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  1. Genome wide and cross species comparisons of amino acid repeats is an intriguing problem in biology mainly due to the highly polymorphic nature and diverse functions of amino acid repeats. Innate protein repea...

    Authors: Mridul K Kalita, Gowthaman Ramasamy, Sekhar Duraisamy, Virander S Chauhan and Dinesh Gupta
    Citation: BMC Bioinformatics 2006 7:336
  2. Microarrays are routinely used to assess mRNA transcript levels on a genome-wide scale. Large amount of microarray datasets are now available in several databases, and new experiments are constantly being perf...

    Authors: Mattia Pelizzola, Norman Pavelka, Maria Foti and Paola Ricciardi-Castagnoli
    Citation: BMC Bioinformatics 2006 7:335
  3. Word sense disambiguation (WSD) is critical in the biomedical domain for improving the precision of natural language processing (NLP), text mining, and information retrieval systems because ambiguous words neg...

    Authors: Hua Xu, Marianthi Markatou, Rositsa Dimova, Hongfang Liu and Carol Friedman
    Citation: BMC Bioinformatics 2006 7:334
  4. DNA microarrays are popular tools for measuring gene expression of biological samples. This ever increasing popularity is ensuring that a large number of microarray studies are conducted, many of which with da...

    Authors: Mathieu Miron, Owen Z Woody, Alexandre Marcil, Carl Murie, Robert Sladek and Robert Nadon
    Citation: BMC Bioinformatics 2006 7:333
  5. Gene regulation and metabolic reactions are two primary activities of life. Although many works have been dedicated to study each system, the coupling between them is less well understood. To bridge this gap, ...

    Authors: Chen-Hsiang Yeang and Martin Vingron
    Citation: BMC Bioinformatics 2006 7:332
  6. Comparison of large protein datasets has become a standard task in bioinformatics. Typically researchers wish to know whether one group of proteins is significantly enriched in certain annotation attributes or...

    Authors: Thorsten Schmidt and Dmitrij Frishman
    Citation: BMC Bioinformatics 2006 7:331
  7. A complete understanding of the regulatory mechanisms of gene expression is the next important issue of genomics. Many bioinformaticians have developed methods and algorithms for predicting transcriptional reg...

    Authors: Seon-Young Kim and YongSung Kim
    Citation: BMC Bioinformatics 2006 7:330
  8. Quantitative descriptions of amino acid similarity, expressed as probabilistic models of evolutionary interchangeability, are central to many mainstream bioinformatic procedures such as sequence alignment, hom...

    Authors: Blazej Bulka, Marie desJardins and Stephen J Freeland
    Citation: BMC Bioinformatics 2006 7:329
  9. ESTs are a tremendous resource for determining the exon-intron structures of genes, but even extensive EST sequencing tends to leave many exons and genes untouched. Gene prediction systems based exclusively on...

    Authors: Chaochun Wei and Michael R Brent
    Citation: BMC Bioinformatics 2006 7:327
  10. The aim of protein design is to predict amino-acid sequences compatible with a given target structure. Traditionally envisioned as a purely thermodynamic question, this problem can also be understood in a wide...

    Authors: Claudia L Kleinman, Nicolas Rodrigue, Cécile Bonnard, Hervé Philippe and Nicolas Lartillot
    Citation: BMC Bioinformatics 2006 7:326
  11. The development and testing of functions for the modeling of protein energetics is an important part of current research aimed at understanding protein structure and function. Knowledge-based mean force potent...

    Authors: Qiwen Dong, Xiaolong Wang and Lei Lin
    Citation: BMC Bioinformatics 2006 7:324
  12. The reliable dissection of large proteins into structural domains represents an important issue for structural genomics/proteomics projects. To provide a practical approach to this issue, we tested the ability...

    Authors: Satoshi Miyazaki, Yutaka Kuroda and Shigeyuki Yokoyama
    Citation: BMC Bioinformatics 2006 7:323
  13. The Lepidoptera Spodoptera frugiperda is a pest which causes widespread economic damage on a variety of crop plants. It is also well known through its famous Sf9 cell line which is used for numerous heterologous ...

