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  1. Currently, there is a gap between purely theoretical studies of the topology of large bioregulatory networks and the practical traditions and interests of experimentalists. While the theoretical approaches emp...

    Authors: Anatolij P Potapov, Björn Goemann and Edgar Wingender
    Citation: BMC Bioinformatics 2008 9:227
    Content type: Methodology article Published on:

  2. Protein structure prediction methods provide accurate results when a homologous protein is predicted, while poorer predictions are obtained in the absence of homologous templates. However, some protein chains ...

    Authors: Lukasz Kurgan, Krzysztof Cios and Ke Chen
    Citation: BMC Bioinformatics 2008 9:226
    Content type: Methodology article Published on:

  3. Genes interact with each other as basic building blocks of life, forming a complicated network. The relationship between groups of genes with different functions can be represented as gene networks. With the d...

    Authors: Jong-Min Kim, Yoon-Sung Jung, Engin A Sungur, Kap-Hoon Han, Changyi Park and Insuk Sohn
    Citation: BMC Bioinformatics 2008 9:225
    Content type: Methodology article Published on:

  5. There are several situations in population biology research where simulating DNA sequences is useful. Simulation of biological populations under different evolutionary genetic models can be undertaken using ba...

    Authors: Antonio Carvajal-Rodríguez
    Citation: BMC Bioinformatics 2008 9:223
    Content type: Software Published on:

  6. RNAmute is an interactive Java application which, given an RNA sequence, calculates the secondary structure of all single point mutations and organizes them into categories according to their similarity to the...

    Authors: Alexander Churkin and Danny Barash
    Citation: BMC Bioinformatics 2008 9:222
    Content type: Methodology article Published on:

  7. Fitting four-parameter sigmoidal models is one of the methods established in the analysis of quantitative real-time PCR (qPCR) data. We had observed that these models are not optimal in the fitting outcome due...

    Authors: Andrej-Nikolai Spiess, Caroline Feig and Christian Ritz
    Citation: BMC Bioinformatics 2008 9:221
    Content type: Methodology article Published on:

  9. Many bioinformatics applications rely on controlled vocabularies or ontologies to consistently interpret and seamlessly integrate information scattered across public resources. Experimental data sets from meta...

    Authors: Irena Spasić, Daniel Schober, Susanna-Assunta Sansone, Dietrich Rebholz-Schuhmann, Douglas B Kell and Norman W Paton
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  10. Several semantic similarity measures have been applied to gene products annotated with Gene Ontology terms, providing a basis for their functional comparison. However, it is still unclear which is the best app...

    Authors: Catia Pesquita, Daniel Faria, Hugo Bastos, António EN Ferreira, André O Falcão and Francisco M Couto
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  11. Although the UniProt KnowledgeBase is not a medical-oriented database, it contains information on more than 2,000 human proteins involved in pathologies. However, these annotations are not standardized, which ...

    Authors: Anaïs Mottaz, Yum L Yip, Patrick Ruch and Anne-Lise Veuthey
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  12. To address the challenges of information integration and retrieval, the computational genomics community increasingly has come to rely on the methodology of creating annotations of scientific literature using ...

    Authors: David P Hill, Barry Smith, Monica S McAndrews-Hill and Judith A Blake
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  13. Bio-ontologies are key elements of knowledge management in bioinformatics. Rich and rigorous bio-ontologies should represent biological knowledge with high fidelity and robustness. The richness in bio-ontologi...

    Authors: Mikel Egaña Aranguren, Erick Antezana, Martin Kuiper and Robert Stevens
    Citation: BMC Bioinformatics 2008 9(Suppl 5):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 9 Supplement 5

  14. Aligning homologous non-coding RNAs (ncRNAs) correctly in terms of sequence and structure is an unresolved problem, due to both mathematical complexity and imperfect scoring functions. High quality alignments,...

    Authors: Andreas Wilm, Kornelia Linnenbrink and Gerhard Steger
    Citation: BMC Bioinformatics 2008 9:219
    Content type: Methodology article Published on:

  16. Metagenomics is an approach to the characterization of microbial genomes via the direct isolation of genomic sequences from the environment without prior cultivation. The amount of metagenomic sequence data is...

    Authors: Katharina J Hoff, Maike Tech, Thomas Lingner, Rolf Daniel, Burkhard Morgenstern and Peter Meinicke
    Citation: BMC Bioinformatics 2008 9:217
    Content type: Methodology article Published on:

  17. Most microarray studies are made using labelling with one or two dyes which allows the hybridization of one or two samples on the same slide. In such experiments, the most frequently used dyes are Cy 3 and Cy 5. ...

