共词分析国内外生物信息学领域研究态势

生物信息学作为自然科学领域中多学科交叉的新兴学科,其发展研究得到了众多学者的关注。为了解生物信息学在国内外的研究态势,以CNKI中文数据库和Web of science外文数据库中生物信息学领域期刊论文为研究对象,利用R语言编程工具,文献计量和共词分析归纳了国内外生物信息学领域的研究现状、热点及趋势。结果表明:国内外生物信息学研究均处于高速发展期,文献量呈逐年增长趋势,研究领域也在不断拓宽;国内外研究热点均聚焦在基因挖掘、蛋白质结构与功能预测、miRNA分析等,但国内偏向于理论研究,而国际更注重其在疾病治疗、药物设计等方面的应用研究。     

可持续生计研究热点与前沿的可视化分析

可持续生计目前已成为全球环境变化研究的热点领域,正日益发展为可持续性科学的重要研究范式之一。论文以Web of science核心库为数据源,应用可视化分析软件CiteS paceⅢ,采取关键词共现分析、文献共被引分析、突现词分析等方法对国际可持续生计研究现状进行系统分析。研究发现,可持续生计研究文献数量呈逐年上升趋势,主要分布在生态、环境、资源及管理相关学科;瓦赫宁恩大学、中国科学院、昆士兰大学、哥伦比亚大学、博茨瓦纳大学等研究机构表现出较强的研究实力;研究人员及机构的成规模的合作网络已经形成。Scoones I、Chambers R、Conway G、Ellis F和Ostrom E等学者及其代表作品对可持续生计理论知识基础的构建及相关研究的推进奠定了坚实的基础。生计与生态环境的相互关系一直是研究重点,交叉学科的综合集成研究将成为可持续生计研究的新热点。     

数据挖掘在生物信息学中的应用——文献计量学视角

基因组和蛋白质结构与功能方面已积累了海量数据。如何从海量数据中获取有效信息成为生物信息学迫切要解决的问题。本文以相关主题词检索文献,分析了该领域历年文章数量、发文最多的机构和作者、被引用频次居前论文、期刊载文量,并对关键词和被引用频次居前论文的作者进行共现分析。我们发现,生物信息学中运用数据挖掘方法的文献逐年增多,该领域30.1%的文献发表在十个期刊上,分类、聚类、特征选择和支持向量机等数据挖掘方法使用较多。本研究描绘了生物信息学与数据挖掘这一交叉领域的研究概况,为后续数据挖掘方法与生物信息学研究相结合提供帮助。     

从文献计量分析看京津冀近65年昆虫学研究发展态势

本文运用文献计量学方法,对新中国成立以来发表在我国主要中文期刊上的京津冀地区昆虫学文献进行检索、整理、分类、统计和分析,共搜集了2457篇相关文献。探讨了这些文献的文献学特征,包括数量年度分布、研究类群分布、研究领域分布、文献载体分布、研究机构分布和学科方向分布,并对昆虫学各分支学科的发展情况进行了阶段分析,以期了解该地区昆虫学研究发展的基本现状和趋势。     

植物学的发展趋势及国家自然科学基金委员会植物学科资助状况

根据植物学的发展趋势和植物学科的特点,对该学科采取的资助策略是“重视前沿领域,扶持弱势学科,关注新的学科生长点”;学科资助项目数和经费数逐年增加,2004年投入经费和资助项目数是2001年的2倍;简要介绍了学科遴选项目的原则和2004年度项目申请和资助的情况,提供了2004年度植物学科资助项目一览表。     

植物学的发展趋势及国家自然科学基金委员会植物学科资助状况

根据植物学的发展趋势和植物学科的特点,对该学科采取的资助策略是"重视前沿领域,扶持弱势学科,关注新的学科生长点";学科资助项目数和经费数逐年增加,2004年投入经费和资助项目数是2001年的2倍;简要介绍了学科遴选项目的原则和2004年度项目申请和资助的情况,提供了2004年度植物学科资助项目一览表.     

关于昆虫学的交叉科学问题

一、什么是交叉科学所谓交叉科学是指突破某一门学科原有的界限,在研究内容和方法上涉及到两门学科以上研究领域的科学。科学的发展有两种形式:一种是单一的,即研究原有的学科,使其不断深化和精细;另一种是交叉的,即研究各种跨学科的课题,并将其融合起来,形成交叉学科。交叉学科可分为三种类型:一种是研究两门科学交界的问题而成长起来的科学。如:生物化学;另一种是综合多学科知识而发展起来的如:环境科学。还有一种是研究各专门学科中的共性问题,即横断学科。现在许多单一科学,其研究方法和内容常具有交叉学科的性质,而且其交叉比重越来越大。交叉学科的发展,将会导致新学     

