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2010 IEEE International Conference on BioInformatics and BioEngineering最新文献

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An Elastic Video Interpolation Methodology for Wireless Capsule Endoscopy Videos 一种用于无线胶囊内窥镜视频的弹性视频插值方法
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.16
A. Karargyris, N. Bourbakis
Wireless Capsule Endoscopy (WCE) is a popular diagnostic technology that enables gastroenterologists to view the human digestive tract and more particularly, the small bowel, searching for various abnormalities like blood-based abnormalities, ulcers and polyps. This technology captures videos that consist of approximately 50,000 frames making its examination a very tedious task. For power consumption reasons the rate at which the frames are taken is extremely low (3 frames / second). This has a negative effect on the smoothness of the captured video and the consistency of the observed objects. This paper proposes a sophisticated video interpolation methodology for creating smooth and visually pleasing intermediate images from consecutive frames, while preserving the structure of the observed objects. It utilizes techniques and concepts from various fields such as optical flow and elasticity. Illustrative results of the methodology are also given in this paper.
无线胶囊内窥镜(WCE)是一种流行的诊断技术,它使胃肠病学家能够观察人类消化道,特别是小肠,寻找各种异常,如血液异常、溃疡和息肉。该技术捕获的视频包含大约50,000帧,使其检查成为一项非常繁琐的任务。由于功耗的原因,帧被采取的速率非常低(3帧/秒)。这对捕获视频的平滑性和观察对象的一致性有负面影响。本文提出了一种复杂的视频插值方法,用于从连续帧中创建平滑且视觉上令人愉悦的中间图像,同时保留观察对象的结构。它利用了各个领域的技术和概念,如光流和弹性。本文还给出了该方法的说明结果。
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引用次数: 4
Quantification and Analysis of Combination Drug Synergy in High-Throughput Transcriptome Studies 高通量转录组研究中联合药物协同作用的定量分析
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.46
Z. Gümüş, F. Siso-Nadal, Ada Gjrezi, P. McDonagh, I. Khalil, P. Giannakakou, H. Weinstein
We present an integrated experimental and computational approach designed to identify the key cellular components that either contribute to or drive therapeutic synergy of drug combinations with anticancer activity. The approach includes (i) quantification of drug synergy in high throughput transcriptome experiments, (ii) data-driven reverse engineering and forward simulation technology to develop an in silico model predictive of drug synergy, and (iii) utilization of databases of interaction and functional information in hypothesis generation that are validated experimentally in a final step (iv). The goal is to develop an integrated framework that aids in understanding the mechanistic details of drug synergy to design better combination drugs. We illustrate this approach with an application to the analysis of transcriptome changes in cells exposed to the synergistic anticancer drug combination of farnesyl transferase inhibitors (FTIs) combined with taxanes.
我们提出了一种综合的实验和计算方法,旨在确定促进或驱动抗癌药物联合治疗协同作用的关键细胞成分。该方法包括(i)在高通量转录组实验中定量药物协同作用,(ii)数据驱动的逆向工程和正向模拟技术,以开发预测药物协同作用的硅模型。(iii)在假设生成中利用相互作用和功能信息数据库,并在最后一步(iv)中进行实验验证。目标是开发一个综合框架,帮助理解药物协同作用的机制细节,以设计更好的联合药物。我们通过应用于分析暴露于法尼基转移酶抑制剂(FTIs)与紫杉烷的协同抗癌药物组合的细胞的转录组变化来说明这种方法。
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引用次数: 0
Using the Semantically Interoperable Biospecimen Repository Application, caTissue: End User Deployment Lessons Learned 使用语义上可互操作的生物标本库应用程序,caTissue:最终用户部署经验教训
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.71
J. London, Devjani Chatterjee
The goal of the National Cancer Institute’s cancer Biomedical Informatics Grid initiative, or caBIG®, is the ability to share data and resources among cancer researchers. One means to achieving this goal is the development of semantically interoperable informatics tools based on common data models and controlled vocabularies. A tool for managing biospecimen repositories, caTissue, enables investigators to query for available tissues that are relevant to the needs of their research. For this functionality, the caTissue application data model must include annotation describing various specimen characteristics, and have this information accessible for query by the researcher end user. Having deployed caTissue over two years at Thomas Jefferson University, we report the lessons learned from our investigators’ use of this complex, semantically interoperable software application. Overall we have found that object model complexity and semantic completeness pose obstacles to end user accessibility that require effective strategies to overcome.
