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  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. The biological information in genomic expression data can be understood, and computationally extracted, in the context of systems of interacting molecules. The automation of this information extraction require...

    Authors: Bruz Marzolf, Eric W Deutsch, Patrick Moss, David Campbell, Michael H Johnson and Timothy Galitski
    Citation: BMC Bioinformatics 2006 7:286
  10. Direct synthesis of genes is rapidly becoming the most efficient way to make functional genetic constructs and enables applications such as codon optimization, RNAi resistant genes and protein engineering. Her...

    Authors: Alan Villalobos, Jon E Ness, Claes Gustafsson, Jeremy Minshull and Sridhar Govindarajan
    Citation: BMC Bioinformatics 2006 7:285
  11. Many important agricultural traits such as weight gain, milk fat content and intramuscular fat (marbling) in cattle are quantitative traits. Most of the information on these traits has not previously been inte...

    Authors: Pavana Polineni, Prathyusha Aragonda, Suresh R Xavier, Richard Furuta and David L Adelson
    Citation: BMC Bioinformatics 2006 7:283
  12. Identification of minor cell populations, e.g. leukemic blasts within blood samples, has become increasingly important in therapeutic disease monitoring. Modern flow cytometers enable researchers to reliably m...

    Authors: Joern Toedling, Peter Rhein, Richard Ratei, Leonid Karawajew and Rainer Spang
    Citation: BMC Bioinformatics 2006 7:282
  13. The genome sequencing projects have shown our limited knowledge regarding gene function, e.g. S. cerevisiae has 5–6,000 genes of which nearly 1,000 have an uncertain function. Their gross influence on the behavio...

    Authors: Irena Spasić, Warwick B Dunn, Giles Velarde, Andy Tseng, Helen Jenkins, Nigel Hardy, Stephen G Oliver and Douglas B Kell
    Citation: BMC Bioinformatics 2006 7:281
  14. The learning of global genetic regulatory networks from expression data is a severely under-constrained problem that is aided by reducing the dimensionality of the search space by means of clustering genes int...

    Authors: David J Reiss, Nitin S Baliga and Richard Bonneau
    Citation: BMC Bioinformatics 2006 7:280
  15. Identifying functional elements, such as transcriptional factor binding sites, is a fundamental step in reconstructing gene regulatory networks and remains a challenging issue, largely due to limited availabil...

    Authors: Weichun Huang, David M Umbach, Uwe Ohler and Leping Li
    Citation: BMC Bioinformatics 2006 7:279
  16. Proteins are comprised of one or several building blocks, known as domains. Such domains can be classified into families according to their evolutionary origin. Whereas sequencing technologies have advanced im...

    Authors: Elon Portugaly, Amir Harel, Nathan Linial and Michal Linial
    Citation: BMC Bioinformatics 2006 7:277
  17. Agile is an iterative approach to software development that relies on strong collaboration and automation to keep pace with dynamic environments. We have successfully used agile development approaches to creat...

    Authors: David W Kane, Moses M Hohman, Ethan G Cerami, Michael W McCormick, Karl F Kuhlmman and Jeff A Byrd
    Citation: BMC Bioinformatics 2006 7:273
  18. Pseudomonas aeruginosa, an opportunistic pathogen, is often encountered in chronic lung diseases such as cystic fibrosis or chronic obstructive pneumonia, as well as acute settings like mechanical ventilation acq...

    Authors: Didier Filopon, Annabelle Mérieau, Gilles Bernot, Jean-Paul Comet, Rozenne LeBerre, Benoit Guery, Benoit Polack and Janine Guespin-Michel
    Citation: BMC Bioinformatics 2006 7:272
  19. Orthologs (genes that have diverged after a speciation event) tend to have similar function, and so their prediction has become an important component of comparative genomics and genome annotation. The gold st...

    Authors: Debra L Fulton, Yvonne Y Li, Matthew R Laird, Benjamin GS Horsman, Fiona M Roche and Fiona SL Brinkman
    Citation: BMC Bioinformatics 2006 7:270
  20. The automation of many common molecular biology techniques has resulted in the accumulation of vast quantities of experimental data. One of the major challenges now facing researchers is how to process this da...

    Authors: Jianghui Xiong, Simon Rayner, Kunyi Luo, Yinghui Li and Shanguang Chen
    Citation: BMC Bioinformatics 2006 7:268
  21. Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies ...

    Authors: Alexander Garcia Castro, Philippe Rocca-Serra, Robert Stevens, Chris Taylor, Karim Nashar, Mark A Ragan and Susanna-Assunta Sansone
    Citation: BMC Bioinformatics 2006 7:267
  22. Algorithms that locate evolutionarily conserved sequences have become powerful tools for finding functional DNA elements, including transcription factor binding sites; however, most methods do not take advanta...

    Authors: Jason Gertz, Justin C Fay and Barak A Cohen
    Citation: BMC Bioinformatics 2006 7:266
  23. Jumping alignments have recently been proposed as a strategy to search a given multiple sequence alignment A against a database. Instead of comparing a database sequence S to the multiple alignment or profile as ...

