Title (题目): ComputationalSystems Biology for Complex Diseases
Speaker (报告人): 陈洛南教授 中国科学院上海生命科学研究院
Time (时间): 2017-04-15 (星期六)8:30-9:20
Place (地点): 数学楼二楼报告厅
Title (题目): 探索增强子的生物学功能
Speaker (报告人): 周天寿教授 中山大学
Time (时间): 2016-04-15 (星期六) 9:20-10:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): 增强子和启动子的结构类似，但增强子的生物学功能还不清楚，实验研究给出一些假设。在这一报告中，我将首先介绍有关增强子的研究背景，然后重点提出若干未解决的问题，供大家参考。
Title (题目): 单细胞模拟的应用：胚胎重编程和炎癌转化
Speaker (报告人): 雷锦誌教授 清华大学
Time (时间): 2016-04-15 (星期六) 10:30-11:20
Place (地点): 数学楼二楼报告厅
Abstract (摘要): 将报告最近使用单细胞模拟技术对两个问题研究的最新成果。分别介绍跨代遗传中胚胎重编程的单细胞模拟和炎癌转化中的单细胞模拟的计算模型和分析方法。
Title (题目): Infiniteswapping simulated tempering Monte Carlo Scheme
Speaker (报告人): 葛颢教授 北京大学
Time (时间): 2016-04-15 (星期六)11:20-12:10
Place (地点): 数学楼二楼报告厅
Title (题目): 基因转录调控动力学
Speaker (报告人): 刘峰教授 南京大学
Time (时间): 2016-04-15 (星期六)13:30-14:20
Place (地点): 数学楼二楼报告厅
.
Title (题目): The N-leapingmethod for stochasticsimulation of coupled chemical
Speaker (报告人): 兰岳恒教授 清华大学
Time (时间): 2016-04-15 (星期六)14:20-15:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): Numericalsimulation of the time evolution of a spatially homogeneous chemical system isalways of greatinterest. Gillespie first developed the exact stochasticsimulation algorithm (SSA), which is accurate but timeconsuming.Recently, manyapproximate schemes of the SSA are proposed to speed up simulation.Presentedhere is the N-leap method, which guarantees the validity of the leapcondition and at the same time keeps theefficiency. In many cases, N-leap hasbetter performance than the widely-used-leap method. The details ofthe N-leapmethod are described and several examples are presented to show its validity.
Title (题目): Informationtheoretic approaches to infer biological networks with strong associations
Speaker (报告人): 李铁军教授 北京大学
Time (时间): 2016-04-15 (星期六)15:30-16:20
Place (地点): 数学楼二楼报告厅
Abstract (摘要): Partialcorrelation (PC) or conditional mutual information (CMI) is widely used indetecting direct dependencies between the observed variables in a network byeliminating indirect correlations/associations, but it fails whenever there aresome strong correlations in the network, due to the inherent underestimationproblem of PC/CMI. We theoretically develop a multiscale association analysisto overcome this difficulty. Specifically, we first show why conditional mutualinformation (CMI)/partial correlation (PC) suffers from an underestimationproblem for biological networks with strong correlations. Then, we propose anew measure, partial association (PA), based on the multiscale conditionalmutual information (MCMI), to solve this problem. We show that linear PA andnonlinear PA can quantify the direct associations in biological networks in anaccurate manner from both theoretical and computational aspects. Both simulatedmodels and real datasets demonstrate that PA is superior to PC and CMI in termsof efficiency and effectiveness. We will also mention some new ideas still inprogressing.
