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Biomedical subjects

Yibo Wang

Publications and source records attributed to Yibo Wang.

4 recordsLinked to original sources
PubMed2026

OmniExtract: an automatic data extraction tool based on large language model and prompt engineering.

Extracting structured information from documents or scientific papers is crucial for data sharing and retrieval. Recent advances in large language models (LLMs) have demonstrated strong capabilities in language understanding, and a number of LLM-based tools have been developed for extraction-oriented tasks. However, it's still difficult to find a universal and user-friendly tool for various practical extraction tasks. To address this challenge, we propose OmniExtract, an automatic data extraction tool with user-friendly configuration files that can adapt to various data extraction tasks. OmniExtract employs a prompt optimization method to refine task-specific prompts and achieve high extraction performance. It also supports comprehensive data extraction from both documents and tables, making it applicable to a broad range of data sources. Evaluation results show that OmniExtract obtains a high accuracy ~90% for three datasets. Furthermore, two additional data extraction applications of OmniExtract in real-world scenarios have been presented, achieving an accuracy of 92.21% and ~90% precision and recall, respectively. Specifically, OmniExtract can handle tabular files of various sizes and formats, and achieve over 99% precision and recall on table information extraction tasks. The data reliability performance shows that OmniExtract is a valuable tool for database updating. An online testing service is available at https://ngdc.cncb.ac.cn/omniextract/. The service can be deployed locally with the code in https://github.com/wyb39/OmniExtract.

Large Language Models↗
PubMed2026

Complete genome sequence of the first alphahypovirus from the phytopathogenic fungus Curvularia americana on Poa pratensis in China.

In the present study, a novel positive-sense single-stranded RNA virus was identified from Curvularia americana strain 32 - 2, a phytopathogenic fungus infecting Poa pratensis in China, which was designated as "Curvularia americana hypovirus 1" (CaHV1). The complete genome of CaHV1 consists of 14,386 nucleotides (nt) with a single large open reading frame (ORF) (nt position 593 to 14035). The ORF encodes a putative polyprotein (4,480 amino acids) containing two potential conserved domains, which includes a Domain of Unknown Function 3525 (DUF3525) and Helicase. BLASTp analysis showed that amino acid sequence of the polyprotein of CaHV1 shared the highest amino acid sequence identity with that of Bipolaris oryzae hypovirus 1 (63.52%). Phylogenetic analysis based on amino acid sequence of the polyprotein indicated that CaHV1 clustered together with members of the genus Alphahypovirus within the family Hypoviridae. To the best of our knowledge, this is the first report of an alphahypovirus infecting C. americana.

Genome, Viral↗
PubMed2026

A single small molecule-based human embryo model reveals V-ATPase requirement in mammalian blastocyst cavitation.

Human naïve pluripotent stem cells (nPSCs) can be induced by various combinations of signaling factors to generate blastocyst-like structures, termed blastoids. Despite rapid progress in human blastoid models, their potential to uncover fundamental mechanisms of early human development remains limited, leaving key morphogenetic processes poorly understood. Here, we describe a simple and robust system in which dimethyl sulfoxide (DMSO) alone induces blastoid formation from human nPSCs. This model recapitulates key pre- and post-implantation features and exhibits enhanced polar trophectoderm (TE) organization, more efficient attachment within an implantation-relevant window, improved epiblast lumenogenesis associated with amniotic cavity formation, and more robust, sustained expansion of embryonic lineages following attachment. Using this system, we reveal a previously unrecognized mechanism underlying TE cavitation and identify lysosome-associated genes - particularly subunits of the proton pump V-ATPase - as essential regulators of blastoid cavitation. DMSO treatment upregulates key V-ATPase subunits (ATP6V0A4 and ATP6V1B1), which are also enriched in the TE of human embryos. Genetic or pharmacological inhibition of V-ATPase activity disrupts lysosomal acidification, blocks intracellular vacuole formation, and impairs blastoid cavitation, whereas overexpression of V-ATPase subunits rescues this phenotype. Furthermore, genetic and pharmacological perturbations of V-ATPase function significantly compromise cavitation in both mouse and human blastocysts. Finally, DMSO treatment induces membrane biomechanical changes characteristic of early embryonic development, suggesting a mode of action distinct from conventional small-molecule, signaling pathway-based induction strategies. This simple DMSO-based blastoid model recapitulates key aspects of human blastocyst development and reveals a conserved requirement for V-ATPase-mediated lysosomal acidification during early mammalian embryogenesis.

Humans↗
PubMed2025

CRISPR-Cas9-mediated knockout of OsKCS11 in rice reveals potential crosstalk between very-long-chain fatty acids and cytokinin.

Very-long-chain fatty acids (VLCFAs) play crucial roles in various physiological processes in plants. Through our investigation using a CRISPR-Cas9 knockout mutant library in rice, we identified a semi-dwarf rice mutant named CRISPR-Cas-based dwarf-1 (csd-1). This mutant displayed multiple developmental defects, such as decreased plant height, panicle length, seed size, and seed-setting rate. Whole-genome resequencing analysis revealed that a T-nucleotide insertion in β-ketoacyl-CoA synthase 11 (KCS11), responsible for the initial step in fatty acid elongation, was responsible for the observed defects in csd-1. The identity of csd-1 was confirmed through genetic complementation and CRISPR-Cas9-mediated knockout. Expression analysis indicated that OsKCS11 was present in various tissues, with differential abundance observed through RT-qPCR and promoter GUS staining, and strong localization at the node position by RNA in situ hybridization; furthermore, OsKCS11 protein was confirmed to be in the endoplasmic reticulum. Furthermore, csd-1 exhibited significantly reduced levels of linolenic acid (18:3), C24:0-OH, C28:0-alkanes, C29:0-alkanes, alpha-tocopherol, and C33:0-alkanes, while trans-nonadecenoic acid and behenic acid levels were increased. Cytokinin analysis revealed significant increases in isopentenyladenine (IPA) and cis-zeatin (cZ) levels in csd-1. Molecular investigations indicated upregulation of genes involved in cytokinin biosynthesis or signaling, suggesting a potential link between VLCFAs and cytokinin synthesis through acetyl-CoA. This study not only proposed an alternative gene mapping method based on whole-genome resequencing but also elucidated the mechanism by which VLCFAs influence cytokinin synthesis and signaling.

Oryza↗