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Meeting report on RECOMB 2013 （the 17th Annual International Conference on Research in computational Molecular biology）

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Frontiers of Electrical and Electronic Engineering in China 2013年第2期8卷 175-181页

作者： Xuegong Zhang Fengzhu Sun MOE Key Laboratory of Bioinformatics and Bioinformatics Division/Center for Synthetic and systems biology TNLIST and Department of Automation Tsinghua University Beijing 100084 China Molecular and computational biology Program University of Southern California Los Angeles CA 90089 USA

RECOMB 2013 was successfully held in Tsinghua University, Beijing, China on April 7-10, 2013, hosted by the Bioinformatics Division and Center for Synthetic and systems biology, Tsinghua National Laboratory for Information Science and Technology （TNLIST）. A total of about 500 professionals from both academia and industry from 29 countries and regions attended the conference and its RECOMB-Seq satellite workshop after the main conference.

关键词： Residual Dipolar Coupling Chromatin Interaction Keynote Speaker Pedigree Reconstruction computational Molecular biology

De novo identification and quantification of single amino-acid variants in human brain

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Journal of Molecular Cell biology 2014年第5期8卷 421-433页

作者： Zhi-Duan Su Quan-Hu Sheng Qing-Run Li Hao Chi Xi Jiang ZhengYan Ning Fu Si-Min He Philipp Khaitovich Jia-Rui Wu Rong Zeng Key Laboratory of systems biology Chinese Academy of Sciences Institute of Biochemistry and Cell Biology Shanghai Institutes for Biological Sciences Shanghai 200031 China Institute of Computing Technology Chinese Academy of Sciences Beijing 100190 China Key Laboratory of computational biology CAS-MPG Partner Institute for Computational Biology Chinese Academy of Sciences Shanghai 200031 China

单个氨基酸的变体(SAV ) 的察觉通常取决于单个核苷酸的多型性(SNP ) 数据库。这里，我们描述发现在 proteome 的 SAV 铺平 SNP 数据的独立人士的一个新奇方法。用定序算法的集体基于 spectrometry 的 de novo，肽候选人被识别并且与理... 详细信息

单个氨基酸的变体(SAV ) 的察觉通常取决于单个核苷酸的多型性(SNP ) 数据库。这里，我们描述发现在 proteome 的 SAV 铺平 SNP 数据的独立人士的一个新奇方法。用定序算法的集体基于 spectrometry 的 de novo，肽候选人被识别并且与理论蛋白质数据库到相比在配对策略下面产生 SAV，它被数据库研究到控制跟随假发现率。在人的大脑纸巾，我们能充满信心地识别知道并且有多样的起源的新奇蛋白质变体。与 DNA/RNA 定序结合了，我们证实 SAV 源于 DNA 变化，拼接的 RNA 选择，和未知 post-transcriptional 机制。而且，在人的大脑纸巾的定量分析揭示 SAV 的几织物特定的微分表情。这条途径提供新奇存取给蛋白质变体的高产量的察觉，它可以为临床的 biomarker 发现和机械学的研究提供潜力。

关键词：氨基酸变异体识别单核苷酸多态性蛋白质水平 RNA剪接人脑从头测序

利用中心原子价层轨道阐释软硬酸碱理论的原理与应用

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化学教育（中英文） 2024年第6期45卷 99-107页

作者：杨雪梅王志鹏张永臻马新雨 Chen Maggie 蒋振雄哈尔滨工业大学(深圳)理学院广东深圳518055 Division of Genetics Department of MedicineBrigham and Women’s HospitalDepartment of Biological Chemistry and Molecular PharmacologyHarvard Medical SchoolBostonMA02115USA Department of Chemistry Texas A&M UniversityCollege StationTX77840USA 清华大学化学系北京100084 澳门科技大学创新工程学院材料科学与工程系中国澳门999078 Department of Chemistry and Chemical biology Harvard UniversityBostonMA02138USA Department of Microbiology Miami UniversityOxfordOH45056USA computational biology and Bioinformatics Program Duke UniversityDurhamNC27703USA

