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Gene classification using expression profiles: a feasibility study 利用表达谱进行基因分类的可行性研究
Michihiro Kuramochi, G. Karypis
As various genome sequencing projects have already been completed or are near completion, genome researchers are shifting their focus to functional genomics. Functional genomics represents the next phase, that expands the biological investigation to studying the functionality of genes of a single organism as well as studying and correlating the functionality of genes across many different organisms. Recently developed methods for monitoring genome-wide mRNA expression changes hold the promise of allowing us to inexpensively gain insights into the function of unknown genes. In this paper we focus on evaluating the feasibility of using supervised machine learning methods for determining the function of genes based solely on their expression profiles. We experimentally evaluate the performance of traditional classification algorithms such as support vector machines and k-nearest neighbors on the yeast genome, and present new approaches for classification that improve the overall recall with moderate reductions in precision. Our experiments show that the accuracies achieved for different classes varies dramatically. In analyzing these results we show that the achieved accuracy is highly dependent on whether or not the genes of that class were significantly active during the various experimental conditions, suggesting that gene expression profiles can become a viable alternative to sequence similarity searches provided that the genes are observed under a wide range of experimental conditions.
随着各种基因组测序项目已经完成或接近完成,基因组研究人员将重点转向功能基因组学。功能基因组学代表了下一个阶段,它将生物学研究扩展到研究单个生物体的基因功能,以及研究和关联许多不同生物体的基因功能。最近开发的监测全基因组mRNA表达变化的方法有望使我们以低廉的成本了解未知基因的功能。在本文中,我们专注于评估使用有监督的机器学习方法来确定仅基于基因表达谱的基因功能的可行性。我们通过实验评估了传统分类算法(如支持向量机和k近邻)在酵母基因组上的性能,并提出了新的分类方法,这些方法可以在适度降低精度的情况下提高总体召回率。我们的实验表明,不同类别的准确率差异很大。在分析这些结果时,我们发现所获得的准确性高度依赖于该类基因在各种实验条件下是否显着活跃,这表明基因表达谱可以成为序列相似性搜索的可行替代方案,前提是在广泛的实验条件下观察到基因。
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引用次数: 86
Utilizing multiple bioinformatics information sources: an XML database approach 利用多种生物信息学信息源:XML数据库方法
R. Wong, William M. Shui
Biological databanks have proven useful to bioscience researchers, especially in the analysis of raw data. Computational tools for sequence identification, structural analysis, and visualization have been built to access these databanks. This paper describes a way to utilize these resources (both data and tools) by integrating different biological databanks into a unified XML framework. An interface to access the embedded bioinformatic tools for this common model is built by leveraging the query language of XML database management system. The proposed framework has been implemented with the emphasis of reusing the existing bioinformatic data and tools. This paper describes the overall architecture of this prototype and some design issues.
生物数据库已被证明对生物科学研究人员很有用,特别是在分析原始数据方面。已经建立了用于序列识别、结构分析和可视化的计算工具来访问这些数据库。本文描述了一种通过将不同的生物数据库集成到统一的XML框架中来利用这些资源(包括数据和工具)的方法。利用XML数据库管理系统的查询语言,构建了用于访问该通用模型的嵌入式生物信息学工具的接口。提出的框架已经实施,重点是重用现有的生物信息学数据和工具。本文介绍了该样机的总体结构和设计要点。
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引用次数: 14
Investigation of ultrasound image based correction of intraoperative brain shift 术中颅脑移位超声图像校正的研究
L. M. Bates, R. Robb
Stereotactic navigational systems are being incorporated into an increasing number of neurosurgical procedures. Preoperatively acquired 3D images are used for planning the procedure, and are also employed in intraoperative navigations to help localize and resect brain lesions. However, as the operation progresses, multiple factors contribute to changes that limit the accuracy of the navigation based on pre-operative images alone. Our method to correct for brain shift involves the use of ultrasound intraoperatively to update patient specific pre-operative MRI scans using a physics based dynamic model. To validate the imaging and modeling process, a phantom was designed that simulates the brain and its shifting patterns resulting from several of the clinical factors present during a brain operation. MRI and ultrasound datasets were acquired for several permutations of phantom parameters. Deformation algorithms were then applied to the phantom data to demonstrate the efficacy of this approach as a method to effectively update the pre-operatively acquired MRI data during an operation.
