2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)最新文献_第3页

An Efficient Algorithm for Identifying Genomic Structural Inversion with Wide-spectrum of Length 一种宽谱长度基因组结构反转的高效识别算法

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-16

Yu Geng, Zhongmeng Zhao, Xingjian Cui, Rong Zhang, Tian Zheng, Xuanping Zhang, Jiayin Wang

{"title":"An Efficient Algorithm for Identifying Genomic Structural Inversion with Wide-spectrum of Length","authors":"Yu Geng, Zhongmeng Zhao, Xingjian Cui, Rong Zhang, Tian Zheng, Xuanping Zhang, Jiayin Wang","doi":"10.1109/BIBE.2017.00-16","DOIUrl":"https://doi.org/10.1109/BIBE.2017.00-16","url":null,"abstract":"Genomic structural inversion is a class of structural variations, and has been widely associated to a series of complex traits and diseases. It has great significance in accurately identifying the inversions from the high-throughput sequencing data for both research and clinical practice. However, detecting inversion is a challenging computational problem. Existing approaches either limit to detect the inversions with specific length intervals or require a significant distribution of the coverage across the candidate interval. In this paper, we propose a novel detection algorithm to accurately identify the inversions with wide-spectrum of length. The proposed algorithm consists of two components: a clustering step and a segmentation and extension step. It first clusters the pair–ended reads to squeeze the candidate intervals. Then, it utilizes the contig assembly strategy to reconstruct the candidate intervals. Meanwhile, a segmentation and extension strategy is implemented. For each candidate interval, a feature vector is calculated, based on the characteristic values. Finally, the algorithm combines the comparison verification results to filter out some potential false positives, and then returns the inversion breakpoints on base-pair resolution. We conduct a series of simulation experiments to verify the performance of proposed algorithm and compare to two very popular approaches, DELLY and Pindel. The results demonstrate that the proposed approach provides better results on handling the inversions with wide-spectrum of length, especially when the inversions with short-to-medium length exist.","PeriodicalId":262603,"journal":{"name":"2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"4 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"133151501","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

Multiple Sequence Alignment using Hybrid Parallel Computing 基于混合并行计算的多序列比对

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-59

Elói Araújo, M. A. Stefanes, Valter de O. Ferlete, L. Rozante

引用次数: 2

The Size of Red Blood Cells Regulates the Extent of Pulmonary Capillary Diameter Effect on Pulmonary Gas Exchange Process 红细胞大小调节肺毛细血管直径对肺气体交换过程的影响程度

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-77

K. Pourfarhangi, Mohammad Sahlabadi

引用次数: 0

Dynamic 3D Print of the Breathing Function 呼吸功能的动态3D打印

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-21

Duc Duong, D. Shastri, Ioannis T. Pavlidis

引用次数: 2

Thyroid Nodule Benignty Prediction by Deep Feature Extraction 基于深度特征提取的甲状腺结节良性预测

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-48

XueYan Mei, Xiaomeng Dong, T. Deyer, Jingyi Zeng, T. Trafalis, Yan Fang

引用次数: 10

Effect of Circulation Chamber Dimensions on Aerosol Delivery Efficiency of a Commercial Dry Powder Inhaler Aerolizer® 循环室尺寸对商用干粉吸入器气溶胶输送效率的影响

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00011

Tijana Tuteric, Aleksandra Vulovic, S. Cvijić, S. Ibrić, N. Filipovic

引用次数: 3

Noninvasive Invastigation of Excitability Parameters of the Finger Branches of Median Nerve by Threshold Tracking Method 阈值追踪法无创性研究正中神经指支兴奋性参数

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00010

N. Dalkilic, S. Tuncer, Ilksen Burat

{"title":"Noninvasive Invastigation of Excitability Parameters of the Finger Branches of Median Nerve by Threshold Tracking Method","authors":"N. Dalkilic, S. Tuncer, Ilksen Burat","doi":"10.1109/BIBE.2017.00010","DOIUrl":"https://doi.org/10.1109/BIBE.2017.00010","url":null,"abstract":"To provide a basis for basic and clinical studies, we aimed to establish the excitability properties of thumb, index and medius fingers innervated by median nerve by using threshold tracking methods from both right and left hands of right-handed volunteers. In addition to that, possible differences were investigated between the fingers of left and right hands. Experiments were performed on 21 right-handed healthy volunteers. The protocols of threshold tracking method were applied to all subjects. To conduct excitability measurements, median nerve was stimulated at elbow, then non-invasive muscle compound action potential recordings were performed from medius, index and thumb fingers of left and right hand with ring-shaped electrodes. During an experiment, threshold electrotonus, recovery cycle, threshold current stimulus-response relationship and the amount of threshold charge-stimulus duration relationship curves were plotted. Some of the excitability parameters such as refractoriness (%) at 2 ms, strength duration time constant (ms), resting current-voltage (I-V) slope, rheobase and 50% stimulus intensity required to have the maximal response (mA) did not differ significantly (p <0.05) for three fingers of left and right hand. The stimulus-response, strength-duration relationship, 40% threshold electrotonus, current-threshold relationship and recovery cycle curves were obtained. For all of these curves, there were no significant difference (p < 0.05), either. The results showed that there was no statistical significance between the observed fingers. Detailed analysis of these curves also indicated that the activities of all fast, slow and rectifier K+ channels in the membrane of median nerve that innervate finger muscles were similar. Similarly, no significant differences were seen for activity of Na+ channels","PeriodicalId":262603,"journal":{"name":"2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"32 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123977317","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

Reference-free Identification of Phage DNA Using Signal Processing on Nanopore Data 利用纳米孔数据进行信号处理的噬菌体DNA无参考鉴定

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-71

K. Kupkova, K. Sedlář, I. Provazník

引用次数: 1

Protein-Protein Interaction Extraction from Text by Selecting Linguistic Features 选择语言特征提取文本中蛋白质-蛋白质相互作用

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-58

T. Phan, T. Ohkawa, Akihiro Yamamoto

{"title":"Protein-Protein Interaction Extraction from Text by Selecting Linguistic Features","authors":"T. Phan, T. Ohkawa, Akihiro Yamamoto","doi":"10.1109/BIBE.2017.00-58","DOIUrl":"https://doi.org/10.1109/BIBE.2017.00-58","url":null,"abstract":"Extracting protein-protein interactions (PPIs) from articles is important in comprehending the underlying biological processes. With advances of natural language processing, many automatic PPI extraction methods from articles such as the machine learning-based methods, including the feature-based methods and the kernel-based ones, have been developed. However, the results of these methods still need to be improved much more. We propose a novel method to extract PPIs from articles. We use many diverse features, including lexical features obtained from sentences and features obtained from parse trees. We also devise new features extracted from shortest dependency paths obtained from dependency trees. In our method, after the training data and the test data are partitioned into subsets based on the basic structures of the sentences and the process of the feature selection (FS) is performed, we decrease the values of all the features, which belong to each group of similar features, of each instance by multiplying them with corresponding shrink coefficients of features. These shrink coefficients are determined automatically. Our experimental results using five corpora show the usefulness of the proposed method.","PeriodicalId":262603,"journal":{"name":"2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE)","volume":"1 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2017-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129411399","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

An mhealth Platform to Evaluate Glycaemic Variability in Type 1 Diabetes 评估1型糖尿病血糖变异性的移动健康平台

2017 IEEE 17th International Conference on Bioinformatics and Bioengineering (BIBE) Pub Date : 2017-10-01 DOI: 10.1109/BIBE.2017.00-42

Georgios I. Gogolos, Eleni I. Georga, E. Rizos, D. Fotiadis

引用次数: 0