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Curation,nomenclature,and topological classification of receptor-like kinases from 528 plant species for novel domain discovery and functional inference

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Molecular Plant 2024年第4期17卷 658-671页

作者： Qian Liu Qiong Fu Yujie Yan Qian Jiang Longfei Mao Long Wang Feng Yu Heping Zheng State Key Laboratory of Chemo/Biosensing and Chemometrics Hunan University College of BiologyChangshaHunan 410082China bioinformatics Center Hunan University College of BiologyChangshaHunan 410082China

Receptor-like kinases(RLKs)are the most numerous signal transduction components in plants and play important roles in determining how different plants adapt to their ecological *** on RLKs has focused mainly on a small number of typical RLK members in a few model *** is an urgent need to study the composition,distribution,and evolution of RLKs at the holistic level to increase our understanding of how RLKs assist in the ecological adaptations of different plant *** this study,we collected the genome assemblies of 528 plant species and constructed an RLK *** this dataset,we identified and characterized 524948 RLK family *** member underwent systematic topological classification and was assigned a gene ID based on a unified nomenclature ***,we identified two novel extracellular domains in some RLKs,designated Xiao and *** analysis of the RLK family revealed that the RLCK-XVII and RLCK-XII-2 classes were present exclusively in dicots,suggesting that diversification of RLKs between monocots and dicots may have led to differences in downstream cytoplasmic *** also used an interaction proteome to help empower data mining for inference of new RLK functions from a global perspective,with the ultimate goal of understanding how RLKs shape the adaptation of different plants to the environments/*** assembled RLK dataset,together with annotations and analytical tools,forms an integrated foundation of multiomics data that is publicly accessible via the metaRLK web portal(http://***).

关键词： RLK RLCK domain signaling pathway receptor-protein interactions

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Simple and robust 3D MINFLUX excitation with a variable phase plate

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Light(Science & Applications) 2024年第7期13卷 1354-1363页

作者： Takahiro Deguchi Jonas Ries European Molecular biology Laboratory Cell Biology and BiophysicsHeidelbergGermany. Max Perutz Labs Vienna Biocenter Campus(VBC)ViennaAustria. University of Vienna Center for Molecular BiologyDepartment of Structural and Computational BiologyViennaAustria. University of Vienna Faculty of PhysicsViennaAustria

MINFLUX has achieved extraordinary resolution in superresolution imaging and single fluorophore *** is based on localizing single fluorophores by rapid probing with a patterned beam that features a local intensity *** implementations,however,are complex and expensive and are limited in speed and ***,we show that a combination of an electro-optical modulator with a segmented birefringent element such as a spatial light modulator produces a variable phase plate for which the phase can be scanned on the MHz *** or top-hat phase patterns generate high-contrast compact excitation point-spread functions for MINFLUX localization in the x,y,and z-direction,respectively,which can be scanned across a fluorophore within a microsecond,switched within 60 microseconds and alternated among different excitation *** discuss how to compensate for non-optimal performance of the components and present a robust 3D and multi-color MINFLUX excitation module,which we envision as an integral component of a high-performance and cost-effective open-source MINFLUX.

关键词： excitation phase switched

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Virus-like nanoparticle vaccines for inducing long-lasting immunity against infectious diseases

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National Science Review 2024年第4期11卷 13-15页

作者： Yi-Nan Zhang Sarah Auclair Jiang Zhu Department of Integrative Structural and computational biology The Scripps Research Institute Department of Immunology and Microbiology The Scripps Research Institute

Prophylactic vaccines that can generate long-lasting protective immune responses are needed for many infectious diseases. Efficient vaccination requires vaccine antigens to be retained and presented to B cells in lymp...

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Deciphering gastric inflammation-induced tumorigenesis through multi-omics data and AI methods

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Cancer biology & Medicine 2024年第4期21卷 312-330页

作者： Qian Zhang Mingran Yang Peng Zhang Bowen Wu Xiaosen Wei Shao Li Institute for TCM-X MOE Key Laboratory of BioinformaticsBioinformatics DivisionBNRISTDepartment of AutomationTsinghua UniversityBeijing 100084China

Gastric cancer(GC), the fifth most common cancer globally, remains the leading cause of cancer deaths worldwide. Inflammation-induced tumorigenesis is the predominant process in GC development;therefore, systematic research in this area should improve understanding of the biological mechanisms that initiate GC development and promote cancer hallmarks. Here, we summarize biological knowledge regarding gastric inflammation-induced tumorigenesis, and characterize the multi-omics data and systems biology methods for investigating GC development. Of note, we highlight pioneering studies in multi-omics data and state-of-the-art network-based algorithms used for dissecting the features of gastric inflammation-induced tumorigenesis, and we propose translational applications in early GC warning biomarkers and precise treatment strategies. This review offers integrative insights for GC research, with the goal of paving the way to novel paradigms for GC precision oncology and prevention.

