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2010 ieee World Congress on computational intelligence

作者： Fober, Thomas Huellermeier, Eyke Univ Marburg Dept Math & Comp Sci D-35041 Marburg Germany

ISBN: (纸本)9781424469208

We propose a method for comparing protein structures or, more specifically, protein binding sites in terms of histogram-based representations. These representation are intended to capture important geometrical and physico-chemical properties. In comparison to hitherto existing approaches in structural bioinformatics, especially graph-based methods and methods from computational geometry, our approach is computationally much more efficient. Moreover, despite its simplicity, first experimental studies suggest that it is able to produce useful measures of similarity.

关键词： bioinformatics computational geometry computational geometry fuzzy histogram comparison fuzzy set theory geometrical properties graph based methods graph theory histogram based representations physico chemical properties protein binding sites protein structures proteins similarity measures structural bioinformatics

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FAST: Fast Annotation with Synchronized Threads 13

FAST: Fast Annotation with Synchronized Threads

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13th ieee Annual conference on computational intelligence in bioinformatics and computational biology (ieee CIBCB)

作者： Kim, Dongjae Hahn, Aria S. Hanson, Niels W. Konwar, Kishori M. Hallam, Steven J. Univ British Columbia Dept Microbiol & Immunol Vancouver BC Canada Koonkie Inc Menlo Pk CA 94025 USA MIT Comp Sci & Artificial Intelligence Lab 77 Massachusetts Ave Cambridge MA 02139 USA Univ British Columbia ECOSCOPE Training Program Vancouver BC Canada Univ British Columbia Dept Comp Sci Vancouver BC Canada Univ British Columbia Grad Program Bioinformat Vancouver BC Canada KPMG LLC Data & Analyt Seattle WA USA

ISBN: (纸本)9781467394727

FAST is a multi-threaded, I/O optimized Seed-and-Extend alignment program. FAST is extensible to nucleotide sequences making it comparable to both BLASTn and BLASTp, and also features several new usage flags reporting only HSPs meeting user defined e-value cut-offs. FASTs threaded database construction allows fast, low memory database construction e.g., RefSeq (9.4GB) can be indexed in under 5 minutes using 20 threads. The threaded database construction gives users the ability to create custom databases on demand which is useful for tasks requiring self-alignment, such as network construction [30]. Finally, FAST supports incremental database construction enabling users to keep their databases up-to-date by adding sequences without suffering the cost of reformatting the entire database. The FAST source is freely available through GitHub https:// ***/hallamlab/FAST and test datasets can be found on Dropbox https://***/sh/xvvavweuzgqybc4/ AAAWCrRnol67ZsXi2qLQWUuOa? © 2016 ieee.

关键词： Database systems

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Towards Extracting Supporting Information About Predicted Protein-Protein Interactions

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ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2018年第4期15卷 1239-1246页

作者： Roth, Adam Subramanian, Sandeep Ganapathiraju, Madhavi K. Univ Pittsburgh Dept Biomed Informat 5607 Baum BlvdSuite 501 Pittsburgh PA 15206 USA Carnegie Mellon Univ Langauge Technol Inst 5000 Forbes Ave Pittsburgh PA 15213 USA

One of the goals of relation extraction is to identify protein-protein interactions (PPIs) in biomedical literature. Current systems are capturing binary relations and also the direction and type of an interaction. Besides assisting in the curation PPIs into databases, there has been little real-world application of these algorithms. We describe UPSITE, a text mining tool for extracting evidence in support of a hypothesized interaction. Given a predicted PPI, UPSITE uses a binary relation detector to check whether a PPI is found in abstracts in PubMed. If it is not found, UPSITE retrieves documents relevant to each of the two proteins separately, and extracts contextual information about biological events surrounding each protein, and calculates semantic similarity of the two proteins to provide evidential support for the predicted PPI. In evaluations, relation extraction achieved an Fscore of 0.88 on the HPRD50 corpus, and semantic similarity measured with angular distance was found to be statistically significant. With the development of PPI prediction algorithms, the burden of interpreting the validity and relevance of novel PPIs is on biologists. We suggest that presenting annotations of the two proteins in a PPI side-by-side and a score that quantifies their similarity lessens this burden to some extent.

关键词： Artificial intelligence computational biology/methods data mining/methods semantics proteins/metabolism natural language processing

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ieee BIBM 2018 Special Section

IEEE TRANSACTIONS ON NANOBIOSCIENCE

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ieee TRANSACTIONS ON NANOBIOSCIENCE 2019年第3期18卷 271-272页

作者： Hu, Xiaohua Drexel Univ Philadelphia PA 19104 USA

bioinformatics and biomedicine research is fundamental to our understanding of complex biological systems, impacting the science and technology of fields ranging from agricultural and environmental sciences to pharmaceutical and medical sciences. This type of research requires close collaboration among multidisciplinary teams of researchers in computer science, statistics, physics, engineering, life sciences and medical sciences, and their interfaces. The ieee International conference on bioinformatics and Biomedicine aims to provide an open and interactive forum to catalyze the cross-fertilization of ideas from these disciplines and to bridge our knowledge gaps.

关键词： Special issues and sections Meetings bioinformatics computational systems biology Genomics

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Channel selection in EEG-based prediction of shoulder/elbow movement intentions involving stroke patients: A computational approach

Channel selection in EEG-based prediction of shoulder/elbow ...

