ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine最新文献_第6页

Are We There Yet? Feasibility of Continuous Stress Assessment via Wireless Physiological Sensors. 我们成功了吗？通过无线生理传感器进行连续压力评估的可行性

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2014-01-01 DOI: 10.1145/2649387.2649433

Mahbubur Rahman, Rummana Bari, Amin Ahsan Ali, Moushumi Sharmin, Andrew Raij, Karen Hovsepian, Syed Monowar Hossain, Emre Ertin, Ashley Kennedy, David H Epstein, Kenzie L Preston, Michelle Jobes, J Gayle Beck, Satish Kedia, Kenneth D Ward, Mustafa al'Absi, Santosh Kumar

{"title":"Are We There Yet? Feasibility of Continuous Stress Assessment via Wireless Physiological Sensors.","authors":"Mahbubur Rahman, Rummana Bari, Amin Ahsan Ali, Moushumi Sharmin, Andrew Raij, Karen Hovsepian, Syed Monowar Hossain, Emre Ertin, Ashley Kennedy, David H Epstein, Kenzie L Preston, Michelle Jobes, J Gayle Beck, Satish Kedia, Kenneth D Ward, Mustafa al'Absi, Santosh Kumar","doi":"10.1145/2649387.2649433","DOIUrl":"10.1145/2649387.2649433","url":null,"abstract":"Stress can lead to headaches and fatigue, precipitate addictive behaviors (e.g., smoking, alcohol and drug use), and lead to cardiovascular diseases and cancer. Continuous assessment of stress from sensors can be used for timely delivery of a variety of interventions to reduce or avoid stress. We investigate the feasibility of continuous stress measurement via two field studies using wireless physiological sensors - a four-week study with illicit drug users (n = 40), and a one-week study with daily smokers and social drinkers (n = 30). We find that 11+ hours/day of usable data can be obtained in a 4-week study. Significant learning effect is observed after the first week and data yield is seen to be increasing over time even in the fourth week. We propose a framework to analyze sensor data yield and find that losses in wireless channel is negligible; the main hurdle in further improving data yield is the attachment constraint. We show the feasibility of measuring stress minutes preceding events of interest and observe the sensor-derived stress to be rising prior to self-reported stress and smoking events.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2014 ","pages":"479-488"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4374173/pdf/nihms-671146.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33047557","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

SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine. SimConcept：简化生物医学中复合命名实体的混合方法。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2014-01-01 DOI: 10.1145/2649387.2649420

Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu

{"title":"SimConcept: A Hybrid Approach for Simplifying Composite Named Entities in Biomedicine.","authors":"Chih-Hsuan Wei, Robert Leaman, Zhiyong Lu","doi":"10.1145/2649387.2649420","DOIUrl":"10.1145/2649387.2649420","url":null,"abstract":"Many text-mining studies have focused on the issue of named entity recognition and normalization, especially in the field of biomedical natural language processing. However, entity recognition is a complicated and difficult task in biomedical text. One particular challenge is to identify and resolve composite named entities, where a single span refers to more than one concept(e.g., BRCA1/2). Most bioconcept recognition and normalization studies have either ignored this issue, used simple ad-hoc rules, or only handled coordination ellipsis, which is only one of the many types of composite mentions studied in this work. No systematic methods for simplifying composite mentions have been previously reported, making a robust approach greatly needed. To this end, we propose a hybrid approach by integrating a machine learning model with a pattern identification strategy to identify the antecedent and conjuncts regions of a concept mention, and then reassemble the composite mention using those identified regions. Our method, which we have named SimConcept, is the first method to systematically handle most types of composite mentions. Our method achieves high performance in identifying and resolving composite mentions for three fundamental biological entities: genes (89.29% in F-measure), diseases (85.52% in F-measure) and chemicals (84.04% in F-measure). Furthermore, our results show that, using our SimConcept method can subsequently help improve the performance of gene and disease concept recognition and normalization.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2014 ","pages":"138-146"},"PeriodicalIF":0.0,"publicationDate":"2014-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4384177/pdf/nihms673019.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33193039","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

Integrated miRNA and mRNA Analysis of Time Series Microarray Data. 时间序列微阵列数据的集成miRNA和mRNA分析。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2014-01-01 DOI: 10.1145/2649387.2649411

