|
2010年
|
| 报告题目： |
The
core structure of complex biological networks |
| 报
告 人： |
Prof.
Kwang-Hyun Cho,Department of Bio and Brain Engineering, Korea
Advanced Institute of Science and Technology (KAIST) |
| 时间地点： |
7月27日（星期二）下午16:00
思源楼1013室 |
| 摘 要： |
Most biological
networks have huge complex structures which daunt us to make
any sense of them. A question then arises as to whether there
exists an essential core subnetwork that actually realizes
most of the key regulatory functions and forms a backbone
structure, within such a large complex network. We have developed
an algorithm by which we can identify such a core structure
in consideration of the relationship between network topology
and dynamics. Intriguingly, we found that such core structures
preserve all the fundamental network dynamics and include
most of the biologically important nodes. The proposed concept
of a core network can provide us with new insights into the
evolutionary design principle of complex biological networks.
|
| |
|
| 报告题目： |
Maximum
Entropy Principle for Composition Vector Method in Phylogenetics |
| 报
告 人： |
Prof.
Raymond H. Chan，Department of Mathematics, The Chinese University
of Hong Kong |
| 时间地点： |
4月29日（星期四）上午10:30
思源楼712室 |
| 摘 要： |
Molecular
Phylogenetics is the study of evolutionary relatedness among
species through molecular sequencing data. The composition vector
(CV) method is an alignment-free method for phylogenetics. Since
biological sequences are often obscured by noise and bias, denoising
is necessary when using the CV method. By using the maximum
entropy principle for denoising and utilizing the special structure
of the constraint matrix to simplify the optimization, we derive
several new denoising formulas. By comparing with existing formulas
on ten different data sets, we found that one of our formulas
gives more accurate phylogenetic trees. An example is the tree
for the tetrapod data set where we can correctly group birds
and reptiles together, a result that cannot be obtained previously
by either alignment method or other denoising formulas |
| |
|
| 报告题目： |
Improving
protein binding sites prediction with consensus approaches |
| 报
告 人： |
Dr.
Bingding Huang,Senior Researcher, Bioinformatics group, Biotec,
TU Dresden, Dresden. Systems Biolgy Division, Zhejiang-California
International Nanosystems Institute (ZCNI), Zhejiang University |
| 时间地点： |
4月15日（星期四）下午3:00
思源楼712室 |
| 摘 要： |
In
the last decades, many computational efforts have been done
to predict protein binding sites based on protein structure
and resulted in a lot of algorithms, software and web-servers.
In this talk, I will present two meta-approaches to predict
protein-ligand binding sites and protein-protein interaction
sites: metaPocket and metaPPI. MetaPocket uses the predicted
pocket sites from four methods: LIGSITEcs, PASS, Q-SiteFinder,
and SURFNET to improve the prediction success rate from 70%
to 75% at the top 1 prediction. For protein-protein binding
site prediction, metaPPI includes PPI-Pred, PPISP, PINUP, Promate
and SPPIDER, which predict enzyme-inhibitor interfaces with
success rates of 23% to 55% and other interfaces with 10% to
28% on a benchmark dataset of 62 complexes. MetaPPI significantly
improves prediction success rates to 70% for enzyme-inhibitor
and 44% for other interfaces. |
| |
|
| 报告题目： |
Dynamical
Systems Analysis of Prostate Cancer |
| 报
告 人： |
Prof.
Kazuyuki Aihara，Institute of Industrial Science, The University
of Tokyo |
| 时间地点： |
3月29日（星期一）上午10:00
思源楼712室 |
| 摘 要： |
Prostate cancer
is recently becoming a serious social problem. It is the secondly
most common cancer in men. Although the incident rate of prostate
cancer is not so high in Asian countries like China and Japan
fortunately, its increasing rate is highest among cancers
of the Japanese men. In this talk, I review our dynamical
systems approach to prostate cancer and its therapy based
on mathematical modeling.
References
(1) A.M. Ideta, G. Tanaka, T. Takeuchi, and K. Aihara: J.
Nonlinear Science, Vol.18, No.6, pp.593-614 (2008).