美国国家癌症研究所的癌症生物医学信息网格计划(caBIG®)的目标是在癌症研究人员之间共享数据和资源。实现这一目标的一种方法是基于公共数据模型和受控词汇表开发语义上可互操作的信息学工具。一个管理生物标本库的工具,caTissue,使研究人员能够查询与他们的研究需要相关的可用组织。为了实现这一功能,caTissue应用程序数据模型必须包含描述各种样本特征的注释,并且研究人员最终用户可以访问这些信息进行查询。在Thomas Jefferson大学部署了caTissue两年多之后,我们报告了从我们的研究人员使用这个复杂的、语义上可互操作的软件应用程序中学到的经验教训。总的来说,我们发现对象模型的复杂性和语义完整性对最终用户的可访问性构成了障碍,需要有效的策略来克服。
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引用次数: 9
Identifying Hidden Confounders in Gene Networks by Bayesian Networks 利用贝叶斯网络识别基因网络中隐藏的混杂因素
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.35
Tomoya Higashigaki, Kaname Kojima, R. Yamaguchi, Masato Inoue, S. Imoto, S. Miyano
In the estimation of gene networks from microarray gene expression data, we propose a statistical method for quantification of the hidden confounders in gene networks, which were possibly removed from the set of genes on the gene networks or are novel biological elements that are not measured by microarrays. Due to high computational cost of the structural learning of Bayesian networks and the limited source of the microarray data, it is usual to perform gene selection prior to the estimation of gene networks. Therefore, there exist missing genes that decrease accuracy and interpretability of the estimated gene networks. The proposed method can identify hidden confounders based on the conflicts of the estimated local Bayesian network structures and estimate their ideal profiles based on the proposed Bayesian networks with hidden variables with an EM algorithm. From the estimated ideal profiles, we can identify genes which are missing in the network or suggest the existence of the novel biological elements if the ideal profiles are not significantly correlated with any expression profiles of genes. To the best of our knowledge, this research is the first study to theoretically characterize missing genes in gene networks and practically utilize this information to refine network estimation.
在从微阵列基因表达数据估计基因网络时,我们提出了一种统计方法来量化基因网络中隐藏的混杂因素,这些混杂因素可能是从基因网络上的一组基因中移除的,或者是微阵列无法测量的新生物元件。由于贝叶斯网络结构学习的计算成本高和微阵列数据来源有限,通常在基因网络估计之前进行基因选择。因此,存在缺失基因,降低了估计基因网络的准确性和可解释性。该方法可以根据估计的局部贝叶斯网络结构的冲突来识别隐藏的混杂因素,并基于所提出的带隐变量的贝叶斯网络,利用EM算法估计其理想轮廓。从估计的理想谱中,我们可以确定网络中缺失的基因,或者如果理想谱与任何基因的表达谱没有显著相关,则可以提示新生物元件的存在。据我们所知,这项研究是第一个从理论上描述基因网络中缺失基因的研究,并实际利用这些信息来改进网络估计。
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引用次数: 3
Fast Phased Small RNA Cycle Counting Algorithms 快速分阶段小RNA循环计数算法
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.30
F. S. Bao, Zhixin Xie, Yuanlin Zhang
Counting phased small RNA cycles (PSRC) from mapped small RNA positions is a repeatedly invoked subproblem in the computation of identifying TRANS-ACTING siRNA (TAS) loci and loci of other small RNAs forming through mechanisms similar to that of trans-acting small interfering RNAs (ta-siRNAs). The efficiency of counting PSRC has a clear impact on the efficiency of the algorithms predicting these loci. There are two closely related variants on counting PSRC in real applications: WPSRC, which counts the number of distinct small RNAs falling onto the phased positions in a sliding window, and MPSRC, which counts the maximum consecutive PSRC from mapped small RNA positions. In this paper, we develop fast algorithms for both WPSRC and MPSRC. Our algorithms have O(max(S)) time complexity, while the existing algorithm and its variant have O(|S|·max(S)) and O(|S|·L) time complexity for MPSRC and WPSRC respectively, where S is a set of mapped small RNA positions and L the length of sliding window for WPSRC. Experimental results on two real-life datasets show that our algorithms are significantly faster than the existing algorithm and its variant. The proposed algorithms are applicable to TAS-like clusters with any PSRC length including 21-nt.