    Authors: Marie-Laure Martin-Magniette, Julie Aubert, Avner Bar-Hen, Samira Elftieh, Frederic Magniette, Jean-Pierre Renou and Jean-Jacques Daudin
    Citation: BMC Bioinformatics 2008 9:216
    Content type: Research article Published on:

  18. In metagenomic studies, a process called binning is necessary to assign contigs that belong to multiple species to their respective phylogenetic groups. Most of the current methods of binning, such as BLAST, k-me...

    Authors: Chon-Kit Kenneth Chan, Arthur L Hsu, Saman K Halgamuge and Sen-Lin Tang
    Citation: BMC Bioinformatics 2008 9:215
    Content type: Methodology article Published on:

  20. Linear motifs (LMs) are abundant short regulatory sites used for modulating the functions of many eukaryotic proteins. They play important roles in post-translational modification, cell compartment targeting, ...

    Authors: Emmanuel Perrodou, Claudia Chica, Olivier Poch, Toby J Gibson and Julie D Thompson
    Citation: BMC Bioinformatics 2008 9:213
    Content type: Research article Published on:

  22. PCR primer design is an everyday, but not trivial task requiring state-of-the-art software. We describe the popular tool GeneFisher and explain its recent restructuring using workflow techniques. We apply a se...

    Authors: Anna-Lena Lamprecht, Tiziana Margaria, Bernhard Steffen, Alexander Sczyrba, Sven Hartmeier and Robert Giegerich
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  23. With Bio-jETI, we introduce a service platform for interdisciplinary work on biological application domains and illustrate its use in a concrete application concerning statistical data processing in R and xcms...

    Authors: Tiziana Margaria, Christian Kubczak and Bernhard Steffen
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  25. Biomedical and chemical databases are large and rapidly growing in size. Graphs naturally model such kinds of data. To fully exploit the wealth of information in these graph databases, a key role is played by ...

    Authors: Alfredo Ferro, Rosalba Giugno, Misael Mongiovì, Alfredo Pulvirenti, Dmitry Skripin and Dennis Shasha
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  26. Significance analysis at single gene level may suffer from the limited number of samples and experimental noise that can severely limit the power of the chosen statistical test. This problem is typically appro...

    Authors: Mirko Francesconi, Daniel Remondini, Nicola Neretti, John M Sedivy, Leon N Cooper, Ettore Verondini, Luciano Milanesi and Gastone Castellani
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  27. Metabolic networks present a complex interconnected structure, whose understanding is in general a non-trivial task. Several formal approaches have been developed to support the investigation of such networks....

    Authors: Chiara Bodei, Andrea Bracciali and Davide Chiarugi
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  28. Research in life sciences is benefiting from a large availability of formal description techniques and analysis methodologies. These allow both the phenomena investigated to be precisely modeled and virtual ex...

    Authors: Andrea Bracciali, Marcello Brunelli, Enrico Cataldo and Pierpaolo Degano
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  29. The recent availability of high-throughput data in molecular biology has increased the need for a formal representation of this knowledge domain. New ontologies are being developed to formalize knowledge, e.g....

    Authors: Andrea Splendiani
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  30. Amines are biogenic amino acid derivatives, which play pleiotropic and very important yet complex roles in animal physiology. For many other relevant biomolecules, biochemical and molecular data are being accu...

    Authors: Ismael Navas-Delgado, Raúl Montañez, Almudena Pino-Ángeles, Aurelio A Moya-García, José Luis Urdiales, Francisca Sánchez-Jiménez and José F Aldana-Montes
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  31. Tissue MicroArray technique is becoming increasingly important in pathology for the validation of experimental data from transcriptomic analysis. This approach produces many images which need to be properly ma...

    Authors: Federica Viti, Ivan Merelli, Andrea Caprera, Barbara Lazzari, Alessandra Stella and Luciano Milanesi
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  32. Complexity and amount of post-genomic data constitute two major factors limiting the application of Knowledge Discovery in Databases (KDD) methods in life sciences. Bio-ontologies may nowadays play key roles i...

    Authors: Adrien Coulet, Malika Smaïl-Tabbone, Pascale Benlian, Amedeo Napoli and Marie-Dominique Devignes
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  33. The engineering of ontologies, especially with a view to a text-mining use, is still a new research field. There does not yet exist a well-defined theory and technology for ontology construction. Many of the o...

