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Bayesian networks: a powerful tool for systems biology study

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Frontiers in biology 2010年第2期5卷 95-96页

作者： Xiu-Jie WANG State Key Laboratory of Plant Genomics Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China

The wide application of omics research approaches caused a burst of biological data in the past decade,and also promoted the growth of systems biology,a research field that studies biological questions from a genome-wide point of *** feature of systems biology study is to integrate and *** only experiments are carried out at whole-genome scales,but also data from various resources,such as genomics,transcriptomics,proteomics,and metabolics data,need to be integrated to identify correlations among targeted ***,plenty amounts of experimental data,robust statistical methods,and reliable network construction models are indispensable for systems biology *** the available network construction models,Bayesian network is considered as one of the most effective methods available so far for biological network predictions(Pe’er,2005).

关键词： network networks plenty

systems biology Approaches to Animal Hibernation

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Systems Biology Approaches to Animal Hibernation

Efficient Numerical Optimization Algorithm Based on New Real-Coded Genetic Algorithm, AREX + JGG, and Application to the Inverse Problem in systems biology

“基因、进化与生理功能多样性”海内外学术研讨会暨中国生理学会第七届比较生理学学术会议

作者：严军 CAS-MPG Partner Institute for Computational biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences

Hibernation is an energy saving strategy adopted by a wide range of mammalian species to survive extreme environments through regulated metabolic suppression. Mammalian hibernators also evolved the

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Applied Mathematics 2012年第10期3卷 1463-1470页

作者： Asako Komori Yukihiro Maki Masahiko Nakatsui Isao Ono Masahiro Okamoto Department of Bioinformatics Graduate School of Systems Life Sciences Kyushu University Fukuoka Japan Department of systems Bioscience for Drug Discovery Graduate School of Pharmaceutical Sciences Kyoto University Kyoto Japan Faculty of Inernational Communications Fukuoka International University Fukuoka Japan Graduate School of Computational Intelligence and systems Science Tokyo Institute of Technology Tokyo Japan

In systems biology, system identification, which infers regulatory network in genetic system and metabolic pathways using experimentally observed time-course data, is one of the hottest issues. The efficient numerical optimization algorithm to estimate more than 100 real-coded parameters should be developed for this purpose. New real-coded genetic algorithm (RCGA), the combination of AREX (adaptive real-coded ensemble crossover) with JGG (just generation gap), have applied to the inference of genetic interactions involving more than 100 parameters related to the interactions with using experimentally observed time-course data. Compared with conventional RCGA, the combination of UNDX (unimodal normal distribution crossover) with MGG (minimal generation gap), new algorithm has shown the superiority with improving early convergence in the first stage of search and suppressing evolutionary stagnation in the last stage of search.

关键词： Inverse Problem S-System Formalism Gene Regulatory Network System Identification Real-Coded Genetic Algorithm

The 7th National Conference on Bioinformatics and systems biology of China

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Frontiers of Electrical and Electronic Engineering in China 2017年第2期5卷 199-201页

作者： Zhirong Sun Kui Hua Xuegong Zhang Feng-Biao Guo Jian Huang MOE Key Laboratory of Bioinformatics School of Life Sciences Tsinghua University Beijing 100084 China MOE Key Laboratory of Bioinformatics Bioinformatics Division and Center for Synthetic & systems biology TNLIST Department of Automation Tsinghua University Beijing 100084 China Bioinformatics Center in School of Life Science and Technology University of Electronic Science and Technology of China Chengdu 610054 China Center of Bioinformatics (COBI) Key Laboratory for Neuro Information of Ministry of Education University of Electronic Science and Technology of China Chengdu 610054 China

The 7th National Conference on Bioinformatics and System biology and the International Workshop on Advanced Bioinformatics and Precision Medicine was successfully held in Chengdu, Sichuan Province, China, on October 7-9, 2016. The conference is organized by Chinese Society for Cell biology （CSCB）, National Natural Science Foundation of China （NSFC）, and MOE Key Laboratory of Bioinformatics, Tsinghua University, and hosted by University of Electronic Science and Technology of China （UESTC）. Prof. Runsheng Chen of Institute of Biophysics, CAS, is the organizing chair of the conference, and Prof. Zhirong Sun of Tsinghua University is the general secretary. Professors Feng-Biao Guo and Jian Huang of UESTC led the local organization team. A total of about 1,047 professionals and graduate students from all over the country and several US universities attended the conference.

