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  1. The identification of promoter regions that are regulated by a given transcription factor has traditionally relied upon the identification and distributions of binding sites recognized by the factor. In this s...

    Authors: Deendayal Dinakarpandian, Venetia Raheja, Saumil Mehta, Erin G Schuetz and Peter K Rogan

    Citation: BMC Bioinformatics 2005 6:204

    Content type: Research article

    Published on:

  2. Peptide Mass Fingerprinting (PMF) is a widely used mass spectrometry (MS) method of analysis of proteins and peptides. It relies on the comparison between experimentally determined and theoretical mass spectra...

    Authors: Witold E Wolski, Maciej Lalowski, Peter Jungblut and Knut Reinert

    Citation: BMC Bioinformatics 2005 6:203

    Content type: Research article

    Published on:

  3. Two of the main objectives of the genomic and post-genomic era are to structurally and functionally annotate genomes which consists of detecting genes' position and structure, and inferring their function (as ...

    Authors: Philippe Gouret, Vérane Vitiello, Nathalie Balandraud, André Gilles, Pierre Pontarotti and Etienne GJ Danchin

    Citation: BMC Bioinformatics 2005 6:198

    Content type: Software

    Published on:

  4. BLAST is a widely used genetic research tool for analysis of similarity between nucleotide and protein sequences. This paper presents a software application entitled "Squid" that makes use of grid technology. ...

    Authors: Paulo C Carvalho, Rafael V Glória, Antonio B de Miranda and Wim M Degrave

    Citation: BMC Bioinformatics 2005 6:197

    Content type: Software

    Published on:

  5. Life processes are determined by the organism's genetic profile and multiple environmental variables. However the interaction between these factors is inherently non-linear [1]. Microarray data is one representat...

    Authors: Kevin Dawson, Raymond L Rodriguez and Wasyl Malyj

    Citation: BMC Bioinformatics 2005 6:195

    Content type: Research article

    Published on:

  6. Protein function is often dependent on subsets of solvent-exposed residues that may exist in a similar three-dimensional configuration in non homologous proteins thus having different order and/or spacing in t...

    Authors: Fabrizio Ferrè, Gabriele Ausiello, Andreas Zanzoni and Manuela Helmer-Citterich

    Citation: BMC Bioinformatics 2005 6:194

    Content type: Methodology article

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  7. SRS (Sequence Retrieval System) has proven to be a valuable platform for storing, linking, and querying biological databases. Due to the availability of a broad range of different scientific databases in SRS, ...

    Authors: Antoine Veldhoven, Don de Lange, Marcel Smid, Victor de Jager, Jan A Kors and Guido Jenster

    Citation: BMC Bioinformatics 2005 6:192

    Content type: Software

    Published on:

  8. A new algorithm for assessing similarity between primer and template has been developed based on the hypothesis that annealing of primer to template is an information transfer process.

    Authors: Youfang Cao, Lianjie Wang, Kexue Xu, Chunhai Kou, Yulei Zhang, Guifang Wei, Junjian He, Yunfang Wang and Liping Zhao

    Citation: BMC Bioinformatics 2005 6:190

    Content type: Software

    Published on:

  9. CGH-Profiler is a program that supports the analysis of genomic aberrations measured by Comparative Genomic Hybridisation (CGH). Comparative genomic hybridisation (CGH) is a well-established, molecular cytogeneti...

    Authors: Falk Schubert, Bernhard Tausch, Stefan Joos and Roland Eils

    Citation: BMC Bioinformatics 2005 6:188

    Content type: Software

    Published on:

  10. The evaluation of statistical significance has become a critical process in identifying differentially expressed genes in microarray studies. Classical p-value adjustment methods for multiple comparisons such ...

    Authors: Nitin Jain, HyungJun Cho, Michael O'Connell and Jae K Lee

    Citation: BMC Bioinformatics 2005 6:187

    Content type: Methodology article

    Published on:

  11. Pathogenicity islands (PAIs), distinct genomic segments of pathogens encoding virulence factors, represent a subgroup of genomic islands (GIs) that have been acquired by horizontal gene transfer event. Up to n...