    Authors: Dimitra Alexopoulou, Thomas Wächter, Laura Pickersgill, Cecilia Eyre and Michael Schroeder
    Citation: BMC Bioinformatics 2008 9(Suppl 4):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 4

  36. The DNA microarray technology allows the measurement of expression levels of thousands of genes under tens/hundreds of different conditions. In microarray data, genes with similar functions usually co-express ...

    Authors: Kin-On Cheng, Ngai-Fong Law, Wan-Chi Siu and Alan Wee-Chung Liew
    Citation: BMC Bioinformatics 2008 9:210
    Content type: Methodology article Published on:

  38. Genes that are co-expressed tend to be involved in the same biological process. However, co-expression is not a very reliable predictor of functional links between genes. The evolutionary conservation of co-ex...

    Authors: Martin Oti, Jeroen van Reeuwijk, Martijn A Huynen and Han G Brunner
    Citation: BMC Bioinformatics 2008 9:208
    Content type: Methodology article Published on:

  39. The increasing amount of published literature in biomedicine represents an immense source of knowledge, which can only efficiently be accessed by a new generation of automated information extraction tools. Nam...

    Authors: Markus Bundschus, Mathaeus Dejori, Martin Stetter, Volker Tresp and Hans-Peter Kriegel
    Citation: BMC Bioinformatics 2008 9:207
    Content type: Research article Published on:

  40. With the completion of the Human Genome Project and recent advancements in mutation detection technologies, the volume of data available on genetic variations has risen considerably. These data are stored in o...

    Authors: Timothy D Smith and Richard GH Cotton
    Citation: BMC Bioinformatics 2008 9:206
    Content type: Software Published on:

  41. Synthesis of data from published human genetic association studies is a critical step in the translation of human genome discoveries into health applications. Although genetic association studies account for a...

    Authors: Wei Yu, Melinda Clyne, Siobhan M Dolan, Ajay Yesupriya, Anja Wulf, Tiebin Liu, Muin J Khoury and Marta Gwinn
    Citation: BMC Bioinformatics 2008 9:205
    Content type: Software Published on:

  42. Single nucleotide polymorphisms (SNPs) are the most common genetic variations in the human genome and are useful as genomic markers. Oligonucleotide SNP microarrays have been developed for high-throughput geno...

    Authors: Cheng Li, Rameen Beroukhim, Barbara A Weir, Wendy Winckler, Levi A Garraway, William R Sellers and Matthew Meyerson
    Citation: BMC Bioinformatics 2008 9:204
    Content type: Research article Published on:

  43. Integrating data from multiple global assays and curated databases is essential to understand the spatio-temporal interactions within cells. Different experiments measure cellular processes at various widths a...

    Authors: Yuji Zhang, Jianhua Xuan, Benildo G de los Reyes, Robert Clarke and Habtom W Ressom
    Citation: BMC Bioinformatics 2008 9:203
    Content type: Research article Published on:

  44. Missing values frequently pose problems in gene expression microarray experiments as they can hinder downstream analysis of the datasets. While several missing value imputation approaches are available to the ...

    Authors: Johannes Tuikkala, Laura L Elo, Olli S Nevalainen and Tero Aittokallio
    Citation: BMC Bioinformatics 2008 9:202
    Content type: Research article Published on:

  45. Malaria parasite secretes various proteins in infected RBC for its growth and survival. Thus identification of these secretory proteins is important for developing vaccine/drug against malaria. The existing mo...

    Authors: Ruchi Verma, Ajit Tiwari, Sukhwinder Kaur, Grish C Varshney and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2008 9:201
    Content type: Research article Published on:

  46. During the last decade, the use of microarrays to assess the transcriptome of many biological systems has generated an enormous amount of data. A common technique used to organize and analyze microarray data i...

    Authors: Piotr Kraj, Ashok Sharma, Nikhil Garge, Robert Podolsky and Richard A McIndoe
    Citation: BMC Bioinformatics 2008 9:200
    Content type: Software Published on:

  48. Determining the function of uncharacterized proteins is a major challenge in the post-genomic era due to the problem's complexity and scale. Identifying a protein's function contributes to an understanding of ...

    Authors: Aaron P Gabow, Sonia M Leach, William A Baumgartner, Lawrence E Hunter and Debra S Goldberg
    Citation: BMC Bioinformatics 2008 9:198
    Content type: Research article Published on:

  50. With the advent of high throughput biotechnology data acquisition platforms such as micro arrays, SNP chips and mass spectrometers, data sets with many more variables than observations are now routinely being ...

    Authors: Harri T Kiiveri
    Citation: BMC Bioinformatics 2008 9:195
    Content type: Methodology article Published on:

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