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2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)最新文献

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Modelling biological pathway dynamics with Timed Automata 用时间自动机建模生物路径动力学
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399719
S. Schivo, J. Scholma, Brend Wanders, R. A. U. Camacho, P. V. D. Vet, M. Karperien, R. Langerak, J. Pol, J. Post
{"title":"Modelling biological pathway dynamics with Timed Automata","authors":"S. Schivo, J. Scholma, Brend Wanders, R. A. U. Camacho, P. V. D. Vet, M. Karperien, R. Langerak, J. Pol, J. Post","doi":"10.1109/BIBE.2012.6399719","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399719","url":null,"abstract":"When analysing complex interaction networks occurring in biological cells, a biologist needs computational support in order to understand the effects of signalling molecules (e.g. growth factors, drugs). ANIMO (Analysis of Networks with Interactive MOdelling) is a tool that allows the user to create and explore executable models of biological networks, helping to derive hypotheses and to plan wet-lab experiments. The tool is based on the formalism of Timed Automata, which can be analysed via the UPPAAL model checker. Thanks to Timed Automata, we can provide a formal semantics for the domain-specific language used to represent signalling networks. This enforces precision and uniformity in the definition of signalling pathways, contributing to the integration of signalling event models into complex, crosstalk-driven networks. We propose an approach to discretization of reaction kinetics that allows us to efficiently use UPPAAL as the computational engine to explore the dynamic cell behaviour. A user friendly interface makes the use of Timed Automata completely transparent to the biologist, while keeping the expressive power intact. This allows to define relatively simple, yet faithful models of complex biological interactions. The resulting timed behaviour is displayed graphically, allowing for an intuitive and interactive modelling experience.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"86 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132800073","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: 26
Monitoring circulating cancer cells by multichannel in vivo flow cytometry 多通道体内流式细胞术监测循环癌细胞
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399751
C. Pitsillides, K. Kapnisis, M. Prokopi, C. Kousparou, A. Anayiotos
{"title":"Monitoring circulating cancer cells by multichannel in vivo flow cytometry","authors":"C. Pitsillides, K. Kapnisis, M. Prokopi, C. Kousparou, A. Anayiotos","doi":"10.1109/BIBE.2012.6399751","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399751","url":null,"abstract":"We report a new approach for potential monitoring of tumor burden in experimental animals using multichannel in vivo flow cytometry, a novel optical technique that enables the realtime, continuous detection and quantification of fluorescently labeled cells in the circulation without the need for blood extraction. The ability to non-invasively track circulating cells in real time and in their native environment, opens up enormous possibilities for new investigations into the mechanisms that govern the complex trafficking and tissue interactions of these cells in a wide range of clinical and biological fields such as cancer, stem cell biology and immunology. We have developed the in vivo flow cytometer in order to track circulating cancer cells in a mouse model and provide a new, non-invasive method for the monitoring of cancer disease progression as well as the response to therapeutic intervention.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"117 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124351578","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
Modeling the activation of a non-homogenous nerve fiber by magnetic stimulation 模拟磁刺激对非同质神经纤维的激活
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399743
M. Crețu, L. Darabant, R. Ciupa
{"title":"Modeling the activation of a non-homogenous nerve fiber by magnetic stimulation","authors":"M. Crețu, L. Darabant, R. Ciupa","doi":"10.1109/BIBE.2012.6399743","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399743","url":null,"abstract":"In this paper we present a model that combines circuit analysis with Maxwell's equations of electromagnetic theory and non-linear cable theory, to explain the action of the induced electric field upon a nerve fiber. The current source and stimulating coil are modeled as a series RLC circuit. The induced electric field distribution within a homogeneous cylindrical volume conductor modeling the arm is calculated for different time courses of the current. The effect of the induced electric field upon the nerve is determined with a cable model which contains active Hodgkin-Huxley elements. The possible non-homogeneities of the nerve's electrical properties are also considered, and we assess their influence on the activation of the nerve.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"33 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"121474445","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
An information retrieval system for expert and consumer users 一个供专家和消费者使用的信息检索系统
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399664
Rena Peraki, E. Petrakis, Angelos Hliaoutakis
