CompBio: Special Focus on Information Processing in Biology

生物学的许多方面越来越多地被视为涉及信息的处理。现代信息和计算机科学在人类基因组测序等重大生物学成就中发挥了重要作用。另一方面，生物学思想可以启发情报学中的新概念和新方法。本项目的动机是这两个观察结果。生物信息处理领域的进展将需要计算机科学家、数学家、物理学家、化学家和生物学家之间的跨学科合作。该项目将围绕一系列研讨会展开，这些研讨会将加强开始形成的跨学科合作，并将优秀的初级人员介绍给研究前沿的问题和主题。智力价值该项目将围绕四个主题的系列研讨会组织：(1)生物信息处理的算法方法；(2)计算机科学、工程和生物学：应用和类比；(3)生物电路和细胞信号；(4)蛋白质组学。其中两个主题代表方法，两个代表这些方法的应用领域。在主题1下，计划的工作坊是关于检测和处理高通量生物数据中的规律性；理解基因调控的机器学习方法；以及计算肿瘤建模。主题2工作坊将涵盖纳米技术和生物学；生物学中的控制、通信和计算；以及RNA干扰过程的机制和应用。对于主题3，将举办关于反向工程生物电路的策略、发展问题中的细胞通信和信息处理、生物网络的动力学和基因调控网络的进化的讲习班。主题4工作坊将讨论分子识别中蛋白质结构的信息处理；蛋白质组网络进化；神经退行性疾病的功能蛋白质组学；以及感染的数学模型和乙肝病毒的分子建模的意义。我们期望该项目产生的研讨会、科学论文和书籍将有助于发展该领域的长期焦点，仔细定义生物学家特别感兴趣的计算机科学、数学、化学和物理方面的问题和方向，并与生物学家合作设计，并产生新的生物学概念，这些概念将有助于未来的生物学和信息科学研究。简而言之，我们预计该项目将在未来几年内促进生物信息处理的研究。广泛的影响在该项目中提出的想法将对无数领域产生影响，并建立跨学科的联系。访客计划将鼓励包括学生在内的高级和初级研究人员参与由研讨会产生的合作研究。每个讲习班都将设立一个基金，用于支持本科生和博士后，讲习班将通过讲授/说明性的演讲，提供大量的教育内容。这一课题很适合本科生的研究，参与的教职员工将与已经存在的本科生研究计划(REU计划)协调主题。为了让项目得到广泛传播，每个研讨会都将有一个网站，上面有相关的参考资料、问题和演示文稿的副本，使其成为大型社区的资源。该项目将对一大批优秀的初级研究人员的职业生涯产生重大影响，并对培养和发展有充分准备成为生物信息处理领域领导者的科学家发挥重要作用。预计该项目的长期影响将远远超过其四年的持续时间，因为该项目的讲习班、访问者和传播部分将使所形成的想法惠及全国和世界各地的数百人。

Increasingly, many aspects of biology can be viewed as involving the processing of information. Moderninformation and computer science have played an important rolein such major biological accomplishmentsas the sequencing of the human genome. On the other hand, biological ideas can inspire new concepts andmethods in information science. This project is motivated by these two observations. Progress in the fieldof biological information processing will require interdisciplinary collaborations among computer scientists,mathematicians, physicists, chemists, and biologists. The project is built around a series of workshops thatwill enhance the interdisciplinary collaborations beginning to form and introduce outstanding junior peopleto problems and topics at the forefront of research.Intellectual MeritThe project will be organized around a series of workshops with four themes: (1) Algorithmic Approachesto Biological Information Processing; (2) Computer Science, Engineering and Biology: Applications andAnalogies; (3) Biological Circuits and Cellular Signaling; (4) Proteomics. Two of these themes representapproaches and two represent areas of application of these approaches. Under theme 1, planned workshopsare on Detecting and Processing Regularities in High Throughput Biological Data; Machine Learning Ap-proaches for Understanding Gene Regulation; and Computational Tumor Modeling. Theme 2 workshops willcover Nanotechnology and Biology; Control, Communication, and Computing in Biology; and The Mecha-nism and Applications of the RNA Interference Process. For Theme 3, there will be workshops on Strategiesfor Reverse Engineering Biological Circuits; Cell Communication and Information Processing in DevelopingTissues; Dynamics of Biological Networks; and Evolution of Gene Regulatory Networks. Theme 4 work-shops will be on Information Processing by Protein Structures in Molecular Recognition; Proteome NetworkEvolution; Functional Proteomics of Neurodegenerative Diseases; and Implications of Mathematical Modelsof Infection and Molecular Modeling of Hepatitis B Virus. We expect that the workshops, scientific papersand books coming out of the project will help to develop the long-term focus of the field, carefully defineproblems and directions in computer science, mathematics, chemistry, andphysics of specific interest to anddesigned in collaboration with biologists, and lead to new biological concepts that will in uence biologicaland information science research in the future. In short, we expect the project to in uence the study ofbiological information processing for years to come.Broader ImpactsThe ideas developed in this project will have impact on a myriad of fields and create cross-disciplinaryconnections. A visitor program will encourage senior and junior researchers, including students, to participatein collaborative research spawned by the workshops. Each workshop will have a fund for support of graduatestudents and postdocs amd workshops will have a substantial educational component through talks of atutorial/expository nature. The topic lends itself well to undergraduate research and participating facultywill coordinate topics with an undergraduate research program (REU program) already in existence. To givethe project widespread dissemination, each workshop will have awebsite with relevant references, problems,and copies of presentations that can make it a resource for a large community. The project should significantlyin uence the careers of a large number of outstanding junior researchers and it should play an importantrole in the training and development of scientists who are well-prepared to become leaders in the field ofbiological information processing. The project is expected to have a long-term impact well beyond its fouryear duration since the workshop, visitor, and dissemination components of the project will allow the ideasdeveloped to reach hundreds of people nationwide and worldwide.