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  1. A fundamental activity in biomedical research is Knowledge Discovery which has the ability to search through large amounts of biomedical information such as documents and data. High performance computational i...

    Authors: Marcello Castellano, Giuseppe Mastronardi, Roberto Bellotti and Gianfranco Tarricone
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S23
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  2. In the biological sciences, the need to analyse vast amounts of information has become commonplace. Such large-scale analyses often involve drawing together data from a variety of different databases, held rem...

    Authors: Steve Pettifer, David Thorne, Philip McDermott, James Marsh, Alice Villéger, Douglas B Kell and Teresa K Attwood
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  3. As biological networks often show complex topological features, mathematical methods are required to extract meaningful information. Clustering methods are useful in this setting, as they allow the summary of ...

    Authors: Franck Picard, Vincent Miele, Jean-Jacques Daudin, Ludovic Cottret and Stéphane Robin
    Citation: BMC Bioinformatics 2009 10(Suppl 6):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 6

  5. The structural analysis of protein ligand binding sites can provide information relevant for assigning functions to unknown proteins, to guide the drug discovery process and to infer relations among distant pr...

    Authors: Gabriele Ausiello, Pier Federico Gherardini, Elena Gatti, Ottaviano Incani and Manuela Helmer-Citterich
    Citation: BMC Bioinformatics 2009 10:182
    Content type: Methodology article Published on:

  6. Interaction graphs (signed directed graphs) provide an important qualitative modeling approach for Systems Biology. They enable the analysis of causal relationships in cellular networks and can even be useful ...

    Authors: Steffen Klamt and Axel von Kamp
    Citation: BMC Bioinformatics 2009 10:181
    Content type: Methodology article Published on:

  7. In moderate-throughput SNP genotyping there was a gap in the workflow, between choosing a set of SNPs and submitting their sequences to proprietary assay design software, which was not met by existing software...

    Authors: Helen I Field, Serena A Scollen, Craig Luccarini, Caroline Baynes, Jonathan Morrison, Alison M Dunning, Douglas F Easton and Paul DP Pharoah
    Citation: BMC Bioinformatics 2009 10:180
    Content type: Software Published on:

  8. Proteomic protein identification results need to be compared across laboratories and platforms, and thus a reliable method is needed to estimate false discovery rates. The target-decoy strategy is a platform-i...

    Authors: Lau Sennels, Jimi-Carlo Bukowski-Wills and Juri Rappsilber
    Citation: BMC Bioinformatics 2009 10:179
    Content type: Research article Published on:

  10. The Enteropathogen Resource Integration Center (ERIC; http://​www.​ericbrc.​org) has a goal of providing bioinformatics support for the scientific communi...

    Authors: Sam Zaremba, Mila Ramos-Santacruz, Thomas Hampton, Panna Shetty, Joel Fedorko, Jon Whitmore, John M Greene, Nicole T Perna, Jeremy D Glasner, Guy Plunkett III, Matthew Shaker and David Pot
    Citation: BMC Bioinformatics 2009 10:177
    Content type: Database Published on:

  11. Analysis of allelic variation for relevant genes and monitoring chromosome segment transmission during selection are important approaches in plant breeding and ecology. To minimize the number of required molec...

    Authors: Ursula K Frei, Bernd Wollenweber and Thomas Lübberstedt
    Citation: BMC Bioinformatics 2009 10:176
    Content type: Software Published on:

  12. DNA sequence comparison is based on optimal local alignment of two sequences using a similarity score. However, some new DNA sequencing technologies do not directly measure the base sequence, but rather an enc...

    Authors: Nils Homer, Barry Merriman and Stanley F Nelson
    Citation: BMC Bioinformatics 2009 10:175
    Content type: Research article Published on:

  14. Microarray analysis of immunoprecipitated chromatin (ChIP-chip) has evolved from a novel technique to a standard approach for the systematic study of protein-DNA interactions. In ChIP-chip, sites of protein-DN...

    Authors: Wei Sun, Michael J Buck, Mukund Patel and Ian J Davis
    Citation: BMC Bioinformatics 2009 10:173
    Content type: Methodology article Published on:

  15. Copy number variations (CNVs) may play an important role in disease risk by altering dosage of genes and other regulatory elements, which may have functional and, ultimately, phenotypic consequences. Therefore...

    Authors: Juan R González, Isaac Subirana, Geòrgia Escaramís, Solymar Peraza, Alejandro Cáceres, Xavier Estivill and Lluís Armengol
    Citation: BMC Bioinformatics 2009 10:172
    Content type: Methodology article Published on:

  16. Despite increasing popularity and improvements in terminal restriction fragment length polymorphism (T-RFLP) and other microbial community fingerprinting techniques, there are still numerous obstacles that ham...