立体定向导航系统正被越来越多的神经外科手术所采用。术前获得的3D图像用于计划手术,也用于术中导航,以帮助定位和切除脑病变。然而,随着手术的进行,多种因素导致的变化限制了仅基于术前图像的导航精度。我们纠正脑偏移的方法包括术中使用超声来更新患者特定的术前MRI扫描,使用基于物理的动态模型。为了验证成像和建模过程,设计了一个模拟大脑及其由大脑手术过程中出现的几种临床因素引起的变化模式的幻影。MRI和超声数据集的幻影参数的几个排列获得。然后将变形算法应用于幻像数据,以证明该方法作为一种有效更新术中术前获得的MRI数据的方法的有效性。
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引用次数: 4
Comparing trees in a phylogenetic relationship repository 在系统发育关系存储库中比较树
John Bluis, Ravi Nori, Hsin-Wei Wang, Pinglei Zhou, J. Gogarten, Dong-Guk Shin
Scientists are able to use many different phylogenetic analysis tools to assist them in their research. The data collection and data analysis processes can take days or weeks to complete. Having this data available in a repository would reduce this process time and allow researchers to spend more time analyzing data instead of collecting it. We collected data for 21 completely sequenced genomes and created an intuitive interface for browsing the genomes. The interface allows users to search this data including the pre-calculated phylogenetic trees that are stored in the database. We have also developed a new method for comparing a large set of phylogenetic trees so users can search the database based on a user given hypothesis tree.
科学家们能够使用许多不同的系统发育分析工具来协助他们的研究。数据收集和数据分析过程可能需要几天或几周才能完成。在存储库中提供这些数据将减少这个过程的时间,并允许研究人员花更多的时间来分析数据,而不是收集数据。我们收集了21个完全测序的基因组数据,并创建了一个直观的基因组浏览界面。该界面允许用户搜索这些数据,包括存储在数据库中的预先计算的系统发育树。我们还开发了一种新的方法来比较大量的系统发育树,这样用户就可以根据用户给定的假设树来搜索数据库。
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引用次数: 1
Medical decision-making and collaborative reasoning 医疗决策和协同推理
J. Quintero, A. Aguilera, M. Abraham, H. Villegas, G. Montilla, B. Solaiman
An overview is presented of different constraints in conventional medical decision-making for improving collaborative reasoning. When designing and implementing an effective assisted diagnoses system it is imperative to make a complete study of reasoning processes used by physicians every day. We are particularly interested in studying the process of conventional decision-making when, at the first stage, a physician faces a diagnosis decision and, later, when this decision is made by several physicians, that is, when collaborative medical reasoning is involved. The design of an architecture that supports the requirements of medical practices in this framework is presented.
概述了传统医疗决策中不同的约束条件,以提高协同推理能力。在设计和实施一个有效的辅助诊断系统时,必须对医生每天使用的推理过程进行完整的研究。我们特别感兴趣的是研究常规决策的过程,在第一阶段,一个医生面临诊断决定,然后,当这个决定是由几个医生做出的,也就是说,当涉及到协同医学推理时。提出了一个支持该框架中医疗实践需求的体系结构设计。
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引用次数: 7
Audio and vision-based evaluation of parkinson~s disease from discourse video 基于音频和视觉的话语视频帕金森病评价
Francis K. H. Quek, R. Bryll, M. Harper, L. Chen, L. Ramig
Parkinson's disease (PD) belongs to a class of neurodegenerative diseases that affect both the patient's speech and motor capabilities. To date, PD diagnosis and the determination of disease progress and treatment efficacy is based entirely on the subjective observation of a trained physician. We present the results of a pilot study of two Idiopathic PD patients who have undergone Lee Silverman Voice Treatment (LSVT). It has been observed subjectively that gestural performance of patients improve in tandem with speech improvements after LSVT. It is hypothesized that these improvements are taking place at a neurological level. Measurements of speech and gesture suggest that LSVT improves the quality of both gesticulation and speech.
帕金森病(PD)属于一类神经退行性疾病,影响患者的语言和运动能力。迄今为止,PD的诊断以及疾病进展和治疗效果的确定完全基于训练有素的医生的主观观察。我们介绍了两名接受李西尔弗曼声音治疗(LSVT)的特发性PD患者的初步研究结果。从主观上观察到,LSVT后患者手势表现的改善与言语能力的改善是同步的。据推测,这些改善发生在神经学层面。语音和手势的测量表明,LSVT提高了手势和语音的质量。
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引用次数: 3
Chemosensory adaptation in an electronic nose 电子鼻的化学感觉适应
R. Gutierrez-Osuna, Nilesh U. Powar, P. Sun
This article presents a computational mechanism inspired by the process of chemosensory adaptation in the mammalian olfactory system. The algorithm operates on multiple subsets of the sensory space, generating a family of discriminant functions for different volatile compounds. A set of selectivity coefficients is associated to each discriminant function on the basis of its behavior in the presence of mixtures. These coefficients are employed to form a weighted average of the discriminant functions and establish a feedback signal that reduces the contribution of certain sensory inputs, inhibiting the overall selectivity of the system to previously detected analytes. The algorithm is validated on a database of organic solvents using an array of temperature-modulated metal-oxide chemoresistors.
