2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)最新文献_第3页

Hypergeometric Similarity Measure for Spatial Analysis in Tissue Imaging Mass Spectrometry 组织成像质谱中空间分析的超几何相似度量

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.113

C. Kaddi, R. M. Parry, May D. Wang

引用次数: 10

Dealing with reusability and reproducibility for scientific workflows 处理科学工作流的可重用性和可再现性

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112441

Sérgio Lifschitz, Luciana S. A. Gomes, S. Rehen

引用次数: 7

YinYang bipolar atom and quantum cellular automation — A unification 阴阳双极原子与量子细胞自动化的统一

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112473

Wen-Ran Zhang

引用次数: 2

A Novel Algorithm for Multi-class Cancer Diagnosis on MALDI-TOF Mass Spectra 基于MALDI-TOF质谱的多类别肿瘤诊断新算法

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.50

Phuong Pham, Li Yu, Minh Nguyen

引用次数: 1

Protein Structure Visualization by Dimension Reduction and Texture Mapping 基于降维和纹理映射的蛋白质结构可视化

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.29

Heng Yang, R. Qureshi, A. Sacan

{"title":"Protein Structure Visualization by Dimension Reduction and Texture Mapping","authors":"Heng Yang, R. Qureshi, A. Sacan","doi":"10.1109/BIBM.2011.29","DOIUrl":"https://doi.org/10.1109/BIBM.2011.29","url":null,"abstract":"Among the biological macromolecules, proteins have attracted special attention from the scientific community due to their rich functional roles. The ability to visualize and manipulate macromolecular structures on graphical display devices has facilitated the identification and analysis of these macromolecules. Structural analyses of the proteins often provide important insights into their biochemical functions. However, such analysis is often limited by the representation of protein structures and the corresponding computational resource requirements. In this study, we focus on the molecular surface of the proteins and investigate computationally and visually effective representations to serve a number of visualization and analysis purposes. Specifically, we \"unfold\" the protein surface onto a planar space, while preserving the local surface features as much as possible. In contrast to classical cartographic projections, our approach is able to preserve local shape features. Several biochemical properties associated with each surface point are mapped to generate a two dimensional map of these features. The 3D-2D mapping of the surface vertices has also been utilized to texture-map an arbitrary image back onto the protein structure to facilitate the visualization of the 3D structure.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"49 1","pages":"437-442"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"82644462","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: 2

On the energy of bifurcated hydrogen bonds for protein structure prediction 分岔氢键能量用于蛋白质结构预测

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112395

Sajal Dash, J. Snoeyink

引用次数: 0

Opening the Door to Electronic Medical Records: Using Informatics to Overcome Terabytes 打开电子医疗记录的大门:利用信息学克服tb

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.130

Michael Farnum, V. Lobanov, F. Defalco, S. Cepeda

{"title":"Opening the Door to Electronic Medical Records: Using Informatics to Overcome Terabytes","authors":"Michael Farnum, V. Lobanov, F. Defalco, S. Cepeda","doi":"10.1109/BIBM.2011.130","DOIUrl":"https://doi.org/10.1109/BIBM.2011.130","url":null,"abstract":"Databases of medical records contain a wealth of information critical to many areas of research including drug safety, health outcomes, clinical epidemiology and translational medicine. Through commercially available databases, researchers can gain a better understanding of the impact of exposure to drugs and medical devices, identify populations at risk for adverse effects, estimate the prevalence and natural history of medical conditions, and assess drug utilization across different demographic groups. However, the daunting size and complexity of these databases as well as lack of convenient tools to mine them have made this information largely inaccessible to all but a few experts with advanced data management and statistical programming skills. Using a combination of a relational data management strategy and a graphical user front-end, we have developed an approach that allows any medical researcher to perform a number of common searches and analyses in a consistent, intuitive and interactive manner, without the assistance of an expert programmer. Moreover, the optimization work done on the database and application sides have dramatically reduced the time needed to analyze the data and, thus, increased the number of studies that can be performed. A crucial part of any such study is the selection of code lists for diseases, procedures, medications, etc., and we have supported this effort by allowing definitions to be queried using common ontologies and shared conveniently across the organization.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"22 1","pages":"659-659"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"88900084","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

Genome-wide identification of TF-miRNA regulatory networks in myogenesis 肌发生中TF-miRNA调控网络的全基因组鉴定

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112512

Leina Lu, Liang Zhou, Eric Z. Chen, K. Sun, P. Jiang, Susie Su, Lijun Wang, Hao Sun, Huating Wang

{"title":"Genome-wide identification of TF-miRNA regulatory networks in myogenesis","authors":"Leina Lu, Liang Zhou, Eric Z. Chen, K. Sun, P. Jiang, Susie Su, Lijun Wang, Hao Sun, Huating Wang","doi":"10.1109/BIBMW.2011.6112512","DOIUrl":"https://doi.org/10.1109/BIBMW.2011.6112512","url":null,"abstract":"MicroRNAs (miRNAs) are non-coding RNAs that regulate gene expression post-transcriptionally, and mounting evidences support the prevalence and functional significance of their interplay with transcription factors (TFs). Here we describe the identification of a regulatory circuit between muscle miRNAs (miR-1, miR-133 and miR-206) and Yin Yang 1 (YY1), an epigenetic repressor of skeletal myogenesis in mouse. Genome-wide identification of potential down-stream targets of YY1 by combining computational prediction with expression profiling data reveals a large number of putative miRNA targets of YY1 during skeletal myoblasts differentiation into myotubes with muscle miRs rank on top of the list. The subsequent experimental results demonstrate that YY1 indeed represses muscle miRs expression in myoblasts and the repression is mediated through multiple enhancers and recruitment of Polycomb complex to several YY1 binding sites. YY1 regulating miR-1 is functionally important for both C2C12 myogenic differentiation and injury-induced muscle regeneration. Furthermore, we demonstrate that miR-1 in turn targets YY1, thus forming a negative feedback loop. Together, these results identify a novel regulatory circuit required for skeletal myogenesis and reinforce the idea that regulatory circuitry involving miRNAs and TFs are prevalent mechanisms.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"17 1","pages":"941-941"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"79232524","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

An initial study of full parsing of clinical text using the Stanford Parser 使用斯坦福解析器对临床文本进行完整解析的初步研究

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112438

Hua Xu, S. Abdelrahman, Min Jiang, Jung-wei Fan, Yang Huang

引用次数: 10

Chronology-Sensitive Hierarchical Clustering of Pyrosequenced DNA Samples of E. coli: A Case Study 大肠杆菌焦焦测序DNA样本的时间敏感分层聚类:一个案例研究

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.99

Aldrin Montana, Alex Dekhtyar, Emily R. Neal, Michael Black, C. Kitts

引用次数: 9