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  1. There are many sources of variation in dual labelled microarray experiments, including data acquisition and image processing. The final interpretation of experiments strongly relies on the accuracy of the meas...

    Authors: Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck and Marie-Hélène Mucchielli-Giorgi
    Citation: BMC Bioinformatics 2009 10:98
    Content type: Methodology article Published on:

  3. An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for p...

    Authors: Stephen C Billups, Margaret C Neville, Michael Rudolph, Weston Porter and Pepper Schedin
    Citation: BMC Bioinformatics 2009 10:96
    Content type: Research article Published on:

  4. A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biologica...

    Authors: Jamie I MacPherson, John W Pinney and David L Robertson
    Citation: BMC Bioinformatics 2009 10:95
    Content type: Software Published on:

  5. Automated microscopy technologies have led to a rapid growth in imaging data on a scale comparable to that of the genomic revolution. High throughput screens are now being performed to determine the localisati...

    Authors: Nicholas A Hamilton, Jack TH Wang, Markus C Kerr and Rohan D Teasdale
    Citation: BMC Bioinformatics 2009 10:94
    Content type: Methodology article Published on:

  6. Pattern discovery in DNA sequences is one of the most fundamental problems in molecular biology with important applications in finding regulatory signals and transcription factor binding sites. An important ta...

    Authors: Fatemeh Zare-Mirakabad, Hayedeh Ahrabian, Mehdei Sadeghi, Abbas Nowzari-Dalini and Bahram Goliaei
    Citation: BMC Bioinformatics 2009 10:93
    Content type: Research article Published on:

  7. A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as...

    Authors: Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner and Peter Meinicke
    Citation: BMC Bioinformatics 2009 10:92
    Content type: Software Published on:

  8. Existing methods for analyzing bacterial CGH data from two-color arrays are based on log-ratios only, a paradigm inherited from expression studies. We propose an alternative approach, where microarray signals ...

    Authors: Lars Snipen, Otto L Nyquist, Margrete Solheim, Ågot Aakra and Ingolf F Nes
    Citation: BMC Bioinformatics 2009 10:91
    Content type: Methodology article Published on:

  9. One of the most challenging problems in mining gene expression data is to identify how the expression of any particular gene affects the expression of other genes. To elucidate the relationships between genes,...

    Authors: Hojung Nam, KiYoung Lee and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  10. Databases containing very large amounts of SNP (Single Nucleotide Polymorphism) data are now freely available for researchers interested in medical and/or population genetics applications. While many of these ...

    Authors: Jorge Amigo, Christopher Phillips, Antonio Salas and Ángel Carracedo
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  12. We present a passage relevance model for integrating syntactic and semantic evidence of biomedical concepts and topics using a probabilistic graphical model. Component models of topics, concepts, terms, and do...

    Authors: Jay Urbain, Ophir Frieder and Nazli Goharian
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  13. Metastasis is the most dangerous step in cancer progression and causes more than 90% of cancer death. Although many researchers have been working on biological features and characteristics of metastasis, most ...

    Authors: Sangwoo Kim and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  14. Accurate estimation of statistical significance of a pairwise alignment is an important problem in sequence comparison. Recently, a comparative study of pairwise statistical significance with database statisti...

    Authors: Ankit Agrawal and Xiaoqiu Huang
    Citation: BMC Bioinformatics 2009 10(Suppl 3):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 3

  15. The versatility of DNA copy number amplifications for profiling and categorization of various tissue samples has been widely acknowledged in the biomedical literature. For instance, this type of measurement te...

    Authors: Pekka Marttinen, Samuel Myllykangas and Jukka Corander
    Citation: BMC Bioinformatics 2009 10:90
    Content type: Research article Published on:

  16. Polyhydroxyalkanoates (PHAs) can be degraded by many microorganisms using intra- or extracellular PHA depolymerases. PHA depolymerases are very diverse in sequence and substrate specificity, but share a common...

    Authors: Michael Knoll, Thomas M Hamm, Florian Wagner, Virginia Martinez and Jürgen Pleiss
    Citation: BMC Bioinformatics 2009 10:89
    Content type: Database Published on:

  18. Data generated from liquid chromatography coupled to high-resolution mass spectrometry (LC-MS)-based studies of a biological sample can contain large amounts of biologically significant information in the form...

    Authors: Navdeep Jaitly, Anoop Mayampurath, Kyle Littlefield, Joshua N Adkins, Gordon A Anderson and Richard D Smith
    Citation: BMC Bioinformatics 2009 10:87
    Content type: Software Published on:

  19. In silico candidate gene prioritisation (CGP) aids the discovery of gene functions by ranking genes according to an objective relevance score. While several CGP methods have been described for identifying human ...

