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Unexpected failure rates for modular assembly of engineered zinc fingers (vol 5, pg 374, 2008)

NATURE METHODS 2008年第6期5卷 575-575页

作者： Ramirez, Cherie L. Foley, Jonathan E. Wright, David A. Mueller-Lerch, Felix Rahman, Shamim H. Cornu, Tatjana I. Winfrey, Ronnie J. Sander, Jeffry D. Fu, Fengli Townsend, Jeffrey A. Cathomen, Toni Voytas, Daniel F. Joung, J. Keith These authors contributed equally to this work. These authors contributed equally to this work. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Interdepartmental Graduate Program in Bioinformatics and Computational Biology 2114 Molecular Biology Building Iowa State University Ames Iowa 50011 USA. Interdepartmental Graduate Program in Bioinformatics and Computational Biology 2114 Molecular Biology Building Iowa State University Ames Iowa 50011 USA. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Charité Medical School Institute of Virology Hindenburgdamm 27 D-12203 Berlin Germany. Department of Genetics Development and Cell Biology Iowa State University 1035A Roy J. Carver Co-Lab Ames Iowa 50011 USA. Department of Pathology Harvard Medical School Boston Massachusetts 02115 USA.

A letter to the editor is presented in response to an article on zinc fingers in a previous issue.

关键词： LETTERS to the editor ZINC

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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2007 IEEE Congress on Evolutionary Computation, CEC 2007

作者： Kim, Sun Kim, Soo-Jin Zhang, Byoung-Tak Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul 151-742 Korea Republic of School of Computer Science and Engineering Seoul National University Seoul 151-744 Korea Republic of

ISBN: (纸本)1424413400

High-throughput microarrays inform us on different outlooks of the molecular mechanisms underlying the function of cells and organisms. While computational analysis for the microarrays show good performance, it is still difficult to infer modules of multiple co-regulated genes. Here, we present a novel classification method to identify the gene modules associated with cancers from microarray data. The proposed approach is based on 'hypernetworks', a hypergraph model consisting of vertices and weighted hyperedges. The hypernetwork model is inspired by biological networks and its learning process is suitable for identifying interacting gene modules. Applied to the analysis of microRNA (miRNA) expression profiles on multiple human cancers, the hypernetwork classifiers identified cancer-related miRNA modules. The results show that our method performs better than decision trees and naive Bayes. The biological meaning of the discovered miRNA modules has been examined by literature search. © 2007 IEEE.

关键词： Microarrays

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Finding cancer-related gene combinations using a molecular evolutionary algorithm

Finding cancer-related gene combinations using a molecular e...

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7th IEEE International Conference on bioinformatics and Bioengineering, BIBE

作者： Park, Chan-Hoon Kim, Soo-Jin Kim, Sun Cho, Dong-Yeon Zhang, Byoung-Tak School of Computer Science and Engineering Seoul National University Seoul 151-742 Korea Republic of Graduate Program in Bioinformatics Seoul National University Seoul 151-742 Korea Republic of

ISBN: (纸本)1424415098

High-throughput data such as microarrays make it possible to investigate the molecular-level mechanism of cancer more efficiently. Computational methods boost the microarray analysis by managing large and complex data systematically. However, combinatorial interactions among genes have not been considered as a unit of the analysis since previous methods mainly focus on a whole gene or a single isolated gene. Here, we introduce a molecular evolutionary algorithm called probabilistic library model (PLM). In the PLM, library elements are generated from gene combinations. An evolutionary procedure is adopted to learn the probabilistic distribution of training samples. We apply the PLM to prostate cancer microarray data. The experimental results show that the PLM classifiers perform better than conventional methods such as neural networks and decision trees in accuracy. We also examine the evolved library to find cancer-related gene combinations. ©2007 IEEE.

