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A Historic Retrospective on the Early Bioinformatics Research in China

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Genomics, Proteomics & Bioinformatics 2023年第5期21卷 897-899页

作者： runsheng chen CAS Key Laboratory of RNA Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101China College of Life Sciences University of Chinese Academy of SciencesBeijing 100049China

With the rapid development of various omics and related technologies,as well as the revolutionary computing power upsurge,bioinformatics has ushered in unprecedented development ***’s bioinformatics research as a cohesive team effort continues to grow,and has also achieved many gratifying discoveries[1,2].The vigorous development of bioinformatics in China today is inseparable from the foundation and promotion of the older generation of scientists who pioneered in bioinformatics research.

关键词： promotion continue today

Early bioinformatics research in China

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Quantitative Biology 2021年第3期9卷 242-250页

作者： runsheng chen Chinese Academy of Sciences Key Laboratory of Nucleic Acid Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101China

This article records the author’s experience in participating in the early human genome and bioinformatics research in China,especially the non-coding sequence of the *** also introduced the beginning of human genome research in china,including the experts and teams involved in the International Human Genome Project All the progress of bioinformatics originates from the inheritance of theoretical biology and the layout of philosophers in china.

关键词： participating layout beginning

AlphaFold2 and its applications in the fields of biology and medicine

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Signal Transduction and Targeted Therapy 2023年第4期8卷 1630-1643页

作者： Zhenyu Yang Xiaoxi Zeng Yi Zhao runsheng chen West China Biomedical Big Data Center West China HospitalSichuan UniversityChengdu 610041China Key Laboratory of Intelligent Information Processing Advanced Computer Research CenterInstitute of Computing TechnologyChinese Academy of SciencesBeijing 100190China Key Laboratory of RNA Biology Center for Big Data Research in HealthInstitute of BiophysicsChinese Academy of SciencesBeijing 100101China Pingshan Translational Medicine Center Shenzhen Bay LaboratoryShenzhen 518118China

AlphaFold2(AF2)is an artificial intelligence(AI)system developed by DeepMind that can predict three-dimensional(3D)structures of proteins from amino acid sequences with atomic-level *** structure prediction is one of the most challenging problems in computational biology and chemistry,and has puzzled scientists for 50 *** advent of AF2 presents an unprecedented progress in protein structure prediction and has attracted much *** release of structures of more than 200 million proteins predicted by AF2 further aroused great enthusiasm in the science community,especially in the fields of biology and ***2 is thought to have a significant impact on structural biology and research areas that need protein structure information,such as drug discovery,protein design,prediction of protein function,et *** the time is not long since AF2 was developed,there are already quite a few application studies of AF2 in the fields of biology and medicine,with many of them having preliminarily proved the potential of *** better understand AF2 and promote its applications,we will in this article summarize the principle and system architecture of AF2 as well as the recipe of its success,and particularly focus on reviewing its applications in the fields of biology and *** of current AF2 prediction will also be discussed.

关键词： system fields Fold

Noncoding RNA:from dark matter to bright star

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Science China(Life Sciences) 2020年第4期63卷 463-468页

作者： Yuanchao Xue runsheng chen Lianghu Qu Xiaofeng Cao Key Laboratory of RNA Biology Institute of BiophysicsChinese Academy of SciencesBeijing 100101China MOE Key Laboratory of Gene Function and Regulation State Key Laboratory for BiocontrolSchool of Life SciencesSun Yat-Sen UniversityGuangzhou 510275China State Key Laboratory of Plant Genomics and National Center for Plant Gene Research(Beijing) Institute of Genetics and Developmental BiologyChinese Academy of SciencesBeijing 100101China University of Chinese Academy of Sciences Beijing 100049China

The central dogma states that genes encoded in the DNA should be first transcribed into messenger RNA(mRNA)and then translated into functional proteins(Crick,1970).This dogma has been written in numerous textbooks and learned by myriad ***,along with the completion of the human genome project in June 2000,an astonishing fact was revealed:only 1.5%of the human genome encodes for proteins(Lander et al.,2001;Venter et al.,2001).This fact raised three fundamental questions:(i)why does the human genome have so few protein-coding genes?(ii)how to explain the apparent differences between humans and other species using the limited coding genes?(iii)what are the roles of the noncoding regions in our genome?

关键词： al. apparent raised

Bioinformatics—Mining the genome for information

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Frontiers of Electrical and Electronic Engineering in China 2010年第3期5卷 391-404页

作者： runsheng chen Geir SKOGERBØ National Laboratory of Biomacromolecules Institute of Biophysics Chinese Academy of Sciences Beijing China

Since the launching of the human genome sequencing project in the 1990s,genomic research has already achieved definite *** the beginning of the present century,the complete genomes of several model organisms have already been sequenced,including a number of prokaryote microorganisms and the eukaryotes yeast(Saccharomyces cerevisiae),nematode(***),fruit fly(Drosophila melanogaster)and thale cress(Arabidopsis thaliana)as well as the major part of the human *** achievements signified that a new era of data mining and analysis on the human genome had *** language of human genetics would gradually be read and understood,and the genetic information underlying metabolism,development,differentiation and evolution would progressively become known to *** amounts of data are already accumulating,but at present many of the rules that should guide the understanding of this information are yet *** research is thus not only becoming more important,but is also faced with severe challenges as well as great opportunities.