    Authors: Frank PY Lin, Enrico Coiera, Ruiting Lan and Vitali Sintchenko
    Citation: BMC Bioinformatics 2009 10:86
    Content type: Research article Published on:

  20. A variety of high-throughput techniques are now available for constructing comprehensive gene regulatory networks in systems biology. In this study, we report a new statistical approach for facilitating in silico

    Authors: Li-Yu D Liu, Chien-Yu Chen, Mei-Ju M Chen, Ming-Shian Tsai, Cho-Han S Lee, Tzu L Phang, Li-Yun Chang, Wen-Hung Kuo, Hsiao-Lin Hwa, Huang-Chun Lien, Shih-Ming Jung, Yi-Shing Lin, King-Jen Chang and Fon-Jou Hsieh
    Citation: BMC Bioinformatics 2009 10:85
    Content type: Research article Published on:

  22. Spectral processing and post-experimental data analysis are the major tasks in NMR-based metabonomics studies. While there are commercial and free licensed software tools available to assist these tasks, resea...

    Authors: Tao Wang, Kang Shao, Qinying Chu, Yanfei Ren, Yiming Mu, Lijia Qu, Jie He, Changwen Jin and Bin Xia
    Citation: BMC Bioinformatics 2009 10:83
    Content type: Software Published on:

  26. Within research each experiment is different, the focus changes and the data is generated from a continually evolving barrage of technologies. There is a continual introduction of new techniques whose usage ra...

    Authors: John Boyle, Hector Rovira, Chris Cavnor, David Burdick, Sarah Killcoyne and Ilya Shmulevich
    Citation: BMC Bioinformatics 2009 10:79
    Content type: Research article Published on:

  27. Single nucleotide polymorphisms (SNPs) may be correlated due to linkage disequilibrium (LD). Association studies look for both direct and indirect associations with disease loci. In a Random Forest (RF) analys...

    Authors: Yan A Meng, Yi Yu, L Adrienne Cupples, Lindsay A Farrer and Kathryn L Lunetta
    Citation: BMC Bioinformatics 2009 10:78
    Content type: Methodology article Published on:

  28. Cross-species gene expression analyses using oligonucleotide microarrays designed to evaluate a single species can provide spurious results due to mismatches between the interrogated transcriptome and arrayed ...

    Authors: Donna M Toleno, Gabriel Renaud, Tyra G Wolfsberg, Munirul Islam, Derek E Wildman, Kimberly D Siegmund and Joseph G Hacia
    Citation: BMC Bioinformatics 2009 10:77
    Content type: Methodology article Published on:

  29. Scanning large genomes with a sliding window in search of locally stable RNA structures is a well motivated problem in bioinformatics. Given a predefined window size L and an RNA sequence S of size N (L < N), ...

    Authors: Yair Horesh, Ydo Wexler, Ilana Lebenthal, Michal Ziv-Ukelson and Ron Unger
    Citation: BMC Bioinformatics 2009 10:76
    Content type: Methodology article Published on:

  30. Despite significant progress in imaging technologies, the efficient detection of edges and elongated features in images of intracellular and multicellular structures acquired using light or electron microscopy...

    Authors: Tobias Gebäck and Petros Koumoutsakos
    Citation: BMC Bioinformatics 2009 10:75
    Content type: Methodology article Published on:

  31. R is the leading open source statistics software with a vast number of biostatistical and bioinformatical analysis packages. To exploit the advantages of R, extensive scripting/programming skills are required.

    Authors: Ilhami Visne, Erkan Dilaveroglu, Klemens Vierlinger, Martin Lauss, Ahmet Yildiz, Andreas Weinhaeusel, Christa Noehammer, Friedrich Leisch and Albert Kriegner
    Citation: BMC Bioinformatics 2009 10:74
    Content type: Software Published on:

  32. Although most of the current disease candidate gene identification and prioritization methods depend on functional annotations, the coverage of the gene functional annotations is a limiting factor. In the curr...

    Authors: Jing Chen, Bruce J Aronow and Anil G Jegga
    Citation: BMC Bioinformatics 2009 10:73
    Content type: Research article Published on:

    The Erratum to this article has been published in BMC Bioinformatics 2009 10:406

  33. Microarray technology is increasingly used to identify potential biomarkers for cancer prognostics and diagnostics. Previously, we have developed the iterative Bayesian Model Averaging (BMA) algorithm for use ...

    Authors: Amalia Annest, Roger E Bumgarner, Adrian E Raftery and Ka Yee Yeung
    Citation: BMC Bioinformatics 2009 10:72
    Content type: Methodology article Published on:

  34. Although microarray-based studies have revealed global view of gene expression in cancer cells, we still have little knowledge about regulatory mechanisms underlying the transcriptome. Several computational me...

