检索结果-南通市图书馆

Detection and characterization of regulatory elements using probabilistic conditional random field and hidden Markov models

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Chinese Journal of Cancer 2013年第4期32卷 186-194页

作者： Hongyan Wang xiaobo zhou Department of Radiology the Methodist Hospital Research Institute Department of Radiology Weill Cornell Medical College

By altering the electrostatic charge of histones or providing binding sites to protein recognition molecules, Chromatin marks have been proposed to regulate gene expression, a property that has motivated researchers to link these marks to cis-regulatory elements. With the help of next generation sequencing technologies, we can now correlate one specific chromatin mark with regulatory elements (e.g. enhancers or promoters) and also build tools, such as hidden Markov models, to gain insight into mark combinations. However, hidden Markov models have limitation for their character of generative models and assume that a current observation depends only on a current hidden state in the chain. Here, we employed two graphical probabilistic models, namely the linear conditional random field model and multivariate hidden Markov model, to mark gene regions with different states based on recurrent and spatially coherent character of these eight marks. Both models revealed chromatin states that may correspond to enhancers and promoters, transcribed regions, transcriptional elongation, and low-signal regions. We also found that the linear conditional random field model was more effective than the hidden Markov model in recognizing regulatory elements, such as promoter-, enhancer-, and transcriptional elongation-associated regions, which gives us a better choice.

关键词： Epigenetics, histone modification, conditional random field, regulatory elements

Cancer bioinformatics:detection of chromatin states, SNP-containing motifs, and functional enrichment modules

在线全文

学校读者我要写书评

暂无评论

Chinese Journal of Cancer 2013年第4期32卷 153-154页

作者： xiaobo zhou Center for Bioinformatics and Systems Biology Wake Forest University-School of Medicine

In this editorial preface, I briefly r eview cancer bioinformatics and introduce the four articles in this special issue highlighting important applications of the field: detection of chromatin states; detection of SNP- containing motifs and association with transcription factor-binding sites; improvements in functional enrichment modules; and gene association studies on aging and cancer. We expect this issue to provide bioinformatics scientists, cancer biologists, and clinical doctors with a better understanding of how cancer bioinformatics can be used to identify candidate biomarkers and targets and to conduct functional analysis.

关键词： Chromatin sates, SNP-containing motifs, functional enrichment analysis, gene association

Nonlinear fusion filters based on prediction and smoothing

在线全文

学校读者我要写书评

暂无评论

Chinese Science Bulletin 2000年第18期45卷 1726-1728页

作者： Qiansheng Cheng xiaobo zhou Xichen Sun Peking Univ Sch Math Sci Beijing 100871 Peoples R China

To attenuate white noise, nonstationary noise and impulse noise are important for signal processing. In this letter, we present nonlinear fusion filters (NFF) based on prediction and smoothing. By means of least square fitting of a polynomial, we define and give the operators of left prediction and right prediction, left smoothing and right smoothing, central smoothing and cross-validation smoothing. In simulated experiments, it is shown that the present method is an effective one.

关键词： prediction smoothing nonlinear fusion filters.

Monocular 3D object detection with Pseudo-LiDAR confidence sampling and hierarchical geometric feature extraction in 6G network

在线全文

学校读者我要写书评

暂无评论

Digital Communications and Networks 2023年第4期9卷 827-835页

作者： Jianlong Zhang Guangzu Fang Bin Wang xiaobo zhou Qingqi Pei Chen Chen School of Electronic Engineering Xidian UniversityXi'an710071China School of Computer Science and Technology College of Intelligence and ComputingTianjin UniversityTianjin300000China School of Telecommunications Engineering Xidian UniversityXi'an710071China

The high bandwidth and low latency of 6G network technology enable the successful application of monocular 3D object detection on vehicle *** 3D-object-detection-based Pseudo-LiDAR is a low-cost,lowpower solution compared to LiDAR solutions in the field of autonomous ***,this technique has some problems,i.e.,(1)the poor quality of generated Pseudo-LiDAR point clouds resulting from the nonlinear error distribution of monocular depth estimation and(2)the weak representation capability of point cloud features due to the neglected global geometric structure features of point clouds existing in LiDAR-based 3D detection ***,we proposed a Pseudo-LiDAR confidence sampling strategy and a hierarchical geometric feature extraction module for monocular 3D object *** first designed a point cloud confidence sampling strategy based on a 3D Gaussian distribution to assign small confidence to the points with great error in depth estimation and filter them out according to the ***,we present a hierarchical geometric feature extraction module by aggregating the local neighborhood features and a dual transformer to capture the global geometric features in the point ***,our detection framework is based on Point-Voxel-RCNN(PV-RCNN)with high-quality Pseudo-LiDAR and enriched geometric features as *** the experimental results,our method achieves satisfactory results in monocular 3D object detection.