Title (题目): 反常扩散下可逆的双分子生化反应系统的统计性质研究
Speaker (报告人): 易鸣教授 华中农业大学
Time (时间): 2016-04-15 (星期六)16:20-17:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): 反常扩散对于生化反应的影响研究是生物物理和非线性研究的前沿热点，我们首先数学上考虑了一个分数阶次扩散方程的 Sturm-Liouville 问题以及Dirichlet 条件的数值方法，讨论了它的级数解以及鲁棒性。进一步理论研究了反常扩散下可逆的双分子化学反应系统 A+B⇌C，基于连续时间随机行走理论首先给定了主方程模型，然后推导了宏观的分数阶反应次扩散方程。我们分析了系统的统计性质，发现分数阶矩也与时间成线性比率关系，深入讨论发现其中一种反应物的定态分布满足指数衰减。
Title (题目): Integrativeanalysis and network construction of multi-dimensional data based on tensorframework
Speaker (报告人): 邹秀芬教授 武汉大学
Time (时间): 2016-04-16 (星期日) 8:30-9:20
Place (地点): 数学楼二楼报告厅
Title (题目): Tristability inthe transition between stem cells states
Speaker (报告人): 田天海教授 Monash University
Time (时间): 2016-04-16 (星期日) 9:20-10:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): In the classicalmodel of haematopoiesis, HSCs undergo stepwise differentiation, first losingtheir self-renewal potential and differentiating into multipotent progenitorsbefore further commitment into different progenitors committed to specificcombinations of lineages. Alternatively, recent single-cell data suggest analternative model of human adult haematopoiesis, in which differentiation doesnot occur as a branching process. This talk will first discuss the recentprogress in this topics and thenpresent some initial research results ofmathematical modelling.
Title (题目): Quantifying thebiological functions in gene regulatory networks
Speaker (报告人): 张磊教授 北京大学
Time (时间): 2016-04-16 (星期日)10:30-11:20
Place (地点): 数学楼二楼报告厅
Abstract (摘要): Gene regulatorynetwork in biology plays a critical role in achieving accurate biologicalfunctions. In this talk, I will start with exploration of the topologies fordual function networks by achieving both adaptation and noise attenuation. Weshow the three-node networks are not able to buffer noise while implementing agood adaptation due to the tradeoff. Thus, we construct a four-node networktopology achieves dual functions, in which the fluctuation in input is dampensignificantly in the upstream reactions and the downstream reactions accomplishthe adaptive behavior. Secondly, I will present the dual role of Nanog duringstem cell differentiation and reprogramming. The low-Nanog state enhances celldifferentiation through serving as an intermediate state to reduce the energybarrier of transition. On the contrary, the existence of low stemness low-Nanogstate will slow down the reprogramming process, and additional Nanog activationis revealed to be essential to attain fully reprogrammed cell state faster.
Title (题目): Landscape andpath of gene networks
Speaker (报告人): 李春贺教授 复旦大学
Time (时间): 2016-04-16 (星期日)11:20-12:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): Cellularfunctions in biological systems are regulated by the underlying gene regulatorynetworks. How to investigate the global properties of gene networks is achallenging problem. In this talk, I will present some approaches we recentlydeveloped, i.e. the potential landscape and path framework, to study thestochastic dynamics of gene networks. The basins on the landscape characterizedifferent cell states. The landscape topography in terms of barrier heightsbetween stable states quantifies the global stability of the gene regulatorysystem.The kinetic paths quantify the transition processes betweendifferentcell states. I will also discuss some applications of this approach in thebiological systems, including cancer, cell cycle, and stem celldifferentiation.
Title (题目): 网络动力学的控制
Speaker (报告人): 王瑞琦教授 上海大学
Time (时间): 2016-04-16 (星期日)13:30-14:20
Place (地点): 数学楼二楼报告厅
Abstract (摘要): 主要通过对网络节点以及控制方法的选取来对分子网络的动力学进行控制。
Title (题目): 缺氧诱导因子HIF-1响应缺氧应激的动力学研究
Speaker (报告人): 张小鹏副教授 南京大学
Time (时间): 2016-04-16 (星期日)14:20-15:10
Place (地点): 数学楼二楼报告厅
Abstract (摘要): 我们主要通过生物网络建模研究了缺氧响应中HIF-1选择性表达下游靶基因的动力学机制。模型考虑了HIF-1的两个羟化酶PHD和FIH对氧气的不同亲和性。结果表明，温和缺氧时PHD首先失活，HIF-1变得稳定，其N-TAD转录域首先激活，可表达糖酵解相关基因；严重缺氧时，HIF-1的C-TAD区域进一步被激活，进而表达血管生成和细胞坏死相关基因；而在极端缺氧条件下，HIF-1则通过氧气非依赖的途径被降解掉。我们的工作揭示了HIF-1在缺氧响应中调控细胞命运的动力学机制，有望加深对细胞响应缺氧机制的理解。
Title (题目): 带条件与时滞的非线性因果网络构建
Speaker (报告人): 林伟教授 复旦大学
Time (时间): 2016-04-16 (星期日)15:30-16:20
Place (地点): 数学楼二楼报告厅