关键词： Microarrays

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Study of equilibrium sense improvement displaying visual information

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Key Engineering Materials 2008年 381-382卷 369-372页

作者： Kim, G.B. Jeong, S.H. Chong, W.S. Kang, H.S. Kim, S.J. Kim, M.H. Hwang, J.W. Hong, C.U. Education Program for 21st Century Chonbuk National University Research Institute of Clinical Medicine Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Computer Engineering Graduate School Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Biomedical Engineering Graduate School Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Pharmacology College of Veterinary Medicine Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Department of Bio and Applied Chemistry Iksan National College Ma-Dong Iksan Chonbuk 570-752 Korea Republic of Department of Thoracic and Cardiovascular Surgery Chonbuk National University Medical Schools Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of Division of Bionics and Bioinformatics Collage of Engineering Chonbuk National University Duckjin-Dong Jeonju Chonbuk 561-756 Korea Republic of

The effectiveness of the visual feedback to improve ability with the sense and muscular strength of human in our bicycle system was quantitatively verified in our study. Experiments were performed to find the factors related to the training of equilibrium sense. The subjects consisted of young and the aged and the group of young people was compared against the group of the aged. We investigated three different training modes, non-visual feedback (NVF), visual feedback of the weight (VFW), and visual feedback of the center of pressure (VFC) and measured the riding time and speed, the weight shift, and the center of pressure (COP) for twenties and seventies. The results showed that the running capability of the young and the aged became much better after repeated training. In addition, it was found out that the ability to control postural balance and the capability of equilibrium sense were improved with the presentation of the visual feedback information. These results will be effective in the diagnosis of equilibrium sense and vestibular function with the aged.

关键词： Feedback

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Analysis of Protein Protein Dimeric Interfaces

Analysis of Protein Protein Dimeric Interfaces

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IEEE International Conference on bioinformatics and Biomedicine (BIBM)

作者： Feihong Wu Fadi Towfic Drena Dobbs Vasant Honavar Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA

We analyzed the structural properties and the local surface environment of surface amino acid residues of proteins using a large, non-redundant dataset of 2383 protein chains in dimeric complexes from PDB. We compared the interface residues and non-interface residues based on six properties: side chain orientation, surface roughness, solid angle, ex value, hydrophobicity and interface cluster size. The results of our analysis show that interface residues have side chains pointing inward; interfaces are rougher, tend to be flat, moderately convex or concave and protrude more relative to non-interface surface residues. Interface residues tend to be surrounded by hydrophobic neighbors and tend to form clusters consisting of three or more interfaces residues. These findings are consistent with previous published studies using much smaller datasets, while allowing for more qualitative conclusions due to our larger dataset. Preliminary results suggest the possibility of using the six the properties to identify putative interface residues.

关键词： Proteins Rough surfaces Surface roughness bioinformatics Amino acids Solids Sequences Biomedical computing Computer interfaces Biomedical measurements

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eXpanda: An integrated platform for network analysis and visualization

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In Silico Biology 2007年第2期7卷 141-144页

作者： Negishi, Yoshiteru Nakamura, Hiroyuki Yachie, Nozomu Saito, Rintaro Tomita, Masaru Institute for Advanced Biosciences Keio University Fujisawa 252-8520 Japan Bioinformatics Program Graduate School of Media and Governance Keio University Fujisawa 252-8520 Japan Department of Environmental Information Keio University Fujisawa 252-8520 Japan

Analysis and visualization of biological networks, such as protein-protein and protein-DNA interactions, are crucially important toward obtaining a thorough understanding of living systems. Here, we present an integrative software platform, eXpanda, which enables an analysis of a very broad range of biological networks, with a special focus on the extraction of characteristic topologies which potentially function as units in the networks. eXpanda is provided as a Perl library which gives full-automatic connections to various biological databases via a Perl programmable interface and can perform topological analysis based on graph theory. The results of these analyses are visualizable by vector graphics. eXpanda is under GNU General Public License. Software package, detailed documentations, source codes, and some sample scripts are downloadable at http://***/expanda/. © 2007 IOS Press. All rights reserved.

关键词： Interactome Network analysis Network visualization Perl library Scalable Vector Graphics (SVG)

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Evolving hypernetwork classifiers for microRNA expression profile analysis

Evolving hypernetwork classifiers for microRNA expression pr...

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Congress on Evolutionary Computation

作者： Sun Kim Soo-Jin Kim Byoung-Tak Zhang The Center for Bioinformatics Technology Graduate Program in Bioinformatics Seoul National University Seoul South Korea The School of Computer Science and Engineering Seoul National University Seoul South Korea

关键词： Cancer Gene expression Biological system modeling Data analysis Support vector machines Support vector machine classification Evolutionary computation Humans Decision trees Diseases

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Structural characterization of RNA-binding sites of proteins: Preliminary results

Structural characterization of RNA-binding sites of proteins...