关键词： Monocular 3D object detection Pseudo-LiDAR Confidence sampling Hierarchical geometric feature extraction

Detection and tracking of clathrin-coated pits in biological images

在线全文

学校读者我要写书评

暂无评论

Chinese Science Bulletin 2012年第7期57卷 729-735页

作者： LIU ZhiFeng GE Yun ZHANG Dong zhou xiaobo School of Electronic Science and Engineering Nanjing UniversityNanjing 210093China HCNR-Center for Bioinformatics Harvard Medical SchoolMA 02215USA

Dynamically tracking hundreds of individual pits is essential to determine whether there exist "hot spots" for the formation of clathrin-coated pits or if the pits formed randomly on the plasma membrane. We propose an automated approach to detect these particles based on an improved á trous wavelet transform decomposition with automatic threshold selection and post processing solution, and to track the dynamic process with a greedy algorithm. The results indicate that the detection method can successfully detect most particles in an image with accuracy of 98.61% and 97.65% for adaptor and clathrin images, respectively, and that the tracking algorithm can resolve merging and splitting issues encountered when analyzing dynamic, live-cell images of clathrin assemblies.

关键词：检测精度生物图像动态跟踪网格小波变换阈值选择贪婪算法跟踪算法

The Integrative Studies on the Functional A-to-I RNA Editing Events in Human Cancers

在线全文

学校读者我要写书评

暂无评论

Genomics, Proteomics & Bioinformatics 2023年第3期21卷 619-631页

作者： Sijia Wu Zhiwei Fan Pora Kim Liyu Huang xiaobo zhou School of Life Science and Technology Xidian UniversityXi’an 710071China West China School of Public Health and West China Fourth Hospital Sichuan UniversityChengdu 610040China Center for Computational Systems Medicine School of Biomedical InformaticsThe University of Texas Health Science Center at HoustonHoustonTX 77030USA

Adenosine-to-inosine(A-to-I)RNA editing,constituting nearly 90%of all RNA editing events in humans,has been reported to contribute to the tumorigenesis in diverse ***,the comprehensive map for functional A-to-I RNA editing events in cancers is still *** fill this gap,we systematically and intensively analyzed multiple tumorigenic mechanisms of A-to-I RNA editing events in samples across 33 cancer types from The Cancer Genome *** individual candidate among1,500,000 quantified RNA editing events,we performed diverse types of downstream functional ***,we identified 24,236 potentially functional A-to-I RNA editing events,including the cases in APOL1,IGFBP3,GRIA2,BLCAP,and *** events might play crucial roles in the scenarios of tumorigenesis,due to their tumor-related editing frequencies or probable effects on altered expression profiles,protein functions,splicing patterns,and microRNA regulations of tumor *** functional A-to-I RNA editing events(https://***/CAeditome/)will help better understand the cancer pathology from the A-to-I RNA editing aspect.

关键词： A-to-I RNA editing Cancer Protein recoding Alternative splicing MicroRNA regulation

An integrated self-healing algorithm for resilient packet ring

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

High Technology Letters 2005年第3期11卷 284-288页

作者： zhou xiaobo（周晓波） Jin Depeng Zeng Lieguang School of Electronics and Information Engineering Beijing Jiaotong University Department of Electronic Engineering Tsinghua University

Resilient Packet Ring (RPR) is a Media Access Control (MAC) layer protocol that operates over a double counter-rotating ring network topology. RPR is designed to enhance Synchronous Digital Hierarchy(SDH) in order to handle data traffic more efficiently. Since Intelligent Protection Switching(IPS) is one of the key technologies in ring networks, RPR provides two intelligent protection algorithms: steering and wrapping. While wrapping in RPR in essence inherits the automatic protection switching(APS) algorithm of SDH, it also wastes the bandwidth on the wrapping ringlets and may result in severe congestion. Whereas steering in RPR provides high bandwidth utilization, its switching speed is low, because it is indeed a high layer's restoration algorithm. In this paper, integrated self-healing(ISH) algorithm as an effective algorithm for RPR is proposed, which synthesizes the merits of the two algorithms by transporting healing signal and computing routing in MAC layer. At last, the performance of ISH algorithm is analyzed and simulated.

