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  1. 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:

  2. 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

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  3. 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

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  4. 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

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  5. 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

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  6. 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

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  7. 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:

  8. 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:

  9. 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:

  10. 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

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  11. 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

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  12. 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

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  13. 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

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  14. 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:

  15. 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

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  16. 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

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  17. 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

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  18. 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

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  19. 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:

  20. 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:

  21. 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:

  22. 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

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  23. Very few analytical approaches have been reported to resolve the variability in microarray measurements stemming from sample heterogeneity. For example, tissue samples used in cancer studies are usually contam...

    Authors: Harri Lähdesmäki, llya Shmulevich, Valerie Dunmire, Olli Yli-Harja and Wei Zhang

    Citation: BMC Bioinformatics 2005 6:54

    Content type: Methodology article

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  24. Gene duplication and gene loss during the evolution of eukaryotes have hindered attempts to estimate phylogenies and divergence times of species. Although current methods that identify clusters of orthologous ...

    Authors: Jaime E Blair, Prachi Shah and S Blair Hedges

    Citation: BMC Bioinformatics 2005 6:53

    Content type: Research article

    Published on:

  25. Normal mode analysis (NMA) has become the method of choice to investigate the slowest motions in macromolecular systems. NMA is especially useful for large biomolecular assemblies, such as transmembrane channe...

    Authors: Siv Midtun Hollup, Gisle Salensminde and Nathalie Reuter

    Citation: BMC Bioinformatics 2005 6:52

    Content type: Software

    Published on:

  26. High throughput microarray analyses result in many differentially expressed genes that are potentially responsible for the biological process of interest. In order to identify biological similarities between g...

    Authors: Blaise TF Alako, Antoine Veldhoven, Sjozef van Baal, Rob Jelier, Stefan Verhoeven, Ton Rullmann, Jan Polman and Guido Jenster

    Citation: BMC Bioinformatics 2005 6:51

    Content type: Software

    Published on:

  27. Proteochemometrics is a new methodology that allows prediction of protein function directly from real interaction measurement data without the need of 3D structure information. Several reported proteochemometr...

    Authors: Eva Freyhult, Peteris Prusis, Maris Lapinsh, Jarl ES Wikberg, Vincent Moulton and Mats G Gustafsson

    Citation: BMC Bioinformatics 2005 6:50

    Content type: Research article

    Published on:

  28. Popular methods to reconstruct molecular phylogenies are based on multiple sequence alignments, in which addition or removal of data may change the resulting tree topology. We have sought a representation of h...

    Authors: Olivier Bastien, Philippe Ortet, Sylvaine Roy and Eric Maréchal

    Citation: BMC Bioinformatics 2005 6:49

    Content type: Research article

    Published on:

  29. Many three-dimensional (3D) images are routinely collected in biomedical research and a number of digital atlases with associated anatomical and other information have been published. A number of tools are ava...

    Authors: Guangjie Feng, Nick Burton, Bill Hill, Duncan Davidson, Janet Kerwin, Mark Scott, Susan Lindsay and Richard Baldock

    Citation: BMC Bioinformatics 2005 6:47

    Content type: Software

    Published on:

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