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  1. Tandem mass spectrometry has emerged as a cornerstone of high throughput proteomic studies owing in part to various high throughput search engines which are used to interpret these tandem mass spectra. However...

    Authors: Fang-Xiang Wu, Pierre Gagné, Arnaud Droit and Guy G Poirier
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  2. In accordance with the increasing amount of information concerning individual differences in drug response and molecular interaction, the role of in silico prediction of drug interaction on the pathway level is b...

    Authors: Takeshi Arikuma, Sumi Yoshikawa, Ryuzo Azuma, Kentaro Watanabe, Kazumi Matsumura and Akihiko Konagaya
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  3. Analysis of gene expression data for tumor classification is an important application of bioinformatics methods. But it is hard to analyse gene expression data from DNA microarray experiments by commonly used ...

    Authors: Xue-Qiang Zeng, Guo-Zheng Li, Jack Y Yang, Mary Qu Yang and Geng-Feng Wu
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  4. Graphs and networks are common analysis representations for biological systems. Many traditional graph algorithms such as k-clique, k-coloring, and subgraph matching have great potential as analysis techniques...

    Authors: George Chin Jr, Daniel G Chavarria, Grant C Nakamura and Heidi J Sofia
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  5. Localization of complex traits by genetic linkage analysis may involve exploration of a vast multidimensional parameter space. The posterior probability of linkage (PPL), a class of statistics for complex trai...

    Authors: Manika Govil, Alberto M Segre and Veronica J Vieland
    Citation: BMC Bioinformatics 2008 9(Suppl 6):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 6

  6. A number of studies have used protein interaction data alone for protein function prediction. Here, we introduce a computational approach for annotation of enzymes, based on the observation that similar protei...

    Authors: Jordi Espadaler, Narayanan Eswar, Enrique Querol, Francesc X Avilés, Andrej Sali, Marc A Marti-Renom and Baldomero Oliva
    Citation: BMC Bioinformatics 2008 9:249
    Content type: Methodology article Published on:

  9. Association testing is a powerful tool for identifying disease susceptibility genes underlying complex diseases. Technological advances have yielded a dramatic increase in the density of available genetic mark...

    Authors: Ie-Bin Lian, Yi-Hsien Lin, Ying-Chao Lin, Hsin-Chou Yang, Chee-Jang Chang and Cathy SJ Fann
    Citation: BMC Bioinformatics 2008 9:246
    Content type: Methodology article Published on:

  10. We have previously described an approach to predicting the substrate specificity of serine-threonine protein kinases. The method, named Predikin, identifies key conserved substrate-determining residues in the kin...

    Authors: Neil FW Saunders, Ross I Brinkworth, Thomas Huber, Bruce E Kemp and Bostjan Kobe
    Citation: BMC Bioinformatics 2008 9:245
    Content type: Software Published on:

  11. The combination of gene expression profiling with linkage analysis has become a powerful paradigm for mapping gene expression quantitative trait loci (eQTL). To date, most studies have searched for eQTL by ana...

    Authors: Shameek Biswas, John D Storey and Joshua M Akey
    Citation: BMC Bioinformatics 2008 9:244
    Content type: Methodology article Published on:

  12. Recent advances in global genomic profiling methodologies have enabled multi-dimensional characterization of biological systems. Complete analysis of these genomic profiles require an in depth look at parallel...

    Authors: Bryan Chi, Ronald J deLeeuw, Bradley P Coe, Raymond T Ng, Calum MacAulay and Wan L Lam
    Citation: BMC Bioinformatics 2008 9:243
    Content type: Software Published on:

  13. Publicly available DNA sequence databases such as GenBank are large, and are growing at an exponential rate. The sheer volume of data being dealt with presents serious storage and data communications problems....

    Authors: W Timothy J White and Michael D Hendy
    Citation: BMC Bioinformatics 2008 9:242
    Content type: Software Published on:

  14. Bioactivity profiling using high-throughput in vitro assays can reduce the cost and time required for toxicological screening of environmental chemicals and can also reduce the need for animal testing. Several pu...

    Authors: Richard Judson, Fathi Elloumi, R Woodrow Setzer, Zhen Li and Imran Shah
    Citation: BMC Bioinformatics 2008 9:241
    Content type: Research article Published on:

  15. Cellular metabolism is one of the most investigated system of biological interactions. While the topological nature of individual reactions and pathways in the network is quite well understood there is still a...

    Authors: Alfredo Braunstein, Roberto Mulet and Andrea Pagnani
    Citation: BMC Bioinformatics 2008 9:240
    Content type: Methodology article Published on:

  16. DNA sequencing is now emerging as an important component in biomedical studies of diseases like cancer. Short-read, highly parallel sequencing instruments are expected to be used heavily for such projects, but...

    Authors: Michael C Wendl and Richard K Wilson
    Citation: BMC Bioinformatics 2008 9:239
    Content type: Research article Published on:

  17. Multifactor Dimensionality Reduction (MDR) has been introduced previously as a non-parametric statistical method for detecting gene-gene interactions. MDR performs a dimensional reduction by assigning multi-lo...

    Authors: William S Bush, Todd L Edwards, Scott M Dudek, Brett A McKinney and Marylyn D Ritchie
    Citation: BMC Bioinformatics 2008 9:238
    Content type: Research article Published on:

  18. With the amount of influenza genome sequence data growing rapidly, researchers need machine assistance in selecting datasets and exploring the data. Enhanced visualization tools are required to represent resul...

    Authors: Leonid Zaslavsky, Yiming Bao and Tatiana A Tatusova
    Citation: BMC Bioinformatics 2008 9:237
    Content type: Methodology article Published on:

  20. Higher eukaryotic genomes are typically large, complex and filled with both genes and multiple classes of repetitive DNA. The repetitive DNAs, primarily transposable elements, are a rapidly evolving genome com...

    Authors: Jeremy D DeBarry, Renyi Liu and Jeffrey L Bennetzen
    Citation: BMC Bioinformatics 2008 9:235
    Content type: Software Published on:

  23. Utilization of alternative initiation sites for protein translation directed by non-AUG codons in mammalian mRNAs is observed with increasing frequency. Alternative initiation sites are utilized for the synthe...

    Authors: Jill L Wegrzyn, Thomas M Drudge, Faramarz Valafar and Vivian Hook
    Citation: BMC Bioinformatics 2008 9:232
    Content type: Research article Published on:

  26. The structure of many eukaryotic cell regulatory proteins is highly modular. They are assembled from globular domains, segments of natively disordered polypeptides and short linear motifs. The latter are invol...

    Authors: Claudia Chica, Alberto Labarga, Cathryn M Gould, Rodrigo López and Toby J Gibson
    Citation: BMC Bioinformatics 2008 9:229
    Content type: Methodology article Published on:

  27. Expression profiles obtained from multiple perturbation experiments are increasingly used to reconstruct transcriptional regulatory networks, from well studied, simple organisms up to higher eukaryotes. Admitt...

    Authors: Philippe Veber, Carito Guziolowski, Michel Le Borgne, Ovidiu Radulescu and Anne Siegel
    Citation: BMC Bioinformatics 2008 9:228
    Content type: Methodology article Published on:

  28. 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:

  29. 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:

  30. 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:

  32. 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:

  33. 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:

  34. 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:

  36. 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

  37. 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

  38. 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

  39. 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

  40. 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

  41. 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:

  43. 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:

  44. 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:

  45. 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:

  46. 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:

  48. 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

  49. 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

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