(2) G. Tanaka, K. Tsumoto, S. Tsuji, and K. Aihara: Physica
D, Vol.237, No.20, pp.2616-2627 (2008).
(3) T. Shimada and K. Aihara: Mathematical Biosciences, Vol.214,
No.1/2, pp.134-139 (2008).
(4) Y. Tao, Q. Guo, and K. Aihara, J. Nonlinear Science (in
press)
Kazuyuki Aihara
received the B.E. degree in electrical engineering in 1977
and the Ph.D. degree in electronic engineering 1982 from the
University of Tokyo, Tokyo, Japan. Currently, he is Professor
in Institute of Industrial Science, Graduate School of Information
Science and Technology, and Graduate School of Engineering,
the University of Tokyo. His research interests include mathematical
modeling of complex systems, parallel distributed processing
with chaotic neural networks, and nonlinear time series analysis.
|
| |
|
| 报告题目： |
Mathematical
modelling and computational analysis of protein folding |
| 报
告 人： |
Prof.
Christof Schuette,Freie Universitaet Berlin德国柏林自由大学 |
| 时间地点： |
3月19日（星期五）下午2:00,思源楼1013室 |
| 摘 要： |
Characterizing
the equilibrium ensemble of folding pathways, including their
relative probability, is one of the major challenges in protein
folding theory today. Although this information is in principle
accessible via all-atom molecular dynamics simulations, it is
difficult to compute in practice because protein folding is
a rare event and the affordable simulation length is typically
not sufficient to observe an appreciable number of folding events,
unless very simplified protein models are used. Here we present
an approach that allows for the reconstruction of the full ensemble
of folding pathways from simulations that are much shorter than
the folding time. This approach is based on partitioning the
state space into small conformational states and constructing
a Markov model between them. The talk will presented the mathematical
theory that allows for the extraction of the full ensemble of
transition pathways from the unfolded to the folded configurations,
and can be likewise applied to many other complex systems exhibiting
metastable effective dynamics. The approach will then be applied
to the folding of a small protein, the PinWW domain in explicit
solvent, where the folding time is two orders of magnitude larger
than the length of individual simulations. The results are in
good agreement with kinetic experimental data and give detailed
insights about the nature of the folding process which is shown
to be surprisingly complex and parallel. The analysis reveals
the existence of misfolded trap states outside the network of
efficient folding intermediates that significantly reduce the
folding speed.
Prof. Christof
Schuette is a full professor in mathematics at Freie Universitaet
Berlin. His speciality is biocomputing. He is one of the Directors
of the Berlin Mathematical School - a joint top graduate school
in mathematics of the research universities in Berlin - as
well as the Vice Director of the Research Center MATHEON -
Mathematics for Key Technologies - funded by the German Science
Foundation (DFG) as a center for excellence.
|
2009年
|
| 报告题目： |
Quantitative
Simulation for Biomolecular Networks |
| 报
告 人： |
Prof.
Luonan Chen，Osaka Sangyo University |
| 时间地点： |
7月22日（星期三）下午2:00
思源楼1013室 |
| 摘 要： |
Explicitly
considering all variables and chemical reactions in a cell is
unrealistic for a biomolecular network from modeling, analyzing
and computing viewpoint. However, in a cell, many different
time scales characterize the gene regulatory processes, which
can be exploited to reduce the complexity of the mathematical
models. For instance, the transcription and translation processes
generally evolve on a time scale that is much slower than that
of phosphorylation, dimerization or binding reactions of transcription
factors. Moreover, in biological systems, a large class of biological
models can be approximately by stochastic hybrid systems in
which some state components are discrete and other are continuous.