    Authors: Steven W Culman, Robert Bukowski, Hugh G Gauch, Hinsby Cadillo-Quiroz and Daniel H Buckley
    Citation: BMC Bioinformatics 2009 10:171
    Content type: Software Published on:

  17. High-throughput molecular approaches for gene expression profiling, such as Serial Analysis of Gene Expression (SAGE), Massively Parallel Signature Sequencing (MPSS) or Sequencing-by-Synthesis (SBS) represent ...

    Authors: Daniel G Pinheiro, Pedro AF Galante, Sandro J de Souza, Marco A Zago and Wilson A Silva Jr
    Citation: BMC Bioinformatics 2009 10:170
    Content type: Software Published on:

  19. Virtual screening methods start to be well established as effective approaches to identify hits, candidates and leads for drug discovery research. Among those, structure based virtual screening (SBVS) approach...

    Authors: Vincent Le Guilloux, Peter Schmidtke and Pierre Tuffery
    Citation: BMC Bioinformatics 2009 10:168
    Content type: Software Published on:

  22. Cluster analysis has become a standard computational method for gene function discovery as well as for more general explanatory data analysis. A number of different approaches have been proposed for that purpo...

    Authors: Xiaofeng Dai, Timo Erkkilä, Olli Yli-Harja and Harri Lähdesmäki
    Citation: BMC Bioinformatics 2009 10:165
    Content type: Methodology article Published on:

  23. One of the main objectives of microarray analysis is to identify differentially expressed genes for different types of cells or treatments. Many statistical methods have been proposed to assess the treatment e...

    Authors: Sin-Ho Jung, Insuk Sohn, Stephen L George, Liping Feng and Phyllis C Leppert
    Citation: BMC Bioinformatics 2009 10:164
    Content type: Methodology article Published on:

  25. Hydrogen/deuterium exchange mass spectrometry (H/DX-MS) experiments implemented to characterize protein interaction and protein folding generate large quantities of data. Organizing, processing and visualizing...

    Authors: Gordon W Slysz, Charles AH Baker, Benjamin M Bozsa, Anthony Dang, Andrew J Percy, Melissa Bennett and David C Schriemer
    Citation: BMC Bioinformatics 2009 10:162
    Content type: Software Published on:

  26. Gene set analysis (GSA) is a widely used strategy for gene expression data analysis based on pathway knowledge. GSA focuses on sets of related genes and has established major advantages over individual gene an...

    Authors: Weijun Luo, Michael S Friedman, Kerby Shedden, Kurt D Hankenson and Peter J Woolf
    Citation: BMC Bioinformatics 2009 10:161
    Content type: Research article Published on:

  27. Internal ribosomal entry sites (IRESs) provide alternative, cap-independent translation initiation sites in eukaryotic cells. IRES elements are important factors in viral genomes and are also useful tools for ...

    Authors: Tzong-Yuan Wu, Chi-Chun Hsieh, Jun-Jie Hong, Chung-Yung Chen and Yuh-Show Tsai
    Citation: BMC Bioinformatics 2009 10:160
    Content type: Methodology article Published on:

  29. Integration and exploration of data obtained from genome wide monitoring technologies has become a major challenge for many bioinformaticists and biologists due to its heterogeneity and high dimensionality. A ...

    Authors: Jaume Mercadé, Antonio Espinosa, José-Enrique Adsuara, Rosa Adrados, Jordi Segura and Tamara Maes
    Citation: BMC Bioinformatics 2009 10:158
    Content type: Software Published on:

  31. The latest generation of Affymetrix microarrays are designed to interrogate expression over the entire length of every locus, thus giving the opportunity to study alternative splicing genome-wide. The Exon 1.0...

    Authors: Mark D Robinson and Terence P Speed
    Citation: BMC Bioinformatics 2009 10:156
    Content type: Methodology article Published on:

  32. Transcriptional responses often consist of regulatory modules – sets of genes with a shared expression pattern that are controlled by the same regulatory mechanisms. Previous methods allow dissecting regulator...

    Authors: Iftach Nachman and Aviv Regev
    Citation: BMC Bioinformatics 2009 10:155
    Content type: Research article Published on:

  33. The introduction of next generation sequencing approaches has caused a rapid increase in the number of completely sequenced genomes. As one result of this development, it is now feasible to analyze large group...

    Authors: Jochen Blom, Stefan P Albaum, Daniel Doppmeier, Alfred Pühler, Frank-Jörg Vorhölter, Martha Zakrzewski and Alexander Goesmann
    Citation: BMC Bioinformatics 2009 10:154
    Content type: Software Published on:

  35. Multilocus Sequence Typing (MLST) is a frequently used typing method for the analysis of the clonal relationships among strains of several clinically relevant microbial species. MLST is based on the sequence o...

