2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)最新文献_第6页

Functional Gene Detection and Clustering from Seed Gene Sets 种子基因集的功能基因检测与聚类

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.48

Alexander Senf, Xue-wen Chen

引用次数: 0

Magnetic resonance angiography study of a normal mouse brain for creating a three-dimensional cerebral vasculature atlas and software for labeling vessels 正常小鼠脑磁共振血管造影研究，用于创建三维脑血管图谱和标记血管的软件

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112522

Rajeshree Joshi, N. Yanasak

引用次数: 2

Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection 丙型肝炎病毒感染急性和慢性阶段高变区1理化性质的变化

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112357

I. Astrakhantseva, David S. Campo, Aufra Araujo, C. Teo, Y. Khudyakov, S. Kamili

{"title":"Variation in physicochemical properties of the hypervariable region 1 during acute and chronic stages of hepatitis C virus infection","authors":"I. Astrakhantseva, David S. Campo, Aufra Araujo, C. Teo, Y. Khudyakov, S. Kamili","doi":"10.1109/BIBMW.2011.6112357","DOIUrl":"https://doi.org/10.1109/BIBMW.2011.6112357","url":null,"abstract":"Differentiation between acute and chronic HCV infections is clinically important given that early treatment of infected patients leads to high rates of sustained virological response. Analysis of HVR1 sequences (n=2179) from samples obtained from patients with acute (n=49) and chronic (n=102) HCV infections showed that intra-host HVR1 diversity was 1.8 times higher in patients with chronic than acute infection. Analysis of molecular variance showed significant differences between sequences from acute and chronic patients. We found statistically significant differences in polarity, volume and hydrophobicity of amino acids at 10 HVR1 positions. A classification model constructed using the 10 positions in HVR1 distinguished between acute and chronic cases with accuracy of 88% in cross-validation experiments. The results indicate that progression from acute to chronic stage of HCV infection is accompanied by characteristic changes in amino acid composition of HVR1, suggesting a substantial regularity of the intra-host HVR1 evolution.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"152 1","pages":"72-78"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83823017","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: 3

Associating gene functional groups with multiple clinical conditions using Jaccard similarity 利用Jaccard相似性将基因功能群与多种临床条件联系起来

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112381

N. A. Yousri, D. Elkaffash

引用次数: 2

An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents 生物医学PDF文档中图形和标题的自动提取系统

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.26

L. D. Lopez, Jingyi Yu, C. Arighi, Hongzhan Huang, H. Shatkay, Cathy H. Wu

{"title":"An Automatic System for Extracting Figures and Captions in Biomedical PDF Documents","authors":"L. D. Lopez, Jingyi Yu, C. Arighi, Hongzhan Huang, H. Shatkay, Cathy H. Wu","doi":"10.1109/BIBM.2011.26","DOIUrl":"https://doi.org/10.1109/BIBM.2011.26","url":null,"abstract":"Figures in biomedical articles often constitute direct evidence of experimental results. Image analysis methods can be coupled with text-based methods to improve knowledge discovery. However, automatically harvesting figures along with their associated captions from full-text articles remains challenging. In this paper, we present an automatic system for robustly harvesting figures from biomedical literature. Our approach relies on the idea that the PDF specification of the document layout can be used to identify encoded figures and figure boundaries within the PDF and enforce constraints among figure-regions. This allows us to harvest fragments of figures (subfigures), from the PDF, correctly identify subfigures that belong to the same figure, and identify the captions associated with each figure. Our method simultaneously recovers figures and captions and applies additional filtering process to remove irrelevant figures such as logos, to eliminate text passages that were incorrectly identified as captions, and to re-group subfigures to generate a putative figure. Finally, we associate figures with captions. Our preliminary experiments suggest that our method achieves an accuracy of 95% in harvesting figures-caption pairs from a set of 2, 035 full-text biomedical documents from Bio Creative III, containing 12, 574 figures.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"55 1","pages":"578-581"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90066222","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: 20

SCOP family fingerprints: An information theoretic approach to structural classification of protein domains SCOP家族指纹图谱:蛋白质结构域结构分类的信息理论方法