    Authors: Sung Ho Yoon, Cheol-Goo Hur, Ho-Young Kang, Yeoun Hee Kim, Tae Kwang Oh and Jihyun F Kim

    Citation: BMC Bioinformatics 2005 6:184

    Content type: Methodology article

    Published on:

  12. There are a number of methods (also called: measures) currently in use that quantify codon usage in genes. These measures are often influenced by other sequence properties, such as length. This can introduce s...

    Authors: Fran Supek and Kristian Vlahoviček

    Citation: BMC Bioinformatics 2005 6:182

    Content type: Methodology article

    Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2010 11:463

  13. Gene expression studies increasingly compare expression responses between different experimental backgrounds (genetic, physiological, or phylogenetic). By focusing on dynamic responses rather than a direct com...

    Authors: Rainer Breitling, Patrick Armengaud and Anna Amtmann

    Citation: BMC Bioinformatics 2005 6:181

    Content type: Methodology article

    Published on:

  14. The current methods of publishing chemical information in bioscience articles are analysed. Using 3 papers as use-cases, it is shown that conventional methods using human procedures, including cut-and-paste ar...

    Authors: Peter Murray-Rust, John BO Mitchell and Henry S Rzepa

    Citation: BMC Bioinformatics 2005 6:180

    Content type: Commentary

    Published on:

  15. During the last few years, DNA sequence analysis has become one of the primary means of taxonomic identification of species, particularly so for species that are minute or otherwise lack distinct, readily obta...

    Authors: R Henrik Nilsson, Erik Kristiansson, Martin Ryberg and Karl-Henrik Larsson

    Citation: BMC Bioinformatics 2005 6:178

    Content type: Software

    Published on:

  16. Gender differences in gene expression were estimated in liver samples from 9 males and 9 females. The study tested 31,110 genes for a gender difference using a design that adjusted for sources of variation ass...

    Authors: Robert R Delongchamp, Cruz Velasco, Stacey Dial and Angela J Harris

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S13

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  17. The acceptance of microarray technology in regulatory decision-making is being challenged by the existence of various platforms and data analysis methods. A recent report (E. Marshall, Science, 306, 630–631, 2004...

    Authors: Leming Shi, Weida Tong, Hong Fang, Uwe Scherf, Jing Han, Raj K Puri, Felix W Frueh, Federico M Goodsaid, Lei Guo, Zhenqiang Su, Tao Han, James C Fuscoe, Z aAlex Xu, Tucker A Patterson, Huixiao Hong, Qian Xie…

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S12

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  18. Microarray-based measurement of mRNA abundance assumes a linear relationship between the fluorescence intensity and the dye concentration. In reality, however, the calibration curve can be nonlinear.

    Authors: Leming Shi, Weida Tong, Zhenqiang Su, Tao Han, Jing Han, Raj K Puri, Hong Fang, Felix W Frueh, Federico M Goodsaid, Lei Guo, William S Branham, James J Chen, Z Alex Xu, Stephen C Harris, Huixiao Hong, Qian Xie…

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S11

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  19. In cluster analysis, the validity of specific solutions, algorithms, and procedures present significant challenges because there is no null hypothesis to test and no 'right answer'. It has been noted that a re...

    Authors: Nikhil R Garge, Grier P Page, Alan P Sprague, Bernard S Gorman and David B Allison

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S10

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  20. Protein-protein, protein-DNA and protein-RNA interactions are of central importance in biological systems. Quadrapole Time-of-flight (Q-TOF) mass spectrometry is a sensitive, promising tool for studying these ...

    Authors: Yong Tang, Yingfeng Chen, Cheryl F Lichti, Roger A Hall, Kevin D Raney and Steven F Jennings

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S9

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  21. This paper describes a microarray study including data quality control, data analysis and the analysis of the mechanism of toxicity (MOT) induced by 1-methyl-4-phenylpyridinium (MPP+) in a rat adrenal pheochromoc...

