IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine最新文献_第5页

The Effect of Human Genome Annotation Complexity on RNA-Seq Gene Expression Quantification. 人类基因组注释复杂性对RNA-Seq基因表达定量的影响。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2012-10-01 DOI: 10.1109/BIBMW.2012.6470224

Po-Yen Wu, John H Phan, May D Wang

引用次数: 9

Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression. 使用个性化二倍体参考基因组进行RNA测序数据的读图定位，减少了检测等位基因特异性表达的偏差。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2012-10-01 DOI: 10.1109/BIBMW.2012.6470225

Shuai Yuan, Zhaohui Qin

{"title":"Read-mapping using personalized diploid reference genome for RNA sequencing data reduced bias for detecting allele-specific expression.","authors":"Shuai Yuan, Zhaohui Qin","doi":"10.1109/BIBMW.2012.6470225","DOIUrl":"https://doi.org/10.1109/BIBMW.2012.6470225","url":null,"abstract":"Next generation sequencing (NGS) technologies have been applied extensively in many areas of genetics and genomics research. A fundamental problem when comes to analyzing NGS data is mapping short sequencing reads back to the reference genome. Most of existing software packages rely on a single uniform reference genome and do not automatically take into the consideration of genetic variants. On the other hand, large proportions of incorrectly mapped reads affect the correct interpretation of the NGS experimental results. As an example, Degner et al. showed that detecting allele-specific expression from RNA sequencing data was biased toward the reference allele. In this study, we developed a method that utilize DirectX 11 enabled graphics processing unit (GPU)'s parallel computing power to produces a personalized diploid reference genome based on all known genetic variants of that particular individual. We show that using such a personalized diploid reference genome can improve mapping accuracy and significantly reduce the bias toward reference allele in allele-specific expression analysis. Our method can be applied to any individual that has genotype information obtained either from array-based genotyping or resequencing. Besides the reference genome, no additional changes to alignment algorithm are needed for performing read mapping therefore one can utilize any of the existing read mapping tools and achieve the improved read mapping result. C++ and GPU compute shader source code of the software program is available at: http://code.google.com/p/diploid-mapping/downloads/list.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2012 ","pages":"718-724"},"PeriodicalIF":0.0,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BIBMW.2012.6470225","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33003100","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 15

Efficient Multiple Samples aCGH Analysis for Rare CNVs Detection 用于稀有CNVs检测的高效多样本aCGH分析

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.38

Maciej Sykulski, T. Gambin, M. Bartnik, K. Derwinska, B. Wiśniowiecka-Kowalnik, P. Stankiewicz, A. Gambin

引用次数: 1

A Web Interface for the Quantification of Microtubule Dynamics. 微管动力学定量的Web界面。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2011-11-01 DOI: 10.1109/BIBMW.2011.6112376

Koon Yin Kong, Adam I Marcus, Paraskevi Giaanakakou, May D Wang

{"title":"A Web Interface for the Quantification of Microtubule Dynamics.","authors":"Koon Yin Kong, Adam I Marcus, Paraskevi Giaanakakou, May D Wang","doi":"10.1109/BIBMW.2011.6112376","DOIUrl":"https://doi.org/10.1109/BIBMW.2011.6112376","url":null,"abstract":"We propose a web interface that allows researchers to quantify and analyze microtubule confocal images online. Most analyses of microtubule confocal images are performed manually using very simple software or tools. Analysis results are stored locally within each collaborator with different styles and formats. This has limited the sharing of data and results when collaborating among different research parties. A web interface provides a simple way for users to process data online. It also allows easy sharing of both data and results among different participating groups. Analysis workflow of the interface is made similar to existing manual protocols. We demonstrate the integration of image processing algorithm in the current workflow to aid the analysis. Our design also allows integration of novel automated analysis algorithms and modules to re-evaluate existing data. This interface can provide a validation platform for new automated algorithm and allow collaboration on microtubule image analysis from different locations.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2011 ","pages":"209-214"},"PeriodicalIF":0.0,"publicationDate":"2011-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BIBMW.2011.6112376","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34711998","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation. RNA-Seq基因表达估计归一化方法的评价。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2011-11-01 DOI: 10.1109/BIBMW.2011.6112354

Po-Yen Wu, John H Phan, Fengfeng Zhou, May D Wang

{"title":"Evaluation of Normalization Methods for RNA-Seq Gene Expression Estimation.","authors":"Po-Yen Wu, John H Phan, Fengfeng Zhou, May D Wang","doi":"10.1109/BIBMW.2011.6112354","DOIUrl":"https://doi.org/10.1109/BIBMW.2011.6112354","url":null,"abstract":"Statistical inferences on RNA-Seq data, e.g., detecting differential gene expression, are meaningful only after proper normalization. However, there is no consensus for choosing a normalization procedure from among the many existing procedures. We evaluated several RNA-Seq normalization procedures by (1) correlating estimated RNA-Seq expression values to those of microarrays, (2) examining the concordance of stable and differential gene detection between the platforms, and (3) applying the procedures to simulated RNA-Seq data. Results suggested that RNA-Seq normalization procedures have little effect on both inter-platform gene expression correlation as well as inter-platform concordance of genes detected as stably or differentially expressed. However, the results of simulated analysis suggested that some normalization procedures are more robust to changes in distribution of differentially expressed genes. These results may provide guidance for selecting RNA-Seq normalization procedures.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2011 ","pages":"50-57"},"PeriodicalIF":0.0,"publicationDate":"2011-11-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BIBMW.2011.6112354","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34313421","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 4

Semantic Predications for Complex Information Needs in Biomedical Literature. 生物医学文献中复杂信息需求的语义预测。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2011-01-01 DOI: 10.1109/BIBM.2011.23

Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo N Mendes, Amit P Sheth, Krishnaprasad Thirunarayan

{"title":"Semantic Predications for Complex Information Needs in Biomedical Literature.","authors":"Delroy Cameron, Ramakanth Kavuluru, Olivier Bodenreider, Pablo N Mendes, Amit P Sheth, Krishnaprasad Thirunarayan","doi":"10.1109/BIBM.2011.23","DOIUrl":"10.1109/BIBM.2011.23","url":null,"abstract":"Many complex information needs that arise in biomedical disciplines require exploring multiple documents in order to obtain information. While traditional information retrieval techniques that return a single ranked list of documents are quite common for such tasks, they may not always be adequate. The main issue is that ranked lists typically impose a significant burden on users to filter out irrelevant documents. Additionally, users must intuitively reformulate their search query when relevant documents have not been not highly ranked. Furthermore, even after interesting documents have been selected, very few mechanisms exist that enable document-to-document transitions. In this paper, we demonstrate the utility of assertions extracted from biomedical text (called semantic predications) to facilitate retrieving relevant documents for complex information needs. Our approach offers an alternative to query reformulation by establishing a framework for transitioning from one document to another. We evaluate this novel knowledge-driven approach using precision and recall metrics on the 2006 TREC Genomics Track.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2011 ","pages":"512-519"},"PeriodicalIF":0.0,"publicationDate":"2011-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330970/pdf/nihms654702.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33399671","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Correction of Copy Number Variation Data Using Principal Component Analysis. 利用主成分分析法校正拷贝数变异数据。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2010-12-01 Epub Date: 2011-01-28 DOI: 10.1109/BIBMW.2010.5703928

Jiayu Chen, Jingyu Liu, Vince D Calhoun

引用次数: 0

TissueWiki^Mobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device. TissueWikiMobile:在移动设备上用于病理知识共享和注释的整合蛋白表达图像浏览器。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2010-12-01 DOI: 10.1109/BIBMW.2010.5703848

Chihwen Cheng, Todd H Stokes, Sovandy Hang, May D Wang

{"title":"TissueWikiMobile: an Integrative Protein Expression Image Browser for Pathological Knowledge Sharing and Annotation on a Mobile Device.","authors":"Chihwen Cheng, Todd H Stokes, Sovandy Hang, May D Wang","doi":"10.1109/BIBMW.2010.5703848","DOIUrl":"https://doi.org/10.1109/BIBMW.2010.5703848","url":null,"abstract":"Doctors need fast and convenient access to medical data. This motivates the use of mobile devices for knowledge retrieval and sharing. We have developed TissueWikiMobile on the Apple iPhone and iPad to seamlessly access TissueWiki, an enormous repository of medical histology images. TissueWiki is a three terabyte database of antibody information and histology images from the Human Protein Atlas (HPA). Using TissueWikiMobile, users are capable of extracting knowledge from protein expression, adding annotations to highlight regions of interest on images, and sharing their professional insight. By providing an intuitive human computer interface, users can efficiently operate TissueWikiMobile to access important biomedical data without losing mobility. TissueWikiMobile furnishes the health community a ubiquitous way to collaborate and share their expert opinions not only on the performance of various antibodies stains but also on histology image annotation.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2010 ","pages":"473-480"},"PeriodicalIF":0.0,"publicationDate":"2010-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BIBMW.2010.5703848","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34313420","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

A distributed system for fast alignment of next-generation sequencing data. 用于下一代测序数据快速校准的分布式系统。

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2010-12-01 DOI: 10.1109/BIBMW.2010.5703865

Jaydeep K Srimani, Po-Yen Wu, John H Phan, May D Wang

{"title":"A distributed system for fast alignment of next-generation sequencing data.","authors":"Jaydeep K Srimani, Po-Yen Wu, John H Phan, May D Wang","doi":"10.1109/BIBMW.2010.5703865","DOIUrl":"https://doi.org/10.1109/BIBMW.2010.5703865","url":null,"abstract":"We developed a scalable distributed computing system using the Berkeley Open Interface for Network Computing (BOINC) to align next-generation sequencing (NGS) data quickly and accurately. NGS technology is emerging as a promising platform for gene expression analysis due to its high sensitivity compared to traditional genomic microarray technology. However, despite the benefits, NGS datasets can be prohibitively large, requiring significant computing resources to obtain sequence alignment results. Moreover, as the data and alignment algorithms become more prevalent, it will become necessary to examine the effect of the multitude of alignment parameters on various NGS systems. We validate the distributed software system by (1) computing simple timing results to show the speed-up gained by using multiple computers, (2) optimizing alignment parameters using simulated NGS data, and (3) computing NGS expression levels for a single biological sample using optimal parameters and comparing these expression levels to that of a microarray sample. Results indicate that the distributed alignment system achieves approximately a linear speed-up and correctly distributes sequence data to and gathers alignment results from multiple compute clients.","PeriodicalId":73283,"journal":{"name":"IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine","volume":"2010 ","pages":"579-584"},"PeriodicalIF":0.0,"publicationDate":"2010-12-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1109/BIBMW.2010.5703865","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34378448","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 2

Mining Association Rules among Gene Functions in Clusters of Similar Gene Expression Maps. 挖掘相似基因表达图簇中基因功能的关联规则

IEEE International Conference on Bioinformatics and Biomedicine workshops. IEEE International Conference on Bioinformatics and Biomedicine Pub Date : 2009-11-01 DOI: 10.1109/BIBMW.2009.5332104

Li An, Zoran Obradovic, Desmond Smith, Olivier Bodenreider, Vasileios Megalooikonomou

引用次数: 0