2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops最新文献_第5页

The role of Eigen-matrix translation in classification of biological datasets 特征矩阵翻译在生物数据集分类中的作用

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392701

Hao Jiang, W. Ching

引用次数: 2

A model of cellular decision making in photodynamic therapy of cancer 肿瘤光动力治疗中的细胞决策模型

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392704

I. Gkigkitzis, Xin-Hua Hu

{"title":"A model of cellular decision making in photodynamic therapy of cancer","authors":"I. Gkigkitzis, Xin-Hua Hu","doi":"10.1109/BIBM.2012.6392704","DOIUrl":"https://doi.org/10.1109/BIBM.2012.6392704","url":null,"abstract":"The aim of this report is to provide a mathematical model of the mechanism for making binary fate decisions about cell death or survival, during and after type II photodynamic therapy (PDT) treatment, and to supply the logical design for this decision mechanism as an application of rate distortion theory to the biochemical processing of information by the physical system of a cell. Based on system biology models of the molecular interactions involved in the PDT processes previously established, and regarding a cellular decision-making system as a noisy communication channel, we use rate distortion theory to design a time dependent three dimensional Blahut-Arimoto algorithm where the input is a stimulus vector composed of the time dependent concentrations of three PDT related cell death signaling molecules and a cell fate decision as output. The molecular concentrations are determined by a group of rate equations. The output is the cell decision with a probability of cell survival or death. The optimality of the cell decision strategy is assessed by the cell survival probability, which might be modified to account for heterogeneous cell resistance to therapy.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"54 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"85444328","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

Aligning ligand binding cavities by optimizing superposed volume 通过优化叠加体积来排列配体结合腔

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392629

Ruobing Chen, K. Scheinberg, B. Chen

引用次数: 3

Jumping low, jumping high: Controlling hopping in the protein energy surface 低跳、高跳:控制蛋白能量面跳跃

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470276

Brian S. Olson, Amarda Shehu

引用次数: 0

A supervised solution for redundant feature detection depending on instances 基于实例的冗余特征检测的监督解决方案

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470320

Xue-Qiang Zeng, Guozheng Li

引用次数: 1

Quantitative models for statistical nucleosome occupancy prediction 统计核小体占用预测的定量模型

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470270

Yu Zhang, Xiuwen Liu, J. Dennis

引用次数: 1

Reconstructing dynamic gene regulatory network for the development process of hepatocellular carcinoma 重建肝细胞癌发生过程的动态基因调控网络

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470298

Hailong Zhu, R. Rao, Luonan Chen

引用次数: 1

Clinical research on rule of acupoint heat-sensitization within patients suffer Bell's palsy 贝尔氏麻痹患者穴位热敏化规律的临床研究

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBMW.2012.6470351

Qingsheng Yang, Z. Gu, Zhenhua Xu, Quanxin Chen

{"title":"Clinical research on rule of acupoint heat-sensitization within patients suffer Bell's palsy","authors":"Qingsheng Yang, Z. Gu, Zhenhua Xu, Quanxin Chen","doi":"10.1109/BIBMW.2012.6470351","DOIUrl":"https://doi.org/10.1109/BIBMW.2012.6470351","url":null,"abstract":"This study is to explore the rule of acupoint heat-sensitization within patients who suffer Bell's palsy. Probe the rule of acupoint heat-sensitization within patients suffer Bell's palsy by recording the phenomenon and contrasting the frequency of acupoints, meridians, patterns of manifestation between healthy control volunteers and patients. We found that there was statistical difference between two groups on the frequency of acupoint heat-sensitization phenomenon (P<;0.01), but not among different types of TCM syndrome when compared on the occurrence rate, patterns of manifestation (the top five patterns: blended sense, diathermanous sense, thermolytic sense, orderly transmission along channels, enjoying the thermal sensation), distribution of meridians (the top five channels: meridian of FOOT-YANG MING, HAND-SHAO YANG, FOOT-SHAO YANG, HAND-TAI YANG, HAND-YANG MING) and distribution of acupuncture points (the five top points: YIFENG(SJ17), XIAGUAN(ST7), QUANLIAO(SL18), YANGBAI(GB14), HEGU(LM)) (P>0.05). Thus we conclude that the frequency of acupoint heat-sensitization phenomenon within Bell's palsy patients is higher than normal volunteers, and the difference of patterns of manifestation, distribution of acupoints and meridians are all associated with channels, but not with the TCM syndromes.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"12 1","pages":"413-417"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"90338331","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

A neural network approach to the identification of b-/y-ions in MS/MS spectra MS/MS光谱中b-/y-离子识别的神经网络方法

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392625

J. P. Cleveland, J. Rose

{"title":"A neural network approach to the identification of b-/y-ions in MS/MS spectra","authors":"J. P. Cleveland, J. Rose","doi":"10.1109/BIBM.2012.6392625","DOIUrl":"https://doi.org/10.1109/BIBM.2012.6392625","url":null,"abstract":"The effectiveness of de novo peptide sequencing algorithms depends on the quality of MS/MS spectra. Since most of the peaks in a spectrum are uninterpretable `noise' peaks it is necessary to carefully pre-filter the spectra to identify the `signal' peaks that likely correspond to b-/y-ions. Selecting the optimal set of peaks for candidate peptide generation is essential for obtaining accurate results. A careful balance must be maintained between the precision and recall of peaks that are selected for further processing and candidate peptide generation. If too many peaks are selected the search space will be too large and the problem becomes intractable. If too few peaks are selected cleavage sites will be missed, the resulting candidate peptides will have large gaps, and sequencing results will be poor. For this reason pre-filtering of MS/MS spectra and accurate selection of peaks for peptide candidate generation is essential to any de novo peptide sequencing algorithm. We present a novel neural network approach for the selection of b-/y-ions using known fragmentation characteristics, and leveraging neural network probability estimates of flanking and complementary ions. We show a significant improvement in precision and recall of peaks corresponding to b-/y-ions and a reduction in search space over approaches used by other de novo peptide sequencing algorithms.","PeriodicalId":6392,"journal":{"name":"2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops","volume":"1 1","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2012-10-04","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"87531277","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: 4

Keyword annotation of biomedicai documents with graph-based similarity methods 基于图的相似度方法的生物医学文献关键词标注

2012 IEEE International Conference on Bioinformatics and Biomedicine Workshops Pub Date : 2012-10-04 DOI: 10.1109/BIBM.2012.6392698

Shuguang Wang, M. Hauskrecht

引用次数: 2