2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops最新文献_第9页

Incorporating semantic similarity into clustering process for identifying protein complexes from Affinity Purification/Mass Spectrometry data 将语义相似度整合到聚类过程中，从亲和纯化/质谱数据中识别蛋白质复合物

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392718

Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang

{"title":"Incorporating semantic similarity into clustering process for identifying protein complexes from Affinity Purification/Mass Spectrometry data","authors":"Bingjing Cai, Haiying Wang, Huiru Zheng, Hui Wang","doi":"10.1109/BIBM.2012.6392718","DOIUrl":"https://doi.org/10.1109/BIBM.2012.6392718","url":null,"abstract":"This paper presents a framework for incorporating semantic similarities in the detection of protein complexes from Affinity Purification/Mass Spectrometry (AP-MS) data. AP-MS data is modeled as a bipartite network, where one set of nodes consist of bait proteins and the other set are prey proteins. Pair-wise similarities of bait proteins are computed by combining similarities based on topological features and functional semantic similarities. A hierarchical clustering algorithm is then applied to obtain `seed clusters' consisting of bait proteins. Starting from these `seed' clusters, an expansion process is developed to recruit prey proteins which are significantly associated with bait proteins, to produce final sets of identified protein complexes. In the application to real AP-MS datasets, we validate biological significance of predicted protein complexes by using curated protein complexes. Six statistical metrics have been applied. Results show that by integrating semantic similarities into the clustering process, the accuracy of identifying complexes has been greatly improved. Meanwhile, clustering results obtained by the proposed framework are better than those from several existent clustering methods.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"190 1","pages":"1-4"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79509611","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 1

A novel non-contact interactive medical image viewing system 一种新型非接触式交互式医学图像查看系统

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470312

Chen Geng, Jian Yang, Tong Li, Yongtian Wang

{"title":"A novel non-contact interactive medical image viewing system","authors":"Chen Geng, Jian Yang, Tong Li, Yongtian Wang","doi":"10.1109/BIBMW.2012.6470312","DOIUrl":"https://doi.org/10.1109/BIBMW.2012.6470312","url":null,"abstract":"Currently, photographic film is the most commonly used medium for viewing medical images in hospitals. However, as digitalized medical images need to be printed on photographic film first, such kind of viewing pattern has an extremely limited use A homogeneous white light source is also needed to observe the anatomic structure clearly. Such observation pattern is very limited to the circumstances in which it is used In this paper, a novel interactive non-contact system is developed to observe multimodal medical images. For this system, a series of gestures is defined, and a depth sensor is used to capture the speckle pattern of infrared laser, which irradiates to the person in front of the system By analyzing the morphologic atlas of the depth photo, the 3-D structure and the motion of the captured image can be obtained in real time. Then, all kinds of operations on medical images, including transformation, contrast adjustment, volume rendering, can be achieved through different gesture regulations. The system developed realizes flexible observation of medical images using digitalized images directly, which greatly reduces expenses for the clinical diagnosis. The system does not need any contact with the medium. Therefore, it can be utilized by doctors doing clinical surgery.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"157 1","pages":"254-259"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"78588356","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

CryoEM skeleton length estimation using a decimated curve 利用抽取曲线估计CryoEM骨架长度

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470283

Andrew McKnight, Kamal Al-Nasr, Dong Si, Andrey N. Chernikov, N. Chrisochoides, Jing He

引用次数: 2

Managing data provenance in genome project workflows 管理基因组计划工作流程中的数据来源

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470215

Renato de Paula, M. Holanda, M. E. Walter, Sérgio Lifschitz

引用次数: 3

Discovery at a distance: Farther journeys in predication space 远方的发现:预测空间中更远的旅程

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470307

T. Cohen, D. Widdows, R. Schvaneveldt, T. Rindflesch

引用次数: 16

Early classification of multivariate time series using a hybrid HMM/SVM model 基于HMM/SVM混合模型的多变量时间序列早期分类

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392654

Mohamed F. Ghalwash, Dusan Ramljak, Z. Obradovic

{"title":"Early classification of multivariate time series using a hybrid HMM/SVM model","authors":"Mohamed F. Ghalwash, Dusan Ramljak, Z. Obradovic","doi":"10.1109/BIBM.2012.6392654","DOIUrl":"https://doi.org/10.1109/BIBM.2012.6392654","url":null,"abstract":"Early classification of time series has been receiving a lot of attention as of late, particularly in the context of gene expression. In the biomédical realm, early classification can be of tremendous help, by identifying the onset of a disease before it has time to fully take hold, or determining that a treatment has done its job and can be discontinued. In this paper we present a state-of-the-art model, which we call the Early Classification Model (ECM), that allows for early, accurate, and patient-specific classification of multivariate time series. The model is comprised of an integration of the widely-used HMM and SVM models, which, while not a new technique per se, has not been used for early classification of multivariate time series classification until now. It attained very promising results on the datasets we tested it on: in our experiments based on a published dataset of response to drug therapy in Multiple Sclerosis patients, ECM used only an average of 40% of a time series and was able to outperform some of the baseline models, which needed the full time series for classification.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"189 1","pages":"1-6"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"75072371","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 34

Mining hub-based protein complexes in massive biological networks 在大规模生物网络中挖掘基于枢纽的蛋白质复合物

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470299

Zhijie Lin, Yan Chen, Shiwei Wu, Yun Xiong, Yangyong Zhu, Guangyong Zheng

引用次数: 0

The experimental introduction of professor Fu's three-step therapy on gouty arthritis 傅教授三步法治疗痛风性关节炎的实验介绍

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470364

Changeai Xie, Nipeng Lin, Jiaxin Zhou, Zhiqi Fan, W. Fu

引用次数: 0

Enriching miRNA binding site specificity with sequence profile based filtering of 3'-UTR region of mRNA 利用基于序列谱的mRNA 3′-UTR区域过滤来增强miRNA结合位点特异性

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470200

Jasjit K. Banwait, H. Ali, D. Bastola

引用次数: 0

An efficient overlap graph coarsening approach for modeling short reads 一种高效的重叠图粗化方法，用于短读段建模

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470223

Julia D. Warnke-Sommer, H. Ali

{"title":"An efficient overlap graph coarsening approach for modeling short reads","authors":"Julia D. Warnke-Sommer, H. Ali","doi":"10.1109/BIBMW.2012.6470223","DOIUrl":"https://doi.org/10.1109/BIBMW.2012.6470223","url":null,"abstract":"Next generation sequencing has quickly emerged as the most exciting yet challenging computational problem in Bioinformatics. Current sequencing technologies are capable of producing several hundreds of thousands to several millions of short sequence reads in a single run. However, current methods for managing, storing, and processing the produced reads remain for the most part simple and lack the complexity needed to model the produced reads efficiently and assemble them correctly. These reads are produced at a high coverage of the original target sequence such that many reads overlap. The overlap relationships are used to align and merge reads into contiguous sequences called contigs. In this paper, we present an overlap graph coarsening scheme for modeling reads and their overlap relationships. Our approach is different from previous read analysis and assembly methods that use a single graph to model read overlap relationships. Instead, we use a series of graphs with different granularities of information to represent the complex read overlap relationships. We present a new graph coarsening algorithm for clustering a simulated metagenomics dataset at various levels of granularity. We also use the proposed graph coarsening scheme along with graph traversal algorithms to find a labeling of the overlap graph that allows for the efficient organization of nodes within the graph data structure.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"6 1","pages":"704-711"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"72920343","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 5