Continuous state components are usually involved in fast reactions
with high copy numbers of molecules, whereas discrete state
components are in slow processes and have low copy numbers of
molecules. In this work, based on the partial Kramers-Moyal
expansion with the central limit theorem, we exploit such properties
to simplify a complicated molecular network to a hybrid system
by giving several models, which can be applied to the quantitative
simulation of a large cellular system. we developed a novel
stochastic hybrid model for representing chemical master equation,
and provided several computational algorithms to efficiently
simulate the stochastically cellular dynamics. |
| |
|
| 报告题目： |
Emerging
of Stochastic Dynamical Equalities and Steady State Thermodynamics
from Darwinian Dynamics |
| 报
告 人： |
敖平
教授 (上海交通大学系统生物医学院) |
| 时间地点： |
2009.6.23(星期二)，10：00，思源楼712室 |
| 摘 要： |
The evolutionary
dynamics first conceived by Darwin and Wallace, referring
to as Darwinian dynamics in the present paper, has been found
to be universally valid in biology. The statistical mechanics
and thermodynamics, while enormous successful in physics,
have been in an awkward situation of wanting a consistent
dynamical understanding. Here we present from a formal point
of view an exploration of the connection between thermodynamics
and Darwinian dynamics and a few related topics. We first
show that the stochasticity in Darwinian dynamics implies
the existence temperature, hence the canonical distribution
of Boltzmann-Gibbs type. In term of relative entropy the Second
Law of thermodynamics is dynamically demonstrated without
detailed balance condition, and is valid regardless of size
of the system. In particular, the dynamical component responsible
for breaking detailed balance condition does not contribute
to the change of the relative entropy. Two types of stochastic
dynamical equalities of current interest are explicitly discussed
in the present approach: One is based on Feynman-Kac formula
and another is a generalization of Einstein relation. Both
are directly accessible to experimental tests. Our demonstration
indicates that Darwinian dynamics represents logically a simple
and straightforward starting point for statistical mechanics
and thermodynamics and is complementary to and consistent
with conservative dynamics that dominates the physical sciences.
Present exploration suggests the existence of a unified stochastic
dynamical framework both near and far from equilibrium.
敖平，1983年获北京大学物理学学士。1985年获美国伊利诺大学香槟分校(University of Illinois
at Urbana-Champaign, UIUC)物理学硕士。1990年获UIUC物理学博士学位，导师为诺贝尔奖获得者Prof.
A. J. Leggett。1990-1994年在美国华盛顿大学(University of Washington)物理系从事博士后研究，合作导师为美国科学院院士Prof.
D. J. Thouless。1994-2000年任瑞典Umea大学物理系副教授。2000-2003年任西雅图的美国系统生物学研究所(United
States Institute for Systems Biology)高级研究科学家及访问教授，与研究所创始人之一美国科学院院士Leory
Hood进行合作研究。2003-2008年任华盛顿大学机械工程系副教授。2008年回国任上海交通大学系统生物医学院特聘教授,
973肥胖症项目首席科学家.
|
| |
|
| 报告题目： |
Integrative
disease classification and phenotype prediction based on cross-platform
microarray data |
| 报
告 人： |
Dr.
Chun-Chi Jim Liu (Molecular and Computational Biology, University
of Southern California) |
| 时间地点： |
2009.1.12
(星期一), 15:00 思源楼712教室 |
| 摘 要： |
.
|
|
|
| 报告题目： |
Boolean
Models and Algorithms for Analyzing Genetic Networks and Metabolic
Networks |
| 报
告 人： |
Prof.
Tatsuya Akutsu (Bioinformatics Center, Institute for Chemical
Research, Kyoto University) |
| 时间地点： |
2009.1.12(星期一),
10:00 思源楼712教室 |
| 摘 要： |
.
|
|
2008年
|
| 报告题目： |
Knowledge-based
Approaches for Reconstruction of Biological Networks |
| 报
告 人： |
Prof.
Yang Dai (Department of Bioengineering University of Illinois
at Chicago) |
| 时间地点： |
2008.7.14
(星期一), 15:00 思源楼1013教室 |
| 摘 要： |
.
|
|
2007年
|
| 报告题目： |
Mathematical
modeling of circadian rhythms |
| 报
告 人： |
Prof.
