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.     

宏基因组研究的生物信息学平台现状

由Handelsman et al(1998)提出的宏基因组(metagenome)泛指特定环境样品(例如:人类和动物的肠道、母乳、土壤、湖泊、冰川和海洋等环境)中微生物群落所有物种的基因组。宏基因组技术起源于环境微生物学研究,而新一代高通量测序技术使其广泛应用成为可能。与基因组学研究相类似,目前宏基因组学发展的瓶颈在于如何高效分析高通量测序产生的海量数据,因此,相关的生物信息学分析方法和平台是宏基因组学研究的关键。该文介绍了目前宏基因组研究领域中主要的生物信息学软件及工具;鉴于目前宏基因组研究所采用的"全基因组测序"(whole genome sequencing)和"扩增子测序"(amplicon sequencing)两大测序方法所获得的数据和相应分析方法有较大差异,文中分别对相应软件平台进行了介绍。     

An international showcase of bioinformatics research

A report on the 11th International Conference on Intelligent Systems for Molecular Biology, Brisbane, Queensland, Australia, 29 June - 3 July 2003.     

Promoting synergistic research and education in genomics and bioinformatics

Bioinformatics and Genomics are closely related disciplines that hold great promises for the advancement of research and development in complex biomedical systems, as well as public health, drug design, comparative genomics, personalized medicine and so on. Research and development in these two important areas are impacting the science and technology.High throughput sequencing and molecular imaging technologies marked the beginning of a new era for modern translational medicine and personalized healthcare. The impact of having the human sequence and personalized digital images in hand has also created tremendous demands of developing powerful supercomputing, statistical learning and artificial intelligence approaches to handle the massive bioinformatics and personalized healthcare data, which will obviously have a profound effect on how biomedical research will be conducted toward the improvement of human health and prolonging of human life in the future. The International Society of Intelligent Biological Medicine (http://www.isibm.org) and its official journals, the International Journal of Functional Informatics and Personalized Medicine (http://www.inderscience.com/ijfipm) and the International Journal of Computational Biology and Drug Design (http://www.inderscience.com/ijcbdd) in collaboration with International Conference on Bioinformatics and Computational Biology (Biocomp), touch tomorrow's bioinformatics and personalized medicine throughout today's efforts in promoting the research, education and awareness of the upcoming integrated inter/multidisciplinary field. The 2007 international conference on Bioinformatics and Computational Biology (BIOCOMP07) was held in Las Vegas, the United States of American on June 25-28, 2007. The conference attracted over 400 papers, covering broad research areas in the genomics, biomedicine and bioinformatics. The Biocomp 2007 provides a common platform for the cross fertilization of ideas, and to help shape knowledge and scientific achievements by bridging these two very important disciplines into an interactive and attractive forum. Keeping this objective in mind, Biocomp 2007 aims to promote interdisciplinary and multidisciplinary education and research. 25 high quality peer-reviewed papers were selected from 400+ submissions for this supplementary issue of BMC Genomics. Those papers contributed to a wide-range of important research fields including gene expression data analysis and applications, high-throughput genome mapping, sequence analysis, gene regulation, protein structure prediction, disease prediction by machine learning techniques, systems biology, database and biological software development. We always encourage participants submitting proposals for genomics sessions, special interest research sessions, workshops and tutorials to Professor Hamid R. Arabnia (hra@cs.uga.edu) in order to ensure that Biocomp continuously plays the leadership role in promoting inter/multidisciplinary research and education in the fields. Biocomp received top conference ranking with a high score of 0.95/1.00. Biocomp is academically co-sponsored by the International Society of Intelligent Biological Medicine and the Research Laboratories and Centers of Harvard University--Massachusetts Institute of Technology, Indiana University--Purdue University, Georgia Tech--Emory University, UIUC, UCLA, Columbia University, University of Texas at Austin and University of Iowa etc. Biocomp--Worldcomp brings leading scientists together across the nation and all over the world and aims to promote synergistic components such as keynote lectures, special interest sessions, workshops and tutorials in response to the advances of cutting-edge research.     

Post-genomic challenges for collaborative research in infectious diseases

Although high-burden pathogens have been prioritized for sequencing, genomic research has yet to yield effective vaccines, diagnostics or therapeutics for the infectious diseases that burden developing countries. International research partnerships are needed more today than ever before, and we propose that increased participation by scientists in endemic areas would overcome current roadblocks and is an essential path towards translational research outcomes.     