软硬酸碱理论作为基础化学的重要理论,其在教学与教材中却存在定义不清、难以应用、适用范围不明、模棱两可等众多问题。借用前线轨道理论的观念,针对核心原子的外层轨道进行系统性讨论,并分类举例说明其适用范围与应用方式,以期对基础... 详细信息

软硬酸碱理论作为基础化学的重要理论,其在教学与教材中却存在定义不清、难以应用、适用范围不明、模棱两可等众多问题。借用前线轨道理论的观念,针对核心原子的外层轨道进行系统性讨论,并分类举例说明其适用范围与应用方式,以期对基础教学和相关科研有助。

关键词：软硬酸碱理论前线轨道理论亲核进攻电负性

Not just a sponge: new functions of circular RNAs discovered

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Science China(Life Sciences) 2015年第4期58卷 407-408页

作者： WANG ZeFeng CAS-MPG Partner Institute of computational biology

One of the most exciting findings in RNA biology is the discovery of numerous circular RNAs(circ RNA)in mammalian *** being considered as low abundance splicing byproducts,circ RNAs are surprisingly

关键词： RNA 圆形内含子序列海绵剪接位点动物基因组生物合成副产品

Synchronization transition of a coupled system composed of neurons with coexisting behaviors near a Hopf bifurcation

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Chinese Physics B 2014年第5期23卷 180-190页

作者：贾冰 Center for computational System biology School of Mathematical ScienceFudan University

The coexistence of a resting condition and period-1 firing near a subcritical Hopf bifurcation point, lying between the monostable resting condition and period-1 firing, is often observed in neurons of the central nervous systems. Near such a bifurcation point in the Morris-Lecar （ML） model, the attraction domain of the resting condition decreases while that of the coexisting period-1 firing increases as the bifurcation parameter value increases. With the increase of the coupling strength, and parameter and initial value dependent synchronization transition processes from non-synchronization to compete synchronization are simulated in two coupled ML neurons with coexisting behaviors： one neuron chosen as the resting condition and the other the coexisting period-1 firing. The complete synchronization is either a resting condition or period-1 firing dependent on the initial values of period-1 firing when the bifurcation parameter value is small or middle and is period- 1 firing when the parameter value is large. As the bifurcation parameter value increases, the probability of the initial values of a period- 1 firing neuron that lead to complete synchronization of period- 1 firing increases, while that leading to complete synchronization of the resting condition decreases. It shows that the attraction domain of a coexisting behavior is larger, the probability of initial values leading to complete synchronization of this behavior is higher. The bifurcations of the coupled system are investigated and discussed. The results reveal the complex dynamics of synchronization behaviors of the coupled system composed of neurons with the coexisting resting condition and period-1 firing, and are helpful to further identify the dynamics of the spatiotemporal behaviors of the central nervous system.

关键词： synchronization neuronal network Hopf bifurcation coexistence

Experimental identification of a comb-shaped chaotic region in multiple parameter spaces simulated by the Hindmarsh–Rose neuron model

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Chinese Physics B 2014年第3期23卷 179-185页

作者：贾冰 Center for computational System biology School of Mathematical Science Fudan University

A comb-shaped chaotic region has been simulated in multiple two-dimensional parameter spaces using the Hindmarsh-Rose （HR） neuron model in many recent studies, which can interpret almost all of the previously simulated bifurcation processes with chaos in neural firing patterns. In the present paper, a comb-shaped chaotic region in a two- dimensional parameter space was reproduced, which presented different processes of period-adding bifurcations with chaos with changing one parameter and fixed the other parameter at different levels. In the biological experiments, different period-adding bifurcation scenarios with chaos by decreasing the extra-cellular calcium concentration were observed from some neural pacemakers at different levels of extra-cellular 4-aminopyridine concentration and from other pacemakers at different levels of extra-cellular caesium concentration. By using the nonlinear time series analysis method, the determin- istic dynamics of the experimental chaotic firings were investigated. The period-adding bifurcations with chaos observed in the experiments resembled those simulated in the comb-shaped chaotic region using the HR model. The experimental results show that period-adding bifurcations with chaos are preserved in different two-dimensional parameter spaces, which provides evidence of the existence of the comb-shaped chaotic region and a demonstration of the simulation results in dif- ferent two-dimensional parameter spaces in the HR neuron model. The results also present relationships between different firing patterns in two-dimensional parameter spaces.