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IEEE International Conference on bioinformatics and Biomedicine Workshops (BIBMW)

作者： Fadi Towfic David C. Gemperline Cornelia Caragea Feihong Wu Drena Dobbs Vasant Honavar Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Biology Department of Chemistry Carthage College Kenosha WI USA Department of Computer Science Iowa State University Ames IA USA Department of Genetics Development and Cell Biology Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA Department of Computer Science Bioinformatics and Computational Biology Graduate Program Iowa State University Ames IA USA

We explore whether protein-RNA interfaces differ from non-interfaces in terms of their structural features and whether structural features vary according to the type of the bound RNA (e.g., mRNA, siRNA...etc), using a non-redundant dataset of 147 protein chains extracted from protein-RNA complexes in the protein data bank. Our analysis of surface roughness, solid angle and CX value of amino acid residues for each of the protein chains in the dataset shows that: The protein-RNA interface residues tend to be protruding compared to non-interface residues and tend to have higher surface roughness and exhibit moderately convex or concave solid angles. Furthermore, the protein chains in protein-RNA interfaces that contain Viral RNA and rRNA significantly differ from those that contain dsRNA, mRNA siRNA, snRNA, SRP RNA and tRNA with respect to their CX values. The results of this analysis sug gests the possibility of using such structural features to reliably identify protein-RNA interface residues when the structure of the protein is available but the structures of complexes formed by the protein with RNA are not.

关键词： RNA Protein engineering Biology computing Amino acids bioinformatics Computer interfaces Rough surfaces Surface roughness Solids Machine learning

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Simulation of developmental changes in action potentials with ventricular cell models

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Systems and Synthetic Biology 2007年第1期1卷 11-23页

作者： Itoh, Hitomi Naito, Yasuhiro Tomita, Masaru Institute for Advanced Biosciences Keio University Fujisawa Kanagawa 252-8520 Japan Bioinformatics Program Graduate School of Media and Governance Keio University Fujisawa Kanagawa 252-8520 Japan Japan Society for the Promotion of Science (DC1) Tokyo Japan Department of Environmental Information Keio University Fujisawa Kanagawa 252-8520 Japan

During cardiomyocyte development, early embryonic ventricular cells show spontaneous activity that disappears at a later stage. Dramatic changes in action potential are mediated by developmental changes in individual ionic currents. Hence, reconstruction of the individual ionic currents into an integrated mathematical model would lead to a better understanding of cardiomyocyte development. To simulate the action potential of the rodent ventricular cell at three representative developmental stages, quantitative changes in the ionic currents, pumps, exchangers, and sarcoplasmic reticulum (SR) Ca²⁺ kinetics were represented as relative activities, which were multiplied by conductance or conversion factors for individual ionic systems. The simulated action potential of the early embryonic ventricular cell model exhibited spontaneous activity, which ceased in the simulated action potential of the late embryonic and neonatal ventricular cell models. The simulations with our models were able to reproduce action potentials that were consistent with the reported characteristics of the cells in vitro. The action potential of rodent ventricular cells at different developmental stages can be reproduced with common sets of mathematical equations by multiplying conductance or conversion factors for ionic currents, pumps, exchangers, and SR Ca ²⁺ kinetics by relative activities. © Springer Science + Business Media B.V. 2007.

关键词： Cardiac ventricular cell Computer modeling Development Electrophysiology Ion channels Spontaneous electrical activity

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Tag clouds for summarizing web search results 07

Tag clouds for summarizing web search results

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16th International World Wide Web Conference, WWW2007

作者： Kuo, Byron Y.-L. Hentrich, Thomas Good, Benjamin M . Wilkinson, Mark D. ICAPTURE Centre for Cardiovascular and Pulmonary Research University of British Columbia St. Paul.s Hospital Vancouver BC V6Z 1Y6 Canada Computing Science Simon Fraser University Burnaby BC Canada Bioinformatics Graduate Program University of British Columbia Vancouver BC Canada

ISBN: (纸本)1595936548

In this paper, we describe an application, PubCloud that uses tagclouds for the summarization of results from queries over thePubMed database of biomedical literature. PubCloud responds toqueries of this database with tag clouds generated from wordsextracted from the abstracts returned by the query. The results ofa user study comparing the PubCloud tag-cloud summarization ofquery results with the standard result list provided by PubMedindicated that the tag cloud interface is advantageous in presenting descriptive information and in reducing user frustrationbut that it is less effective at the task of enabling users to discoverrelations between concepts.

关键词： Online searching

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