Speaker: Professor Chen Luonan, Professor, Electronics, Information and Communication Engineering, Osaka Sangyo University, Director, Institute of Systems Biology, Shanghai University and Former Editor-in-Chief, IET Journal on Systems Biology

Topic 1: Biomolecular Networks - Methods and Applications

Date: 16 March 2009 (Monday)
Time: 3:00pm - 6:00pm
Venue: Room 222, Lady Shaw Building
Abstract: This talk comprehensively covers the contents and the topics on inferring and analyzing biomolecular networks in cellular systems based on available experiment data, in particular stressing on the aspects of network and system, with specific biological problems and novel computational methods. The specific topics include:
1. Inferring gene regulatory network and transcription regulatory network
2. Inferring Protein-protein interaction network, and reconstructing complexes
3. Alignment of biomolecular networks for different species and different tissues
4. Identifying active pathways, and recovering signaling transduction networks
5. Drug target detection in metabolic networks

Topic 2: Modeling Biomolecular Networks - Structures and Dynamics

Date: 17 March 2008 (Tuesday)
Time: 3:00pm - 6:00pm
Venue: Room 222, Lady Shaw Building
Abstract: This talk will cover contents or topics on modeling molecular networks and analyzing nonlinear dynamics in cellular systems in a comprehensive manner, in particular stressing on the aspects of systems and engineering. Attention will be focused on deriving general theoretical results and revealing the essential principles of biological systems based on nonlinear dynamical and control theory. Specifically, I will describe how to model or construct a general molecular network in a single cell, how to construct a molecular network with specific functions or structures, such as gene switching networks and gene oscillating networks in individual cells at the molecular level, and how to model a general multicellular system with the consideration of external fluctuations and intercellular coupling of signal biomolecules, how to design a biomolecular network from forward engineering viewpoint, and how to analyze and further control the nonlinear phenomena of living organisms at the molecula level, such as switching behaviors, cooperative dynamics or synchronization of biological oscillators in mult cellular systems.

Speaker: Professor Yu Zu-guo, School of Mathematical Science
Queensland University of Technology, Australia
Venue: Room 232, Lady Shaw Building, CUHK

Talk 1: Predictive methods using DNA sequences and protein sequences and structure, pairwise and multiple sequence alignment

Date: 13 May 2008 (Tuesday)
Time: 2:30am - 5:30pm
Abstract: This talk includes two parts of contents. In the first part, we talk about the prediction methods in bioinformatics such as gene prediction methods, DNA promoter analysis characterization and prediction, predicting features of individual residues, predicting function, protein structure prediction, protein structure evaluation, protein structure comparison and protein secondary structure prediction. In the second part, we talk about the widely used sequence alignment algorithms. This part includes global versus local sequence alignments, dot-plots, score matrices, multiple alignment, structural and evolutionary alignment,etc

Talk 2: Visualization of biological sequences, fractal methods for coding and noncoding DNA sequence distinguish and protein structural classification

Date: 14 May 2008 (Wednesday)
Time: 2:30am - 5:30pm
Abstract: In this talk we first give a short introduction of the fractal theory, then give some graphic and numerical representation of DNA sequences and protein sequences. These representations include DNA walk models (one-dimensional DNA walk, two-dimensional DNA walk, higher-dimensional DNA walk), chaos game representation of biological sequences and their recurrent iterated function simulation, two-dimensional portrait representation of DNA sequences (fractal dimension of the fractal set for a given tag), onedimensional measure representation of biological sequences, Z curve representation of DNA sequences, number sequence of DNA sequences. We will also talk about how to use these representations to distinguish coding and non-coding DNA sequence from the same genome, or identify the species from the fragments of the genome, and discuss protein structural classes based on their amino sequences.

Talk 3: Phylogenetic analysis without sequence alignment

Date: 19 May 2008 (Monday)
Time: 2:30am - 5:30pm
Abstract: The complete genomes of living organisms have provided much information on their phylogenetic relationships. Similarly, the complete genomes of the chloroplast and mitochondria have helped to resolve the evolution of these organelles in photosynthetic eukaryotes and vertebrates respectively. Existing tools and traditional sequence distance methods for phylogenetic analysis, e.g., multiple alignment and various sequence evolutionary models, do not directly apply to complete genomes. Some distance methods without alignment have been developed for phylogenetic analysis using complete genomes. In this talk we will show some distance methods without sequence alignment based on SVD method, Markov model, dynamical language model, Fourier method and log-correlation distance, Entropy density profile with log-correlation distance, mutual information distance. The above distance methods have been used to analyse the phylogenetic relationship of bacteria, viruses and vertebrates based on the genomes. The results are largely in agreement with the current understanding on these organisms.

Speaker: Dr. Wu Ling-yun, Institute of Applied Mathematics, Academy of Mathematics and Systems Science, Chinese Academy of Sciences
Venue: Room 232, Lady Shaw Building, CUHK

Talk 1: Brief Introduction to Bioinformatics

Date: 11 May 2007 (Friday)
Time: 2:00pm - 5:00pm
Abstract: In this lecture, we will first talk about what's bioinformatics, and the brief history of bioinformatics research. Then we will introduce the basic concepts in molecular biology, which is necessary to understand bioinformatics problem. Finally, we will discuss bioinformatics databases and how to access the required biological data.

Talk 2: Sequence, Structure and Functions

Date: 18 May 2007 (Friday)
Time: 9:30am - 12:30pm
Abstract: A fundamental axiom of biology is the cascade that amino-acid sequence determines protein structure, and in turn protein structure determines protein function. In this lecture, we will introduce the mathematical problems and methods for analyzing and modeling DNA sequence and protein structure, such as DNA sequencing, sequence alignment, haplotype reconstruction, protein structure prediction, protein structure alignment.

Talk 3: Biological Networks

Date: 25 May 2007 (Friday)
Time: 9:30am - 12:30pm
Abstract: Systems biology is the study of the interactions between the components of a biological system, and how these interactions give rise to the function and behavior of that system. Most systems studied in systems biology are represented as networks. This lecture will focus on the mathematical models and related problems of biological networks such as gene regulatory networks and protein-protein interaction networks.