在计算识别反式作用小RNA (TAS)位点和通过类似于反式作用小干扰RNA (ta-siRNA)的机制形成的其他小RNA的位点时,从小RNA定位中计算阶段性小RNA周期(PSRC)是一个反复被调用的子问题。计数PSRC的效率对预测这些基因座的算法的效率有明显的影响。在实际应用中,有两种密切相关的PSRC计数变体:WPSRC计数在滑动窗口中落在相位位置上的不同小RNA的数量,MPSRC计数从映射的小RNA位置连续的最大PSRC。在本文中,我们开发了WPSRC和MPSRC的快速算法。我们的算法的时间复杂度为0 (max(S)),而现有的MPSRC和WPSRC算法及其变体的时间复杂度分别为O(|S|·max(S))和O(|S|·L),其中S是映射的小RNA位置集,L是WPSRC的滑动窗口长度。在两个真实数据集上的实验结果表明,我们的算法明显快于现有算法及其变体。该算法适用于任意PSRC长度(包括21-nt)的类tas聚类。
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引用次数: 1
Estimating the Expression of Transcript Isoforms from mRNA-Seq via Nonnegative Least Squares 利用非负最小二乘法估计mRNA-Seq转录异构体的表达
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.61
Hyunsoo Kim, Y. Bi, R. Davuluri
mRNA-Seq is an emerging massive parallel sequencing based technology for identification and quantification of gene transcripts. Although gene level expression can easily be estimated from mRNA-Seq data, estimating the isoform level expression poses serious problems, and appropriate methods are required. In this paper, we introduce a mathematical method to estimate transcript isoform concentrations, i.e. transcript isoform expression estimation via nonnegative least squares (TIEE/NLS).
mRNA-Seq是一种新兴的大规模平行测序技术,用于鉴定和定量基因转录物。虽然从mRNA-Seq数据可以很容易地估计基因水平表达,但估计异构体水平表达是一个严重的问题,需要适当的方法。本文介绍了一种估计转录异构体浓度的数学方法,即通过非负最小二乘(TIEE/NLS)估计转录异构体表达。
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引用次数: 5
An Accurate Prediction Method for Protein Structural Class from Signal Patterns of NMR Spectra in the Absence of Chemical Shift Assignments 在没有化学移位赋值的情况下,利用核磁共振光谱信号模式准确预测蛋白质结构类别的方法
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.15
Hiromi Arai, N. Tochio, Tsuyoshi Kato, T. Kigawa, M. Yamamura
The structural class information about a protein is important to understand its biological properties. NMR is one of the most powerful tools to obtain structural information of proteins in atomic resolution. However, an analysis of protein three-dimensional structure from NMR spectra usually requires laborious chemical shift assignment. We developed a new method for predicting the protein structural class directly from the NMR spectra without any chemical shift assignment. The results show that our method outperforms the methods using current secondary structure prediction.
蛋白质的结构类信息对了解其生物学特性非常重要。核磁共振是在原子分辨率下获取蛋白质结构信息的最有力工具之一。然而,从核磁共振光谱分析蛋白质三维结构通常需要费力的化学位移分配。我们开发了一种新的方法,可以直接从核磁共振光谱预测蛋白质的结构类别,而不需要任何化学位移分配。结果表明,该方法优于现有的二级结构预测方法。
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引用次数: 3
Use of Hilbert Huang Transform in Uterine Contraction Analysis 黄氏变换在子宫收缩分析中的应用
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.70
Kemal Aydın, R. M. Demirer, Coskun Bayrak
Proposed approach, Hilbert-Huang Transform (HHT), has already been successfully applied in many engineering fields. In this work, unique properties of the HHT approach, like (1) decomposing and expansion of data into components so-called Intrinsic Mode Functions (IMFs) (2) localizing events in time-frequency space by using temporal frequency energy distribution. An experiment conducted to show that it is possible to extract the contraction locations in the uterine MMG signal.
