CompBio: Special Focus on Information Processing in Biology

越来越多地，生物学的许多方面可以被视为涉及信息处理。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信息科学的新概念和新方法。这个项目的动机是这两个观察。生物信息处理领域的进步需要计算机科学家、数学家、物理学家、化学家和生物学家之间的跨学科合作。该项目围绕一系列研讨会展开，这些研讨会将加强跨学科合作，并向优秀的年轻人介绍研究前沿的问题和主题。该项目将围绕以下四个主题举办一系列研讨会：(1)生物信息处理的算法方法；(2)计算机科学、工程与生物学：应用与类比；(3)生物电路与细胞信号传导；(4)蛋白质组学。其中两个主题代表了方法，两个主题代表了这些方法的应用领域。主题1：拟举办高通量生物数据检测与处理规律专题研讨会；机器学习方法——理解基因调控的方法和计算肿瘤建模。主题二工作坊将涵盖纳米科技及生物学；生物学中的控制、通信与计算RNA干扰过程的机制和应用。关于主题3，将有关于逆向工程生物电路策略的研讨会；发育组织中的细胞通讯和信息处理生物网络动力学；基因调控网络的进化。主题四：分子识别中蛋白质结构的信息处理；蛋白质组NetworkEvolution;神经退行性疾病的功能蛋白质组学研究乙型肝炎病毒感染的数学模型和分子模型的意义我们期望从该项目中产生的研讨会、科学论文和书籍将有助于发展该领域的长期焦点，仔细定义计算机科学、数学、化学和物理学中特定兴趣的问题和方向，并与生物学家合作设计，并导致新的生物学概念，这些概念将影响未来的生物和信息科学研究。简而言之，我们期望这个项目在未来几年对生物信息处理的研究产生影响。更广泛的影响在这个项目中产生的想法将对无数领域产生影响，并建立跨学科的联系。访问计划将鼓励高级和初级研究人员，包括学生，参与由研讨会产生的合作研究。每个研讨会将有一个基金来支持研究生和博士后，研讨会将有一个实质性的教育组成部分，通过指导/说明性的谈话。该主题适合本科研究，参与的教师将与已经存在的本科研究计划（REU计划）协调主题。为了使项目广泛传播，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，可以使其成为大型社区的资源。该项目将对一大批优秀青年科研人员的职业生涯产生重大影响，并对培养和发展生物信息处理领域的领军人才发挥重要作用。该项目预计将产生长期影响，远远超过其四年的持续时间，因为该项目的研讨会、访客和传播组成部分将使所开发的想法接触到全国乃至全世界的数百人。

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.