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Identifying essential proteins based on dynamic protein-protein interaction networks and RNA-Seq datasets

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Science China(Information Sciences) 2016年第7期59卷 61-71页

作者： xuequn shang Yu WANG Bolin CHEN School of Computer Science Northwestern Polytechnical University

The identification of essential proteins is not only important for understanding organism structure on the molecular level, but also beneficial to drug-target detection and genetic disease prevention. Traditional methods often employ various centrality indices of static protein-protein interaction(PPI) networks and/or gene expression profiles to predict essential proteins. However, the prediction accuracy of most methods still has room to be further improved. In this study, we propose a strategy to increase the prediction accuracy of essential protein identification in three ways. Firstly, RNA-Seq datasets are employed to construct integrated dynamic PPI networks. Using a RNA-Seq dataset is expected to give more accurate predictions than using microarray gene expression profiles. Secondly, a novel integrated dynamic PPI network is constructed by considering both the co-expression pattern and the co-expression level of the RNA-Seq data. Thirdly, a novel two-step strategy is proposed to identify essential proteins from two known centrality indices. Numerical experiments have shown that the proposed strategy can increase the prediction accuracy dramatically, which can be generalized to many existing methods and centrality indices.

关键词： essential protein dynamic protein network RNA-Seq data gene co-expression pattern M2 measure

Flexibility and rigidity index for chromosome packing,flexibility and dynamics analysis

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Frontiers of Computer Science 2022年第4期16卷 203-213页

作者： Jiajie Peng Jinjin Yang D Vijay Anand xuequn shang Kelin Xia School of Computer Science Northwestern Polytechnical UniversityXi’an710129China Key Laboratory of Big Data Storage and Management Northwestern Polytechnical UniversityMinistry of Industry and Information TechnologyXi’an710129China Division of Mathematical Sciences School of Physical and Mathematical SciencesNanyang Technological UniversitySingapore637371Singapore School of Biological Sciences Nanyang Technological UniversitySingapore637371Singapore

The packing of genomic DNA from double helix into highly-order hierarchical assemblies has a great impact on chromosome flexibility,dynamics and *** open and accessible regions of chromosomes are primary binding positions for regulatory elements and are crucial to nuclear processes and biological *** by the success of flexibility-rigidity index(FRI)in biomolecular flexibility analysis and drug design,we propose an FRI-based model for quantitatively characterizing chromosome *** on Hi-C data,a flexibility index for each locus can be ***,flexibility is tightly related to packing *** compacted regions are usually more rigid,while loosely packed regions are more ***,a strong correlation is found between our flexibility index and DNase and ATAC values,which are measurements for chromosome *** addition,the genome regions with higher chromosome flexibility have a higher chance to be bound by transcription ***,the Gaussian network model(GNM)is applied to analyze the chromosome accessibility and a mobility profile has been proposed to characterize chromosome *** with GNM,our FRI is slightly more accurate(1%to 2%increase)and significantly more efficient in both computational time and *** a 5Kb resolution Hi-C data,the flexibility evaluation process only takes FRI a few minutes on a single-core *** contrast,GNM requires 1.5 hours on 10 ***,interchromosome interactions can be easily combined into the flexibility evaluation,thus further enhancing the accuracy of our *** contrast,the consideration of interchromosome information into GNM will significantly increase the size of its Laplacian(or Kirchhoff)matrix,thus becoming computationally extremely challenging for the current *** software and supplementary document are available at https://***/jiajiepeng/FRI_chrFle.

