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  1. 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

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

  2. 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

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

  3. 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

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

  4. 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

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

  5. 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

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

  6. 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

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

  7. 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

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

  8. 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

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

  9. 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

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

  10. 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

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

  11. 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
  12. 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
  13. 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
  14. 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
  15. 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
  16. 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
  17. 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
  18. 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
  19. 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
  20. 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
  21. 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
  22. 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
  23. 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
  24. 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
  25. 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
  26. Massive text mining of the biological literature holds great promise of relating disparate information and discovering new knowledge. However, disambiguation of gene symbols is a major bottleneck.

    Authors: Bob JA Schijvenaars, Barend Mons, Marc Weeber, Martijn J Schuemie, Erik M van Mulligen, Hester M Wain and Jan A Kors
    Citation: BMC Bioinformatics 2005 6:149
  27. In the clinical context, samples assayed by microarray are often classified by cell line or tumour type and it is of interest to discover a set of genes that can be used as class predictors. The leukemia datas...

    Authors: Thanyaluk Jirapech-Umpai and Stuart Aitken
    Citation: BMC Bioinformatics 2005 6:148
  28. Sequencing of EST and BAC end datasets is no longer limited to large research groups. Drops in per-base pricing have made high throughput sequencing accessible to individual investigators. However, there are f...

    Authors: Stephen E Diener, Thomas D Houfek, Sam E Kalat, DE Windham, Mark Burke, Charles Opperman and Ralph A Dean
    Citation: BMC Bioinformatics 2005 6:147
  29. To date, 35 human diseases, some of which also exhibit anticipation, have been associated with unstable repeats. Anticipation has been reported in a number of diseases in which repeat expansion may have a role...

    Authors: Perseus I Missirlis, Carri-Lyn R Mead, Stefanie L Butland, BF Francis Ouellette, Rebecca S Devon, Blair R Leavitt and Robert A Holt
    Citation: BMC Bioinformatics 2005 6:145
  30. Gene set enrichment analysis (GSEA) is a microarray data analysis method that uses predefined gene sets and ranks of genes to identify significant biological changes in microarray data sets. GSEA is especially...

    Authors: Seon-Young Kim and David J Volsky
    Citation: BMC Bioinformatics 2005 6:144
  31. 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 investigation...

    Authors: Barend Mons
    Citation: BMC Bioinformatics 2005 6:142
  32. Chemical information is now seen as critical for most areas of life sciences. But unlike Bioinformatics, where data is openly available and freely re-usable, most chemical information is closed and cannot be r...

    Authors: Peter Murray-Rust, John BO Mitchell and Henry S Rzepa
    Citation: BMC Bioinformatics 2005 6:141

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