关键词： Gastric cancer inflammation-induced tumorigenesis multi-omics artificial intelligence network-based methods

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Small extrachromosomal circular DNA in amyotrophic lateral sclerosis matter

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Neural Regeneration Research 2025年第5期20卷 1411-1413页

作者： Marcos J.Arauzo-Bravo Daniela Gerovska Matthias Schwab Alexandra Kretz computational biology and Systems Biomedicine Biodonostia Health Research InstituteSan SebastianSpain Basque Foundation for Science IKERBASQUEBilbaoSpainMax Planck Institute for Molecular BiomedicineComputational Biology and Bioinformatics GroupMünsterNorth Rhine-WestphaliaGermany Department of Cell biology and Histology Faculty of Medicine and NursingUniversity of Basque Country(UPV/EHU)LeioaSpain Department of Neurology Jena University HospitalJenaThuringiaGermany

Comprehensive studies identify motor neuron spectrum disorders including amyotrophic lateral sclerosis(ALS)as globally rising fatal disorders with the highest prevalence in aging populations,influenced by ethnicity and ancestry(GBD 2016 Motor Neuron Disease Colla borators,2018).While~10% of diagnoses involve a family history(fALS),most cases are considered sporadic(sALS).However,population-based studies suggest that even cases without a common index mutation impart heritability(Ryan et al.,2019),indicating a crucial role of rare and as yet unknown genetic denominators.

关键词： amyotrophic sclerosis

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Interplant communication:an emerging battlefield in plant-aphid-virus interactions

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Science China(Life Sciences) 2024年第5期67卷 1069-1071页

作者： Yunjing Wang Qian Gong Yule Liu MOE Key Laboratory of bioinformatics and Center for Plant biology School of Life SciencesTsinghua UniversityBeijing 100084China Tsinghua-Peking Center for Life Sciences Beijing 100084China

Plants constantly face threats from various organisms,including pathogens and *** the pathogens,plant viruses are obligate intracellular parasites that infect plants and cause serious crop yield losses.

关键词： plant Plants communication

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Identification of Proteins and Genes Associated with Hedgehog Signaling Pathway Involved in Neoplasm Formation Using Text-Mining Approach

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Big Data Mining and Analytics 2024年第1期7卷 107-130页

作者： Nadezhda Yu.Biziukova Sergey M.Ivanov Oga A.Tarasova Department of bioinformatics Institute of Biomedical ChemistryMoscow 119121Russia Department of bioinformatics Pirogov Russian National Research Medical UniversityMoscow 117997Russia

Analysis of molecular mechanisms that lead to the development of various types of tumors is essential for biology and medicine,because it may help to find new therapeutic opportunities for cancer treatment and cure including personalized treatment *** of the pathways known to be important for the development of neoplastic diseases and pathological processes is the Hedgehog signaling pathway that normally controls human embryonic *** accumulation of various types of biological data,including interactions between proteins,regulation of genes transcription,proteomics,and metabolomics experiments results,allows the application of computational analysis of these big data for identification of key molecular mechanisms of certain diseases and pathologies and promising therapeutic *** aim of this study is to develop a computational approach for revealing associations between human proteins and genes interacting with the Hedgehog pathway components,as well as for identifying their roles in the development of various types of *** automatically collect sets of abstract texts from the NCBI PubMed bibliographic *** recognition of the Hedgehog pathway proteins and genes and neoplastic diseases we use a dictionary-based named entity recognition approach,while for all other proteins and genes machine learning method is *** association extraction,we develop a set of semantic *** complete the results of the text analysis with the gene set enrichment *** identified key pathways that may influence the Hedgehog pathway and their roles in tumor development are then verified using the information in the literature.