关键词： flexibility-rigidity index 3D genome chromosome flexibility

Copy number variation related disease genes

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Frontiers of Electrical and Electronic Engineering in China 2018年第2期6卷 99-112页

作者： Chaima Aouiche xuequn shang Bolin Chen School of Computer Science Northwestern Polytechnical University Xi'an 710072 China

Background： One of the most important and challenging issues in biomedicine and genomics is how to identify disease related genes. Datasets from high-throughput biotechnologies have been widely used to overcome this issue from various perspectives, e.g., epigenomics, genomics, transcriptomics, proteomics, metabolomics. At the genomic level, copy number variations （CNVs） have been recognized as critical genetic variations, which contribute significantly to genomic diversity. They have been associated with both common and complex diseases, and thus have a large influence on a variety of Mendelian and somatic genetic disorders. Results： In this review, based on a variety of complex diseases, we give an overview about the critical role of using CNVs for identifying disease related genes, and discuss on details the different high-throughput and sequencing methods applied for CNV detection. Some limitations and challenges concerning CNV are also highlighted. Conclusions： Reliable detection of CNVs will not only allow discriminating driver mutations for various diseases, but also helps to develop personalized medicine when integrating it with other genomic features.

关键词： CNV disease gene complex disease targeted approach genome-wide approach whole exome sequencing

Constrained query of order-preserving submatrix in gene expression data

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Frontiers of Computer Science 2016年第6期10卷 1052-1066页

作者： Tao JIANG Zhanhuai LI xuequn shang Bolin CHEN Weibang LI Zhilei YIN School of Computer Science and Technology Northwestern Polytechnical University Xi'an 710072 China

Order-preserving submatrix （OPSM） has become important in modelling biologically meaningful subspace cluster, capturing the general tendency of gene expressions across a subset of conditions. With the advance of microarray and analysis techniques, big volume of gene expression datasets and OPSM mining results are produced. OPSM query can efficiently retrieve relevant OPSMs from the huge amount of OPSM datasets. However, improving OPSM query relevancy remains a difficult task in real life exploratory data analysis processing. First, it is hard to capture subjective interestingness aspects, e.g., the analyst＇s expectation given her/his domain knowledge. Second, when these expectations can be declaratively specified, it is still challenging to use them during the computational process of OPSM queries. With the best of our knowledge, existing methods mainly fo- cus on batch OPSM mining, while few works involve OPSM query. To solve the above problems, the paper proposes two constrained OPSM query methods, which exploit userdefined constraints to search relevant results from two kinds of indices introduced. In this paper, extensive experiments are conducted on real datasets, and experiment results demonstrate that the multi-dimension index （cIndex） and enumerating sequence index （esIndex） based queries have better performance than brute force search.

关键词： gene expression data OPSM constrained query brute-force search feature sequence cIndex

Power-law patterns in the Phanerozoic sedimentary records of carbon, oxygen, sulfur,and strontium isotopes

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Journal of Palaeogeography 2024年第1期13卷 116-126页

作者： Haitao shang Institute of Ecology and Evolution University of OregonEugeneOR97403USA

Power-law patterns appear in a variety of natural systems on the modern Earth;nevertheless,whether such behaviors appeared in the deep-time environment has rarely been studied. Isotopic records in sedimentary rocks, which are widely used to reconstruct the geological/geochemical conditions in paleoenvironments and the evolutionary trajectories of biogeochemical cycles, offer an opportunity to investigate power laws in ancient geological systems. In this study, I focus on the Phanerozoic sedimentary records of carbon, oxygen, sulfur, and strontium isotopes, which have well documented and extraordinarily comprehensive datasets. I perform statistical analyses on these datasets and show that the variations in the sedimentary records of the four isotopes exhibit power-law behaviors. The exponents of these power laws range between 2.2 and 2.9;this narrow interval indicates that the variations in carbon, oxygen, sulfur, and strontium isotopes likely belong to the same universality class, suggesting that these systematic power-law patterns are governed by universal, scale-free mechanisms. I then derive a general form for these power laws from a minimalistic model based on basic physical principles and geosystem-specific assumptions, which provides an interpretation for the power-law patterns from the perspective of thermodynamics. The fundamental mechanisms regulating such patterns might have been ubiquitous in paleoenvironments, implying that similar power-law behaviors may exist in the sedimentary records of other isotopes.