Julian Dymacek, Nancy Lan Guo

引用次数: 6

Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data. 利用模拟序列数据对RNA-Seq定量工具进行系统评估。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2013-09-01 DOI: 10.1145/2506583.2506648

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

{"title":"Systematic Assessment of RNA-Seq Quantification Tools Using Simulated Sequence Data.","authors":"Raghu Chandramohan, Po-Yen Wu, John H Phan, May D Wang","doi":"10.1145/2506583.2506648","DOIUrl":"10.1145/2506583.2506648","url":null,"abstract":"RNA-sequencing (RNA-seq) technology has emerged as the preferred method for quantification of gene and isoform expression. Numerous RNA-seq quantification tools have been proposed and developed, bringing us closer to developing expression-based diagnostic tests based on this technology. However, because of the rapidly evolving technologies and algorithms, it is essential to establish a systematic method for evaluating the quality of RNA-seq quantification. We investigate how different RNA-seq experimental designs (i.e., variations in sequencing depth and read length) affect various quantification algorithms (i.e., HTSeq, Cufflinks, and MISO). Using simulated data, we evaluate the quantification tools based on four metrics, namely: (1) total number of usable fragments for quantification, (2) detection of genes and isoforms, (3) correlation, and (4) accuracy of expression quantification with respect to the ground truth. Results show that Cufflinks is able to use the largest number of fragments for quantification, leading to better detection of genes and isoforms. However, HTSeq produces more accurate expression estimates. Moreover, each quantification algorithm is affected differently by varying sequencing depth and read length, suggesting that the selection of quantification algorithms should be application-dependent.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2013 ","pages":""},"PeriodicalIF":0.0,"publicationDate":"2013-09-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/2506583.2506648","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34378450","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: 3

Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images. 组织病理学整张切片图像中形态学模式的生物学解读。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2012-10-01 DOI: 10.1145/2382936.2382964

Sonal Kothari, John H Phan, Adeboye O Osunkoya, May D Wang

{"title":"Biological Interpretation of Morphological Patterns in Histopathological Whole-Slide Images.","authors":"Sonal Kothari, John H Phan, Adeboye O Osunkoya, May D Wang","doi":"10.1145/2382936.2382964","DOIUrl":"10.1145/2382936.2382964","url":null,"abstract":"We propose a framework for studying visual morphological patterns across histopathological whole-slide images (WSIs). Image representation is an important component of computer-aided decision support systems for histopathological cancer diagnosis. Such systems extract hundreds of quantitative image features from digitized tissue biopsy slides and produce models for prediction. The performance of these models depends on the identification of informative features for selection of appropriate regions-of-interest (ROIs) from heterogeneous WSIs and for development of models. However, identification of informative features is hindered by the semantic gap between human interpretation of visual morphological patterns and quantitative image features. We address this challenge by using data mining and information visualization tools to study spatial patterns formed by features extracted from sub-sections of WSIs. Using ovarian serous cystadenocarcinoma (OvCa) WSIs provided by the cancer genome atlas (TCGA), we show that (1) individual and (2) multivariate image features correspond to biologically relevant ROIs, and (3) supervised image feature selection can map histopathology domain knowledge to quantitative image features.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2012 ","pages":"218-225"},"PeriodicalIF":0.0,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5859578/pdf/nihms807306.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35939491","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

A Collective Ranking Method for Genome-wide Association Studies. 全基因组关联研究的集体排序方法。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2012-10-01 DOI: 10.1145/2382936.2382976

Jie Liu, Humberto Vidaillet, Elizabeth Burnside, David Page

{"title":"A Collective Ranking Method for Genome-wide Association Studies.","authors":"Jie Liu, Humberto Vidaillet, Elizabeth Burnside, David Page","doi":"10.1145/2382936.2382976","DOIUrl":"https://doi.org/10.1145/2382936.2382976","url":null,"abstract":"Genome-wide association studies (GWAS) analyze genetic variation (SNPs) across the entire human genome, searching for SNPs that are associated with certain phenotypes, most often diseases, such as breast cancer. In GWAS, we seek a ranking of SNPs in terms of their relevance to the given phenotype. However, because certain SNPs are known to be highly correlated with one another across individuals, it can be beneficial to take into account these correlations when ranking. If a SNP appears associated with the phenotype, and we question whether this association is real, the extent to which its neighbors (correlated SNPs) also appear associated can be informative. Therefore, we propose CollectRank, a ranking approach which allows SNPs to reinforce one another via the correlation structure. CollectRank is loosely analogous to the well-known PageRank algorithm. We first evaluate CollectRank on synthetic data generated from a variety of genetic models under different settings. The numerical results suggest CollectRank can significantly outperform common GWAS methods at the cost of a small amount of extra computation. We further evaluate CollectRank on two real-world GWAS on breast cancer and atrial fibrillation/flutter, and CollectRank performs well in both studies. We finally provide a theoretical analysis that also suggests CollectRank's advantages.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2012 ","pages":"313-320"},"PeriodicalIF":0.0,"publicationDate":"2012-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/2382936.2382976","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"37889997","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

Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study. 利用预测的伴侣特异性蛋白质-蛋白质界面对蛋白质-蛋白质复合物进行排序对接模型：初步研究。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2011-08-01 DOI: 10.1145/2147805.2147866

Li C Xue, Rafael A Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar

{"title":"Ranking Docked Models of Protein-Protein Complexes Using Predicted Partner-Specific Protein-Protein Interfaces: A Preliminary Study.","authors":"Li C Xue, Rafael A Jordan, Yasser El-Manzalawy, Drena Dobbs, Vasant Honavar","doi":"10.1145/2147805.2147866","DOIUrl":"10.1145/2147805.2147866","url":null,"abstract":"Computational protein-protein docking is a valuable tool for determining the conformation of complexes formed by interacting proteins. Selecting near-native conformations from the large number of possible models generated by docking software presents a significant challenge in practice. We introduce a novel method for ranking docked conformations based on the degree of overlap between the interface residues of a docked conformation formed by a pair of proteins with the set of predicted interface residues between them. Our approach relies on a method, called PS-HomPPI, for reliably predicting protein-protein interface residues by taking into account information derived from both interacting proteins. PS-HomPPI infers the residues of a query protein that are likely to interact with a partner protein based on known interface residues of the homo-interologs of the query-partner protein pair, i.e., pairs of interacting proteins that are homologous to the query protein and partner protein. Our results on Docking Benchmark 3.0 show that the quality of the ranking of docked conformations using our method is consistently superior to that produced using ClusPro cluster-size-based and energy-based criteria for 61 out of the 64 docking complexes for which PS-HomPPI produces interface predictions. An implementation of our method for ranking docked models is freely available at: http://einstein.cs.iastate.edu/DockRank/.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2011 ","pages":"441-445"},"PeriodicalIF":0.0,"publicationDate":"2011-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4403796/pdf/nihms314851.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"33243558","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

Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data. 多个共线性基因组数据的动态可视化与比较分析。

ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine Pub Date : 2011-08-01 DOI: 10.1145/2147805.2147846

Jeremy Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan

{"title":"Dynamic Visualization and Comparative Analysis of Multiple Collinear Genomic Data.","authors":"Jeremy Wang, Fernando Pardo-Manuel de Villena, Leonard McMillan","doi":"10.1145/2147805.2147846","DOIUrl":"https://doi.org/10.1145/2147805.2147846","url":null,"abstract":"We have developed a novel tool for visualizing and analyzing multiple collinear genomes. Unlike previous genome browsers and viewers, ours allows for simultaneous and comparative analysis. Our browser is web-based and provides intuitive selection and interactive navigation about features of interest. Dynamic visualizations adjust to scale and data content making analysis at variable resolutions and of multiple data sets more informative. Our tool illustrates genome-sequence similarity through a mosaic of intervals representing local phylogeny, subspecific origin, and haplotype identity. Comparative analysis is facilitated through reordering and clustering of tracks, which can vary throughout the genome. In addition, we provide local phylogenetic trees as an alternate visualization to assess local variations. We demonstrate our genome browser for an extensive set of genomic data sets composed of almost 200 distinct mouse strains.","PeriodicalId":72044,"journal":{"name":"ACM-BCB ... ... : the ... ACM Conference on Bioinformatics, Computational Biology and Biomedicine. ACM Conference on Bioinformatics, Computational Biology and Biomedicine","volume":"2011 ","pages":"335-339"},"PeriodicalIF":0.0,"publicationDate":"2011-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://sci-hub-pdf.com/10.1145/2147805.2147846","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35594879","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