关键词： chaos neural firing bifurcation Hindmarsh-Rose model

Factors That Affect the Centrality Controllability of Scale-Free Networks

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Chinese Physics Letters 2015年第12期32卷 174-177页

作者：胡栋孙先李平陈雁张捷 Center for Intelligent and Networked Systemest School of Computer Science Southwest Petroleum University Chengdu 610500 Center for computational systems biology Fudan University Shanghai 200433

The influence of a node in a network can be characterized by its macroscopic properties such as eigenvector centrality. An issue of significant theoretical and practical interest is to modify the influence or roles of the nodes in a network, and recent advances indicate that this can be achieved by just controlling a subset of nodes： the socalled controllers. However, the relationship between the structural properties of a network and its controllability, e.g., the control of node importance, is still not well understood. Here we systematically＂ explore this relationship by constructing scale-free networks with a fixed degree sequence and tunable network characteristics. We calculate the relative size （nc＊） of the minimai controlling set required to controi the importance of each individual node in a network. It is found that while clustering has no significant impact on nc＊, changes in degree-degree correlations, heterogeneity and the average degree of networks demonstrate a discernible impact on its controllability.

关键词： net Factors That Affect the Centrality Controllability of Scale-Free Networks

Coordinate-wise monotonic transformations enable privacy-preserving age estimation with 3D face point cloud

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Science China(Life Sciences) 2024年第7期67卷 1489-1501页

作者： Xinyu Yang Runhan Li Xindi Yang Yong Zhou Yi Liu Jing-Dong J.Han School of Life Sciences Peking UniversityBeijing 100871China Peking-Tsinghua Center for Life Sciences Academy for Advanced Interdisciplinary StudiesCenter for Quantitative Biology(CQB)Peking UniversityBeijing 100871China Beijing Key Lab of Traffic Data Analysis and Mining School of Computer and Information TechnologyBeijing Jiaotong UniversityBeijing 100044China Clinical Research Institute Shanghai General HospitalShanghai Jiao Tong University School of MedicineShanghai 200025China

The human face is a valuable biomarker of aging,but the collection and use of its image raise significant privacy *** we present an approach for facial data masking that preserves age-related features using coordinate-wise monotonic *** first develop a deep learning model that estimates age directly from non-registered face point clouds with high accuracy and *** show that the model learns a highly indistinguishable mapping using faces treated with coordinate-wise monotonic transformations,indicating that the relative positioning of facial information is a low-level biomarker of facial *** visual perception tests and computational3D face verification experiments,we demonstrate that transformed faces are significantly more difficult to perceive for human but not for machines,except when only the face shape information is *** study leads to a facial data protection guideline that has the potential to broaden public access to face datasets with minimized privacy risks.

关键词： face point cloud age estimation face verification privacy coordinate-wise monotonic transformation

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An effective description of a periodic one-dimensional hopping model

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Science China(Physics,Mechanics & Astronomy) 2011年第3期54卷 401-405页

作者： ZHANG YunXin Shanghai Key Laboratory for Contemporary Applied Mathematics Centre for Computational Systems Biology School of Mathematical Sciences Fudan University Shanghai 200433 China

The periodic one-dimensional hopping model is useful for studying the motion of microscopic particles in the thermal noise environment. Based on the explicit formulations of mean velocity, mean first passage time and effective diffusion constant, a general N internal states or even infinite internal states model can be approximated by a one state model that retains the basic properties of the original process. This effective description aids the analysis of biochemical and biophysical problems. This effective description also implies that, to some extent, many processes can be well described by simple two-state models, or even one-state models.

关键词：跳跃模型一维周期状态模型平均速度微观粒子噪声环境物理问题