Biology subjects

Yuan, M.-L.

Publications and source records attributed to Yuan, M.-L..

3 recordsLinked to original sources

bioRxiv2026

dbGIST: An LLM-Assisted Multi-Omics Resource for Target Exploration and Cross-Dataset Validation in Gastrointestinal Stromal Tumors

Gastrointestinal stromal tumors (GISTs) are the most common mesenchymal neoplasms of the gastrointestinal tract, yet GIST-specific omics evidence remains scattered across small cohorts and is not represented as a dedicated disease project in major cancer genomics resources, limiting reproducible target exploration. Here, we present dbGIST (https://www.dbgist.com), a dedicated GIST-focused multi-omics resource built to make dispersed GIST evidence searchable, analyzable, and reusable. dbGIST harmonizes data from 37 centers and 1,991 samples, including pathologically verified in-house cohorts, across genomics, bulk transcriptomics, proteomics, phosphoproteomics, and single-cell transcriptomics, and couples these data with curated clinical annotations covering survival, mutation status, risk stratification, metastasis or recurrence, mitotic index, tumor site and size, and imatinib response. The platform supports cohort-level molecular-clinical association, survival, enrichment, immune-infiltration, drug-sensitivity, and single-cell analyses through interactive visualizations, downloadable source data, and public APIs for programmatic access to reusable analysis outputs and visualization-ready data. An optional LLM-assisted interface helps users navigate analyses and interpret outputs. Using MCM7 as a case study, dbGIST linked a resource-derived candidate to survival, risk features, metastatic or recurrent disease, imatinib-response phenotypes, proliferative cell states, and in vitro GIST-cell behavior. dbGIST therefore provides a traceable and interoperable resource for target exploration and precision oncology research in GIST.

cancer biology↗

bioRxiv2023

Mitochondrial phylogeography of grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) endemic to the Qinghai-Tibetan Plateau

Grassland caterpillars (Lepidoptera: Lymantriinae: Gynaephora) are the most damaging pests to alpine meadows in the Qinghai-Tibetan Plateau (QTP). Here, we conducted extensive sampling from 39 geographic populations covering almost the entire distribution of the eight Gynaephora species in the QTP to investigate phylogeographic patterns and speciation based on two mitochondrial genes (cox1 and nad5). A total of 40 haplotypes were detected in the 39 populations, with >70% of haplotypes specific to single population. The monophyletic QTP Gynaephora migrated from non-QTP regions during the Pliocene, corresponding to the uplift of the QTP, suggesting a mode of transport into the QTP. Among the eight QTP Gynaephora species described by morphological characteristics, two species (G. alpherakii and G. menyuanensis) were recovered as monophyletic groups (Clades B and C), while the remaining six species formed two monophyletic clades: Clade A (G. qinghaiensis, G. jiuzhiensis, and G. qumalaiensis) and Clade D (G. aureate, G. rouergensis, and G. minora). These results suggested that the number of the QTP Gynaephora species may be overestimated and further studies based on both morphological and nuclear gene data are needed. Genetic differentiation and speciation were driven by intensive uplifts of the QTP and associated climate fluctuations during the Pleistocene, suggesting that isolation and subsequent divergence was the dominant mode of speciation. The Sanjiangyuan region (i.e., Clade A, characterized by high genetic diversity) may have been a glacial refugium of the QTP Gynaephora, as supported by analyses of gene flow and biogeography. High levels of genetic diversity were found in QTP Gynaephora, without population expansion, which may explain the high-altitude adaptation and outbreaks of grassland caterpillars in alpine meadows of the QTP. This study provides the largest phylogeographic analysis of QTP Gynaephora and improves our understanding of the diversity and speciation of QTP insects.

zoology↗

bioRxiv2020

Complete genome characterisation of a novel coronavirus associated with severe human respiratory disease in Wuhan, China

Emerging and re-emerging infectious diseases, such as SARS, MERS, Zika and highly pathogenic influenza present a major threat to public health1-3. Despite intense research effort, how, when and where novel diseases appear are still the source of considerable uncertainly. A severe respiratory disease was recently reported in the city of Wuhan, Hubei province, China. At the time of writing, at least 62 suspected cases have been reported since the first patient was hospitalized on December 12nd 2019. Epidemiological investigation by the local Center for Disease Control and Prevention (CDC) suggested that the outbreak was associated with a sea food market in Wuhan. We studied seven patients who were workers at the market, and collected bronchoalveolar lavage fluid (BALF) from one patient who exhibited a severe respiratory syndrome including fever, dizziness and cough, and who was admitted to Wuhan Central Hospital on December 26th 2019. Next generation metagenomic RNA sequencing4 identified a novel RNA virus from the family Coronaviridae designed WH-Human-1 coronavirus (WHCV). Phylogenetic analysis of the complete viral genome (29,903 nucleotides) revealed that WHCV was most closely related (89.1% nucleotide similarity similarity) to a group of Severe Acute Respiratory Syndrome (SARS)-like coronaviruses (genus Betacoronavirus, subgenus Sarbecovirus) previously sampled from bats in China and that have a history of genomic recombination. This outbreak highlights the ongoing capacity of viral spill-over from animals to cause severe disease in humans.

pathology↗