生物信息学数据库研究文献引文与热点分析

以Web of Science为数据源,简要概括生物信息学数据库研究的发展趋势。利用Cite Space可视化工具展现生物信息学数据库研究的知识基础和研究热点图谱,为开展生物信息学数据库领域相关的理论研究和实践活动提供借鉴,以便推动生物信息学数据库研究的发展。研究表明：1990年Altschul SF发表的＂局部比对搜索工具——BLAST＂是生物信息学数据库研究的重要知识来源文献;热点主题集中在序列库、基因组数据库、分类数据库、蛋白质数据库、数据库更新、集成系统等。     

基于CNKI数据库的构树研究文献计量分析

以中国期刊全文数据库为统计数据源,对构树近10年(2010～2019)的年度发文量、学科分布、被引用情况、研究机构等内容进行统计分析.结果表明:有关构树研究发文数量平均在27篇/年,且主要集中于农业科学领域,占总文献的69.57％;刊载文献最多的是《安徽农业科学》杂志;构树相关研究最多的单位是贵州大学;单篇引用率最高的...     

β-淀粉样蛋白研究热点与内容分析

为探究当前β-淀粉样蛋白研究领域的研究热点和发展趋势,以2008～2017年Web of Science核心合集数据库中收录的21 312篇β-淀粉样蛋白相关文献为数据来源,利用CiteSpaceV进行可视化处理和分析。结果显示:β-淀粉样蛋白研究发文量呈逐年增长的趋势,美国和中国是β-淀粉样蛋白研究领域的主要研究力量;β-淀粉样蛋白研究的高频共被引文献主要关注淀粉样蛋白级联假说、阿兹海默症诊断标准、β-淀粉样蛋白低聚体的神经毒性等问题。阿兹海默症及相关疾病研究、动物模型研究、体内病理特征研究以及体外机理研究是近十年来β-淀粉样蛋白研究的主要研究热点。β-淀粉样蛋白研究前沿和未来研究趋势将围绕在阿兹海默症前期认知障碍的诊断与干预、β-淀粉样蛋白沉积的降解等相关问题上。本研究的知识图谱研究揭示了近十年来β-淀粉样蛋白研究领域的动态发展规律,为相关学科研究提供了切实而有价值的参考。     

Investment in plant research and development bears fruit in China

Recent rapid progress in plant science and biotechnology in China demonstrates that China’s stronger support for funding in plant research and development (R&D) has borne fruit. Chinese groups have contributed major advances in a range of fields, such as rice biology, plant hormone and developmental biology, genomics and evolution, plant genetics and epigenetics, as well as plant biotechnology. Strigolactone studies including those identifying its receptor and dissecting its complex structure and signaling are representative of the recent researches from China at the forefront of the field. These advances are attributable in large part to interdisciplinary studies among scientists from plant science, chemistry, bioinformatics, structural biology, and agronomy. The platforms provided by national facilities facilitate this collaboration. As well, efficient restructuring of the top–down organization of state programs and free exploration of scientists’ interests have accelerated achievements by Chinese researchers. Here, we provide a general outline of China’s progress in plant R&D to highlight fields in which Chinese research has made significant contributions.     

生物信息学本科人才培养的调研与思考

近年来,生物信息学已经逐步发展成为现代生物学和医学等领域的关键技术方法,社会对生物信息学专业人才的需求不断扩大,生物信息学的本科教育也受到了越来越多的关注和重视。为了探索更加合理的人才培养模式、完善课程设置和教学计划,本文以中美两国开设生物信息学本科专业的高校为对象,分别选取一些代表高校并进行深入调研,对比分析课程设置和人才培养现状。结果显示,生物信息学的跨学科性质在各高校中均得到一定体现,培养学生具有多元化的知识结构已经成为生物信息学人才培养的一项共识。同时,根据调研的结果,也对国内生物信息学本科教育提出一些启发与建议。     

Bioconductor: open software development for computational biology and bioinformatics

The Bioconductor project is an initiative for the collaborative creation of extensible software for computational biology and bioinformatics. The goals of the project include: fostering collaborative development and widespread use of innovative software, reducing barriers to entry into interdisciplinary scientific research, and promoting the achievement of remote reproducibility of research results. We describe details of our aims and methods, identify current challenges, compare Bioconductor to other open bioinformatics projects, and provide working examples.     