{"title":"An information retrieval system for expert and consumer users","authors":"Rena Peraki, E. Petrakis, Angelos Hliaoutakis","doi":"10.1109/BIBE.2012.6399664","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399664","url":null,"abstract":"The requirements for the design and implementation of a medical information retrieval system for expert and consumer users are discussed. The proposed approach is based on the integration of state-of-the-art tools and methodologies of systems design and document management. Relying on term extraction by natural language processing, the system supports automatic categorization as well as, indexing and retrieval of medical documents by user profile (novice users and experts). This is achieved by mapping document terms to external lexical resources such as WordNet, and MeSH (the medical thesaurus of NLM). Evaluation results of all methods are presented and discussed as well.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"52 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"124936682","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
Intraoperative registration of preoperative 4D cardiac anatomy with real-time MR images 术中利用实时MR图像对术前4D心脏解剖进行配准
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399737
Xifeng Gao, N. Navkar, D. Shah, N. Tsekos, Z. Deng
{"title":"Intraoperative registration of preoperative 4D cardiac anatomy with real-time MR images","authors":"Xifeng Gao, N. Navkar, D. Shah, N. Tsekos, Z. Deng","doi":"10.1109/BIBE.2012.6399737","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399737","url":null,"abstract":"Co-registering pre- and intra- operative MR data is an important yet challenging problem due to different acquisition parameters, resolutions, and plane orientations. Despite its importance, previous approaches are often computationally intensive and thus cannot be employed in real-time. In this paper, a novel three-step approach is proposed to dynamically register pre-operative 4D MR data with intra-operative 2D RT-MRI to guide intracardiac procedures. Specifically, a novel preparatory step, executed in the pre-operative phase, is introduced to generate bridging information that can be used to significantly speed up the on-the-fly registration in the intraoperative procedure. Our experimental results demonstrate an accuracy of 0.42 mm and a processing speed of 26 FPS of the proposed approach on an off-the-shelf PC. This approach, is in particularly developed for performing intra-cardiac procedures with real-time MR guidance.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"10 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"128496965","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: 21
Open source workflow systems in life sciences informatics 生命科学信息学中的开源工作流系统
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399732
K. Achilleos, Christos C. Kannas, C. Nicolaou, C. Pattichis, V. Promponas
{"title":"Open source workflow systems in life sciences informatics","authors":"K. Achilleos, Christos C. Kannas, C. Nicolaou, C. Pattichis, V. Promponas","doi":"10.1109/BIBE.2012.6399732","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399732","url":null,"abstract":"A simple yet powerful programming tool enabling in silico experimentation, end-to-end data management through web services as well as use of grid and cloud processing power is scientific workflows. This technology is receiving considerable interest in recent years primarily due to its ability to promote and support scientific collaboration among large distributed research teams. The paper reviews the Scientific Workflows Management Systems (SWMS) field and investigates in detail popular open source workflow systems used commonly in life sciences informatics. Emphasis is placed on features which make these systems attractive for scientific use, e.g. user friendliness, use of distributed resources, reusability, provenance, collaboration, data integration, etc. Our conclusions indicate that although SWMS, including open source ones, have several open issues, their unique features and strong momentum clearly suggest that it is only a matter of time before they are adopted in even more scientific fields.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"77 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"122026525","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: 8
Fast searching in biological sequences using multiple hash functions 使用多个哈希函数在生物序列中快速搜索
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399669
S. Faro, T. Lecroq
{"title":"Fast searching in biological sequences using multiple hash functions","authors":"S. Faro, T. Lecroq","doi":"10.1109/BIBE.2012.6399669","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399669","url":null,"abstract":"With the availability of large amounts of DNA data, exact matching of nucleotide sequences has become an important application in modern computational biology and in meta-genomics. In this paper we present an efficient method based on multiple hashing functions which improves the performance of existing string matching algorithms when used for searching DNA sequences. From our experimental results it turns out that the new proposed technique leads to algorithms which are up to 8 times faster than the best algorithm known for matching multiple patterns. It turns out also that the gain in performances is larger when searching for larger sets. Thus, considering the fact that the number of reads produced by next generation sequencing equipments is ever growing, the new technique serves a good basis for massive multiple long pattern search applications.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"68 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"129575654","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: 8
Adaptive nonlinear probabilistic filter for Positron Emission Tomography 正电子发射层析成像的自适应非线性概率滤波
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399753
Musa Alrefaya, H. Sahli
