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Adaptive candidate estimation-assisted multi-objective particle swarm optimization

Science China(Technological Sciences) 2022年第8期65卷 1685-1699页

作者： HAN HongGui ZHANG LinLin HOU Ying QIAO JunFei Faculty of Information Technology Beijing University of TechnologyBeijing 100124China Beijing Key Laboratory of computational Intelligence and Intelligent System Beijing 100124China Engineering Research center of Digital Community Ministry of EducationBeijing 100124China

The selection of global best(Gbest) exerts a high influence on the searching performance of multi-objective particle swarm optimization algorithm(MOPSO). The candidates of MOPSO in external archive are always estimated to select Gbest. However,in most estimation methods, the candidates are considered as the Gbest in a fixed way, which is difficult to adapt to varying evolutionary requirements for balance between convergence and diversity of MOPSO. To deal with this problem, an adaptive candidate estimation-assisted MOPSO(ACE-MOPSO) is proposed in this paper. First, the evolutionary state information,including both the global dominance information and global distribution information of non-dominated solutions, is introduced to describe the evolutionary states to extract the evolutionary requirements. Second, an adaptive candidate estimation method,based on two evaluation distances, is developed to select the excellent leader for balancing convergence and diversity during the dynamic evolutionary process. Third, a leader mutation strategy, using the elite local search(ELS), is devised to select Gbest to improve the searching ability of ACE-MOPSO. Fourth, the convergence analysis is given to prove the theoretical validity of ACE-MOPSO. Finally, this proposed algorithm is compared with popular algorithms on twenty-four benchmark functions. The results demonstrate that ACE-MOPSO has advanced performance in both convergence and diversity.

关键词： multi-objective particle swarm optimization evolutionary state information adaptive candidate estimation convergence and diversity convergence analysis

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C4 Rice-an Ideal Arena for Systems biology Research

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Journal of Integrative Plant biology 2010年第8期52卷 762-770页

作者： Xin-Guang Zhu Lanlan Shan Yu Wang William Paul Quick Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Shanghai Institutes for Biologica Sciences Chinese Academy of Sciences Shanghai 200031 China The International Rice Research Institute Los Banos Philippines

Engineering the C4 photosynthetic pathway into C3 crops has the potential to dramatically increase the yields of major C3 crops. The genetic control of features involved in C4 photosynthesis are still far from being understood; which partially explains why we have gained little success in C4 engineering thus far. Next generation sequencing techniques and other high throughput technologies are offering an unprecedented opportunity to elucidate the developmental and evolutionary processes of C4 photosynthesis. Two contrasting hypotheses about the evolution of C4 photosynthesis exist, i.e. the master switch hypothesis and the incremental gain hypothesis. These two hypotheses demand two different research strategies to proceed in parallel to maximize the success of C4 engineering. In either case, systems biology research will play pivotal roles in identifying key regulatory elements controlling development of C4 features, identifying essential biochemical and anatomical features required to achieve high photosynthetic efficiency, elucidating genetic mechanisms underlining C4 differentiation and ultimately identifying viable routes to engineer C4 rice. As a highly interdisciplinary project, the C4 rice project will have far-reaching impacts on both basic and applied research related to agriculture in the 21st century.

关键词： Engineering Engines Engineers Viverridae Genetics Crops Oesophagus Forecasting Rice Technology

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Understanding the “Horizontal Dimension” of Molecular Evolution to Annotate, Classify, and Discover Proteins with Functional Domains

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Journal of Computer Science & Technology 2010年第1期25卷 82-94页

作者： Gloria Rendon Mao-Feng Ger Ruth Kantorovitz Shreedhar Natarajan Jeffrey Tilson Eric Jakobsson National center for Supercomputing Applications University of Illinois at Urbana-Champaign Beckman Institute for Advanced Science and Technology University of Illinois at Urbana-Champaign center for Biophysics and computational biology University of Illinois at Urbana-Champaign Department of Mathematics University of Illinois at Urbana-Champaign Department of biology University of Pennsylvania Renaissance Computing Institute

Protein evolution proceeds by two distinct processes： 1） individual mutation and selection for adaptive mutations and 2） rearrangement of entire domains within proteins into novel combinations, producing new protein families that combine functional properties in ways that previously did not exist. Domain rearrangement poses a challenge to sequence alignment-based search methods, such as BLAST, in predicting homology since the methodology implicitly assumes that related proteins primarily differ from each other by individual mutations. Moreover, there is ample evidence that the evolutionary process has used （and continues to use） domains as building blocks, therefore, it seems fit to utilize computational, domain-based methods to reconstruct that process. A challenge and opportunity for computational biology is how to use knowledge of evolutionary domain recombination to characterize families of proteins whose evolutionary history includes such recombination, to discover novel proteins, and to infer protein-protein interactions. In this paper we review techniques and databases that exploit our growing knowledge of “horizontal” protein evolution, and suggest possible areas of future development. We illustrate the power of the domain-based methods and the possible directions of future development by a case history in progress aiming at facilitating a particular approach to understanding microbial pathogenicity.