所提出的希尔伯特-黄变换(Hilbert-Huang Transform, HHT)方法已经成功地应用于许多工程领域。在这项工作中,HHT方法的独特特性,如:(1)将数据分解并扩展为所谓的内禀模态函数(IMFs)组件;(2)通过使用时间频率能量分布在时频空间中定位事件。实验表明,可以提取子宫MMG信号中的收缩位置。
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引用次数: 0
A Comparison between Transmembrane Helices and Reentrant Loops 跨膜螺旋和重入环的比较
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.54
Changhui Yan, Jingru Luo
Reentrant loops are an important structure motif in a-helical transmembrane proteins. A reentrant loop goes half way through the membrane and turns and exits the membrane in the same side it has entered. To better predict the topology of transmembrane proteins and understand their function, it is important to investigate why the reentrant loops form such a unique topology. Herein, we compare the reentrant loops with transmembrane helices and find that the two types of structure motifs differ significantly in residue composition and the difference in reside composition is sufficient to discriminate reentrant loops from transmembrane helices based on the amino acid sequence. Our study shows that the difference in residue composition makes the reentrant loops less hydrophobic than the transmembrane helices. Because of the hydrophobic environment of the lipid membrane, this reduced hydrphobicity in the reentrant loops will make them less stable inside the membrane. That may be one of the many factors that make the reentrant loops to form such a unique topology.
重入环是a-螺旋跨膜蛋白的重要结构基序。一个可重入环穿过膜的一半,然后在它进入的同一侧转出膜。为了更好地预测跨膜蛋白的拓扑结构并了解它们的功能,研究为什么重入环形成如此独特的拓扑结构是很重要的。本文将重入环与跨膜螺旋进行比较,发现这两种结构基序在残基组成上存在显著差异,而残基组成的差异足以根据氨基酸序列区分重入环和跨膜螺旋。我们的研究表明,残基组成的差异使得重入环比跨膜螺旋更疏水。由于脂质膜的疏水环境,重入环疏水性的降低将使它们在膜内的稳定性降低。这可能是使可重入回路形成如此独特拓扑结构的众多因素之一。
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引用次数: 1
Dynamic Complexity of the Temporal Transcriptional Regulation Program in Human Endotoxemia 人类内毒素血症中时间转录调控程序的动态复杂性
Pub Date : 2010-05-31 DOI: 10.1109/BIBE.2010.27
Tung T. Nguyen, P. T. Foteinou, I. Androulakis, S. Calvano, S. Lowry
Human endotoxemia is a well-accepted surrogate model for studying the acute inflammatory responses. In order to discover the complex underlying dynamics, identifying biologically relevant transcriptional regulators as well as their putative regulatory interactions with target genes is an essential step. However, prediction of relevant transcriptional regulators in higher eukaryotes remains a challenge both in silico and in vivo. In this study, we analyzed gene expression data from human blood leukocytes to extract four significant patterns of highly coexpressed genes that capture the essence of inflammatory phases. Upon identification of these patterns, a number of inflammation-specific pathways are selected by evaluating the enrichment of the corresponding subsets. Subsequently, statistically significant cis-regulatory modules (CRMs) are selected and decomposed into a list of relevant transcription factors (34 TFs) which are further validated from prior experiments and computational studies in literature. Additionally, our analysis also allows for the construction of a putative dynamic representation of the transcriptional regulatory program, making it become a critical enabler for unraveling regulatory interactions which is an essential step towards a quantification of dynamic transcriptional regulatory networks.
人类内毒素血症是研究急性炎症反应的一个公认的替代模型。为了发现复杂的潜在动力学,识别生物学相关的转录调控因子以及它们与靶基因的推定调控相互作用是必不可少的一步。然而,预测高等真核生物中相关的转录调控因子仍然是一个挑战,无论是在硅和体内。在这项研究中,我们分析了来自人类血液白细胞的基因表达数据,以提取四种重要的高共表达基因模式,这些模式捕捉了炎症阶段的本质。在确定这些模式后,通过评估相应子集的富集程度来选择一些炎症特异性途径。随后,选择具有统计学意义的顺式调控模块(CRMs)并将其分解为相关转录因子列表(34个TFs),并通过先前的实验和文献中的计算研究进一步验证。此外,我们的分析还允许构建转录调控程序的假定动态表示,使其成为揭示调控相互作用的关键推动者,这是动态转录调控网络量化的重要一步。
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引用次数: 0
期刊
2010 IEEE International Conference on BioInformatics and BioEngineering
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