{"title":"Adaptive nonlinear probabilistic filter for Positron Emission Tomography","authors":"Musa Alrefaya, H. Sahli","doi":"10.1109/BIBE.2012.6399753","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399753","url":null,"abstract":"Radiologists face difficulties when reading and interpreting Positron Emission Tomography (PET) images because of the high noise level in the raw-projection data (i.e. the sinogram). The later may lead to erroneous diagnoses. Aiming at finding a suitable denoising technique for PET images, in our first work, we investigated filtering the sinogram with a constraint curvature motion filter where we computed the edge stopping function in terms of edge probability under a marginal prior on the noise free gradient. In this paper, we show that the Chi-square is the appropriate prior for finding the edge probability in the sinogram noise-free gradient. Since the sinogram noise is uncorrelated and follows a Poisson distribution, we then propose an adaptive probabilistic diffusivity function where the edge probability is computed at each pixel. We demonstrate quantitatively and qualitatively through simulations that the performance of the proposed method substantially surpasses that of state-of-art methods, both visually and in terms of statistical measures.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"539 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"127649928","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
Legal and ethical issues in integrating and sharing databases for translational medical research within the EU 在欧盟内部整合和共享转化医学研究数据库的法律和伦理问题
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399764
Iheanyi Nwankwo, Stefanie Hänold, N. Forgó
{"title":"Legal and ethical issues in integrating and sharing databases for translational medical research within the EU","authors":"Iheanyi Nwankwo, Stefanie Hänold, N. Forgó","doi":"10.1109/BIBE.2012.6399764","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399764","url":null,"abstract":"Apart from technical challenges, legal and ethical issues form part of the considerations when pooling together and sharing databases for translational medical research. Questions referring to data protection, data security and intellectual property rights, which are even made more complex because of the transnational aspect of such research, have to be addressed in order to make data sharing legally compliant. Additionally, medical research brings along ethical requirements such as protecting the autonomy and the well-being of the patients. In all, a wide net of rules has to be considered, and in most cases this may hinder the flexibility needed for clinical researches. This paper aims to give an overview of these issues and an insight of the p-medicine's approach at navigating these requirements, which can serve as a guide to similar projects, especially within the EU.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"117321484","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: 6
Electronic Health Record diagnosis tool and a cross reference between coding standards 电子健康记录诊断工具和编码标准之间的交叉参考
2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE) Pub Date : 2012-11-11 DOI: 10.1109/BIBE.2012.6399702
Harris Soteriades, K. Neokleous, George Tsouloupas, A. Jossif, C. Schizas
{"title":"Electronic Health Record diagnosis tool and a cross reference between coding standards","authors":"Harris Soteriades, K. Neokleous, George Tsouloupas, A. Jossif, C. Schizas","doi":"10.1109/BIBE.2012.6399702","DOIUrl":"https://doi.org/10.1109/BIBE.2012.6399702","url":null,"abstract":"Many computer applications have been released targeting the implementation of a general Electronic Health Record (EHR) system. The main goal of an EHR system is to digitally store useful medical information about a patient's history and to share it across different health care units. Furthermore, the EHR systems should provide important information to the medical doctors during or after an encounter of care that will facilitate their decisions on making the correct diagnosis. A major problem however, for adopting an EHR system, especially from older doctors corresponds to the time that is needed to become familiar with the tool and thus either prevents them from enjoying the full benefits of an advanced EHR system, or leads to a complete rejection of the system. Therefore one of the fundamental concepts for implementing an EHR system is to incorporate proper and easy to use tools that will enhance and guide the doctors' decisions in an optimal way without taking significant time of their usually busy schedule. In this paper we aim to tackle part of this problem by proposing an application tool that will help the doctor with the patient's diagnosis by suggesting a matching disease code based on the user's (doctor's) notes. In addition, the tool will offer cross reference functionality between two international standards, the International Classification of Diseases (ICD-10) and the Systematized Nomenclature of Medicine - Clinical Terms (SNOMED-CT). This tool will be tested as a freemed-software module add-on and it will be implemented in a private group practice (the Center). With their cooperation and the feedback from the users the tool will be evaluated for the possibility to be used in other EHR applications.","PeriodicalId":330164,"journal":{"name":"2012 IEEE 12th International Conference on Bioinformatics & Bioengineering (BIBE)","volume":"8 1","pages":"0"},"PeriodicalIF":0.0,"publicationDate":"2012-11-11","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132331511","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
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