Biomedical subjects

Ang Li

Publications and source records attributed to Ang Li.

3 recordsLinked to original sources

PubMed2026

Modtector: ultra-fast modification signal mining on mapped sequencing reads.

SUMMARY: Existing tools for RNA epitranscriptomic modification and structural signal analysis are often fragmented, inefficiency, and limited to single signal types. We developed Modtector, an unified tool for extracting mutation and reverse-transcription stop signals from aligned sequencing reads. By using a "count-then-correct" strategy, Modtector reduces computational complexity and enables efficient dual-signal analysis. It achieves multi-fold speedups on large-genome and high-coverage datasets, including completing HEK293 22G data analysis in 5 minutes, and show strong scalability on single-cell datasets with speedups exceeding 50-fold. AVAILABILITY: The source code is available at GitHub (https://github.com/TongZhou2017/modtector) and Crates.io (https://crates.io/crates/modtector). The archived source-code snapshot used in this study is available at Zenodo (DOI: 10.5281/zenodo.20967747), corresponding to GitHub commit 7c60e9d. Workflow examples, datasets, and analysis scripts are available at Zenodo (DOI: 10.5281/zenodo.17316476 and 10.5281/zenodo.18523297).

Humans↗

PubMed2026

Plasma Proteomic Profiling Identifies Candidate Biomarkers for Pancreatic Ductal Adenocarcinoma.

BACKGROUND: Pancreatic ductal adenocarcinoma (PDAC) is a highly lethal malignancy that is often diagnosed after curative treatment is no longer feasible. Existing biomarkers, particularly CA19-9, have limited sensitivity and specificity. Plasma proteins that capture tumor-associated biological alterations may therefore provide useful signals for earlier detection. METHODS: Plasma samples from 99 patients with PDAC and 30 healthy controls were analyzed using data-independent acquisition (DIA) proteomics. Differentially expressed proteins were identified using predefined statistical thresholds and further examined by functional enrichment analysis. Selected candidate biomarkers were validated by ELISA in an independent subset. RESULTS: Among 565 quantified plasma proteins, 52 were differentially expressed between PDAC and controls. These proteins were enriched in extracellular processes, cholesterol metabolism, complement and coagulation cascades, and pancreatic secretion pathways. ELISA validation confirmed higher plasma levels of Cathepsin S, CTRB2, MARCO, PIGR, PRDX6, REG1A, Trypsin-2, and PEP-FAP in patients with PDAC compared with healthy controls. ROC analyses showed moderate-to-good discriminatory performance for several candidates, and the MARCO + PEP-FAP model improved classification compared with either marker alone. CONCLUSION: These findings reveal circulating proteins linked to key PDAC-related biological processes and identify eight candidates for further evaluation in multi-protein diagnostic panels. Larger validation studies incorporating clinically relevant disease control groups are warranted to determine their diagnostic specificity and clinical utility.

Humans↗

PubMed2025

Genome-wide profiling the integration patterns with T7-PCR.

Integration of exogenous gene fragments into the host genomes is a widely used and powerful method for studying gene functions, advancing molecular breeding, and conducting gene therapy. Accurately identifying the integration sites is essential for ensuring both the safety and efficacy of genome engineering efforts. However, current mapping techniques are constrained by high costs and a low signal-to-noise ratio. In this study, we developed an innovative tool for mapping integration sites, leveraging T7 polymerase-mediated in vitro transcription (T7-IVT) to capture the junction fragments surrounding integration loci. This approach converts genomic flanking sequences into RNA, enabling the simultaneous enrichment of junction fragments and the elimination of background genomic DNA, thereby significantly enhancing the signal-to-noise ratio. We have validated the efficiency of this method, named T7-PCR, across yeast, plant, and human cells under diverse integration scenarios. T7-PCR outperforms current next-generation sequencing (NGS)-based mapping strategies in terms of efficiency and accuracy, with minimal positional effects. This method is highly applicable for high-throughput transgene screening and also supports the development of next-generation tools for targeted integration of large fragments.

Humans↗