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Data-driven systems biology approaches

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分子细胞生物学报：英文版 2017年第6期9卷 435-435页

作者： Luonan Chen Institute of Biochemistry and Cell biology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Shanghai 200031 China

Rapid accumulation of biological data is driving the system-level study from describing complex phenomena to understanding molecular mechanisms, from analyzing individual components to understanding their networks and systems (Chen et al., 2009; Chen and Wu, 2015). Data-driven systems biology approaches are emerging as essential tools to gain new insights into biological processes or systems. In this issue, we collect several research articles, which are all related to such data-driven methodologies or their applications, ranged from new computational tools (GWAS and signal pathway studies) to molecular biology (CSRE inference) and disease analyses (detection of the disease tipping point by DNBs and key genes during glioma progression).

关键词：生物学途径驾驶系统数据驱动计算工具生物数据生物过程方法论 DNB

Integrated systems biology and Chemical biology Approach to Exploring Mechanisms of Traditional Chinese Medicines

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Chinese Herbal Medicines 2016年第2期8卷 99-106页

作者： Gang Bai Yuan-yuan Hou Min Jiang Jie Gao State Key Laboratory of Medicinal Chemical biology and Tianjin Key Laboratory of Molecular Drug Research College of Pharmacy Nankai University

After thousands of years of development, traditional Chinese medicines （TCMs） have evolved into a complete scientific system characterized by multiple components, targets, and pathways, which mediates numerous pharmacological activities and efficacies. The development of ＂-omics＂ technology, including systems biology and network pharmacology, has enabled the illustration of TCMs from a more systematic view. Although the network adequately reflects the overall philosophy of TCMs, its complexity hinders the relevant research to a hover. In addition, the strategies involved appear to be in contrast to the original concise and efficacious disease therapy oriented focus on classic Chinese material medica （CMM）. Based on the established holistic view and reductionism, in this review, we discuss an integrated systems biology and chemical biology research approach that will facilitate and accelerate the understanding of the mechanisms of TCMs. Furthermore, we are optimistic that it will elucidate the associated interactions between active natural products and their targets, and ultimately improve the strategies for complex disease therapies.

关键词： chemical biology network pharmacology systems biology traditional Chinese medicines

ATPID:an integrative platform for plant systems biology

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ATPID:an integrative platform for plant systems biology

Comprehensive identification and function study of Arabidopsis chloroplast proteome through systems biology approaches

第二届植物代谢国际会议

作者： Peng Li Weidong Zang Tieliu Shi Center for Bioinformatics and Computational biology and The Institute of Biomedical Sciences School of Life Science East China Normal University 500 Dong chuan Road Shanghai 200241 Center for Bioinformatics and Computational biology and The Institute of Biomedical Sciences Schoolof Life Science East China Normal University 500 Dong chuan Road Shanghai 200241 Center for Bioinformatics and Computational Biology and The Institute of Biomedical Sciences S

＜正＞Protein interactions are involved in important cellular functions and biological processes that are the fundamentals of all life activities. With improvements in experimental techniques and progress in research,

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Comprehensive identification and function study of Arabidops...

Phase-driven progress in nanophotonic biosensing

第十届上海市植物生物学青年学术研讨会

作者： Yiheng Lan Peng Li Wenjuan Wu Ivan K.Chu Jirong Huang Tieliu Shi The Center for Bioinformatics and Computational biology Shanghai Key Laboratory of Regulatory Biology the Institute of Biomedical Sciences and School of Life Sciences East China Normal University The institute of plant physiology and ecology Shanghai Institutes for Biological Sciences Chinese Academy of Sciences Department of Chemistry The University of Hong Kong

Although chloroplast plays crucial roles in plant growth and development,its proteome remains further *** present study,three Arabidopsis mutants were used to identify chloroplast proteome,among which,low level of Fts...

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Light(Science & Applications) 2024年第5期13卷 798-800页

作者： Isabel Barth Hakho Lee Center for systems biology Massachusetts General HospitalHarvard Medical SchoolBostonMA 02114USA

In the continuous pursuit of enhancing the sensitivity of nanophotonic biosensors by leveraging phase phenomena,a recent development involved the engineering of an atomically thin Ge2Sb2Te5 layer on a silver nanofilm ... 详细信息

关键词： silver Ge2Sb2Te5 pursuit