    Authors: Zengjun Xu, Tucker A Patterson, Jonathan D Wren, Tao Han, Leming Shi, Helen Duhart, Syed F Ali and William Slikker Jr

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S8

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  22. Clustering the ESTs from a large dataset representing a single species is a convenient starting point for a number of investigations into gene discovery, genome evolution, expression patterns, and alternativel...

    Authors: Ronald L Frank and Fikret Ercal

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S7

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  23. The completion of the sequencing of human, mouse and rat genomes and knowledge of cross-species gene homologies enables studies of differential gene expression in animal models. These types of studies have the...

    Authors: H Fang, W Tong, R Perkins, L Shi, H Hong, X Cao, Q Xie, SH Yim, JM Ward, HC Pitot and YP Dragan

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S6

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  24. Proteomic profiling of complex biological mixtures by the ProteinChip technology of surface-enhanced laser desorption/ionization time-of-flight (SELDI-TOF) mass spectrometry (MS) is one of the most promising a...

    Authors: Huixiao Hong, Yvonne Dragan, Joshua Epstein, Candee Teitel, Bangzheng Chen, Qian Xie, Hong Fang, Leming Shi, Roger Perkins and Weida Tong

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S5

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  25. Systematic evaluation and study of single nucleotide polymorphisms (SNPs) made possible by high throughput genotyping technologies and bioinformatics promises to provide breakthroughs in the understanding of c...

    Authors: Qian Xie, Luke D Ratnasinghe, Huixiao Hong, Roger Perkins, Ze-Zhong Tang, Nan Hu, Philip R Taylor and Weida Tong

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S4

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  26. The continuous flow of EST data remains one of the richest sources for discoveries in modern biology. The first step in EST data mining is usually associated with EST clustering, the process of grouping of ori...

    Authors: Andrey Ptitsyn and Winston Hide

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S3

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  27. There is an enormous amount of information encoded in each genome – enough to create living, responsive and adaptive organisms. Raw sequence data alone is not enough to understand function, mechanisms or inter...

    Authors: Jonathan D Wren, David Johnson and Le Gruenwald

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S2

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  28. The MCBIOS 2004 conference brought together regional researchers and students in biology, computer science and bioinformatics on October 7th-9th 2004 to present their latest work. This editorial describes the ...

    Authors: Jonathan D Wren and William Slikker Jr

    Citation: BMC Bioinformatics 2005 6(Suppl 2):S1

    Content type: Proceedings

    Published on:

    This article is part of a Supplement: Volume 6 Supplement 2

  29. Functional analysis of data from genome-scale experiments, such as microarrays, requires an extensive selection of differentially expressed genes. Under many conditions, the proportion of differentially expres...

    Authors: J Peter Svensson, Renée X de Menezes, Ingela Turesson, Micheline Giphart-Gassler and Harry Vrieling

    Citation: BMC Bioinformatics 2005 6:177

    Content type: Methodology article

    Published on:

  30. Predicting the subcellular localization of proteins is important for determining the function of proteins. Previous works focused on predicting protein localization in Gram-negative bacteria obtained good resu...

    Authors: Jiren Wang, Wing-Kin Sung, Arun Krishnan and Kuo-Bin Li

    Citation: BMC Bioinformatics 2005 6:174

    Content type: Research article

    Published on:

  31. The PD-(D/E)XK nuclease superfamily, initially identified in type II restriction endonucleases and later in many enzymes involved in DNA recombination and repair, is one of the most challenging targets for pro...

    Authors: Jan Kosinski, Marcin Feder and Janusz M Bujnicki

    Citation: BMC Bioinformatics 2005 6:172

    Content type: Research article

    Published on:

  32. Public databases now contain multitude of complete bacterial genomes, including several genomes of the same species. The available data offers new opportunities to address questions about bacterial genome evol...

    Authors: H Chiapello, I Bourgait, F Sourivong, G Heuclin, A Gendrault-Jacquemard, M-A Petit and M El Karoui

    Citation: BMC Bioinformatics 2005 6:171

    Content type: Research article

    Published on:

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