关键词： domain-based discovery domain-based orthology domain interactions InterPro MEME/MAST

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eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

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National Science Review 2019年第5期6卷 867-869页

作者： Dalang Yu Lili Dong Fangqi Yan Hailong Mu Bixia Tang Xiao Yang Tao Zeng Qing Zhou Feng Gao Zhonghuang Wang Ziqian Hao Hongen Kang Yi Zheng Hongwei Huang Yuzhang Wei Wei Pan Yaochen Xu Junwei Zhu Shilei Zhao Ciran Wang Pengyu Wang Long Dai Mushan Li Li Lan Yiwei Wang Hua Chen Yi-Xue Li Yun-Xin Fu Zhen Shao Yiming Bao Fangqing Zhao Luo-Nan Chen Guo-Qing Zhang Wenming Zhao Haipeng Li CAS Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Shanghai Institute of Nutrition and HealthShanghai Institutes for Biological SciencesUniversity of Chinese Academy of Sciences Chinese Academy of Sciences University of Chinese Academy of Sciences BIG Data center Beijing Institute of GenomicsChinese Academy of Sciences Shanghai center for Bioinformation Technology Key Laboratory of Systems biology Center for Excellence in Molecular Cell Science Shanghai Institute of Biochemistry and Cell Biology Chinese Academy of Sciences Shanghai Institute of Biochemistry and Cell biology Chinese Academy of Sciences CAS Laboratory of Genomic and Precision Medicine Beijing Institute of Genomics Chinese Academy of Sciences center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Department of Biostatistics and Data Science School of Public Health University of Texas Health Science Center at Houston computational Genomics Lab Beijing Institutes of Life Science Chinese Academy of Sciences Shanghai Research center for Brain Science and Brain-Inspired Intelligence

It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic ***, we describe multi-functional software named evolutionary GenotypePhenotype Systems (eGPS) that en... 详细信息

关键词： GPS eGPS 1.0 comprehensive software for multi-omic and evolutionary analyses

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Genomic convergence underlying high-altitude adaptation in alpine plants

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Journal of Integrative Plant biology 2023年第7期65卷 1620-1635页

作者： Xu Zhang Tianhui Kuang Wenlin Dong Zhihao Qian Huajie Zhang Jacob BLandis Tao Feng Lijuan Li Yanxia Sun Jinling Huang Tao Deng Hengchang Wang Hang Sun CAS Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture The Chinese Academy of SciencesWuhan Botanical GardenWuhan 430074China center of Conservation biology Core Botanical GardensThe Chinese Academy of SciencesWuhan 430074China Yunnan International Joint Laboratory for Biodiversity of Central Asia Key Laboratory for Plant Diversity and Biogeography of East AsiaKunming Institute of BotanyThe Chinese Academy of SciencesKunming 650201China University of Chinese Academy of Sciences Beijing 100049China School of Integrative Plant Science Section of Plant Biology and the L.H.Bailey HortoriumCornell UniversityIthacaNew York 14850USA BTI computational biology center Boyce Thompson InstituteIthacaNew York 14853USA State Key Laboratory of Crop Stress Adaptation and Improvement School of Life SciencesHenan UniversityKaifeng 475004China Department of biology East Carolina UniversityGreenvilleNorth Carolina 27858USA

evolutionary convergence is one of the most striking examples of adaptation driven by natural ***, genomic evidence for convergent adaptation to extreme environments remains ***, we assembled reference genomes of two alpine plants, Saussurea obvallata(Asteraceae)and Rheum alexandrae(Polygonaceae), with 37,938 and 61,463 annotated protein-coding genes. By integrating an additional five alpine genomes,we elucidated genomic convergence underlying high-altitude adaptation in alpine plants. Our results detected convergent contractions of diseaseresistance genes in alpine genomes, which might be an energy-saving strategy for surviving in hostile environments with only a few pathogens *** identified signatures of positive selection on a set of genes involved in reproduction and respiration(e.g., MMD1, NBS1, and HPR), and revealed signatures of molecular convergence on genes involved in self-incompatibility, cell wall modification,DNA repair and stress resistance, which may underlie adaptation to extreme cold, high ultraviolet radiation and hypoxia environments. Incorporating transcriptomic data, we further demonstrated that genes associated with cuticular wax and flavonoid biosynthetic pathways exhibit higher expression levels in leafy bracts, shedding light on the genetic mechanisms of the adaptive “greenhouse” morphology. Our integrative data provide novel insights into convergent evolution at a high-taxonomic level,aiding in a deep understanding of genetic adaptation to complex environments.

