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  1. G- Protein coupled receptors (GPCRs) comprise the largest group of eukaryotic cell surface receptors with great pharmacological interest. A broad range of native ligands interact and activate GPCRs, leading to...

    Authors: Nikolaos G Sgourakis, Pantelis G Bagos, Panagiotis K Papasaikas and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2005 6:104
    Content type: Research article Published on:

  4. Microarray analysis has become a widely used technique for the study of gene-expression patterns on a genomic scale. As more and more laboratories are adopting microarray technology, there is a need for powerf...

    Authors: Michael Maurer, Robert Molidor, Alexander Sturn, Juergen Hartler, Hubert Hackl, Gernot Stocker, Andreas Prokesch, Marcel Scheideler and Zlatko Trajanoski
    Citation: BMC Bioinformatics 2005 6:101
    Content type: Software Published on:

  10. To facilitate efficient selection and the prioritization of candidate complex disease susceptibility genes for association analysis, increasingly comprehensive annotation tools are essential to integrate, visu...

    Authors: Judith E Stenger, Hong Xu, Carol Haynes, Elizabeth R Hauser, Margaret Pericak-Vance, Pascal J Goldschmidt-Clermont and Jeffery M Vance
    Citation: BMC Bioinformatics 2005 6:95
    Content type: Software Published on:

  11. Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open readi...

    Authors: Nicole Donofrio, Ravi Rajagopalon, Douglas Brown, Stephen Diener, Donald Windham, Shelly Nolin, Anna Floyd, Thomas Mitchell, Natalia Galadima, Sara Tucker, Marc J Orbach, Gayatri Patel, Mark Farman, Vishal Pampanwar, Cari Soderlund, Yong-Hwan Lee…
    Citation: BMC Bioinformatics 2005 6:94
    Content type: Software Published on:

  12. BLAST is one of the most common and useful tools for Genetic Research. This paper describes a software application we have termed Windows .NET Distributed Basic Local Alignment Search Toolkit (W.ND-BLAST), whi...

    Authors: Scot E Dowd, Joaquin Zaragoza, Javier R Rodriguez, Melvin J Oliver and Paxton R Payton
    Citation: BMC Bioinformatics 2005 6:93
    Content type: Software Published on:

  14. We have developed the program PERMOL for semi-automated homology modeling of proteins. It is based on restrained molecular dynamics using a simulated annealing protocol in torsion angle space. As main restrain...

    Authors: Andreas Möglich, Daniel Weinfurtner, Till Maurer, Wolfram Gronwald and Hans Robert Kalbitzer
    Citation: BMC Bioinformatics 2005 6:91
    Content type: Software Published on:

  15. Most current DNA diagnostic tests for identifying organisms use specific oligonucleotide probes that are complementary in sequence to, and hence only hybridise with the DNA of one target species. By contrast, ...

    Authors: Mark J Gibbs, John S Armstrong and Adrian J Gibbs
    Citation: BMC Bioinformatics 2005 6:90
    Content type: Methodology article Published on:

  18. Computational methods for problem solving need to interleave information access and algorithm execution in a problem-specific workflow. The structures of these workflows are defined by a scaffold of syntactic, se...

    Authors: Alexander Garcia Castro, Samuel Thoraval, Leyla J Garcia and Mark A Ragan
    Citation: BMC Bioinformatics 2005 6:87
    Content type: Methodology article Published on:

  19. Many efforts in microarray data analysis are focused on providing tools and methods for the qualitative analysis of microarray data. HDBStat! (High-Dimensional Biology-Statistics) is a software package designe...

    Authors: Prinal Trivedi, Jode W Edwards, Jelai Wang, Gary L Gadbury, Vinodh Srinivasasainagendra, Stanislav O Zakharkin, Kyoungmi Kim, Tapan Mehta, Jacob PL Brand, Amit Patki, Grier P Page and David B Allison
    Citation: BMC Bioinformatics 2005 6:86
    Content type: Software Published on:

  20. Array CGH (Comparative Genomic Hybridisation) is a molecular cytogenetic technique for the genome wide detection of chromosomal imbalances. It is based on the co-hybridisation of differentially labelled test a...

    Authors: Wei Chen, Fikret Erdogan, H-Hilger Ropers, Steffen Lenzner and Reinhard Ullmann
    Citation: BMC Bioinformatics 2005 6:85
    Content type: Software Published on:

  21. Transcription factor binding site (TFBS) prediction is a difficult problem, which requires a good scoring function to discriminate between real binding sites and background noise. Many scoring functions have b...

    Authors: Markus Friberg, Peter von Rohr and Gaston Gonnet
    Citation: BMC Bioinformatics 2005 6:84
    Content type: Research article Published on:

  22. Two central problems in computational biology are the determination of the alignment and phylogeny of a set of biological sequences. The traditional approach to this problem is to first build a multiple alignm...

