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7th IEEE International Conference on Bioinformatics and Bioengineering, BIBE

作者： Alterovitz, Gil Muso, Taro Malalur, Paresh Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Children's Hospital Informatics Program Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States

ISBN: (纸本)1424415098

The accumulation of genomic and proteomic data of many organisms presents an opportunity to analyze entire phylogenetic trees in a systematic, quantified manner. The universal tree of life, constructed by genomic data, provides an evolutionary context for proteomic data of individual organisms. Using proteomic information mapped to biological functions, we survey the tree of life for evolutionary trends, where trends are low p-value linear regressions of relative protein diversity against an evolutionary timeline. These trends provide quantified perspectives across evolution that would be otherwise difficult to discern from the large amount of available bioinformatic data. We analyzed 22,762 functions across 167 proteomes for approximately 3.8 million information content calculations. Of particular interest is the rise of protein-protein interactions along the path of mammalian evolution. Of general interest are the numerous uncovered trends that open the door to future queries of focused scope. ©2007 IEEE.

关键词： Information theory

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Correcting base-assignment errors in repeat regions of shotgun assembly

Correcting base-assignment errors in repeat regions of shotg...

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作者： Zhi, Degui Keich, Uri Pevzner, Pavel Heber, Steffen Tang, Haixu Bioinformatics Program University of California San Diego San Diego CA 92093 Department of Computer Science 4130 Upson Hall Cornell University Ithaca NY 14853 Department of Computer Science and Engineering University of California San Diego San Diego CA 92093 North Carolina State University Raleigh NC 27695-7566 School of Informatics Center for Genomics and Bioinformatics Indiana University Bloomington IN 47408

Accurate base-assignment in repeat regions of a whole genome shotgun assembly is an unsolved problem. Since reads in repeat regions cannot be easily attributed to a unique location in the genome, current assemblers may place these reads arbitrarily. As a result, the base-assignment error rate in repeats is likely to be much higher than that in the rest of the genome. We developed an iterative algorithm, EULER-AIR, that is able to correct base-assignment errors in finished genome sequences in public databases. The Wolbachia genome is among the best finished genomes. Using this genome project as an example, we demonstrated that EULER-AIR can 1) discover and correct base-assignment errors, 2) provide accurate read assignments, 3) utilize finishing reads for accurate base-assignment and 4) provide guidance for designing finishing experiments. In the genome of Wolbachia, EULER-AIR found 16 positions with ambiguous base-assignment and two positions with erroneous bases. Besides Wolbachia, many other genome sequencing projects have significantly fewer finishing reads and, hence, are likely to contain more base-assignment errors in repeats. We demonstrate that EULER-AIR is a software tool that can be used to find and correct base-assignment errors in a genome assembly project. © 2007 IEEE.

关键词： Error analysis

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A Middleware for OSCAR and Wireless Sensor Network Environments

A Middleware for OSCAR and Wireless Sensor Network Environme...

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IEEE International Symposium on High Performance Computing Systems and Applications (HPCS)

作者： D. J. Ferreira M.A.R. Dantas A. R. Pinto C. Montez Martius Rodriguez Departament of Informatics and Statistics (INE) University of Santa Catarina (UFSC) Florianopolis Brazil Graduation Program in Electrical Engineering University of Santa Catarina (UFSC) Florianopolis Brazil Fluminense Federal University (UFF) Niteroi Rio de Janeiro

There has been a steady increase in the use of mobile computing, especially with appliances such as sensors. The main challenge in this scenario is to increase network sensor lifetime. Cluster computing integration with wireless sensor networks can represent an interesting answer for high-performance computing to monitor several environments. Computational resources available from cluster configurations are cost effective components to improve several classes of applications in many organizations. Scientific, industrial and commercial applications are more relying on cluster performance. OSCAR is a useful open software approach to manage cluster of workstations. In this article, we present a middleware design and implementation that integrates an OSCAR cluster configuration with a wireless sensor network environment.

关键词： Middleware Wireless sensor networks Application software Distributed computing Statistics Computer networks Workstations Space technology Batteries Prototypes

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An information theoretic framework for ontology-based bioinformatics

An information theoretic framework for ontology-based bioinf...

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2007 Information Theory and Applications Workshop, ITA

作者： Alterovitz, Gil Xiang, Michael Ramoni, Marco F. Division of Health Sciences and Technology Harvard Medical School Massachusetts Institute of Technology Boston MA United States Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA United States Children's Hospital Informatics Program Boston MA United States Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA United States Department of Biology Massachusetts Institute of Technology Cambridge MA United States

ISBN: (纸本)9780615153148

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the Gene Ontology (GO). We have developed a novel framework-based on the well established foundations of information theory - that allows for the evaluation of new types of hypotheses. The framework, encapsulated in Open Biomedical Ontology-Based Exploration and Search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***. net.