关键词： adaptation alpine plants evolutionary rates genomic convergence “greenhouse”morphology high altitude

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Single-cell transcriptomic landscape of the sheep rumen provides insights into physiological programming development and adaptation of digestive strategies

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Zoological Research 2022年第4期43卷 634-647页

作者： Yuan Yuan Da-Ming Sun Tao Qin Sheng-Yong Mao Wei-Yun Zhu Yu-Yang Yin Jie Huang Rasmus Heller Zhi-Peng Li Jun-Hua Liu Qiang Qiu School of Ecology and Environment Northwestern Polytechnical UniversityXi’anShaanxi 710072China Ruminant Nutrition and Feed Engineering Technology Research center College of Animal Science and TechnologyNanjing Agricultural UniversityNanjingJiangsu 210095China Laboratory of Gastrointestinal Microbiology Jiangsu Key Laboratory of Gastrointestinal Nutrition and Animal HealthNational Center for International Research on Animal Gut NutritionCollege of Animal Science and TechnologyNanjing Agricultural UniversityNanjingJiangsu 210095China Huzhou Academy of Agricultural Sciences HuzhouZhejiang 313000China Section for computational and RNA biology Department of BiologyUniversity of CopenhagenCopenhagen DK-2200Denmark College of Animal Science and Technology Jilin Agricultural UniversityChangchunJilin 130118China

As an important evolutionary innovation and unique organ,the rumen has played a crucial role in ruminant adaptation to complex ecological ***,the cellular basis of its complex morphology and function remains largely *** this study,we identified eight major cell types from seven representative prenatal and postnatal rumen samples using~56600 single-cell *** captured the dynamic changes and high heterogeneity in cellular and molecular profiles before,during,and after the appearance of keratinized stratified squamous epithelium with neatly arranged papillae and functional *** cells,keratinocytes,differentiating keratinocytes,terminally differentiated keratinocytes,and special spinous cells provided the cellular basis for rumen epithelium ***,we obtained clear evidence of two keratinization processes involved in early papillogenesis and papillae keratinization and identified TBX3 as a potential marker ***,enriched stratum spinosum cells played crucial roles in volatile fatty acid(VFA)metabolism and immune *** results provide a comprehensive transcriptional landscape of rumen development at single-cell resolution,as well as valuable insight into the interactions between dietary metabolism and the rumen.

关键词： Rumen scRNA-seq Ruminal epithelium Keratinization

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Dog10K: the International Consortium of Canine Genome Sequencing

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National Science Review 2019年第4期6卷 611-613页

作者： Guo-Dong Wang Greger Larson Jeffrey M.Kidd Bridgett M.von Holdt Elaine A.Ostrander Ya-Ping Zhang State Key Laboratory of Genetic Resources and Evolution Kunming Institute of Zoology Chinese Academy of Sciences center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Palaeogenomics and Bio-Archaeology Research Network School of Archaeology University of Oxford Department of Human Genetics and Department of computational Medicine and Bioinformatics University of Michigan Medical School Ecology & evolutionary biology Princeton University National Human Genome Research Institute National Institutes of Health

Dogs (Canis lupus familiaris) were the first species to enter into a domestic relationship with people [1] and are a source of fascination all over the world, not only due to their history of domestication and dispersal along with human beings [2],but also because of their diverse phenotypes and behaviors, driven by both artificial and natural selection [3]. Dogs

关键词： the International Consortium of Canine Genome Sequencing Dog10K

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Global cold-chain related SARS-CoV-2 transmission identified by pandemic-scale phylogenomics

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Zoological Research 2022年第5期43卷 871-874页

作者： Dalang Yu Junwei Zhu Jianing Yang Yi-Hsuan Pan Hailong Mu Ruifang Cao Bixia Tang Guangya Duan Zi-Qian Hao Long Dai Guo-Ping Zhao Ya-Ping Zhang Wenming Zhao Guoqing Zhang Haipeng Li National Genomics Data center&Bio-Med Big Data center CAS Key Laboratory of Computational BiologyShanghai Institute of Nutrition and HealthChinese Academy of SciencesShanghai 200031China National Genomics Data center Beijing Institute of GenomicsChinese Academy of Sciences and China National Center for BioinformationBeijing 100101China Key Laboratory of Brain Functional Genomics of Ministry of Education School of Life ScienceEast China Normal UniversityShanghai 200062China State Key Laboratory of Genetic Resources and Evolution Yunnan Laboratory of Molecular Biology of Domestic AnimalsKunming Institute of ZoologyChinese Academy of SciencesKunmingYunnan 650223China Key Laboratory of Synthetic biology CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and EcologyChinese Academy of SciencesShanghai 200032China School of Life and Health Sciences Hangzhou Institute for Advanced StudyUniversity of Chinese Academy of SciencesHangzhouZhejiang 310024China Shanghai Southgene Technology Co.Ltd Shanghai 201203China University of Chinese Academy of Sciences Beijing 100049China

