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  1. 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:

  4. 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:

  6. 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

  7. 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:

  8. 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:

  10. 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:

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  21. 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

  22. 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

  23. 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

  24. 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:

  27. 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:

  29. 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:

  30. 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:

  33. We previously developed GoMiner, an application that organizes lists of 'interesting' genes (for example, under-and overexpressed genes from a microarray experiment) for biological interpretation in the contex...

    Authors: Barry R Zeeberg, Haiying Qin, Sudarshan Narasimhan, Margot Sunshine, Hong Cao, David W Kane, Mark Reimers, Robert M Stephens, David Bryant, Stanley K Burt, Eldad Elnekave, Danielle M Hari, Thomas A Wynn, Charlotte Cunningham-Rundles, Donn M Stewart, David Nelson…
    Citation: BMC Bioinformatics 2005 6:168
    Content type: Software Published on:

  34. Proteins carrying twin-arginine (Tat) signal peptides are exported into the periplasmic compartment or extracellular environment independently of the classical Sec-dependent translocation pathway. To complemen...

    Authors: Jannick Dyrløv Bendtsen, Henrik Nielsen, David Widdick, Tracy Palmer and Søren Brunak
    Citation: BMC Bioinformatics 2005 6:167
    Content type: Methodology article Published on:

  38. Signal transduction pathways convey information from the outside of the cell to transcription factors, which in turn regulate gene expression. Our objective is to analyze tumor gene expression data from microa...

    Authors: Thomas Breslin, Morten Krogh, Carsten Peterson and Carl Troein
    Citation: BMC Bioinformatics 2005 6:163
    Content type: Research article Published on:

  40. Interpreting the results of high-throughput experiments, such as those obtained from DNA-microarrays, is an often time-consuming task due to the high number of data-points that need to be analyzed in parallel....

    Authors: Felix Kokocinski, Nicolas Delhomme, Gunnar Wrobel, Lars Hummerich, Grischa Toedt and Peter Lichter
    Citation: BMC Bioinformatics 2005 6:161
    Content type: Software Published on:

  43. All eukaryotic organisms need to distinguish each of their chromosomes. A few protein complexes have been described that recognise entire, specific chromosomes, for instance dosage compensation complexes and t...

    Authors: Per Stenberg, Fredrik Pettersson, Anja O Saura, Anders Berglund and Jan Larsson
    Citation: BMC Bioinformatics 2005 6:158
    Content type: Research article Published on:

  44. The ability to distinguish between genes and proteins is essential for understanding biological text. Support Vector Machines (SVMs) have been proven to be very efficient in general data mining tasks. We explo...

    Authors: Tapio Pahikkala, Filip Ginter, Jorma Boberg, Jouni Järvinen and Tapio Salakoski
    Citation: BMC Bioinformatics 2005 6:157
    Content type: Research article Published on:

  46. Recent advances in molecular biology techniques provide an opportunity for developing detailed mathematical models of biological processes. An iterative scheme is introduced for model identification using avai...

    Authors: Kapil G Gadkar, Rudiyanto Gunawan and Francis J Doyle III
    Citation: BMC Bioinformatics 2005 6:155
    Content type: Methodology article Published on:

  47. The extraction of biological knowledge from genome-scale data sets requires its analysis in the context of additional biological information. The importance of integrating experimental data sets with molecular...

    Authors: David J Reiss, Iliana Avila-Campillo, Vesteinn Thorsson, Benno Schwikowski and Timothy Galitski
    Citation: BMC Bioinformatics 2005 6:154
    Content type: Software Published on:

  48. Ambiguity is a problem in biosequence analysis that arises in various analysis tasks solved via dynamic programming, and in particular, in the modeling of families of RNA secondary structures with stochastic c...

    Authors: Janina Reeder, Peter Steffen and Robert Giegerich
    Citation: BMC Bioinformatics 2005 6:153
    Content type: Research article Published on:

  49. Protein subcellular localization is an important determinant of protein function and hence, reliable methods for prediction of localization are needed. A number of prediction algorithms have been developed bas...

    Authors: Deepak Sarda, Gek Huey Chua, Kuo-Bin Li and Arun Krishnan
    Citation: BMC Bioinformatics 2005 6:152
    Content type: Research article Published on:

  50. Analysis of variance is a powerful approach to identify differentially expressed genes in a complex experimental design for microarray and macroarray data. The advantage of the anova model is the possibility t...

    Authors: Christelle Hennequet-Antier, Hélène Chiapello, Karine Piot, Séverine Degrelle, Isabelle Hue, Jean-Paul Renard, François Rodolphe and Stéphane Robin
    Citation: BMC Bioinformatics 2005 6:150
    Content type: Software Published on:

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