    Authors: Gerton Lunter, István Miklós, Alexei Drummond, Jens Ledet Jensen and Jotun Hein
    Citation: BMC Bioinformatics 2005 6:83
    Content type: Methodology article Published on:

  23. Detection of sequence homologues represents a challenging task that is important for the discovery of protein families and the reliable application of automatic annotation methods. The presence of domains in p...

    Authors: Igor V Tetko, Axel Facius, Andreas Ruepp and Hans-Werner Mewes
    Citation: BMC Bioinformatics 2005 6:82
    Content type: Methodology article Published on:

  24. Structural and functional research often requires the computation of sets of protein structures based on certain properties of the proteins, such as sequence features, fold classification, or functional annota...

    Authors: Silke Trißl, Kristian Rother, Heiko Müller, Thomas Steinke, Ina Koch, Robert Preissner, Cornelius Frömmel and Ulf Leser
    Citation: BMC Bioinformatics 2005 6:81
    Content type: Database Published on:

  25. There are currently a number of competing techniques for low-level processing of oligonucleotide array data. The choice of technique has a profound effect on subsequent statistical analyses, but there is no me...

    Authors: Alexander Ploner, Lance D Miller, Per Hall, Jonas Bergh and Yudi Pawitan
    Citation: BMC Bioinformatics 2005 6:80
    Content type: Methodology article Published on:

  26. Cis-regulatory modules are combinations of regulatory elements occurring in close proximity to each other that control the spatial and temporal expression of genes. The ability to identify them in a genome-wide m...

    Authors: Voichita D Marinescu, Isaac S Kohane and Alberto Riva
    Citation: BMC Bioinformatics 2005 6:79
    Content type: Software Published on:

  27. Online Mendelian Inheritance in Man (OMIM) is a computerized database of information about genes and heritable traits in human populations, based on information reported in the scientific literature. Our objec...

    Authors: Chris D Bajdik, Byron Kuo, Shawn Rusaw, Steven Jones and Angela Brooks-Wilson
    Citation: BMC Bioinformatics 2005 6:78
    Content type: Software Published on:

  36. We observe two trends in bioinformatics: (i) analyses are increasing in complexity, often requiring several applications to be run as a workflow; and (ii) multiple CPU clusters and Grids are available to more ...

    Authors: Francis Tang, Ching Lian Chua, Liang-Yoong Ho, Yun Ping Lim, Praveen Issac and Arun Krishnan
    Citation: BMC Bioinformatics 2005 6:69
    Content type: Software Published on:

  39. We present a complete re-implementation of the segment-based approach to multiple protein alignment that contains a number of improvements compared to the previous version 2.2 of DIALIGN. This previous version is...

    Authors: Amarendran R Subramanian, Jan Weyer-Menkhoff, Michael Kaufmann and Burkhard Morgenstern
    Citation: BMC Bioinformatics 2005 6:66
    Content type: Research article Published on:

  40. Microscopists are familiar with many blemishes that fluorescence images can have due to dust and debris, glass flaws, uneven distribution of fluids or surface coatings, etc. Microarray scans show similar artef...

    Authors: Mayte Suárez-Fariñas, Asifa Haider and Knut M Wittkowski
    Citation: BMC Bioinformatics 2005 6:65
    Content type: Methodology article Published on:

  44. Taxon specific hybridization probes in combination with a variety of commonly used hybridization formats nowadays are standard tools in microbial identification. A frequently applied technology, fluorescence in s...

    Authors: Yadhu Kumar, Ralf Westram, Sebastian Behrens, Bernhard Fuchs, Frank Oliver Glöckner, Rudolf Amann, Harald Meier and Wolfgang Ludwig
    Citation: BMC Bioinformatics 2005 6:61
    Content type: Software Published on:

  47. Development of robust and efficient methods for analyzing and interpreting high dimension gene expression profiles continues to be a focus in computational biology. The accumulated experiment evidence supports...

    Authors: Zheng Guo, Tianwen Zhang, Xia Li, Qi Wang, Jianzhen Xu, Hui Yu, Jing Zhu, Haiyun Wang, Chenguang Wang, Eric J Topol, Qing Wang and Shaoqi Rao
    Citation: BMC Bioinformatics 2005 6:58
    Content type: Methodology article Published on:

  48. As the use of microarray technology becomes more prevalent it is not unusual to find several laboratories employing the same microarray technology to identify genes related to the same condition in the same sp...

    Authors: John R Stevens and RW Doerge
    Citation: BMC Bioinformatics 2005 6:57
    Content type: Methodology article Published on:

  50. Regions of interest identified through genetic linkage studies regularly exceed 30 centimorgans in size and can contain hundreds of genes. Traditionally this number is reduced by matching functional annotation...

    Authors: Euan A Adie, Richard R Adams, Kathryn L Evans, David J Porteous and Ben S Pickard
    Citation: BMC Bioinformatics 2005 6:55
    Content type: Research article Published on:

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