Explanipedia

Incorporating LLM Embeddings for Variation Across the Human Genome Open

Hui Niu, Jordan Bryan, Xihao Li, Didong Li · 2025

Recent advances in large language model (LLM) embeddings have enabled powerful representations for biological data, but most applications to date focus only on gene-level information. We present one of the first systematic frameworks to ge…

A Porcine Monoclonal Antibody Targeting a Conserved GP4 Epitope Protects against In Vivo Infection via the Induction of Broad‐Spectrum PRRSV Neutralization Open

Xu Chen, Jiakai Zhao, Pinpin Ji, Xiaoxuan Li, Hui Niu , et al. · 2025

Porcine reproductive and respiratory syndrome virus (PRRSV) imposes substantial economic losses on global swine production. While modified live vaccines remain the primary prevention tool, their efficacy is compromised by the genetic varia…

Revealing lactylation-mediated mechanisms and hub genes in heart failure pathogenesis Open

Hongguang Xie, Yiqiang Wang, Xing Zhu, Lili Zhang, Hui Niu , et al. · 2025

Purpose This study explores lactylation's pivotal role in the disease progression of heart failure (HF). Methods The GSE57345 dataset, encompassing 177 HF samples and 136 normal controls (CTL), was sourced from Gene Expression Omnibus (GEO…

Incorporating Large Language Model-Derived Information into Hypothesis Testing for Genomics Open

Jordan Bryan, Hui Niu, Didong Li · 2025

We propose strategies for incorporating the information in large language models (LLMs) into statistical hypothesis tests in genomics studies. Using gene embeddings derived from text inputs to OpenAI’s GPT-3.5 model, we show that biologica…

Unraveling the impact of air pollution on serum lipid markers: a machine learning-driven risk assessment Open

Hui Niu, Jiayuan Feng, Hua Hao, Sijing Zhu, Xiao-Xue Li , et al. · 2025

Exploring the world of small proteins in plant biology and bioengineering Open

Louise Petri, Anne Van Humbeeck, Hui Niu, Casper Ter Waarbeek, Ashleigh Edwards , et al. · 2024

Small proteins are ubiquitous in all kingdoms of life. MicroProteins, initially characterized as small proteins with protein interaction domains that enable them to interact with larger multidomain proteins, frequently modulate the functio…

Sustainable food systems under environmental footprints: The delicate balance from farm to table Open

Hui Niu, Zhihe Li, Chunhong Zhang, Min‐Hui Li · 2024

In today's world, agriculture is not only about food production but also a critical factor in global environmental change, economic stability, and human health, among other aspects. With population growth and increasingly scarce resources,…

<i>Yinshan Zhengyao</i>: exploring the power of food and inheriting healthy thoughts Open

Hui Niu, Aruhan, Seesregdorj Surenjidiin, Liming Zhang, Chunhong Zhang , et al. · 2024

Yinshan Zhengyao stands as a classic in health preservation, gathering the principles of the homology of food and medicine. The book is divided into three volumes, emphasizing the significance of food in the prevention and treatment of chr…

Screening of mRNA markers in early bovine tuberculosis blood samples Open

Dongfeng Jiang, Xiaoyi Song, Liyu Yang, Zheng Li, Kaifeng Niu , et al. · 2024

Bovine tuberculosis (bTB) is a chronic zoonotic disease caused by Mycobacterium bovis . A large number of cattle are infected with bTB every year, resulting in huge economic losses. How to control bTB is an important issue in the current g…

Impact and Mechanisms of Digital Inclusive Finance in Relation to Farmland Transfer: Evidence from China Open

Ziqin Xu, Hui Niu, Yuxuan Wei, Yiping Wu, Yang Yu · 2024

Land use efficiency is primarily limited by the fragmentation of land management. China’s fragmented farmland poses a significant threat to the country’s food security and rural revitalization. Therefore, promoting land transfer to establi…

Analysis of lncRNA, miRNA, and mRNA Expression Profiling in Type I IFN and Type II IFN Overexpressed in Porcine Alveolar Macrophages Open

Congcong Li, Haoyuan Han, Xiuling Li, Jiao Wu, Xinfeng Li , et al. · 2021

Current data is scarce regarding the function of noncoding RNAs (ncRNAs) such as microRNAs (miRNAs) and long noncoding RNAs (lncRNAs) in the interferon- (IFN-) mediated immune response. This is a comprehensive study that analyzes the lncRN…

Immunomodulatory Effect of Colistin and its Protective Role in Rats with Methicillin-Resistant Staphylococcus aureus-induced Pneumonia Open

Hui Niu, Tianli Yang, Jin Wang, Rui Wang, Yun Cai · 2021

Objectives: Colistin is the last resort of antimicrobials against multi-drug resistant Gram-negative pathogens. Previous studies in Caenorhabditis elegans and macrophages of rats have suggested that colistin possesses the immunomodulatory …

Immunomodulatory Effects of Colistin on Macrophages in Rats by Activating the p38/MAPK Pathway Open

Jin Wang, Weili Shao, Hui Niu, Tianli Yang, Yuning Wang , et al. · 2019

Objectives: Colistin has been identified in a Caenorhabditis elegans chemical screening as an immunostimulatory agent that activates the conserved p38/PMK-1 pathway and provides protection against pathogens. Here we aimed to …

Long non-coding RNA AK027294 involves in the process of proliferation, migration, and apoptosis of colorectal cancer cells Open

Hui Niu, Zhaoyang Hu, Hui Liu, Guoliang Hu, Bo Yang , et al. · 2016

This study is aimed to investigate the differentially expressed long non-coding RNAs (lncRNAs) in colorectal cancer and its potential biological function. Colorectal adenoma is the precancerous lesions of colorectal cancer, so in this stud…

DNA sequence polymorphism within the bovine adenosine monophosphate deaminase 1 (AMPD1) is associated with production traits in Chinese cattle Open

Changyong Wei, J.-Q. Wang, F.-Y. Chen, Hui Niu, Ke Li · 2015

The objectives of the present study were to detect an 18-bp deletion mutation in the bovine adenosine monophosphate deaminase 1 (AMPD1) gene and analyze its effect on growth traits in 2 Chinese cattle breeds using DNA sequencing and agaros…

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