关键词： bioinformatics genome algorithm noncoding RNA biological network

Fluid Evolution and Scheelite Precipitation Mechanism of the Large-Scale Shangfang Quartz-Vein-Type Tungsten Deposit, South China: Constraints from Rare Earth Element(REE) Behaviour during Fluid/Rock Interaction

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Journal of Earth Science 2020年第4期31卷 635-652页

作者： runsheng chen Luyun Zhu Shao-Yong Jiang Ying Ma Qinghai Hu State Key Laboratory of Geological Processes and Mineral Resources School of Earth ResourcesChina University of GeosciencesWuhan 430074China Fujian Institute of Geological Survey and Research Fuzhou 350013China Key Laboratory of Geochemical Exploration Institute of Geophysical and Geochemical ExplorationCA GSLangfang 065000China

Unlike classic skarn-type scheelite deposits directly acquiring sufficient Ca2+ from surrounding limestones, all of the scheelite orebodies of the Shangfang tungsten(W) deposit occur mainly in amphibolite, and this provides a new perspective on the mineralization mechanism of W deposits. The ability of hydrothermal scheelite(CaWO4) to bind REE3+ in their Ca2+ crystal lattices makes it a useful mineral for tracing fluid-rock interactions in hydrothermal mineralization systems. In this study, the REE compositions of scheelite and some silicate minerals were measured systematically in-situ by laser ablation inductively coupled plasma mass spectrometry(LA-ICP-MS) to assess the extent of fluid-rock interactions for the Late Mesozoic quartz-vein-type Shangfang W deposits. According to the variations in CaO and REE among scheelite and silicate minerals, the amphibole and actinolite in amphibolite may be able to release large amounts of Ca2+ and REE3+ into the ore-forming fluids during chlorite alteration, which is critical for scheelite precipitation. Furthermore, an improved batch crystallization model was adopted for simulating the process of scheelite precipitation and fluid evolution. The results of both the in-situ measurements and model calculations demonstrate that the precipitation of early-stage scheelite with medium rare-earth elements(MREE)-rich and [Eu/Eu*]N1. Even though the partition coefficient of REE is constant, the later-stage scheelite will also inherit a certain degree of MREE-depletion and [Eu/Eu*]N future from the residual fluids. As a common mineral, sheelite forms in various types of hydrothermal ore deposits(e.g., tungsten and gold deposits). Hence, the improved batch crystallization model is also possible for obtaining detailed information regarding fluid evolution for other types

关键词： scheelite quartz vein type REE pattern Eu anomaly fluid evolution

Analysis of the p53/CEP-1 regulated non-coding transcriptome in C. elegans by an NSR-seq strategy

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Protein & Cell 2014年第10期5卷 770-782页

作者： Derong Xu Guifeng Wei Ping Lu Jianjun Luo Xiaomin chen Geir Skogerbo runsheng chen Laboratory of Non-coding RNA Institute of Biophysics University of Chinese Academy of Sciences Beijing 100101 China Graduate University of Chinese Academy of Sciences Beijing 100080 China Key Laboratory of Forest Protection State Forestry Administration/Research Institute of Forest Ecology Environment andProtection Chinese Academy of Forestry Beijing 100091 China

In recent years, large numbers of non-coding RNAs （ncR- NAs） have been identified in C. elegans but their functions are still not well studied. In C. elegans, CEP-1 is the sole homolog of the p53 family of genes. In order to obtain transcription profiles of ncRNAs regulated by CEP-1 under normal and UV stressed conditions, we applied the ＇not-so- random＇ hexamers priming strategy to RNA sequencing in C. elegans, This NSR-seq strategy efficiently depleted rRNA transcripts from the samples and showed high technical replicability. We identified more than 1,000 ncR- NAs whose apparent expression was repressed by CEP-1, while around 200 were activated. Around 40% of the CEP-1 activated ncRNAs promoters contain a putative CEP-1- binding site. CEP-1 regulated ncRNAs were frequently clustered and concentrated on the X chromosome. These results indicate that numerous ncRNAs are involved in CEP-1 transcriptional network and that these are espe- cially enriched on the X chromosome in C. elegans.

关键词： p53/CEP-1 C. elegans ncRNA removalrRNA NSR-seq high technical replicability

One Novel Long Noncoding RNA lnc10 in Drosophila

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Journal of Genetics and Genomics 2014年第2期41卷 79-82页

作者： Meixia Li Mengbo Xu Shengyun Wen Baoyan Bai runsheng chen Li Liu State Key Laboratory of Brain and Cognitive Science Institute of BiophysicsChinese Academy of Sciences Key Laboratory of Noncoding RNA Institute of BiophysicsChinese Academy of Sciences

With the development of computational methods and RNA sequencing technology for assembling the transcriptome, it is becoming clear that the mammal genome is pervasively tran- scribed, and large numbers of long noncoding RNAs （lncRNAs） composing the major part of the transcriptome have been identified （Ravasi et al., 2006; Birney et al., 2007;

关键词： RNA One Novel Long Noncoding RNA lnc10 in Drosophila RACE PCR length body ORF

Molecular dynamics simulation of site-directed mutagenesis of HIV-1 Tat trans-activator

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Chinese Science Bulletin 1999年第8期44卷 708-711页

作者： Yan Cui Lunjiang Ling runsheng chen Longchuan Bai Jiangang Yuan Boqin Qiang Chinese Acad Sci Inst Biophys Beijing 100101 Peoples R China Chinese Acad Med Sci Inst Basic Med Sci Beijing 100005 Peoples R China

The Cys-rich domain, core region and basic domain are highly conserved and very important to the trans-activation activity of HIV-1 Tat trans-activator. The three-dimensional structures of 6 mutants of HIV-1 Tat protein were constructed with the methods of molecular dynamics simulation. The variations of the structures of the mutants have been analyzed and the factors that led to abolishment of trans-activation activity have been discussed.

关键词： human immunodeficiency virus type 1 ( HIV-1) molecular dynamics simulation site-directed mutagenesis Tat protein.