Biology subjects

Liu, C.-m.

Publications and source records attributed to Liu, C.-m..

2 recordsLinked to original sources

bioRxiv2024

AutoPM3: Enhancing Variant Interpretation via LLM-driven PM3 Evidence Extraction from Scientific Literature

Rare diseases, affecting 300 million people globally, often result from genetic variants. Wholegenome sequencing has made variant detection more cost-effective, but interpreting these variants remains challenging. Current clinical practice combines quantitative evidence and literature, which is complex and time-consuming. We introduce AutoPM3, a method for automating the extraction of ACMG/AMP PM3 evidence from scientific literature using open-source LLMs. It combines an optimized RAG system for text comprehension and a TableLLM equipped with Text2SQL for data extraction. We evaluated AutoPM3 using our collected PM3-Bench, a dataset from ClinGen with 1,027 variant-publication pairs. AutoPM3 significantly outperformed other methods in variant hit and in trans variant identification, thanks to the four key modules. Additionally, we wrapped AutoPM3 with a user-friendly interface to enhance its accessibility. This study presents a powerful tool to improve rare disease diagnosis workflows by facilitating PM3-relevant evidence extraction from scientific literature.

bioinformatics↗

bioRxiv2019

Calcium/calmodulin-dependent protein kinase II regulates mammalian axon growth by affecting F-actin length in growth cone

While axon regeneration is a key determinant of functional recovery of the nervous system after injury, it is often poor in the mature nervous system. Influx of extracellular calcium (Ca2+) is one of the first phenomena that occur following axonal injury, and calcium/calmodulin-dependent protein kinase (CaMKII), a target protein for calcium ions, regulates the status of cytoskeletal proteins such as F-actin. Herein, we found that peripheral axotomy activates CaMKII in dorsal root ganglion (DRG) sensory neurons, and inhibition of CaMKII impairs axon growth in both the peripheral and central nervous systems (PNS and CNS, respectively). Most importantly, we also found that activation of CaMKII promotes PNS and CNS axon growth, and regulatory effects of CaMKII on axon growth occur via affecting the length of the F-actin. Thus, we believe our findings provide clear evidence that CaMKII is a critical modulator of mammalian axon regeneration.

neuroscience↗