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ieee Symposium on computational intelligence in bioinformatics and computational biology

作者： Zhou, Jie Yedida, Sundeep Northern Illinois Univ Dept Comp Sci De Kalb IL 60115 USA

ISBN: (纸本)9781424407101

Brain computer Interface (BCI) has gained a lot of attention recently, as a means to detect individuals' intents using brain signals such as electroencephalographic (EEG) for control of machines. In order to achieve the possible use of BCI in stroke rehabilitation, computational intelligent algorithms are important for reliable separation of shoulder versus elbow movement intentions. Efforts have been made on developing data processing and classification algorithm for such task Differently, this paper investigates the optimal use of electrodes and signal channels, which is formulated as a data-driven feature selection problem. 163 EEG electrodes are used to collect scalp recordings to predict shoulder abduction and elbow flexion intentions in healthy and stroke subjects. We combine the support vector channel selection with a time-frequency synthesized classification algorithm and examine the performances of using different subsets of channel inputs. Preliminary results show that 1) a reduced number of electrodes can be used to achieve the same or better performance than using the full set of signal channels;2) besides the fact that the accuracy on able-bodied subjects is expectedly higher than the stroke subject, the stroke subject tends to need more electrodes to achieve the best performance;3) visualization of spatial distribution of channel rankings shows reasonable connection with functional motor cortex areas.

关键词： Electrodes

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Guest Editorial for the International conference on Genome Informatics (GIW 2013)

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ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2014年第1期11卷 5-6页

作者： Eisenhaber, Frank Sung, Wing-Kin Wong, Limsoon Agcy Sci Technol & Res Bioinformat Inst Singapore 138671 Singapore Natl Univ Singapore Dept Biol Sci Singapore 117597 Singapore Nanyang Technol Univ Sch Comp Engn Singapore 637553 Singapore Natl Univ Singapore Sch Comp Singapore 117417 Singapore Genome Inst Singapore Singapore 138672 Singapore

The nine papers in this special section were presented at the 2013 International conference on Genome Informatics.

关键词： Special Issues And Sections Meetings Genomics bioinformatics Informatics

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Guest Editorial for the 12th Asia Pacific bioinformatics conference

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ieee-ACM TRANSACTIONS ON computational biology AND bioinformatics 2014年第4期11卷 614-615页

作者： Zhou, Shuigeng Chen, Yi-Ping Phoebe Fudan Univ Shanghai Key Lab Intelligent Informat Proc Shanghai 200433 Peoples R China Fudan Univ Sch Comp Sci Shanghai 200433 Peoples R China La Trobe Univ Dept Comp Sci & Comp Engn Melbourne Vic Australia

The eight papers in this special section were presented at the Twelfth Asia Pacific bioinformatics conference (APBC2014), which was held in Shanghai, China, 17-19 January, 2014. The papers cover diverse topics, including protein complex prediction, nucleosome positioning, biological data classification and clustering, sequence comparison, genome reconstruction, and enhancers etc.

关键词： Special Issues And Sections bioinformatics Meetings Informatics

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An improved quick algorithm for aligning DNA/RNA sequences

An improved quick algorithm for aligning DNA/RNA sequences

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International conference on computational intelligence and Security

作者： Zou, Quan Guo, Maozu Liu, Yang Zhang, Taotao Harbin Inst Technol Sch Comp Sci & Technol Harbin 150001 Peoples R China

ISBN: (纸本)9780769530734

biology sequence database search is an important problem for bioinformatics research. The main search software BLAST is based on the BYP algorithm([1]). In BYP, if the length of hit region is set long, it may lose similar appearance. Otherwise, there may he too many r-length regions from Aho-Corasik algorithm. Checking where exists any approximate alignments for the DNA or RNA sequence always spends much time, although the expected running time of BYP is linear. A new algorithm is proposed from the viewpoint of shorting the length and increasing the number of the regions, which can make most of the false r-length regions excluded Thus the algorithm can align the DNA or RNA sequences quickly since the rate of real r-length regions is increased. Experimental results show that the proposed algorithm is computational efficient and achieves good performance.

关键词： bioinformatics

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Information technology and computational biology in human reproduction technologies. Perspectives and bioethical issues for clinical practice

Information technology and computational biology in human re...

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Joint Meeting of the 3rd ieee EMBS International conference on Information Technology Applications in Biomedicine/3rd Workshop of the Int-Telemedical-Information-Society

作者： Tritto, J St Louis Univ Hosp Dept Urol Serv Surg Androl Paris France

ISBN: (纸本)078036449X

Information Technology and computational biology applications in Human Reproduction represent a new growing area of basic and clinical researches in Reproductive Sciences. Human Assisted Reproductive Technologies (ARTs) are changing the clinical practice in male and female infertility therapeutic strategics, imposing new perspectives, but also specific bioethical issues for large scale applications. ReproGen programs, based on bioinformatics and computational biology, must be proposed in order to evaluate the real impact of the genetic approaches (genomics and gene therapies) in human reproduction and fertility.

关键词： bioinformatics computational biology human reproduction genetics bioethics

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Intellectual Property Protection for bioinformatics and computational biology 1

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3rd International Work-conference on bioinformatics and Biomedical Engineering (IWBBIO)

作者： Fernandez, Dennis Maninang, Antonia Kobayashi, Shumpei Bhatia, Shashank Kraatz, Carina Fernandez & Associates LLP Alterton CA USA Stanford Hosp Stanford CA USA

ISBN: (数字)9783319164830

ISBN: (纸本)9783319164830;9783319164823

bioinformatics, and computational biology are two ever-growing fields that require careful attention to intellectual property rights (IPR) and strategies. The American patent system is currently going through the biggest reformation since the passage of Patent Act of 1952, and many changes apply directly to the field of biology that utilize computational intelligence. Basic IP definitions, recent IP developments, and advanced protection strategies are discussed in order to better understand the status quo of intellectual property (IP) specifically in the field of evolutionary computation, bioinformatics, and computational biology.

关键词： computational biology bioinformatics Intellectual Property America Invents Act Patent Portfolio

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