    Authors: Anne-Kathrin Schultz, Ming Zhang, Thomas Leitner, Carla Kuiken, Bette Korber, Burkhard Morgenstern and Mario Stanke
    Citation: BMC Bioinformatics 2006 7:265
  24. Array-based comparative genomic hybridization (array-CGH) is a recently developed technique for analyzing changes in DNA copy number. As in all microarray analyses, normalization is required to correct for exp...

    Authors: Pierre Neuvial, Philippe Hupé, Isabel Brito, Stéphane Liva, Élodie Manié, Caroline Brennetot, François Radvanyi, Alain Aurias and Emmanuel Barillot
    Citation: BMC Bioinformatics 2006 7:264
  25. The number of sequenced eukaryotic genomes is rapidly increasing. This means that over time it will be hard to keep supplying customised gene finders for each genome. This calls for procedures to automatically...

    Authors: Kasper Munch and Anders Krogh
    Citation: BMC Bioinformatics 2006 7:263
  26. Understanding the molecular details of protein-DNA interactions is critical for deciphering the mechanisms of gene regulation. We present a machine learning approach for the identification of amino acid residu...

    Authors: Changhui Yan, Michael Terribilini, Feihong Wu, Robert L Jernigan, Drena Dobbs and Vasant Honavar
    Citation: BMC Bioinformatics 2006 7:262
  27. Assessment of array quality is an essential step in the analysis of data from microarray experiments. Once detected, less reliable arrays are typically excluded or "filtered" from further analysis to avoid mis...

    Authors: Matthew E Ritchie, Dileepa Diyagama, Jody Neilson, Ryan van Laar, Alexander Dobrovic, Andrew Holloway and Gordon K Smyth
    Citation: BMC Bioinformatics 2006 7:261
  28. Amino acids in proteins are not used equally. Some of the differences in the amino acid composition of proteins are between species (mainly due to nucleotide composition and lifestyle) and some are between pro...

    Authors: Alberto Pasamontes and Santiago Garcia-Vallve
    Citation: BMC Bioinformatics 2006 7:257
  29. The Tissue Microarray (TMA) facilitates high-throughput analysis of hundreds of tissue specimens simultaneously. However, bottlenecks in the storage and manipulation of the data generated from TMA reviews have...

    Authors: Catherine M Conway, Deirdre O'Shea, Sallyann O'Brien, Darragh K Lawler, Graham D Dodrill, Anthony O'Grady, Helen Barrett, Christian Gulmann, Lorraine O'Driscoll, William M Gallagher, Elaine W Kay and Daniel G O'Shea
    Citation: BMC Bioinformatics 2006 7:256
  30. The identification of statistically overrepresented sequences in the upstream regions of coregulated genes should theoretically permit the identification of potential cis-regulatory elements. However, in pract...

    Authors: Jonathan M Carlson, Arijit Chakravarty, Radhika S Khetani and Robert H Gross
    Citation: BMC Bioinformatics 2006 7:254
  31. As phenotypic features derived from heritable characters, the topologies of metabolic pathways contain both phylogenetic and phenetic components. In the post-genomic era, it is possible to measure the "phyloph...

    Authors: Yong Zhang, Shaojuan Li, Geir Skogerbø, Zhihua Zhang, Xiaopeng Zhu, Zefeng Zhang, Shiwei Sun, Hongchao Lu, Baochen Shi and Runsheng Chen
    Citation: BMC Bioinformatics 2006 7:252
  32. Gene expression microarray data is notoriously subject to high signal variability. Moreover, unavoidable variation in the concentration of transcripts applied to microarrays may result in poor scaling of the s...

    Authors: Martino Barenco, Jaroslav Stark, Daniel Brewer, Daniela Tomescu, Robin Callard and Michael Hubank
    Citation: BMC Bioinformatics 2006 7:251
  33. The statistical modeling of biomedical corpora could yield integrated, coarse-to-fine views of biological phenomena that complement discoveries made from analysis of molecular sequence and profiling data. Here...

    Authors: DM Blei, K Franks, MI Jordan and IS Mian
    Citation: BMC Bioinformatics 2006 7:250
  34. A central goal of molecular biology is to understand the regulatory mechanisms of gene transcription and protein synthesis. Because of their solid basis in statistics, allowing to deal with the stochastic aspe...

    Authors: Norbert Dojer, Anna Gambin, Andrzej Mizera, Bartek Wilczyński and Jerzy Tiuryn
    Citation: BMC Bioinformatics 2006 7:249
  35. Chaos game representation of genome sequences has been used for visual representation of genome sequence patterns as well as alignment-free comparisons of sequences based on oligonucleotide frequencies. Howeve...

    Authors: Jijoy Joseph and Roschen Sasikumar
    Citation: BMC Bioinformatics 2006 7:243

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