Albert Goldbeter (Université Libre de Bruxelles, Belgium) |
| 时间地点： |
2007.5.30
(星期三), 15:30 思源楼1013教室 |
| 摘 要： |
Circadian oscillations
occur spontaneously with a period of about 24 h in nearly
all living organisms. These oscillations originate from intertwined
feedback processes in genetic regulatory networks. Based on
experimental observations, mathematical models of increasing
complexity have been proposed for the molecular mechanism
of circadian rhythms. Deterministic models were first proposed
for circadian rhythms in Drosophila. These models account
for the occurrence of sustained oscillations of the limit
cycle type and for a variety of dynamical properties such
as phase shifting or long-term suppression by light pulses
and entrainment by light-dark cycles. Stochastic versions
of the models are needed to examine how molecular noise affects
the emergence and robustness of circadian oscillations. Extending
the model to the case of the mammalian circadian clock allows
us to address the dynamical bases of physiological disorders
of the sleep-wake cycle in humans.
References :
Leloup, J.C. and
Goldbeter, A. 2003. Toward a detailed computational model
for the mammalian circadian clock. Proc. Natl. Acad. Sci.
USA 100, 7051-7056.
Leloup, J.C. and
Goldbeter, A. 2004. Modeling the mammalian circadian clock
: Sensitivity analysis and multiplicity of oscillatory mechanisms.
J. Theor. Biol. 230, 541-562.
|
|
2006年
|
| 报告题目： |
A
Knowledge-Based, Statistical Informatics Approach for Protein
Structure Refinement |
| 报
告 人： |
Prof.
Zhijun Wu (Department of Mathematics, Program on Bioinformatics
and Computational Biology Iowa State University, USA ) |
| 时间地点： |
2006.12.21
(星期四), 15:00 思源楼712教室 |
| 摘 要： |
The
protein structures determined by conventional techniques usually
are not as accurate as desired. Further refinement including
human intervention is always required and sometimes critical.
Therefore, the development of an efficient refinement technique
is important, and as more and more structures are determined,
the need is even more urgent, as the CASP prediction center
explained for the call for a structure refinement competition
in spring 2006. Here, we describe a computational approach of
deriving distance constraints from databases of known protein
structures for structure refinement. We calculate the distributions
of the distances of various types in known protein structures,
and use them to obtain the most probable ranges or the mean-force
potentials for the distances. We then impose the constraints
on the structures to be refined or include the mean-force potentials
in energy minimization so that more plausible structural models
may be built. We show that many inter-atomic distances in low-resolution
structures deviate significantly from their average distributions
in known protein structures, and the structures can be refined
when a selected set of distances are constrained to their most
probable ranges or optimized with corresponding mean-force potentials.
We present the results from refining a set of NMR-determined
protein structures by using database derived distance constraints
and mean-force potentials, and show the improvements on the
structures in terms of several standard measures. We also discuss
our results from participating in the CASPR 2006 structural
refinement experiments for comparative model refinement, using
energy minimization, database derived distance constraints,
and massively parallel computing. We describe the development
of a database of protein inter-atomic distances that supports
computing the distributions of the distances of various types
in known protein structures and generating the constraints or
potentials for the distances automatically. We discuss the possibilities
of extending the system to a broader sense of protein geometry
database and using it for structure analysis, classification,
as well as refinement. |
|
|
|
| 报告题目： |
Evolutionary
matching of surface patterns for predicting protein functions
and binding specificities |
| 报
告 人： |
Prof.
Jie Liang （Department of Bioengineering University of Illinois
at Chicago, USA Institute of Systems Biomedicine Shanghai Jiaotong
University, CHINA ) |
| 时间地点： |
2006.10.27
(星期五), 15:00 思源楼712教室 |
| 摘 要： |
Predicting
protein functions is a challenging task, as evolutionary relationship
reflected by global
sequence and structure similarities are often unreliable for
function prediction. For proteins binding to similar substrates
or ligands and carrying out similar functions, their binding
surfaces experience similar physicochemical constraints, and
hence the sets of allowed and forbidden residue substitutions
are similar. We develop a method for predicting protein functions
by incorporating evolutionary information specific to an individual
binding region and by rapidly matching local surfaces. Our method
is based on the estimation of substitution rates of amino acids.
It computes a profile which characterizes protein binding activities
that may involve multiple substrates or ligands. We show that
our method can be used to predict enzyme functions, to identify
potential substrates, and to assess binding specificity. In
an objective large
scale test of 100 enzyme families with 2,196 structures, our
predictions are sensitive and specific: At the stringent specificity
level of 99.98%, we can correctly predict enzyme functions for
80.55% of the proteins. The overall area under the Receiver
Operating Characteristic curve measuring the performance of
our prediction is 0.955. Our method also works well in predicting
the biochemical functions of orphan proteins from structural
genomics project. |
|
|
| 报告题目： |
Multiple
Sequence Alignment Using Partial Order Graphs |
| 报
告 人： |
Dr.
