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  1. The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for pro...

    Authors: Jan Kosinski, Marcin Feder and Janusz M Bujnicki

    Citation: BMC Bioinformatics 2005 6:172

    Content type: Research article

    Published on:

  2. Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evol...

    Authors: H Chiapello, I Bourgait, F Sourivong, G Heuclin, A Gendrault-Jacquemard, M-A Petit and M El Karoui

    Citation: BMC Bioinformatics 2005 6:171

    Content type: Research article

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  3. We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the contex...

    Authors: Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W Kane, Mark Reimers, Robert M Stephens, David Bryant, Stanley K Burt, Eldad Elnekave, Danielle M Hari, Thomas A Wynn, Charlotte Cunningham-Rundles, Donn M Stewart, David Nelson…

    Citation: BMC Bioinformatics 2005 6:168

    Content type: Software

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  4. Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Sec-dependent translocation pathway. To complemen...

    Authors: Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak

    Citation: BMC Bioinformatics 2005 6:167

    Content type: Methodology article

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  5. Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microa...

    Authors: Thomas Breslin, Morten Krogh, Carsten Peterson and Carl Troein

    Citation: BMC Bioinformatics 2005 6:163

    Content type: Research article

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  6. Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel....

    Authors: Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt and Peter Lichter

    Citation: BMC Bioinformatics 2005 6:161

    Content type: Software

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  7. All eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and t...

    Authors: Per Stenberg, Fredrik Pettersson, Anja O Saura, Anders Berglund and Jan Larsson

    Citation: BMC Bioinformatics 2005 6:158

    Content type: Research article

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  8. The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very efficient in general data mining tasks. We explo...

    Authors: Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen and Tapio Salakoski

    Citation: BMC Bioinformatics 2005 6:157

    Content type: Research article

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  9. Recent advances in molecular biology techniques provide an opportunity for developing detailed mathematical models of biological processes. An iterative scheme is introduced for model identification using avai...

    Authors: Kapil G Gadkar, Rudiyanto Gunawan and Francis J Doyle III

    Citation: BMC Bioinformatics 2005 6:155

    Content type: Methodology article

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  10. The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular...

    Authors: David J Reiss, Iliana Avila-Campillo, Vesteinn Thorsson, Benno Schwikowski and Timothy Galitski

    Citation: BMC Bioinformatics 2005 6:154

    Content type: Software

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  11. Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of RNA secondary structures with stochastic c...

    Authors: Janina Reeder, Peter Steffen and Robert Giegerich

    Citation: BMC Bioinformatics 2005 6:153

    Content type: Research article

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  12. Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed bas...

    Authors: Deepak Sarda, Gek Huey Chua, Kuo-Bin Li and Arun Krishnan

    Citation: BMC Bioinformatics 2005 6:152

    Content type: Research article

    Published on:

  13. Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility t...

    Authors: Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot, Séverine Degrelle, Isabelle Hue, Jean-Paul Renard, François Rodolphe and Stéphane Robin

    Citation: BMC Bioinformatics 2005 6:150

    Content type: Software

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  14. Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.

    Authors: Bob JA Schijvenaars, Barend Mons, Marc Weeber, Martijn J Schuemie, Erik M van Mulligen, Hester M Wain and Jan A Kors

    Citation: BMC Bioinformatics 2005 6:149

    Content type: Research article

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  15. In the clinical context, samples assayed by microarray are often classified by cell line or tumour type and it is of interest to discover a set of genes that can be used as class predictors. The leukemia datas...

    Authors: Thanyaluk Jirapech-Umpai and Stuart Aitken

    Citation: BMC Bioinformatics 2005 6:148

    Content type: Research article

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  16. Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are f...

    Authors: Stephen E Diener, Thomas D Houfek, Sam E Kalat, DE Windham, Mark Burke, Charles Opperman and Ralph A Dean

    Citation: BMC Bioinformatics 2005 6:147

    Content type: Software

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  17. To date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role...

    Authors: Perseus I Missirlis, Carri-Lyn R Mead, Stefanie L Butland, BF Francis Ouellette, Rebecca S Devon, Blair R Leavitt and Robert A Holt

    Citation: BMC Bioinformatics 2005 6:145

    Content type: Database

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  18. Gene set enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets and ranks of genes to identify significant biological changes in microarray data sets. GSEA is especially...

    Authors: Seon-Young Kim and David J Volsky

    Citation: BMC Bioinformatics 2005 6:144

    Content type: Methodology article

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  19. Computational Biology needs computer-readable information records. Increasingly, meta-analysed and pre-digested information is being used in the follow up of high throughput experiments and other investigation...

    Authors: Barend Mons

    Citation: BMC Bioinformatics 2005 6:142

    Content type: Commentary

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  20. Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be r...

    Authors: Peter Murray-Rust, John BO Mitchell and Henry S Rzepa

    Citation: BMC Bioinformatics 2005 6:141

    Content type: Commentary

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  21. A number of algorithms for steady state analysis of metabolic networks have been developed over the years. Of these, Elementary Mode Analysis (EMA) has proven especially useful. Despite its low user-friendline...

    Authors: Roland Schwarz, Patrick Musch, Axel von Kamp, Bernd Engels, Heiner Schirmer, Stefan Schuster and Thomas Dandekar

    Citation: BMC Bioinformatics 2005 6:135

    Content type: Software

    Published on:

  22. Codon substitution probabilities are used in many types of molecular evolution studies such as determining Ka/Ks ratios, creating ancestral DNA sequences or aligning coding DNA. Until the recent dramatic incre...

    Authors: Adrian Schneider, Gina M Cannarozzi and Gaston H Gonnet

    Citation: BMC Bioinformatics 2005 6:134

    Content type: Research article

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  23. Despite the continuous production of genome sequence for a number of organisms, reliable, comprehensive, and cost effective gene prediction remains problematic. This is particularly true for genomes for which ...

    Authors: Eduardo Eyras, Alexandre Reymond, Robert Castelo, Jacqueline M Bye, Francisco Camara, Paul Flicek, Elizabeth J Huckle, Genis Parra, David D Shteynberg, Carine Wyss, Jane Rogers, Stylianos E Antonarakis, Ewan Birney, Roderic Guigo and Michael R Brent

    Citation: BMC Bioinformatics 2005 6:131

    Content type: Research article

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  24. Phylogenetic footprinting is the identification of functional regions of DNA by their evolutionary conservation. This is achieved by comparing orthologous regions from multiple species and identifying the DNA ...

    Authors: Matthew J Wakefield, Peter Maxwell and Gavin A Huttley

    Citation: BMC Bioinformatics 2005 6:130

    Content type: Software

    Published on:

  25. Global regulatory mechanisms involving chromatin assembly and remodelling in the promoter regions of genes is implicated in eukaryotic transcription control especially for genes subjected to spatial and tempor...

    Authors: Mythily Ganapathi, Pragya Srivastava, Sushanta Kumar Das Sutar, Kaushal Kumar, Dipayan Dasgupta, Gajinder Pal Singh, Vani Brahmachari and Samir K Brahmachari

    Citation: BMC Bioinformatics 2005 6:126

    Content type: Research article

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  26. Our approach to Task 1A was inspired by Tanabe and Wilbur's ABGene system [1, 2]. Like Tanabe and Wilbur, we approached the problem as one of part-of-speech tagging, adding a GENE tag to the standard tag set. Whe...

    Authors: Shuhei Kinoshita, K Bretonnel Cohen, Philip V Ogren and Lawrence Hunter

    Citation: BMC Bioinformatics 2005 6(Suppl 1):S4

    Content type: Report

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 1

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