    Authors: Alexandre P Francisco, Miguel Bugalho, Mário Ramirez and João A Carriço
    Citation: BMC Bioinformatics 2009 10:152
    Content type: Methodology article Published on:

  36. DNA sequence integrity, mRNA concentrations and protein-DNA interactions have been subject to genome-wide analyses based on microarrays with ever increasing efficiency and reliability over the past fifteen yea...

    Authors: Alexandre Gattiker, Leandro Hermida, Robin Liechti, Ioannis Xenarios, Olivier Collin, Jacques Rougemont and Michael Primig
    Citation: BMC Bioinformatics 2009 10:151
    Content type: Database Published on:

  37. Protein-protein interaction (PPI) is essential to most biological processes. Abnormal interactions may have implications in a number of neurological syndromes. Given that the association and dissociation of pr...

    Authors: Nazar Zaki, Sanja Lazarova-Molnar, Wassim El-Hajj and Piers Campbell
    Citation: BMC Bioinformatics 2009 10:150
    Content type: Research article Published on:

  38. Proteases of human pathogens are becoming increasingly important drug targets, hence it is necessary to understand their substrate specificity and to interpret this knowledge in practically useful ways. New me...

    Authors: Thorsteinn Rögnvaldsson, Terence A Etchells, Liwen You, Daniel Garwicz, Ian Jarman and Paulo JG Lisboa
    Citation: BMC Bioinformatics 2009 10:149
    Content type: Methodology article Published on:

  39. Advances in high-throughput technologies available to modern biology have created an increasing flood of experimentally determined facts. Ordering, managing and describing these raw results is the first step w...

    Authors: Szymon Kaczanowski, Pawel Siedlecki and Piotr Zielenkiewicz
    Citation: BMC Bioinformatics 2009 10:148
    Content type: Software Published on:

  41. Time-course microarray experiments produce vector gene expression profiles across a series of time points. Clustering genes based on these profiles is important in discovering functional related and co-regulat...

    Authors: Tianqing Liu, Nan Lin, Ningzhong Shi and Baoxue Zhang
    Citation: BMC Bioinformatics 2009 10:146
    Content type: Methodology article Published on:

  43. Mass spectrometry-based biomarker discovery has long been hampered by the difficulty in reconciling lists of discriminatory peaks identified by different laboratories for the same diseases studied. We describe...

    Authors: Niclas C Tan, Wayne G Fisher, Kevin P Rosenblatt and Harold R Garner
    Citation: BMC Bioinformatics 2009 10:144
    Content type: Research article Published on:

  44. Next generation sequencing technologies hold great potential for many biological questions. While mainly used for genomic sequencing, they are also very promising for gene expression profiling. Sequencing of c...

    Authors: Robert Kofler, Tatiana Teixeira Torres, Tamas Lelley and Christian Schlötterer
    Citation: BMC Bioinformatics 2009 10:143
    Content type: Software Published on:

  46. Quantitative measurements of specific protein phosphorylation sites, as presented here, can be used to investigate signal transduction pathways, which is an important aspect of cell dynamics. The presented met...

    Authors: Claus A Andersen, Stefano Gotta, Letizia Magnoni, Roberto Raggiaschi, Andreas Kremer and Georg C Terstappen
    Citation: BMC Bioinformatics 2009 10:141
    Content type: Methodology article Published on:

  48. High-throughput genotyping and phenotyping projects of large epidemiological study populations require sophisticated laboratory information management systems. Most epidemiological studies include subject-rela...

    Authors: Sebastian Schönherr, Hansi Weißensteiner, Stefan Coassin, Günther Specht, Florian Kronenberg and Anita Brandstätter
    Citation: BMC Bioinformatics 2009 10:139
    Content type: Database Published on:

  49. Microarray technology is so expensive and powerful that it is essential to extract maximum value from microarray data, specially from large-sample-series microarrays. Our web tools attempt to respond to these ...

    Authors: Mario Huerta, Juan Cedano, Dario Peña, Antonio Rodriguez and Enrique Querol
    Citation: BMC Bioinformatics 2009 10:138
    Content type: Software Published on:

  50. The problem of finding the shortest absent words in DNA data has been recently addressed, and algorithms for its solution have been described. It has been noted that longer absent words might also be of intere...

    Authors: Armando J Pinho, Paulo JSG Ferreira, Sara P Garcia and João MOS Rodrigues
    Citation: BMC Bioinformatics 2009 10:137
    Content type: Research article Published on:

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