    Authors: Atsushi Niida, Andrew D Smith, Seiya Imoto, Hiroyuki Aburatani, Michael Q Zhang and Tetsu Akiyama
    Citation: BMC Bioinformatics 2009 10:71
    Content type: Research article Published on:

  35. Recent increases in the volume and diversity of life science data and information and an increasing emphasis on data sharing and interoperability have resulted in the creation of a large number of biological o...

    Authors: Anna Maria Masci, Cecilia N Arighi, Alexander D Diehl, Anne E Lieberman, Chris Mungall, Richard H Scheuermann, Barry Smith and Lindsay G Cowell
    Citation: BMC Bioinformatics 2009 10:70
    Content type: Research article Published on:

  36. New rapid high-throughput sequencing technologies have sparked the creation of a new class of assembler. Since all high-throughput sequencing platforms incorporate errors in their output, short-read assemblers...

    Authors: Douglas W Bryant Jr, Weng-Keen Wong and Todd C Mockler
    Citation: BMC Bioinformatics 2009 10:69
    Content type: Software Published on:

  39. We introduce Approximate Entropy as a mathematical method of analysis for microarray data. Approximate entropy is applied here as a method to classify the complex gene expression patterns resultant of a clinic...

    Authors: Shaleen K Botting, Jerome P Trzeciakowski, Michelle F Benoit, Salama A Salama and Concepcion R Diaz-Arrastia
    Citation: BMC Bioinformatics 2009 10:66
    Content type: Research article Published on:

  41. An algorithm for the analysis of Affymetrix Genechips is presented. This algorithm, referred to as the Inverse Langmuir Method (ILM), estimates the binding of transcripts to complementary probes using DNA/RNA ...

    Authors: Geert CWM Mulders, Gerard T Barkema and Enrico Carlon
    Citation: BMC Bioinformatics 2009 10:64
    Content type: Research article Published on:

  42. Genome-wide association studies with single nucleotide polymorphisms (SNPs) show great promise to identify genetic determinants of complex human traits. In current analyses, genotype calling and imputation of ...

    Authors: Zhaoxia Yu, Chad Garner, Argyrios Ziogas, Hoda Anton-Culver and Daniel J Schaid
    Citation: BMC Bioinformatics 2009 10:63
    Content type: Methodology article Published on:

  43. Researchers in the field of bioinformatics often face a challenge of combining several ordered lists in a proper and efficient manner. Rank aggregation techniques offer a general and flexible framework that al...

    Authors: Vasyl Pihur, Susmita Datta and Somnath Datta
    Citation: BMC Bioinformatics 2009 10:62
    Content type: Software Published on:

  44. Various normalisation techniques have been developed in the context of microarray analysis to try to correct expression measurements for experimental bias and random fluctuations. Major techniques include: tot...

    Authors: Monica Chiogna, Maria Sofia Massa, Davide Risso and Chiara Romualdi
    Citation: BMC Bioinformatics 2009 10:61
    Content type: Methodology article Published on:

  46. Crucial foundations of any quantitative systems biology experiment are correct genome and proteome annotations. Protein databases compiled from high quality empirical protein identifications that are in turn b...

    Authors: Sandra N Loevenich, Erich Brunner, Nichole L King, Eric W Deutsch, Stephen E Stein, Ruedi Aebersold and Ernst Hafen
    Citation: BMC Bioinformatics 2009 10:59
    Content type: Database Published on:

  47. Development of a fast and accurate scoring function in virtual screening remains a hot issue in current computer-aided drug research. Different scoring functions focus on diverse aspects of ligand binding, and...

    Authors: Honglin Li, Hailei Zhang, Mingyue Zheng, Jie Luo, Ling Kang, Xiaofeng Liu, Xicheng Wang and Hualiang Jiang
    Citation: BMC Bioinformatics 2009 10:58
    Content type: Methodology article Published on:

  49. Metagenomics, or the sequencing and analysis of collective genomes (metagenomes) of microorganisms isolated from an environment, promises direct access to the "unculturable majority". This emerging field offer...

    Authors: Naryttza N Diaz, Lutz Krause, Alexander Goesmann, Karsten Niehaus and Tim W Nattkemper
    Citation: BMC Bioinformatics 2009 10:56
    Content type: Methodology article Published on:

  50. Computational enzyme design is far from being applicable for the general case. Due to computational complexity and limited knowledge of the structure-function interplay, heuristic methods have to be used.

    Authors: André Fischer, Nils Enkler, Gerd Neudert, Marco Bocola, Reinhard Sterner and Rainer Merkl
    Citation: BMC Bioinformatics 2009 10:54
    Content type: Methodology article Published on:

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