Past and future trends in cancer and biomedical research: a comparison between Egypt and the World using PubMed-indexed publications

ABSTRACT: BACKGROUND: PubMed is a free web literature search service that contains almost 21 millions of abstracts and publications with almost 5 million user queries daily. The purposes of the study were to compare trends in PubMed-indexed cancer and biomedical publications from Egypt to that of the world and to predict future publication volumes. METHODS: The PubMed was searched for the biomedical publications between 1991 and 2010 (publications dates). Affiliation was then limited to Egypt. Further limitation was applied to cancer, human and animal publications. Poisson regression model was used for prediction of future number of publications between 2011 and 2020. RESULTS: Cancer publications contributed 23% to biomedical publications both for Egypt and the world. Egyptian biomedical and cancer publications contributed about 0.13% to their world counterparts. This contribution was more than doubled over the study period. Egyptian and world's publications increased from year to year with rapid rise starting the year 2003. Egyptian as well as world's human cancer publications showed the highest increases. Egyptian publications had some peculiarities; they showed some drop at the years 1994 and 2002 and apart from the decline in the animal: human ratio with time, all Egyptian publications in the period 1991-2000 were significantly more than those in 2001-2010 (P<0.05 for all). By 2020, Egyptian biomedical and cancer publications will increase by 158.7% and 280% relative to 2010 to constitute 0.34% and 0.17% of total PubMed publications, respectively. CONCLUSIONS: The Egyptian contribution to world's biomedical and cancer publications needs significant improvements through research strategic planning, setting national research priorities, adequate funding and researchers' training.     

How Multidisciplinary Are the Multidisciplinary Journals Science and Nature?

Interest in cross-disciplinary research knowledge interchange runs high. Review processes at funding agencies, such as the U.S. National Science Foundation, consider plans to disseminate research across disciplinary bounds. Publication in the leading multidisciplinary journals, Nature and Science, may signify the epitome of successful interdisciplinary integration of research knowledge and cross-disciplinary dissemination of findings. But how interdisciplinary are they? The journals are multidisciplinary, but do the individual articles themselves draw upon multiple fields of knowledge and does their influence span disciplines? This research compares articles in three fields (Cell Biology, Physical Chemistry, and Cognitive Science) published in a leading disciplinary journal in each field to those published in Nature and Science. We find comparable degrees of interdisciplinary integration and only modest differences in cross-disciplinary diffusion. That said, though the rate of out-of-field diffusion might be comparable, the sheer reach of Nature and Science, indicated by their potent Journal Impact Factors, means that the diffusion of knowledge therein can far exceed that of leading disciplinary journals in some fields (such as Physical Chemistry and Cognitive Science in our samples).     

后基因组时代生物信息学的发展趋势

介绍生物信息学产生背景、发展过程以及研究现状,讨论了后基因组时代分子生物学的主要研究领域功能基因组学、蛋白质组学、比较基因组学、药物基因组学之间的关系。在分析基因组时代和后基因组时代生物信息学所研究内容的差异基础上．说明了基于分层递阶结构的系统结构、特征分析方法以及相应的软件系统开发将成为生物信息学发展的基本趋势之一。     

Cell biology, chemogenomics and chemoproteomics

The scientific techniques used in molecular biological research and drug discovery have changed dramatically over the past 10 years due to the influence of genomics, proteomics and bioinformatics. Furthermore, genomics and functional genomics are now merging into a new scientific approach called chemogenomics. Advancements in the study of molecular cell biology are dependent upon "omics" researchers realizing the importance of and using the experimental tools currently available to cell biologists. For example, novel microscopic techniques utilizing advanced computer imaging allow for the examination of live specimens in a fourth dimension, viz., time. Yet, molecular biologists have not taken full advantage of these and other traditional and novel cell biology techniques for the further advancement of genomic and proteomic-oriented research. The application of traditional and novel cellular biological techniques will enhance the science of genomics. The authors hypothesize that a stronger interdisciplinary approach must be taken between cell biology (and its closely related fields) and genomics, proteomics and bio-chemoinformatics. Since there is a lot of confusion regarding many of the "omics" definitions, this article also clarifies some of the basic terminology used in genomics, and related fields. It also reviews the current status and future potential of chemogenomics and its relationship to cell biology. The authors also discuss and expand upon the differences between chemogenomics and the relatively new term--chemoproteomics. We conclude that the advances in cell biology methods and approaches and their adoption by "omics" researchers will allow scientists to maximize our knowledge about life.     

Evolving research trends in bioinformatics

The cross-disciplinary nature of bioinformatics entails co-evolution with other biomedical disciplines, whereby some bioinformatics applications become popular in certain disciplines and, in turn, these disciplines influence the focus of future bioinformatics development efforts. We observe here that the growth of computational approaches within various biomedical disciplines is not merely a reflection of a general extended usage of computers and the Internet, but due to the production of useful bioinformatics databases and methods for the rest of the biomedical scientific community. We have used the abstracts stored both in the MEDLINE database of biomedical literature and in NIH-funded project grants, to quantify two effects. First, we examine the biomedical literature as a whole and find that the use of computational methods has become increasingly prevalent across biomedical disciplines over the past three decades, while use of databases and the Internet have been rapidly increasing over the past decade. Second, we study the recent trends in the use of bioinformatics topics. We observe that molecular sequence databases are a widely adopted contribution in biomedicine from the field of bioinformatics, and that microarray analysis is one of the major new topics engaged by the bioinformatics community. Via this analysis, we were able to identify areas of rapid growth in the use of informatics to aid in curriculum planning, development of computational infrastructure and strategies for workforce education and funding.