Skip to main content


Page 234 of 242

  1. 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
  2. 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
  3. 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
  4. 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
  5. 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
  6. 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
  7. 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
  8. 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
  9. 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
  10. 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
  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. 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
  27. 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
  28. wFleaBase is a database with the necessary infrastructure to curate, archive and share genetic, molecular and functional genomic data and protocols for an emerging model organism, the microcrustacean Daphnia. Com...

    Authors: John K Colbourne, Vasanth R Singan and Don G Gilbert
    Citation: BMC Bioinformatics 2005 6:45

Featured videos

View featured videos from across the BMC-series journals

Annual Journal Metrics

  • 2022 Citation Impact
    3.0 - 2-year Impact Factor
    4.3 - 5-year Impact Factor
    0.938 - SNIP (Source Normalized Impact per Paper)
    1.100 - SJR (SCImago Journal Rank)

    2022 Speed
    12 days submission to first editorial decision for all manuscripts (Median)
    135 days submission to accept (Median)

    2022 Usage
    14,511 Altmetric mentions

Sign up for article alerts and news from this journal