    Authors: Vincent Nègre, Thierry Hôtelier, Anne-Nathalie Volkoff, Sylvie Gimenez, François Cousserans, Kazuei Mita, Xavier Sabau, Janick Rocher, Miguel López-Ferber, Emmanuelle d'Alençon, Pascaline Audant, Cécile Sabourault, Vincent Bidegainberry, Frédérique Hilliou and Philippe Fournier
    Citation: BMC Bioinformatics 2006 7:322
  14. It has recently been demonstrated that organism identifications can be recovered from mass spectra using various methods including base-specific fragmentation of nucleic acids. Because mass spectrometry is ext...

    Authors: George W Jackson, Roger J McNichols, George E Fox and Richard C Willson
    Citation: BMC Bioinformatics 2006 7:321
  15. Due to the large number of genes in a typical microarray dataset, feature selection looks set to play an important role in reducing noise and computational cost in gene expression-based tissue classification w...

    Authors: Chia Huey Ooi, Madhu Chetty and Shyh Wei Teng
    Citation: BMC Bioinformatics 2006 7:320
  16. In the post-genomic era, systems-level studies are being performed that seek to explain complex biological systems by integrating diverse resources from fields such as genomics, proteomics or transcriptomics. ...

    Authors: Julie D Thompson, Arnaud Muller, Andrew Waterhouse, Jim Procter, Geoffrey J Barton, Frédéric Plewniak and Olivier Poch
    Citation: BMC Bioinformatics 2006 7:318
  17. The main aim of this study was to develop and implement an algorithm for the rapid, accurate and automated identification of paths leading from buried protein clefts, pockets and cavities in dynamic and static...

    Authors: Martin Petřek, Michal Otyepka, Pavel Banáš, Pavlína Košinová, Jaroslav Koča and Jiří Damborský
    Citation: BMC Bioinformatics 2006 7:316
  18. Gene function analysis often requires a complex and laborious sequence of laboratory and computer-based experiments. Choosing an effective experimental design generally results from hypotheses derived from pri...

    Authors: Oliver Laule, Matthias Hirsch-Hoffmann, Tomas Hruz, Wilhelm Gruissem and Philip Zimmermann
    Citation: BMC Bioinformatics 2006 7:311
  19. Many biological processes involve the physical interaction between protein domains. Understanding these functional associations requires knowledge of the molecular structure. Experimental investigations though...

    Authors: Stefano Lise, Alice Walker-Taylor and David T Jones
    Citation: BMC Bioinformatics 2006 7:310
  20. White Spot Syndrome Virus, a member of the virus family Nimaviridae, is a large dsDNA virus infecting shrimp and other crustacean species. Although limited information is available on the mode of transcription, p...

    Authors: Hendrik Marks, Xin-Ying Ren, Hans Sandbrink, Mariëlle CW van Hulten and Just M Vlak
    Citation: BMC Bioinformatics 2006 7:309
  21. Gene expression microarrays allow the quantification of transcript accumulation for many or all genes in a genome. This technology has been utilized for a range of investigations, from assessments of gene regu...

    Authors: Daniel J Kliebenstein, Marilyn AL West, Hans van Leeuwen, Olivier Loudet, RW Doerge and Dina A St Clair
    Citation: BMC Bioinformatics 2006 7:308
  22. There are several isolated tools for partial analysis of microarray expression data. To provide an integrative, easy-to-use and automated toolkit for the analysis of Affymetrix microarray expression data we ha...

    Authors: Gabriela G Loots, Patrick SG Chain, Shalini Mabery, Amy Rasley, Emilio Garcia and Ivan Ovcharenko
    Citation: BMC Bioinformatics 2006 7:307
  23. REX1 and REX2 are protein components of the RNA editing complex (the editosome) and function as exouridylylases. The exact roles of REX1 and REX2 in the editosome are unclear and the consequences of the presen...

    Authors: I Saira Mian, Elizabeth A Worthey and Reza Salavati
    Citation: BMC Bioinformatics 2006 7:305
  24. The number of sequences compiled in many genome projects is growing exponentially, but most of them have not been characterized experimentally. An automatic annotation scheme must be in an urgent need to reduc...

