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  1. In recent years, clustering algorithms have been effectively applied in molecular biology for gene expression data analysis. With the help of clustering algorithms such as K-means, hierarchical clustering, SOM...

    Authors: Yi Lu, Shiyong Lu, Farshad Fotouhi, Youping Deng and Susan J Brown
    Citation: BMC Bioinformatics 2004 5:172
  2. Kernel-based learning algorithms are among the most advanced machine learning methods and have been successfully applied to a variety of sequence classification tasks within the field of bioinformatics. Conven...

    Authors: Peter Meinicke, Maike Tech, Burkhard Morgenstern and Rainer Merkl
    Citation: BMC Bioinformatics 2004 5:169
  3. Motivated by a biomedical database set up by our group, we aimed to develop a generic database front-end with embedded knowledge discovery and analysis features. A major focus was the human-oriented representa...

    Authors: Dominik Seelow, Raffaello Galli, Siegrun Mebus, Hans-Peter Sperling, Hans Lehrach and Silke Sperling
    Citation: BMC Bioinformatics 2004 5:168
  4. For the purposes of finding and aligning noncoding RNA gene- and cis-regulatory elements in multiple-genome datasets, it is useful to be able to derive multi-sequence stochastic grammars (and hence multiple align...

    Authors: Ian Holmes
    Citation: BMC Bioinformatics 2004 5:166
  5. While researchers have utilized versions of the Affymetrix human GeneChip® for the assessment of expression patterns in non human primate (NHP) samples, there has been no comprehensive sequence analysis study und...

    Authors: Zhining Wang, Mark G Lewis, Martin E Nau, Alma Arnold and Maryanne T Vahey
    Citation: BMC Bioinformatics 2004 5:165
  6. To identify differentially expressed genes, it is standard practice to test a two-sample hypothesis for each gene with a proper adjustment for multiple testing. Such tests are essentially univariate and disreg...

    Authors: Yuanhui Xiao, Robert Frisina, Alexander Gordon, Lev Klebanov and Andrei Yakovlev
    Citation: BMC Bioinformatics 2004 5:164
  7. In the emerging field of environmental genomics, direct cloning and sequencing of genomic fragments from complex microbial communities has proven to be a valuable source of new enzymes, expanding the knowledge...

    Authors: Hanno Teeling, Jost Waldmann, Thierry Lombardot, Margarete Bauer and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2004 5:163
  8. Substantial amounts of data on cell signaling, metabolic, gene regulatory and other biological pathways have been accumulated in literature and electronic databases. Conventionally, this information is stored ...

    Authors: Michael Hsing, Joel L Bellenson, Conor Shankey and Artem Cherkasov
    Citation: BMC Bioinformatics 2004 5:156
  9. Identifying protein-protein interactions is fundamental for understanding the molecular machinery of the cell. Proteome-wide studies of protein-protein interactions are of significant value, but the high-throu...

    Authors: Nan Lin, Baolin Wu, Ronald Jansen, Mark Gerstein and Hongyu Zhao
    Citation: BMC Bioinformatics 2004 5:154
  10. Microarray-based comparative genome hybridization experiments generate data that can be mapped onto the genome. These data are interpreted more easily when represented graphically in a genomic context.

    Authors: Ihab AB Awad, Christian A Rees, Tina Hernandez-Boussard, Catherine A Ball and Gavin Sherlock
    Citation: BMC Bioinformatics 2004 5:151
  11. The rapidly increasing number of completely sequenced genomes led to the establishment of the COG-database which, based on sequence homologies, assigns similar proteins from different organisms to clusters of ...

    Authors: Florian Meereis and Michael Kaufmann
    Citation: BMC Bioinformatics 2004 5:150
  12. The hit criterion is a key component of heuristic local alignment algorithms. It specifies a class of patterns assumed to witness a potential similarity, and this choice is decisive for the selectivity and sen...

    Authors: Laurent Noé and Gregory Kucherov
    Citation: BMC Bioinformatics 2004 5:149
  13. A key step in the analysis of microarray expression profiling data is the identification of genes that display statistically significant changes in expression signals between two biological conditions.

    Authors: Dietmar E Martin, Philippe Demougin, Michael N Hall and Michel Bellis
    Citation: BMC Bioinformatics 2004 5:148
  14. Researchers who use MEDLINE for text mining, information extraction, or natural language processing may benefit from having a copy of MEDLINE that they can manage locally. The National Library of Medicine (NLM...

    Authors: Diane E Oliver, Gaurav Bhalotia, Ariel S Schwartz, Russ B Altman and Marti A Hearst
    Citation: BMC Bioinformatics 2004 5:146
  15. Serial Analysis of Gene Expression (SAGE) is a method of large-scale gene expression analysis that has the potential to generate the full list of mRNAs present within a cell population at a given time and thei...