Update in research and methods in proteomics and bioinformatics

The 3rd International Conference on Proteomics & Bioinformatics (Proteomics 2013)

Philadelphia, PA, USA, 15–17 July 2013

The Third International Conference on Proteomics & Bioinformatics (Proteomics 2013) was sponsored by the OMICS group and was organized in order to strengthen the future of proteomics science by bringing together professionals, researchers and scholars from leading universities across the globe. The main topics of this conference included the integration of novel platforms in data analysis, the use of a systems biology approach, different novel mass spectrometry platforms and biomarker discovery methods. The conference was divided into proteomic methods and research interests. Among these two categories, interactions between methods in proteomics and bioinformatics, as well as other research methodologies, were discussed. Exceptional topics from the keynote forum, oral presentations and the poster session have been highlighted. The topics range from new techniques for analyzing proteomics data, to new models designed to help better understand genetic variations to the differences in the salivary proteomes of HIV-infected patients.     

Architectural design and the collaborative research environment

Given that science is a collaborative endeavor, architects are striving to design new research buildings that not only provide a more pleasant work space but also facilitate interactions among researchers.     

Lessons for collaborative research in a changing operating environment

This Comment records the details of an unusual multipartner ecological research programme studying Temperate Highland Peat Swamps on Sandstone in the Sydney Basin‐Blue Mountains area of New South Wales. We draw lessons from the experience of designing and managing this multipartner ecological programme, which was based on a nontraditional funding source – that is an enforceable undertaking required of a coal mining company related to an occurrence at a mine site. The research programme encompassed geomorphology, ecohydrology and ecology of a number of sites. Given the currently constrained public‐good environmental research funding and pressures for both researchers and managers to find new, collaborative ways of funding and implementing research, lessons drawn from such innovative experiences may be of wider utility. In particular, lessons are drawn from the programme regarding the time required to design collaborative processes and the need for explicit programme management capacities.     

生物信息学在毒理基因组学研究中的应用

毒理基因组学主要在基因组水平上研究机体对环境因子的应答反应,了解基因和环境交互作用在疾病发生中的作用。生物信息学与毒理基因组学研究的结合为环境与健康研究开辟了新的方法。本文对毒理基因组学的研究手段、意义及面临的挑战,生物信息学在毒理基因组学研究中的作用以及存在的问题和展望进行了综述。     

A brief history of genome research and bioinformatics in France

The development of in silico genomics has progressed slowly in France for a number of political reasons. Two administrative organizations, the Groupement de Recherche sur les Génomes (GREG) and the Groupement de Recherche 1029 (GDR 1029) of the Centre National de la Recherche Scientifique (CNRS) have been established. These organizations have created the dynamics that hopefully will place France (which coordinated consortia that completed several of the first large microbial genomes) among the developed nations that support Large-Scale Biology.     

Learning genetics through an authentic research simulation in bioinformatics

Following the rationale that learning is an active process of knowledge construction as well as enculturation into a community of experts, we developed a novel web-based learning environment in bioinformatics for high-school biology majors in Israel. The learning environment enables the learners to actively participate in a guided inquiry process by solving a problem in the context of authentic research in genetics. Through the learning environment, the learners are exposed to a genetics problem which was developed on the basis of research in which a mutated gene, which causes deafness, was identified. They follow, step by step, the way scientists try to solve it, using the current geneticists' toolbox. The environment uses an adapted version of the BLAST program (a bioinformatics tool which enables to find similarities between sequences), which was modified in a way that enables the teachers and students to use it easily. Using quantitative and qualitative research approaches, we were able to show that learning through the bioinformatics environment promotes construction of new knowledge structures and influences students' acquisition of a deeper and multidimensional understanding of the genetics domain. In addition, learning through the bioinformatics environment influences students' comprehension of the practices and scientific ways of thinking.     

Apple gene function and gene family database: an integrated bioinformatics database for apple research

The apple (Malus domestica) is one of the most economically important fruit crops in the world, due its importance to human nutrition and health. To analyze the function and evolution of different apple genes, we developed apple gene function and gene family database (AppleGFDB) for collecting, storing, arranging, and integrating functional genomics information of the apple. The AppleGFDB provides several layers of information about the apple genes, including nucleotide and protein sequences, chromosomal locations, gene structures, and any publications related to these annotations. To further analyze the functional genomics data of apple genes, the AppleGFDB was designed to enable users to easily retrieve information through a suite of interfaces, including gene ontology, protein domain and InterPro. In addition, the database provides tools for analyzing the expression profiles and microRNAs of the apple. Moreover, all of the analyzed and collected data can be downloaded from the database. The database can also be accessed using a convenient web server that supports a full-text search, a BLAST sequence search, and database browsing. Furthermore, to facilitate cooperation among apple researchers, AppleGFDB is presented in a user-interactive platform, which provides users with the opportunity to modify apple gene annotations and submit publication information for related genes. AppleGFDB is available at http://www.applegene.org or http://gfdb.sdau.edu.cn/.