    Authors: Shih-Hau Chiu, Chien-Chi Chen, Gwo-Fang Yuan and Thy-Hou Lin
    Citation: BMC Bioinformatics 2006 7:304
  25. Single Nucleotide Polymorphisms (SNPs) are the most common type of polymorphisms found in the human genome. Effective genetic association studies require the identification of sets of tag SNPs that capture as ...

    Authors: Pierre Nicolas, Fengzhu Sun and Lei M Li
    Citation: BMC Bioinformatics 2006 7:303
  26. Gene Ontology (GO) is a standard vocabulary of functional terms and allows for coherent annotation of gene products. These annotations provide a basis for new methods that compare gene products regarding their...

    Authors: Andreas Schlicker, Francisco S Domingues, Jörg Rahnenführer and Thomas Lengauer
    Citation: BMC Bioinformatics 2006 7:302
  27. The accuracy of protein secondary structure prediction has steadily improved over the past 30 years. Now many secondary structure prediction methods routinely achieve an accuracy (Q3) of about 75%. We believe ...

    Authors: Scott Montgomerie, Shan Sundararaj, Warren J Gallin and David S Wishart
    Citation: BMC Bioinformatics 2006 7:301
  28. Recently, a large number of methods for the analysis of microarray data have been proposed but there are few comparisons of their relative performances. By using so-called spike-in experiments, it is possible ...

    Authors: Patrik Rydén, Henrik Andersson, Mattias Landfors, Linda Näslund, Blanka Hartmanová, Laila Noppa and Anders Sjöstedt
    Citation: BMC Bioinformatics 2006 7:300
  29. The genomic information of a species allows for the genome-scale reconstruction of its metabolic capacity. Such a metabolic reconstruction gives support to metabolic engineering, but also to integrative bioinf...

    Authors: Richard A Notebaart, Frank HJ van Enckevort, Christof Francke, Roland J Siezen and Bas Teusink
    Citation: BMC Bioinformatics 2006 7:296
  30. One of the important goals of microarray research is the identification of genes whose expression is considerably higher or lower in some tissues than in others. We would like to have ways of identifying such ...

    Authors: Koji Kadota, Jiazhen Ye, Yuji Nakai, Tohru Terada and Kentaro Shimizu
    Citation: BMC Bioinformatics 2006 7:294
  31. The increasing number of known protein structures provides valuable information about pharmaceutical targets. Drug binding sites are identifiable and suitable lead compounds can be proposed. The flexibility of...

    Authors: Stefan Günther, Christian Senger, Elke Michalsky, Andrean Goede and Robert Preissner
    Citation: BMC Bioinformatics 2006 7:293
  32. Non-coding DNA sequences comprise a very large proportion of the total genomic content of mammals, most other vertebrates, many invertebrates, and most plants. Unraveling the functional significance of non-cod...

    Authors: Jun Wang, Peter D Keightley and Toby Johnson
    Citation: BMC Bioinformatics 2006 7:292
  33. Genomic functional information is valuable for biomedical research. However, such information frequently needs to be extracted from the scientific literature and structured in order to be exploited by automati...

    Authors: Marco Masseroli, Halil Kilicoglu, François-Michel Lang and Thomas C Rindflesch
    Citation: BMC Bioinformatics 2006 7:291
  34. An alternative to standard approaches to uncover biologically meaningful structures in micro array data is to treat the data as a blind source separation (BSS) problem. BSS attempts to separate a mixture of si...

    Authors: Attila Frigyesi, Srinivas Veerla, David Lindgren and Mattias Höglund
    Citation: BMC Bioinformatics 2006 7:290
  35. Migration is an important aspect of cellular behaviour and is therefore widely studied in cell biology. Numerous components are known to participate in this process in a highly dynamic manner. In order to obta...

    Authors: Lennart Martens, Geert Monsieur, Christophe Ampe, Kris Gevaert and Joël Vandekerckhove
    Citation: BMC Bioinformatics 2006 7:289
  36. In order to maintain the most comprehensive structural annotation databases we must carry out regular updates for each proteome using the latest profile-profile fold recognition methods. The ability to carry o...

    Authors: Liam J McGuffin, Richard T Smith, Kevin Bryson, Søren-Aksel Sørensen and David T Jones
    Citation: BMC Bioinformatics 2006 7:288

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