DEAR EDITOR,The COVID-19 pandemic caused by SARS-CoV-2 continues to pose a tremendous threat to human society. SARS-CoV-2is airborne and transmits primarily through social contact;however, whether cold chain-related transmission has occurred remains highly debated(Han & Liu, 2022;Lewis,2021;Ma et al., 2021;Mallapaty et al., 2021;Pang et al.,2020;Wu et al., 2021). Here, we present a novel method and identify two transmission routes based on lineage-specific reductions in the SARS-CoV-2 evolutionary rate.

关键词： primarily EDIT identif

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Micro-coevolution of host genetics with gut microbiome in three Chinese ethnic groups

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Journal of Genetics and Genomics 2021年第11期48卷 972-983页

作者： Mingyue Cheng Xueling Ge Chaofang Zhong Ruiqing Fu Kang Ning Shuhua Xu Key Laboratory of Molecular Biophysics of the Ministry of Education Hubei Key Laboratory of Bioinformatics and Molecular-imagingCenter of AI BiologyDepartment of Bioinformatics and Systems BiologyCollege of Life Science and TechnologyHuazhong University of Science and TechnologyWuhan 430074China Key Laboratory of computational biology Shanghai Institute of Nutrition and HealthUniversity of Chinese Academy of SciencesChinese Academy of SciencesShanghai 200031China State Key Laboratory of Genetic Engineering Center for Evolutionary BiologyCollaborative Innovation Center for Genetics and DevelopmentSchool of Life SciencesFudan UniversityShanghai 200438China School of Life Science and Technology ShanghaiTech UniversityShanghai 201210China center for Excellence in Animal Evolution and Genetics Chinese Academy of SciencesKunming 650223China Henan Institute of Medical and Pharmaceutical Sciences Zhengzhou UniversityZhengzhou 450052China Human Phenome Institute Fudan UniversityShanghai 201203China

Understanding the micro-coevolution of the human gut microbiome with host genetics is challenging but essential in both evolutionary and medical *** gain insight into the interactions between host genetic variation and the gut microbiome,we analyzed both the human genome and gut microbiome collected from a cohort of 190 students in the same boarding college and representing 3 ethnic groups,Uyghur,Kazakh,and Han *** found that differences in gut microbiome were greater between genetically distinct ethnic groups than those genetically closely related ones in taxonomic composition,functional composition,enterotype stratification,and microbiome genetic *** also observed considerable correlations between host genetic variants and the abundance of a subset of gut microbial ***,interactions between gut microbiome species and host genetic variants might have coordinated effects on specific human *** ovatus,previously reported to modulate intestinal immunity,is significantly correlated with the host genetic variant rs12899811(meta-P=5.55×10^(-5)),which regulates the VPS33B expression in the colon,acting as a tumor suppressor of colorectal *** results advance our understanding of the micro-coevolution of the human gut microbiome and their interactive effects with host genetic variation on phenotypic diversity.

关键词： Micro-coevolution Gut microbiome Host genetics Uyghur Kazakh Han Chines

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Strategies to increase tolerance and robustness of industrial microorganisms

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Synthetic and Systems Biotechnology 2022年第1期7卷 533-540页

作者： Marta Tous Mohedano Oliver Konzock Yun Chen Division of Systems and Synthetic biology Department of Biology and Biological EngineeringChalmers University of TechnologyGöteborgSweden

The development of a cost-competitive bioprocess requires that the cell factory converts the feedstock into the product of interest at high rates and ***,microbial cell factories are exposed to a variety of different stresses during the fermentation *** stresses can be derived from feedstocks,metabolism,or industrial production processes,limiting production capacity and diminishing *** stress tolerance and robustness allows for more efficient production and ultimately makes a process more economically *** review summarises general trends and updates the most recent developments in technologies to improve the stress tolerance of *** first look at evolutionary,systems biology and computational methods as examples of non-rational *** we review the(semi-)rational approaches of membrane and tran-scription factor engineering for improving tolerance *** further discuss challenges and perspectives associated with these different approaches.

关键词： Toxicity Novel synthetic biology tools Systems biology Genome-scale model Membrane engineering Transcription factor engineering

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