关键词： resilient packet ring (RPR) media access control (MAC) self-healing ring intelligent protection switching (IPS)

Identification of SNP-containing regulatory motifs in the myelodysplastic syndromes model using SNP arrays and gene expression arrays

维普期刊数据库评论

在线全文

维普期刊数据库

学校读者我要写书评

暂无评论

Chinese Journal of Cancer 2013年第4期32卷 170-185页

作者： Jing Fan Jennifer G. Dy Chung-Che Chang xiaobo zhou Department of Electrical and Computer Engineering Northeastern University Department of Pathology Florida Hospital University of Central Florida Department of Radiology The Methodist Hospital Research Institute Weill Medical College & Cornell University

Myelodysplastic syndromes have increased in frequency and incidence in the American population, but patient prognosis has not significantly improved over the last decade. Such improvements could be realized if biomarkers for accurate diagnosis and prognostic stratification were successfully identified. In this study, we propose a method that associates two state-of-the-art array technologies-single nucleotide polymorphism (SNP) array and gene expression array-with gene motifs considered transcription factor -binding sites (TFBS). We are particularly interested in SNP-containing motifs introduced by genetic variation and mutation as TFBS. The potential regulation of SNP-containing motifs affects only when certain mutations occur. These motifs can be identified from a group of co-expressed genes with copy number variation. Then, we used a sliding window to identify motif candidates near SNPs on gene sequences. The candidates were filtered by coarse thresholding and fine statistical testing. Using the regression-based LARS-EN algorithm and a level-wise sequence combination procedure, we identified 28 SNP-containing motifs as candidate TFBS. We confirmed 21 of the 28 motifs with ChIP-chip fragments in the TRANSFAC database. Another six motifs were validated by TRANSFAC via searching binding fragments on coregulated genes. The identified motifs and their location genes can be considered potential biomarkers for myelodysplastic syndromes. Thus, our proposed method, a novel strategy for associating two data categories, is capable of integrating information from different sources to identify reliable candidate regulatory SNP-containing motifs introduced by genetic variation and mutation.

关键词： Association study, genetic variation and mutation, transcription factor-binding sites, myelodysplastic syndromes

Autonomic Performance and Power Control on Virtualized Servers:Survey, Practices, and Trends

在线全文

学校读者我要写书评

暂无评论

Journal of Computer Science & Technology 2014年第4期29卷 631-645页

作者：周笑波蒋昌俊 IEEE ACM Department of Computer Science University of Colorado Colorado Springs U.S.A. The Key Laboratory of Embedded System and Service Computing Ministry of Education Tongji University CCF Department of Computer Science and Technology Tongji University

Modern datacenter servers hosting popular Internet services face significant and multi-facet challenges in performance and power control. The user-perceived performance is the result of a complex interaction of complex workloads in a very complex underlying system. Highly dynamic and bursty workloads of Internet services fluctuate over multiple time scales, which has a significant impact on processing and power demands of datacenter servers. High-density servers apply virtualization technology for capacity planning and system manageability. Such virtuMized computer systems are increasingly large and complex. This paper surveys representative approaches to autonomic performance and power control on virtualized servers, which control the quality of service provided by virtualized resources, improve the energy efficiency of the underlying system, and reduce the burden of complex system management from human operators. It then presents three designed self-adaptive resource management techniques based on machine learning and control for percentile-based response time assurance, non-intrusive energy-efficient performance isolation, and joint performance and power guarantee on virtualized servers. The techniques were implemented and evaluated in a testbed of virtualized servers hosting benchmark applications. Finally, two research trends are identified and discussed for sustainable cloud computing in green datacenters.

关键词： autonomic computing joint performance and power control virtualized server Internet application sustainable computing