    Authors: Céline Keime, Francesca Damiola, Dominique Mouchiroud, Laurent Duret and Olivier Gandrillon
    Citation: BMC Bioinformatics 2004 5:143
  16. Microarray is a high-throughput technology to study expression of thousands of genes in parallel. A critical aspect of microarray production is the design aimed at space optimization while maximizing the numbe...

    Authors: Anu Sharma, Gyan Prakash Srivastava, Vineet K Sharma and Srinivasan Ramachandran
    Citation: BMC Bioinformatics 2004 5:142
  17. When publishing large-scale microarray datasets, it is of great value to create supplemental websites where either the full data, or selected subsets corresponding to figures within the paper, can be browsed. ...

    Authors: Christian A Rees, Janos Demeter, John C Matese, David Botstein and Gavin Sherlock
    Citation: BMC Bioinformatics 2004 5:141
  18. MicroRNAs are ~17–24 nt. noncoding RNAs found in all eukaryotes that degrade messenger RNAs via RNA interference (if they bind in a perfect or near-perfect complementarity to the target mRNA), or arrest transl...

    Authors: Neil R Smalheiser and Vetle I Torvik
    Citation: BMC Bioinformatics 2004 5:139
  19. The insect exoskeleton or cuticle is a bi-partite composite of proteins and chitin that provides protective, skeletal and structural functions. Little information is available about the molecular structure of ...

    Authors: Christiana K Magkrioti, Ioannis C Spyropoulos, Vassiliki A Iconomidou, Judith H Willis and Stavros J Hamodrakas
    Citation: BMC Bioinformatics 2004 5:138
  20. Mutations in rpoB, the gene encoding the β subunit of DNA-dependent RNA polymerase, are associated with rifampin resistance in Mycobacterium tuberculosis. Several studies have been conducted where minimum inhibit...

    Authors: Michael P Cummings and Mark R Segal
    Citation: BMC Bioinformatics 2004 5:137
  21. Microarray experiments are becoming a powerful tool for clinical diagnosis, as they have the potential to discover gene expression patterns that are characteristic for a particular disease. To date, this probl...

    Authors: Bing Liu, Qinghua Cui, Tianzi Jiang and Songde Ma
    Citation: BMC Bioinformatics 2004 5:136
  22. This paper presents the use of Support Vector Machines (SVMs) for prediction and analysis of antisense oligonucleotide (AO) efficacy. The collected database comprises 315 AO molecules including 68 features eac...

    Authors: Gustavo Camps-Valls, Alistair M Chalk, Antonio J Serrano-López, José D Martín-Guerrero and Erik LL Sonnhammer
    Citation: BMC Bioinformatics 2004 5:135
  23. Novel proteins entering the food chain, for example by genetic modification of plants, have to be tested for allergenicity. Allermatch™ http://​allermatch.​org

    Authors: Mark WEJ Fiers, Gijs A Kleter, Herman Nijland, Ad ACM Peijnenburg, Jan Peter Nap and Roeland CHJ van Ham
    Citation: BMC Bioinformatics 2004 5:133
  24. Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and...

    Authors: Sook Jung, Christopher Jesudurai, Margaret Staton, Zhidian Du, Stephen Ficklin, Ilhyung Cho, Albert Abbott, Jeffrey Tomkins and Dorrie Main
    Citation: BMC Bioinformatics 2004 5:130
  25. The discovery of cis-regulatory modules in metazoan genomes is crucial for understanding the connection between genes and organism diversity. It is important to quantify how comparative genomics can improve co...

    Authors: Saurabh Sinha, Mark D Schroeder, Ulrich Unnerstall, Ulrike Gaul and Eric D Siggia
    Citation: BMC Bioinformatics 2004 5:129
  26. Proteins having similar functions from different sources can be identified by the occurrence in their sequences, a conserved cluster of amino acids referred to as pattern, motif, signature or fingerprint. The ...

    Authors: Anuradha Vivekanandan Giri, Sharmila Anishetty and Pennathur Gautam
    Citation: BMC Bioinformatics 2004 5:127
  27. Thousands of genes in a genomewide data set are tested against some null hypothesis, for detecting differentially expressed genes in microarray experiments. The expected proportion of false positive genes in a...

    Authors: J Aubert, A Bar-Hen, J-J Daudin and S Robin
    Citation: BMC Bioinformatics 2004 5:125

    The Erratum to this article has been published in BMC Bioinformatics 2005 6:42

  28. The prediction of ancestral protein sequences from multiple sequence alignments is useful for many bioinformatics analyses. Predicting ancestral sequences is not a simple procedure and relies on accurate align...

    Authors: Richard J Edwards and Denis C Shields
    Citation: BMC Bioinformatics 2004 5:123

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