关键词： Information theory

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The generation challenge programme platform: Semantic standards and workbench for crop science

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International Journal of Plant Genomics 2008年第1期2008卷 369601页

作者： Bruskiewich, Richard Senger, Martin Davenport, Guy Ruiz, Manuel Rouard, Mathieu Hazekamp, Tom Takeya, Masaru Doi, Koji Satoh, Kouji Costa, Marcos Simon, Reinhard Balaji, Jayashree Akintunde, Akinnola Mauleon, Ramil Wanchana, Samart Shah, Trushar Anacleto, Mylah Portugal, Arllet Ulat, Victor Jun Thongjuea, Supat Braak, Kyle Ritter, Sebastian Dereeper, Alexis Skofic, Milko Rojas, Edwin Martins, Natalia Pappas, Georgios Alamban, Ryan Almodiel, Roque Barboza, Lord Hendrix Detras, Jeffrey Manansala, Kevin Mendoza, Michael Jonathan Morales, Jeffrey Peralta, Barry Valerio, Rowena Zhang, Yi Gregorio, Sergio Hermocilla, Joseph Echavez, Michael Yap, Jan Michael Farmer, Andrew Schiltz, Gary Lee, Jennifer Casstevens, Terry Jaiswal, Pankaj Meintjes, Ayton Wilkinson, Mark Good, Benjamin Wagner, James Morris, Jane Marshall, David Collins, Anthony Kikuchi, Shoshi Metz, Thomas McLaren, Graham Van Hintum, Theo Crop Research Informatics Laboratory International Rice Research Institute (IRRI) DAPO Box 7777 Metro Manila Philippines Crop Research Informatics Laboratory International Maize and Wheat Improvement Center (CIMMYT) DF 06600 Mexico Apdo. Postal 6-641 Mexico Centre International de Recherche Agronomique Pour le Développement (CIRAD) 34398 Montpellier Cedex 5 Avenue Agropolis France Bioversity International 00057 Maccarese (Fiumicino) Rome Via dei Tre Denari 472/a Italy National Institute for Agrobiological Sciences (NIAS) Tsukuba Ibaraki 305-8602 Kannondai 2-1-2 Japan Empresa Brasileira de Pesquisa Agropecuaria (EMBRAPA) Brasilia DF 70770-900 Parque Estaçao Biologia Final W5 Norte Brazil Centro Internacional de la Papa (CIP) Lima 12 Avenida La Molina 1895 La Molina Peru International Crops Research Institute for the Semi-Arid Tropics Patancheru Andhra Pradesh 502324 India International Center for Agricultural Research in the Dry Areas Aleppo P.O. Box 5466 Syrian Arab Republic National Center for Genetic Engineering and Biotechnology 113 Thailand Science Park Klong Luang Pathumthani 12120 Phahonyothin Road Klong 1 Thailand Institute of Computer Science College of Arts and Sciences University of the Philippines Los Banos Laguna 4031 Philippines Department of Computer Science University of the Philippines Melchor Hall Diliman Quezon City 1101 Philippines National Center for Genome Resources Santa Fe NM 87505 2935 Rodeo Park Drive East United States Scottish Crop Research Institute Invergowrie Dundee DD2 5DA United Kingdom Department of Plant Breeding Cornell University Ithaca NY 14853 United States African Centre for Gene Technologies Lynnwood Ridge 0040 P.O. Box 75011 South Africa Department of Medical Genetics Faculty of Medicine University of British Columbia Vancouver BC V6T 1Z3 Canada School of Computing Science Simon Fraser Universtiy Burnaby BC V5A 1S6 8888 University Drive Canada Bioinformatics Graduate Program Genome Sciences Centre BC

The Generation Challenge programme (GCP) is a global crop research consortium directed toward crop improvement through the application of comparative biology and genetic resources characterization to plant breeding. A key consortium research activity is the development of a GCP crop bioinformatics platform to support GCP research. This platform includes the following: (i) shared, public platform-independent domain models, ontology, and data formats to enable interoperability of data and analysis flows within the platform;(ii) web service and registry technologies to identify, share, and integrate information across diverse, globally dispersed data sources, as well as to access high-performance computational (HPC) facilities for computationally intensive, high-throughput analyses of project data;(iii) platform-specific middleware reference implementations of the domain model integrating a suite of public (largely open-access/-source) databases and software tools into a workbench to facilitate biodiversity analysis, comparative analysis of crop genomic data, and plant breeding decision making.

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An Information Theoretic Framework for Ontology-based Bioinformatics

An Information Theoretic Framework for Ontology-based Bioinf...

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Information Theory and Applications Workshop, ITA

作者： Gil Alterovitz Michael Xiang Marco F. Ramoni Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA USA Department of Electrical Engineering and Computer Science Massachusetts Institute of Technology Cambridge MA USA Department of Biology Massachusetts Institute of Technology Cambridge MA USA Division of Health Sciences and Technology Harvard Medical School and Massachusetts Institute of Technology Boston MA Children's Hospital Informatics Program Boston MA Harvard Partners Center for Genetics and Genomics Harvard Medical School Boston MA.

