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  1. Large-scale compilation of gene expression microarray datasets across diverse biological phenotypes provided a means of gathering a priori knowledge in the form of identification and annotation of bimodal gene...

    Authors: Michael Gormley and Aydin Tozeren
    Citation: BMC Bioinformatics 2008 9:486
    Content type: Research article Published on:

  2. For the past few years, scientific controversy has surrounded the large number of errors in forensic and literature mitochondrial DNA (mtDNA) data. However, recent research has shown that using mtDNA phylogeny...

    Authors: Hwan Young Lee, Injee Song, Eunho Ha, Sung-Bae Cho, Woo Ick Yang and Kyoung-Jin Shin
    Citation: BMC Bioinformatics 2008 9:483
    Content type: Software Published on:

  4. Recently, microarray data analyses using functional pathway information, e.g., gene set enrichment analysis (GSEA) and significance analysis of function and expression (SAFE), have gained recognition as a way ...

    Authors: Rongheng Lin, Shuangshuang Dai, Richard D Irwin, Alexandra N Heinloth, Gary A Boorman and Leping Li
    Citation: BMC Bioinformatics 2008 9:481
    Content type: Methodology article Published on:

  5. Microarray techniques are one of the main methods used to investigate thousands of gene expression profiles for enlightening complex biological processes responsible for serious diseases, with a great scientif...

    Authors: Luca Corradi, Marco Fato, Ivan Porro, Silvia Scaglione and Livia Torterolo
    Citation: BMC Bioinformatics 2008 9:480
    Content type: Software Published on:

  8. Alternative splicing is a major contributor to the diversity of eukaryotic transcriptomes and proteomes. Currently, large scale detection of alternative splicing using expressed sequence tags (ESTs) or microar...

    Authors: Rileen Sinha, Michael Hiller, Rainer Pudimat, Ulrike Gausmann, Matthias Platzer and Rolf Backofen
    Citation: BMC Bioinformatics 2008 9:477
    Content type: Research article Published on:

  11. The prediction of a consensus structure for a set of related RNAs is an important first step for subsequent analyses. RNAalifold, which computes the minimum energy structure that is simultaneously formed by a ...

    Authors: Stephan H Bernhart, Ivo L Hofacker, Sebastian Will, Andreas R Gruber and Peter F Stadler
    Citation: BMC Bioinformatics 2008 9:474
    Content type: Methodology article Published on:

  12. The epidermal physiology results from a complex regulated homeostasis of keratinocyte proliferation, differentiation and death and is tightly regulated by a specific protein expression during cellular maturati...

    Authors: Thora Pommerencke, Thorsten Steinberg, Hartmut Dickhaus, Pascal Tomakidi and Niels Grabe
    Citation: BMC Bioinformatics 2008 9:473
    Content type: Methodology article Published on:

  13. Researchers interested in analysing the expression patterns of functionally related genes usually hope to improve the accuracy of their results beyond the boundaries of currently available experimental data. G...

    Authors: Tao Xu, LinFang Du and Yan Zhou
    Citation: BMC Bioinformatics 2008 9:472
    Content type: Research article Published on:

  14. Detection of non coding RNA (ncRNA) molecules is a major bioinformatics challenge. This challenge is particularly difficult when attempting to detect H/ACA molecules which are involved in converting uridine to...

    Authors: Inna Myslyuk, Tirza Doniger, Yair Horesh, Avraham Hury, Ran Hoffer, Yaara Ziporen, Shulamit Michaeli and Ron Unger
    Citation: BMC Bioinformatics 2008 9:471
    Content type: Research article Published on:

  15. Metabolomics, or metabonomics, refers to the quantitative analysis of all metabolites present within a biological sample and is generally carried out using NMR spectroscopy or Mass Spectrometry. Such analysis ...

    Authors: Kenneth Bryan, Lorraine Brennan and Pádraig Cunningham
    Citation: BMC Bioinformatics 2008 9:470
    Content type: Software Published on:

  16. Despite the widespread usage of DNA microarrays, questions remain about how best to interpret the wealth of gene-by-gene transcriptional levels that they measure. Recently, methods have been proposed which use...

    Authors: Nathan L Tintle, Aaron A Best, Matthew DeJongh, Dirk Van Bruggen, Fred Heffron, Steffen Porwollik and Ronald C Taylor
    Citation: BMC Bioinformatics 2008 9:469
    Content type: Methodology article Published on:

  18. Probability based statistical learning methods such as mutual information and Bayesian networks have emerged as a major category of tools for reverse engineering mechanistic relationships from quantitative bio...

    Authors: Weijun Luo, Kurt D Hankenson and Peter J Woolf
    Citation: BMC Bioinformatics 2008 9:467
    Content type: Research article Published on:

  19. Identification of approximate tandem repeats is an important task of broad significance and still remains a challenging problem of computational genomics. Often there is no single best approach to periodicity ...

    Authors: Vladimir Paar, Nenad Pavin, Ivan Basar, Marija Rosandić, Matko Glunčić and Nils Paar
    Citation: BMC Bioinformatics 2008 9:466
    Content type: Research article Published on:

  20. Medium- to large-scale expression profiling using quantitative polymerase chain reaction (qPCR) assays are becoming increasingly important in genomics research. A major bottleneck in experiment preparation is ...