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112408

A. Casagrande, Francesco Fabris

引用次数: 1

Professional tennis player ranking strategy based Monte Carlo feature selection 基于蒙特卡洛特征选择的职业网球选手排名策略

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112370

Ruifei Xie, Bin Han, Lihua Li, Juan Zhang, Lei Zhu

引用次数: 1

Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum 微阵列数据反卷积预测恶性疟原虫转录调节蛋白激酶

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.31

Wei Zhao, J. Dauwels, J. Niles, Jianshu Cao

{"title":"Deconvolution of Microarray Data Predicts Transcriptionally Regulated Protein Kinases of Plasmodium falciparum","authors":"Wei Zhao, J. Dauwels, J. Niles, Jianshu Cao","doi":"10.1109/BIBM.2011.31","DOIUrl":"https://doi.org/10.1109/BIBM.2011.31","url":null,"abstract":"We have developed a computational approach which predicts the protein kinases that may regulate the transition between the blood developmental stages of Plasmodium falciparum (P. falciparum). To improve the accuracy of our prediction, synchronized gene expression levels are reconstructed from the observed micro array data generated by the ensembles of non-synchronized cells. Peaks in annotated protein kinase transcript levels are hypothesized to directly correlate with the period when the encoded protein kinases function temporally. Therefore, protein kinases, which putatively regulate a given developmental stage transition, are identified by their peak in synchronized gene expression levels. By analyzing publicly available micro array data set, a few protein kinases are considered to be strongly associated with developmental stage transition. Two of these (PF13 0211, PFB0815w) have recently been implicated in the schizont to ring transition [1], [2]. Another one of these identified (MAL7P1.144) has been found to influence erythrocyte membrane in both trophozoite and schizont [3]. Overall, these results suggest that further functional analysis of the other protein kinases we have predicted may reveal new insights into P. falciparum blood stage development.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"5 1","pages":"286-289"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86516660","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

Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization 从总变异的下一代测序数据中检测拷贝数变异惩罚最小二乘优化

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBMW.2011.6112348

Junbo Duan, Ji-Gang Zhang, J. Lefante, H. Deng, Yu-ping Wang

{"title":"Detection of copy number variation from next generation sequencing data with total variation penalized least square optimization","authors":"Junbo Duan, Ji-Gang Zhang, J. Lefante, H. Deng, Yu-ping Wang","doi":"10.1109/BIBMW.2011.6112348","DOIUrl":"https://doi.org/10.1109/BIBMW.2011.6112348","url":null,"abstract":"The detection of copy number variation is important to understand complex diseases such as autism, schizophrenia, cancer, etc. In this paper we propose a method to detect copy number variation from next generation sequencing data. Compared with conventional methods to detect copy number variation like array comparative genomic hybridization (aCGH), the next generation sequencing data provide higher resolution of genomic variations. There are a lot of methods to detect copy number variation from next sequencing data, and most of them are based on statistical hypothesis testing. In this paper, we consider this problem from an optimization point of view. The proposed method is based on optimizing a total variation penalized least square criterion, which involves ℓ-1 norm. Inspired by the analytical study of a statics system, we propose an iterative algorithm to find the optimal solution of this optimization problem. The comparative study with other existing methods on simulated data demonstrates that our method can detect relatively small copy number variants (low copy number and small single copy length) with low false positive rate.","PeriodicalId":6345,"journal":{"name":"2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW)","volume":"46 1","pages":"3-12"},"PeriodicalIF":0.0,"publicationDate":"2011-11-12","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"86556174","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: 12

Prediction of Heme Binding Sites in Heme Proteins Using an Integrative Sequence Profile Coupling Evolutionary Information with Physicochemical Properties 利用结合进化信息和物理化学性质的综合序列图谱预测血红素蛋白中的血红素结合位点

2011 IEEE International Conference on Bioinformatics and Biomedicine Workshops (BIBMW) Pub Date : 2011-11-12 DOI: 10.1109/BIBM.2011.8

Y. Xiong, Wen Zhang, Tao Zeng, Juan Liu

引用次数: 0