关键词： text-mining data mining Hedgehog pathway neoplastic processes enrichment analysis pathology molecularmechanisms

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Understanding the cooperative effects in the catalysis of homodimeric fluoroacetate dehalogenase

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Science China Chemistry 2024年第7期67卷 2382-2391页

作者： Ke-Wei Chen Jia-Nan Chen Jun Zhang Chao Wang Tian-Yu Sun Yun-Dong Wu Key Laboratory of computational Chemistry and Drug Design State Key Laboratory of Chemical OncogenomicSchool of Chemical Biology and BiotechnologyPeking University Shenzhen Graduate SchoolShenzhen 518055China Institute of Chemical biology Shenzhen Bay LaboratoryShenzhen 518132China College of Chemistry and Molecular Engineering Peking UniversityBeijing 100871China Changping Laboratory Beijing 102200China

Fluoroacetate dehalogenases(FAcD),a homodimeric enzyme,catalyzes the conversion of fluoroacetic acid to glycolic acid(GoA).It has been proved that the enzyme has a half-of-the-site ***,its catalytic(C)subunit converts the first substrate to a covalent intermediate;then,the non-catalytic(NC)subunit binds a second substrate and promotes the conversion of the intermediate in the C subunit into the final *** the release of the product,the C subunit becomes the NC subunit,and the previous NC subunit becomes the C *** elucidate the detailed mechanism behind this cooperative catalysis,we have conducted microsecond-scale MD simulations along the reaction *** simulations indicate that the substrate in the NC subunit induces W185 and Y141 adopting an open conformation in the C *** opening of W185(C)facilitates the entry of catalytic water,enhancing the catalytic activity for product formation,while the opening of Y141(C)creates an unfavorable environment for product binding,promoting its *** interaction network analysis reveals that the substrate in the NC subunit can induce conformational changes through a conserved water chain at the interface.

关键词： enzyme catalysis molecular dynamics cooperative effect pre-reaction state

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scEpiTools: a database to comprehensively interrogate analytic tools for single-cell epigenomic data

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Journal of Genetics and Genomics 2024年第4期51卷 462-465页

作者： Zijing Gao Xiaoyang Chen Zhen Li Xuejian Cui Qun Jiang Keyi Li Shengquan Chen Rui Jiang Ministry of Education Key Laboratory of bioinformatics Bioinformatics Division at the Beijing National Research Center for Information Science and TechnologyCenter for Synthetic and Systems BiologyDepartment of AutomationTsinghua UniversityBeijing 100084China School of Mathematical Sciences and LPMC Nankai UniversityTianjin 300071China

Recent advances in single-cell sequencing technologies provide significant implications for understanding cellular heterogeneity,developmental biology,and disease *** fully exploit the potential of these data,numerous tools have been proposed for upstream and downstream *** the the single-cell RNA sequencing(scRNA-seq)community,scRNA-tools(Zappia et al.,2018)was proposed to help researchers navigate the plethora of tools by *** its inception,scRNA-tools has been widely used and its updated version further reveals trends in the field with over 1000 collected tools(Zappia and Theis,2021),providing a valuable guidance in selecting tools for analyses.

关键词： analytic selecting Tools

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NeoHunter:Flexible software for systematically detecting neoantigens from sequencing data

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Quantitative biology 2024年第1期12卷 70-84页

作者： Tianxing Ma Zetong Zhao Haochen Li Lei Wei Xuegong Zhang MOE Key Lab of bioinformatics Bioinformatics Division of BNRIST and Department of AutomationTsinghua UniversityBeijingChina School of Medicine Tsinghua UniversityBeijingChina School of Life Sciences Tsinghua UniversityBeijingChina

Complicated molecular alterations in tumors generate various mutant *** of these mutant peptides can be presented to the cell surface and then elicit immune responses,and such mutant peptides are called *** detection of neoantigens could help to design personalized cancer *** some computational frameworks for neoantigen detection have been proposed,most of them can only detect SNV-and indel-derived *** addition,current frameworks adopt oversimplified neoantigen prioritization *** factors hinder the comprehensive and effective detection of *** developed NeoHunter,flexible software to systematically detect and prioritize neoantigens from sequencing data in different *** can detect not only SNV-and indel-derived neoantigens but also gene fusion-and aberrant splicing-derived *** supports both direct and indirect immunogenicity evaluation strategies to prioritize candidate *** strategies utilize binding characteristics,existing biological big data,and T-cell receptor specificity to ensure accurate detection and *** applied NeoHunter to the TESLA dataset,cohorts of melanoma and non-small cell lung cancer *** achieved high performance across the TESLA cancer patients and detected 79%(27 out of 34)of validated neoantigens in ***-and indel-derived neoantigens accounted for 90%of the top 100 candidate neoantigens while neoantigens from aberrant splicing accounted for 9%.Gene fusion-derived neoantigens were detected in one *** is a powerful tool to‘catch all’neoantigens and is available for free academic use on Github(XuegongLab/NeoHunter).

关键词： cancer vaccine molecular alteration neoantigen neoantigen prioritization

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