关键词： Power laws Phanerozoic sedimentary records Carbon isotope(δ~(13)C) Oxygen isotope(δ~(18)O) Sulfur isotope(δ~(34)S) Strontium isotope(~(87)Sr/~(86)Sr)

Review on Security Defense Technology Research in Edge Computing Environment

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Chinese Journal of Electronics 2024年第1期33卷 1-18页

作者： Ke shang Weizhen HE Shuai ZHANG National Digital Switching System Engineering and Technological R&D Center

Edge computing, which achieves quick data processing by sinking data computing and storage to the network edge, has grown rapidly along with the Internet of things. The new network architecture of edge computing brings new security challenges. Based on this, this paper investigates the edge computing security literature published in recent years and summarizes and analyzes research work on edge computing security from different attack surfaces. We start with the definition and architecture of edge computing. From the attack surface between device and edge server, as well as on edge servers, the research describes the security threats and defense methods of edge computing. In addition, the cause of the attack and the pros and cons of defense methods is introduced. The challenges and future research directions of edge computing are given.

关键词： Cloud computing Systems architecture Computer architecture Network architecture Data processing Security Servers

Cybersecurity Landscape on Remote State Estimation:A Comprehensive Review

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IEEE/CAA Journal of Automatica Sinica 2024年第4期11卷 851-865页

作者： Jing Zhou Jun shang Tongwen Chen the Department of Electrical and Computer Engineering University of AlbertaEdmonton AB T6G 1H9Canada the Department of Control Science and Engineering and shanghai Research Institute for Intelligent Autonomous Systems Tongji UniversityShanghai 200092China

Cyber-physical systems(CPSs)have emerged as an essential area of research in the last decade,providing a new paradigm for the integration of computational and physical units in modern control *** state estimation(RSE)is an indispensable functional module of ***,it has been demonstrated that malicious agents can manipulate data packets transmitted through unreliable channels of RSE,leading to severe estimation performance *** paper aims to present an overview of recent advances in cyber-attacks and defensive countermeasures,with a specific focus on integrity attacks against ***,two representative frameworks for the synthesis of optimal deception attacks with various performance metrics and stealthiness constraints are discussed,which provide a deeper insight into the vulnerabilities of ***,a detailed review of typical attack detection and resilient estimation algorithms is included,illustrating the latest defensive measures safeguarding RSE from ***,some prevalent attacks impairing the confidentiality and data availability of RSE are examined from both attackers'and defenders'***,several challenges and open problems are presented to inspire further exploration and future research in this field.

关键词： Cyber-attacks Kalman filtering remote state estimation unreliable transmission channels

Target parameter estimation for OTFS-integrated radar and communications based on sparse reconstruction preprocessing

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Frontiers of Information Technology & Electronic Engineering 2024年第5期25卷 742-754页

作者： Zhenkai ZHANG Xiaoke shang Yue XIAO Ocean College Jiangsu University of Science and TechnologyZhenjiang 212003China

Orthogonal time-frequency space(OTFS)is a new modulation technique proposed in recent years for high Doppler wireless *** solve the parameter estimation problem of the OTFS-integrated radar and communications system,we propose a parameter estimation method based on sparse reconstruction preprocessing to reduce the computational effort of the traditional weighted subspace fitting(WSF)***,an OTFS-integrated echo signal model is ***,the echo signal is transformed to the time domain to separate the target angle from the range,and the range and angle of the detected target are coarsely estimated by using the sparse reconstruction ***,the WSF algorithm is used to refine the search with the coarse estimate at the center to obtain an accurate *** simulations demonstrate the effectiveness and superiority of the proposed parameterestimation algorithm.

关键词： Integrated radar and communications system Orthogonal time-frequency space Target parameter estimation Sparse reconstruction Weighted subspace fitting

Hall Algebras and Quantum Symmetric Pairs of Kac-Moody Type Ⅱ

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Acta Mathematica Sinica,English Series 2024年第3期40卷 806-822页

作者： Ming LU Run Ze shang Department of Mathematics Sichuan UniversityChengdu 610064P.R.China

We extend the ■Hall algebra realization of ■quantum groups arising from quantum symmetric pairs,which establishes an injective homomorphism from the universal ■quantum group of Kac-Moody type to the ■Hall algebra ... 详细信息

关键词： Quantum symmetric pairs Hall algebras Quiver with involutions