Christopher Lee（Chemistry & Biochemistry Department University
of California at Los Angeles, USA ) |
| 时间地点： |
2006.8.30
(星期三), 15:00 思源楼712教室 |
| 摘 要： |
|
|
|
| 报告题目： |
Inferring
Protein Interactions with Correlated Domains by Integrative
Databases |
| 报
告 人： |
Prof.
Luonan Chen（Osaka Sangyo University, Japan ) |
| 时间地点： |
2006.8.23
(星期三), 15:00 思源楼712教室 |
| 摘 要： |
|
|
|
| 报告题目： |
A
Systems Biology Approach for Studying Gene Function and Pathway
through Mining Functional Genomic Data |
| 报
告 人： |
Prof.
Dong Xu（Digital Biology Laboratory, Computer Science Department
and Life Sciences Center, University of Missouri-Columbia, Columbia,
MO, USA ) |
| 时间地点： |
2006.5.31
(星期三), 15:00 思源楼712教室 |
| 摘 要： |
We
have developed a number of computational approaches to infer
gene function and pathway through utilizing various functional
genomic data, including protein-protein interactions, protein
complexes, microarray data, and genomic sequences. We quantify
the relationship between functional similarity in the Gene Ontology
biological process and functional data, and coded the relationship
into a "functional linkage graph", where each node
represents one gene and the weight of each edge is characterized
by the Bayesian probability of function similarity between the
two connected genes. We utilized the graph to predict gene function
and signaling pathways in yeast and Arabidopsis. We also analyzed
Arabidopsis tiling array data to predict anti-sense gene silencing
and validated the prediction using EST data. Some anti-sense
predictions were confirmed through RT-PCR. |
|
|
| 报告题目： |
Mathematical
analysis of genetic network: Function, Dynamics and Noise |
| 报
告 人： |
Dr.
Sanyi Tang(Warwick University, UK ) |
| 时间地点： |
2005.12.01 (星期四), 15:00 晨兴510室 |
| 摘 要： |
|
|
2005年
|
| 报告题目： |
计算模型与复杂适应系统 |
| 报
告 人： |
张江 博士(北京交通大学经济管理学院 ) |
| 时间地点： |
2005.11.01 (星期二), 15:30 思源楼712室 |
| 摘 要： |
计算模型是研究复杂适应系统的主要手段之一，它不仅可以对复杂系统进行模拟和仿真，提供一种可操作的试验平台，而且可以用隐喻的方法为人们提供对复杂适应系统的深刻洞察。本报告主要介绍width我开发的两个计算模型：Autolife和AEM。Autolife是一个数字人工生命系统，运用该模型我们可以研究Agent个体的进化行为、群体的适应性行为、生命和环境的关系，以及组织的涌现、演化、社会性寄生和自修复等现象。AEM是一个模拟的经济系统，从著名的人工社会模型Sugarscape扩展得来。Agent的层级适应性决策建模技术使得我们可以探讨虚拟经济系统的价格波动、社会分工、市场组织的形成与演化、交易网络、Agent流和商品流的形成与演化等规律。 |
|
|
| 报告题目： |
DNA
Screening and Pooling Designs |
| 报
告 人： |
Prof. Ding-Zhu
Du (University of Texas at Dallas )
|
| 时间地点： |
2005.11.01
(星期二), 14:30 思源楼712室 |
| 摘 要： |
A
recent important development in biology is the success of Human
Genome Project. As the technology for obtaining sequenced genome
data is getting mature, more and more sequenced genome data
are available to scientific research community, so that the
study of gene functions has become a popular research direction.
The study of gene functions requires to obtain DNA library of
high quality through a large amount of testing and screening.
Pooling design is a mathematical tool to reduce the number of
tests for DNA library screening. In this talk, we introduce
a new method to construct pooling designs. |