With myriad information being generated from high-throughput experiments such as microarrays and sequencing technologies, an ever-increasing amount of data is being recorded and analyzed with the help of hierarchical ontologies, such as the gene ontology (GO). We have developed a novel framework- based on the well established foundations of information theory- that allows for the evaluation of new types of hypotheses. The framework, encapsulated in open biomedical ontology-based exploration and search (OBOES), has already been applied in the investigation of different kinds of questions. The resulting framework enables the new field of information theoretic ontology-based analysis. We have applied this framework to create methods to re-engineer ontologies, explore fundamental questions on the evolution of biological complexity, determine optimal ontology terms for bioinformatics analysis, and quantify the usefulness of biofluids as proxies for tissues/diseases. In each case, we found that our methods provide novel, significant findings. An open source Java implementation of OBOES is available at: http://***.

关键词： Ontologies Bioinformatics Genomics Information analysis Biological information theory Information theory Genetic communication Humans Biochemistry Frequency

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Algorithm-based analysis of collective decoherence in quantum search

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Progress in informatics 2006年第3期 5-18页

作者： Master, Cyrus P. Utsunomiya, Shoko Yamamoto, Yoshihisa National Institute of Informatics Tokyo Japan E.L. Ginzton Laboratory Stanford University Stanford CA Department of Information and Communication Engineering University of Tokyo Tokyo Japan National Institute of Informatics Stanford University University of Tokyo Stanford University Applied Physics and Electrical Engineering National Institute of Informatics NTT R and D JST CREST Program on Quantum Information

A major challenge in the implementation of quantum computers is mitigating the impact of undesired couplings with the environment that lead to decoherence. Here, we discuss an error-avoiding strategy that is based upon freedoms inherent in decomposing a quantum algorithm into fundamental gates. Although this approach is specific to a particular algorithm and a collective noise model, it does not the require complicated encodings or significant additional qubit resources of more general error-correcting codes. This paper also includes an overview of quantum computation, including a discussion of the quantum search algorithm. © 2006 National Instiute of informatics.

关键词： Quantum theory

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Semantic atomicity and multilinguality in the medical domain: Design considerations for the MORPHOSAURUS Subword Lexicon 5

Semantic atomicity and multilinguality in the medical domain...

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5th International Conference on Language Resources and Evaluation, LREC 2006

作者： Schulz, Stefan Markó, Kornél Daumke, Philipp Hahn, Udo Hanser, Susanne Nohama, Percy De Andrade, Roosewelt Leite Pacheco, Edson Romacker, Martin Department of Medical Informatics Freiburg University Hospital Freiburg Germany Health Informatics Laboratory Paraná Catholic University Curitiba Brazil Graduate Program in Electrical Engineering and Industrial Informatics CEFET-PR Curitiba Brazil Text Mining in Life Sciences Informatics Novartis Basel Switzerland Lab. Jena Germany

We present the lexico-semantic foundations underlying a multilingual lexicon the entries of which are constituted by so-called subwords. These subwords reflect semantic atomicity constraints in the medical domain which diverge from canonical lexicological understanding in NLP. We focus here on criteria to identify and delimit reasonable subword units, to group them into functionally adequate synonymy classes and to relate them by two types of lexical relations. The lexicon we implemented on the basis of these considerations forms the lexical backbone for MORPHOSAURUS, a cross-language document retrieval engine for the medical domain.

关键词： Semantics

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Importance and measurement of univariance in high dimensional model representation for multivariate analysis

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WSEAS Transactions on Computers 2006年第9期5卷 1788-1794页

作者： Demiralp, Metin Computational Science and Engineering Program Informatics Institute Istanbul Technical University Maslak 34469 Istanbul Turkey

High Dimensional Model Representation (HDMR) presents the possibility to measure how constant, how constant, how univariate, how bivariate (and so on) a given uniform discrete multivariate data or the multivariate function under consideration of HDMR is. Amongst these measurements the most important one is the one for univariance since univariance means additive separability which is the best thing to facilitate the computations in computers. In this paper we define the HDMR's univariance level for a given discrete data. We discuss the possibility of increasing univariance by using certain mappings although the details will not be explicitly given. The basic tool to this end is the recently developed Logarithmic High Dimensional Model Representation and related issues.

关键词： Mathematical models

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Illustrative implementations to show how logarithm based high dimensional model representation works for various functions structures

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WSEAS Transactions on Computers 2006年第6期5卷 1339-1344页

作者： Demiralp, Metin Computational Science and Engineering Program Informatics Institute Istanbul Technical University Maslak 34469 Istanbul Turkey

This paper is aimed at the illustration of how a recently proposed logarithm based high dimensional model representation (HDMR) works on the functions which have different structures. The main focus of the paper is on the dominantly multiplicative functions. Since the logarithm converts multiplicativity to additivity what we expect from this new representation is the sufficiency of less number of these new HDMR components than the number of components of plain High Dimensional Model Representation which works well for dominantly additive functions. In implementations we use MuPAD Computer Algebra System to have any desired precision in calculations and to use its symbolic programming nature. We do not use continuous functions instead we take discrete data about the function under consideration. However these data is produced from continuous functions for illustrative purposes. The comparison of the given function values and the values evaluated by truncated Logarithm Based HDMR.

关键词： Computer graphics

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