dentistry has increasingly utilized advanced image analysis
techniques, such as image classification and disease diagnosis, to improve clinical …

UNet-Att: a self-supervised denoising and recovery model for two-photon microscopic image

Y Lu, Y Ying, C Lin, Y Wang, J **, X Jiang… - Complex & Intelligent …, 2025 - Springer
Two-photon microscopy is indispensable in cell and molecular biology for its high-resolution
visualization of cellular and molecular dynamics. However, the inevitable low signal-to-noise …

Dear‐PSM: A deep learning‐based peptide search engine enables full database search for proteomics

Q He, X Li, J Zhong, G Yang, J Han, J Shuai - Smart Medicine, 2024 - Wiley Online Library
Peptide spectrum matching is the process of linking mass spectrometry data with peptide
sequences. An experimental spectrum can match thousands of candidate peptides with …