    Authors: Samuel Arvidsson, Miroslaw Kwasniewski, Diego Mauricio Riaño-Pachón and Bernd Mueller-Roeber
    Citation: BMC Bioinformatics 2008 9:465
    Content type: Software Published on:

  22. Authors: Regina Bohnert, Georg Zeller, Richard M Clark, Kevin L Childs, Victor Ulat, Renee Stokowski, Dennis Ballinger, Kelly Frazer, David Cox, Richard Bruskiewich, C Robin Buell, Jan Leach, Hei Leung, Kenneth L McNally, Detlef Weigel and Gunnar Rätsch
    Citation: BMC Bioinformatics 2008 9(Suppl 10):O8
    Content type: Oral presentation Published on:

    This article is part of a Supplement: Volume 9 Supplement 10

  34. In this meeting report we give an overview of the talks and presentations from the Fourth International Society for Computational Biology (ISCB) Student Council Symposium held as part of the annual Intelligent...

    Authors: Lucia Peixoto, Nils Gehlenborg and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2008 9(Suppl 10):I1
    Content type: Meeting report Published on:

    This article is part of a Supplement: Volume 9 Supplement 10

  37. The rapid annotation of genes on a genome-wide scale is now possible for several organisms using high-throughput RNA interference assays to knock down the expression of a specific gene. To date, dozens of RNA ...

    Authors: Matthew T Weirauch, Christopher K Wong, Alexandra B Byrne and Joshua M Stuart
    Citation: BMC Bioinformatics 2008 9:463
    Content type: Research article Published on:

  38. Inferring cluster structure in microarray datasets is a fundamental task for the so-called -omic sciences. It is also a fundamental question in Statistics, Data Analysis and Classification, in particular with ...

    Authors: Raffaele Giancarlo, Davide Scaturro and Filippo Utro
    Citation: BMC Bioinformatics 2008 9:462
    Content type: Research article Published on:

  39. This paper presents the R/Bioconductor package minet (version 1.1.6) which provides a set of functions to infer mutual information networks from a dataset. Once fed with a microarray dataset, the package returns ...

    Authors: Patrick E Meyer, Frédéric Lafitte and Gianluca Bontempi
    Citation: BMC Bioinformatics 2008 9:461
    Content type: Software Published on:

  40. In current comparative proteomics studies, the large number of images generated by 2D gels is currently compared using spot matching algorithms. Unfortunately, differences in gel migration and sample variabili...

    Authors: Sabine Pérès, Laurence Molina, Nicolas Salvetat, Claude Granier and Franck Molina
    Citation: BMC Bioinformatics 2008 9:460
    Content type: Software Published on:

  42. The analysis of large-scale data sets via clustering techniques is utilized in a number of applications. Biclustering in particular has emerged as an important problem in the analysis of gene expression data s...

    Authors: Peter A DiMaggio Jr, Scott R McAllister, Christodoulos A Floudas, Xiao-Jiang Feng, Joshua D Rabinowitz and Herschel A Rabitz
    Citation: BMC Bioinformatics 2008 9:458
    Content type: Research article Published on:

  43. DNA methylation patterns have been shown to significantly correlate with different tissue types and disease states. High-throughput methylation arrays enable large-scale DNA methylation analysis to identify in...

    Authors: Hailong Meng, Edward L Murrelle and Guoya Li
    Citation: BMC Bioinformatics 2008 9:457
    Content type: Research article Published on:

  44. The increasing availability of fungal genome sequences provides large numbers of proteins for evolutionary and phylogenetic analyses. However the heterogeneity of data, including the quality of genome annotati...

    Authors: Sylvain Marthey, Gabriela Aguileta, François Rodolphe, Annie Gendrault, Tatiana Giraud, Elisabeth Fournier, Manuela Lopez-Villavicencio, Angélique Gautier, Marc-Henri Lebrun and Hélène Chiapello
    Citation: BMC Bioinformatics 2008 9:456
    Content type: Database Published on:

  45. The regulation of gene expression is complex and occurs at many levels, including transcriptional and post-transcriptional, in metazoans. Transcriptional regulation is mainly determined by sequence elements wi...

    Authors: Christina Chaivorapol, Collin Melton, Grace Wei, Ru-Fang Yeh, Miguel Ramalho-Santos, Robert Blelloch and Hao Li
    Citation: BMC Bioinformatics 2008 9:455
    Content type: Software Published on:

  46. Secondary metabolites biosynthesized by polyketide synthase (PKS) and nonribosomal peptide synthetase (NRPS) family of enzymes constitute several classes of therapeutically important natural products like eryt...

    Authors: Mohd Zeeshan Ansari, Jyoti Sharma, Rajesh S Gokhale and Debasisa Mohanty
    Citation: BMC Bioinformatics 2008 9:454
    Content type: Research article Published on:

  49. Feature selection is a pattern recognition approach to choose important variables according to some criteria in order to distinguish or explain certain phenomena (i.e., for dimensionality reduction). There are...

    Authors: Fabrício Martins Lopes, David Corrêa Martins Jr and Roberto M Cesar Jr
    Citation: BMC Bioinformatics 2008 9:451
    Content type: Software Published on:

  50. The Bluejay genome browser has been developed over several years to address the challenges posed by the ever increasing number of data types as well as the increasing volume of data in genome research. Beginni...

    Authors: Jung Soh, Paul MK Gordon, Morgan L Taschuk, Anguo Dong, Andrew C Ah-Seng, Andrei L Turinsky and Christoph W Sensen
    Citation: BMC Bioinformatics 2008 9:450
    Content type: Software Published on:

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