BMC Bioinformatics Tutorials

1. MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes

By MAPPER: a search engine for the computational identification of putative transcription factor binding sites in multiple genomes Voichita D Marinescu , Isaac S Kohane and Alberto Riva BMC Bioinformatics 2005, 6:79     doi:10.1186/1471-2105-6-79 Published   30 March 2005 Abstrac... read more

2. RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs

By RIO: Analyzing proteomes by automated phylogenomics using resampled inference of orthologs Christian M Zmasek and Sean R Eddy Howard Hughes Medical Institute and Department of Genetics, Washington University School of Medicine, St. Louis, MO 63110, USA BMC Bioinformatics 2002, 3:14     doi:10.1186/1471-2105-3-14 The elect... read more

3. Enhanced protein domain discovery using taxonomy

By Enhanced protein domain discovery using taxonomy Lachlan Coin , Alex Bateman and Richard Durbin Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA, UK BMC Bioinformatics 2004, 5:56     doi:10.1186/1471-2105-5-56 The electronic version of this article is the complete one and can be f... read more

4. Discovery of protein-protein interactions using a combination of linguistic, statistical and graphical information

By Background: The rapid publication of important research in the biomedical literature makes it increasingly difficult for researchers to keep current with significant work in their area of interest. Results: This paper reports a scalable method for the discovery of protein-protein interactions in Medline abstracts, using a combination of text analytics, statistical and graphical analysis, and a... read more

5. Efficient Boolean implementation of universal sequence maps (bUSM)

By Efficient Boolean implementation of universal sequence maps (bUSM) John Schwacke and Jonas S Almeida Department of Biometry and Epidemiology, Medical University of South Carolina, 135 Cannon Street, Suite 303, PO Box 250835, Charleston SC 29425, USA BMC Bioinformatics 2002, 3:28     doi:10.1186/1471-2105-3-28 The electron... read more

6. Delayed impact: ISI's citation tracking choices are keeping scientists in the dark

By Delayed impact: ISI's citation tracking choices are keeping scientists in the dark Matthew J Cockerill BioMed Central Ltd, 34-42, Middlesex House, London, W1T 4LB, UK BMC Bioinformatics 2004, 5:93     doi:10.1186/1471-2105-5-93 The electronic version of this article is the complete one and can be found online at: http://ww... read more

7. Cancer characterization and feature set extraction by discriminative margin clustering

By Cancer characterization and feature set extraction by discriminative margin clustering Kamesh Munagala1 , Robert Tibshirani2 and Patrick O Brown3 1Department of Biochemistry, Stanford University School of Medicine. Address: 466 Gates Computer Science, Stanford CA 94305, USA 2Department of Health Research and Policy, ... read more

8. Comparative analysis of chromatin landscape in regulatory regions of human housekeeping and tissue specific genes.

By Background: 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 temporal regulation. The potential to utilize global regulatory mechanisms for controlling gene expression might depend upon the architecture of the chromatin in and around the gene. I... read more

9. Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering

By Influence of microarrays experiments missing values on the stability of gene groups by hierarchical clustering Alexandre G de Brevern1 , Serge Hazout1 and Alain Malpertuy2 1Equipe de Bioinformatique Génomique et Moléculaire (EBGM), INSERM E0346, Université Denis DIDEROT-Paris 7, case 7113, 2, place Jussieu, 75251 Pa... read more

10. Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals

By Refined repetitive sequence searches utilizing a fast hash function and cross species information retrievals Jeff Reneker and Chi-Ren Shyu BMC Bioinformatics 2005, 6:111     doi:10.1186/1471-2105-6-111 Published   3 May 2005 Abstract (provisional) read more

11. An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage

By An SVD-based comparison of nine whole eukaryotic genomes supports a coelomate rather than ecdysozoan lineage Gary W Stuart1, 2 and Michael W Berry3 1Department of Life Sciences, Indiana State University, Terre Haute, IN 47809, USA 2Visiting Scientist, Center for Genomics and Bioinformatics, Indiana University, Bloomi... read more

12. Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization

By Domain analysis of the tubulin cofactor system: a model for tubulin folding and dimerization Marcin Grynberg1, 2 , Lukasz Jaroszewski3 and Adam Godzik2 1Institute of Biochemistry and Biophysics, Polish Academy of Sciences, 5A Pawinskiego St, 02-106 Warsaw, Poland 2The Burnham Institute, 10901 N. Torrey Pin... read more

13. Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis

By Match-Only Integral Distribution (MOID) Algorithm for high-density oligonucleotide array analysis Yingyao Zhou1 and Ruben Abagyan1, 2 1Genomics Institute of the Novartis Research Foundation, 3115 Merryfield Row, San Diego, CA 92121, USA 2The Scripps Research Institute, Department of Molecular Biology, 10550 North Tor... read more

14. Which gene did you mean?

By 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 investigations that yield massive data sets. Semantic enrichment of plain text is crucial for computer aided analysis. In general people will think about semantic tagging as just another form or text mini... read more

15. Probabilistic estimation of microarray data reliability and underlying gene expression

By Probabilistic estimation of microarray data reliability and underlying gene expression Sven Bilke1 , Thomas Breslin1 and Mikael Sigvardsson2 1Complex Systems Division, Department of Theoretical Physics, University of Lund, Sölvegatan 14A, SE-223 62 Lund, Sweden 2The Laboratory for Cell Differentiation Studies, D... read more

16. Scoring functions for transcription factor binding site prediction

By Scoring functions for transcription factor binding site prediction Markus Friberg , Peter von Rohr and Gaston Gonnet BMC Bioinformatics 2005, 6:84     doi:10.1186/1471-2105-6-84 Published   4 April 2005 Abstract (provisional) read more

17. Gene finding in the chicken genome

By Background: 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 there is not a large collection of known gene sequences, such as the recently published chicken genome. We used the chicken sequence to test comparative and homology-based gene-f... read more

18. IdentiCS – Identification of coding sequence and in silico reconstruction of the metabolic network directly f

By IdentiCS – Identification of coding sequence and in silico reconstruction of the metabolic network directly from unannotated low-coverage bacterial genome sequence Jibin Sun and An-Ping Zeng Department of Genome Analysis, GBF-German Research Center for Biotechnology, Mascheroder Weg 1, Braunschweig, 38124, Germany BMC Bioinformatics 2004, 5:112  ... read more

19. Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer

By Noise filtering and nonparametric analysis of microarray data underscores discriminating markers of oral, prostate, lung, ovarian and breast cancer Virginie M Aris1, 2, 3 , Michael J Cody1 , Jeff Cheng1, 2 , James J Dermody3 , Patricia Soteropoulos1, 3 , Michael Recce1, 2<... read more

20. Cluster stability scores for microarray data in cancer studies

By Cluster stability scores for microarray data in cancer studies Mark Smolkin1 and Debashis Ghosh2 1Department of Health Evaluation Sciences, University of Virginia Medical Center, Charlottesville, Virginia, USA 2Department of Biostatistics, University of Michigan Ann Arbor, Michigan, USA BMC Bioinformatics 2003, 4:36... read more

21. AutoFACT: An Automatic Functional Annotation and Classification Tool.

By Background: Assignment of function to new molecular sequence data is an essential step in genomics projects. The usual process involves similarity searches of a given sequence against one or more databases, an arduous process for large datasets. Results: We present AutoFACT, a fully-automated and customizable annotation tool that assigns biologically informative functions to a sequence. Key featu... read more

22. EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments

By EvDTree: structure-dependent substitution profiles based on decision tree classification of 3D environments Jean-Christophe Gelly , Laurent Chiche and Jérôme Gracy Centre de Biochimie Structurale, Faculté de Pharmacie, Université Montpellier I, 15 avenue Charles Flahault, 34093 Montpellier Cedex 5, France BMC Bioinformatics 2005, 6:4 &nb... read more

23. A computational approach for ordering signal transduction pathway components from genomics and proteomics Data

By A computational approach for ordering signal transduction pathway components from genomics and proteomics Data Yin Liu1 and Hongyu Zhao2 1Program of Computational Biology and Bioinformatics, Yale University, New Haven, CT, 06520, USA 2Department of Epidemiology and Public Health, Yale University School of Medicine, 60 College S... read more

24. Modelling the correlation between the activities of adjacent genes in drosophila

By Modelling the correlation between the activities of adjacent genes in drosophila Helene H Thygesen and Aeilko H Zwinderman Clinical Epidemiology and Biostatistics, Academisch Medisch Centrum, University of Amsterdam, Meibergdreef 9, 1100 DD Amsterdam, Netherlands BMC Bioinformatics 2005, 6:10     doi:10.1186/1471-2105-6-10 read more