本文提出了一种受哺乳动物嗅觉系统化学感觉适应过程启发的计算机制。该算法在感觉空间的多个子集上运行,为不同的挥发性化合物生成一系列判别函数。根据每个判别函数在存在混合物时的行为,将一组选择性系数与之相关联。这些系数被用来形成判别函数的加权平均值,并建立一个反馈信号,减少某些感官输入的贡献,抑制系统对先前检测到的分析物的总体选择性。该算法在使用温度调制金属氧化物化学电阻阵列的有机溶剂数据库上进行了验证。
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引用次数: 1
Discovering common structural motifs from SSU 16 S ribosomal RNA secondary structures 从SSU 16s核糖体RNA二级结构中发现共同结构基序
Hsien-Da Huang, Shu-Fen Fang, Jorng-Tzong Horng, Cheng-Yan Kao
Some structural motifs, like tetra-loops, in ribosomal RNA are known to functionally implicate in virtually every aspect of protein synthesis. Our aim in this study is to discover common structural motifs (CSMs), which are related to specific domains or functions, within the secondary structures of ribosomal RNAs in a data set constructed. After applying data mining techniques to mine the common structural motifs, a machine learning approach is used to find significant discriminating common structural motifs from groups of organisms. By applying to several data sets constructed in this study, it suggests that the CSMs can provide effective information to classify organisms and help biologists understand the functions of ribosomal RNA. From the experiments of the classification of organisms and the construction of phylogenetic trees by CSMs mined, we find our approach is promising.
核糖体RNA中的一些结构基序,如四环,在功能上几乎涉及蛋白质合成的各个方面。本研究的目的是在构建的数据集中发现核糖体rna二级结构中与特定结构域或功能相关的共同结构基序(csm)。在应用数据挖掘技术挖掘共同结构基序之后,使用机器学习方法从生物体群体中找到具有显著区别的共同结构基序。通过应用于本研究构建的多个数据集,表明csm可以为生物分类提供有效的信息,并帮助生物学家了解核糖体RNA的功能。从利用csm进行生物分类和构建系统发育树的实验来看,我们的方法是很有前途的。
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引用次数: 0
Profile combinatorics for fragment selection in comparative protein structure modeling 比较蛋白质结构建模中片段选择的剖面组合学
Deacon J. Sweeney, G. Alter, M. Raymer, T. Doom
Sequencing of the human genome was a great stride towards modeling cellular complexes, massive systems whose key players are proteins and DNA. A major bottleneck limiting the modeling process is structure and function annotation for the new genes. Contemporary protein structure prediction algorithms represent the sequence of every protein of known structure with a profile to which the profile of a protein sequence of unknown structure is compared for recognition. We propose a novel approach to increase the scope and resolution of protein structure profiles. Our technique locates equivalent regions among the members of a structurally similar fold family, and clusters these region by structural similarity. Equivalent substructures can then be swapped on the common regions to generate an array of profiles which represent hypothetical structures to supplement profiles of known structures. Strategies for a specific implementation of the strategy are discussed, including application to multiple template comparative modeling.
人类基因组测序是向细胞复合体建模迈出的一大步,细胞复合体是一个以蛋白质和DNA为主要参与者的庞大系统。新基因的结构和功能标注是制约新基因建模的主要瓶颈。当前的蛋白质结构预测算法是将每个已知结构的蛋白质序列与未知结构的蛋白质序列的特征进行比较以进行识别。我们提出了一种新的方法来增加蛋白质结构谱的范围和分辨率。我们的技术在结构相似的折叠家族成员之间定位等效区域,并根据结构相似性对这些区域进行聚类。然后可以在公共区域上交换等效子结构以生成代表假设结构的轮廓阵列,以补充已知结构的轮廓。讨论了该策略的具体实现策略,包括在多模板比较建模中的应用。
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引用次数: 1
PSST... the probabilistic sequence search tool 嘘……概率序列搜索工具
Crispin J. Miller, T. Attwood
Whole genome comparison and clustering cannot be routinely performed without access to significant resources. If as expected, repositories continue to grow at the current rate, increasingly large and expensive systems will be required in order to maintain the status quo. The high-proportion of uncharacterised gene-sequences, combined with the fact that the majority of sequence analysis techniques are alignment-based, raises the possibility that alternative approaches might be able to identify relationships that have otherwise been missed. There is a need for alternative ways to predict function. PSST is an analysis tool with parallels to both pairwise algorithms and multiple motif-based pattern approaches. It is significantly faster than BLAST, and for some families including GPCRs, the tool is more sensitive and selective as well. For others it is worse. This paper describes the algorithm, its implementation, its evaluation against a diverse set of protein families, and discusses the reasons behind its behaviour.
如果没有大量资源,全基因组比较和聚类不能常规进行。如果像预期的那样,存储库继续以当前的速度增长,那么将需要越来越大和昂贵的系统来维持现状。高比例的未表征基因序列,加上大多数序列分析技术是基于比对的事实,提出了替代方法可能能够识别否则被遗漏的关系的可能性。我们需要另一种方法来预测功能。PSST是一种分析工具,与成对算法和基于多图案的模式方法相似。它比BLAST快得多,而且对于包括gpcr在内的一些家族,该工具也更加敏感和选择性。对其他人来说,情况更糟。本文描述了该算法,它的实现,它对多种蛋白质家族的评估,并讨论了其行为背后的原因。
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引用次数: 3
期刊
Proceedings 2nd Annual IEEE International Symposium on Bioinformatics and Bioengineering (BIBE 2001)
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