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生物物理学报告(英文)
生物物理学报告(英文)
生物物理学报告(英文)/Journal Biophysics Reports
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    Foundation models in molecular biology

    Yunda SiJiawei ZouYicheng GaoGuohui Chuai...
    135-151页
    查看更多>>摘要:Determining correlations between molecules at various levels is an important topic in molecular biolo-gy.Large language models have demonstrated a remarkable ability to capture correlations from large amounts of data in the field of natural language processing as well as image generation,and correla-tions captured from data using large language models can also be applicable to solving a wide range of specific tasks,hence large language models are also referred to as foundation models.The massive amount of data that exists in the field of molecular biology provides an excellent basis for the develop-ment of foundation models,and the recent emergence of foundation models in the field of molecular bi-ology has really pushed the entire field forward.We summarize the foundation models developed based on RNA sequence data,DNA sequence data,protein sequence data,single-cell transcriptome da-ta,and spatial transcriptome data respectively,and further discuss the research directions for the de-velopment of foundation models in molecular biology.

    Developing ChatGPT for biology and medicine:a complete review of biomedical question answering

    Qing LiLei LiYu Li
    152-171页
    查看更多>>摘要:ChatGPT explores a strategic blueprint of question answering(QA)to deliver medical diagnoses,treat-ment recommendations,and other healthcare support.This is achieved through the increasing incorpo-ration of medical domain data via natural language processing(NLP)and multimodal paradigms.By transitioning the distribution of text,images,videos,and other modalities from the general domain to the medical domain,these techniques have accelerated the progress of medical domain question an-swering(MDQA).They bridge the gap between human natural language and sophisticated medical do-main knowledge or expert-provided manual annotations,handling large-scale,diverse,unbalanced,or even unlabeled data analysis scenarios in medical contexts.Central to our focus is the utilization of lan-guage models and multimodal paradigms for medical question answering,aiming to guide the research community in selecting appropriate mechanisms for their specific medical research requirements.Specialized tasks such as unimodal-related question answering,reading comprehension,reasoning,di-agnosis,relation extraction,probability modeling,and others,as well as multimodal-related tasks like vision question answering,image captioning,cross-modal retrieval,report summarization,and genera-tion,are discussed in detail.Each section delves into the intricate specifics of the respective method under consideration.This paper highlights the structures and advancements of medical domain explo-rations against general domain methods,emphasizing their applications across different tasks and datasets.It also outlines current challenges and opportunities for future medical domain research,paving the way for continued innovation and application in this rapidly evolving field.This comprehen-sive review serves not only as an academic resource but also delineates the course for future probes and utilization in the field of medical question answering.

    Decoder-seq:a technology for high sensitivity,high resolution,and low-cost spatial RNA sequencing

    Siquan LiJin LiHe Huang
    172-174页

    The gut-liver axis calibrates PEDF production for ISC homeostasis

    Ying HuangXinran WangLulu Sun
    175-177页

    Digital counting of force accumulation during mechanotransduction

    Xinyu ZhangBei Liu
    178-179页

    Unfolding rates of 1:1 and 2:1 complex of CX-5461 and c-MYC promoter G-quadruplexes revealed by single-molecule force spectroscopy

    Hui PengYashuo ZhangQun LuoXinyu Wang...
    180-189页
    查看更多>>摘要:CX-5461,also known as pidnarulex,is a strong G4 stabilizer and has received FDA fast-track designa-tion for BRCA1-and BRCA2-mutated cancers.However,quantitative measurements of the unfolding rates of CX-5461-G4 complexes which are important for the regulation function of G4s,remain lacking.Here,we employ single-molecule magnetic tweezers to measure the unfolding force distributions of c-MYC G4s in the presence of different concentrations of CX-5461.The unfolding force distributions ex-hibit three discrete levels of unfolding force peaks,corresponding to three binding modes.In combina-tion with a fluorescent quenching assay and molecular docking to previously reported ligand-c-MYC G4 structure,we assigned the~69 pN peak corresponding to the 1∶1(ligand:G4)complex where CX-5461 binds at the G4's 5'-end.The~84 pN peak is attributed to the 2:1 complex where CX-5461 occupies both the 5'and 3'.Furthermore,using the Bell-Arrhenius model to fit the unfolding force distributions,we determined the zero-force unfolding rates of 1∶1,and 2∶1 complexes to be(2.4±0.9)× 10-8 s-1 and(1.4±1.0)× 10-9 s-1 respectively.These findings provide valuable insights for the development of G4-targeted ligands to combat c-MYC-driven cancers.