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  3. Microarray technology has become very popular for globally evaluating gene expression in biological samples. However, non-linear variation associated with the technology can make data interpretation unreliable...

    Authors: Carl R Pelz, Molly Kulesz-Martin, Grover Bagby and Rosalie C Sears
    Citation: BMC Bioinformatics 2008 9:520
    Content type: Methodology article Published on:

  4. Proteomic profiling using mass spectrometry (MS) is one of the most promising methods for the analysis of complex biological samples such as urine, serum and tissue for biomarker discovery. Such experiments ar...

    Authors: David A Cairns, David N Perkins, Anthea J Stanley, Douglas Thompson, Jennifer H Barrett, Peter J Selby and Rosamonde E Banks
    Citation: BMC Bioinformatics 2008 9:519
    Content type: Methodology article Published on:

  5. OMA is a project that aims to identify orthologs within publicly available, complete genomes. With 657 genomes analyzed to date, OMA is one of the largest projects of its kind.

    Authors: Alexander CJ Roth, Gaston H Gonnet and Christophe Dessimoz
    Citation: BMC Bioinformatics 2008 9:518
    Content type: Methodology article Published on:

  7. Due to recent progress in genome sequencing, more and more data for phylogenetic reconstruction based on rearrangement distances between genomes become available. However, this phylogenetic reconstruction is a...

    Authors: Martin Bader, Mohamed I Abouelhoda and Enno Ohlebusch
    Citation: BMC Bioinformatics 2008 9:516
    Content type: Methodology article Published on:

  8. Accurate peptide identification is important to high-throughput proteomics analyses that use mass spectrometry. Search programs compare fragmentation spectra (MS/MS) of peptides from complex digests with theor...

    Authors: Allison Gehrke, Shaojun Sun, Lukasz Kurgan, Natalie Ahn, Katheryn Resing, Karen Kafadar and Krzysztof Cios
    Citation: BMC Bioinformatics 2008 9:515
    Content type: Research article Published on:

  9. Reliable prediction of antibody, or B-cell, epitopes remains challenging yet highly desirable for the design of vaccines and immunodiagnostics. A correlation between antigenicity, solvent accessibility, and fl...

    Authors: Julia Ponomarenko, Huynh-Hoa Bui, Wei Li, Nicholas Fusseder, Philip E Bourne, Alessandro Sette and Bjoern Peters
    Citation: BMC Bioinformatics 2008 9:514
    Content type: Software Published on:

  10. The power of haplotype-based methods for association studies, identification of regions under selection, and ancestral inference, is well-established for diploid organisms. For polyploids, however, the difficu...

    Authors: Shu-Yi Su, Jonathan White, David J Balding and Lachlan JM Coin
    Citation: BMC Bioinformatics 2008 9:513
    Content type: Research article Published on:

  12. The nucleotide substitution rate matrix is a key parameter of molecular evolution. Several methods for inferring this parameter have been proposed, with different mathematical bases. These methods include coun...

    Authors: Maribeth Oscamou, Daniel McDonald, Von Bing Yap, Gavin A Huttley, Manuel E Lladser and Rob Knight
    Citation: BMC Bioinformatics 2008 9:511
    Content type: Research article Published on:

  13. Protein remote homology detection and fold recognition are central problems in bioinformatics. Currently, discriminative methods based on support vector machine (SVM) are the most effective and accurate method...

    Authors: Bin Liu, Xiaolong Wang, Lei Lin, Qiwen Dong and Xuan Wang
    Citation: BMC Bioinformatics 2008 9:510
    Content type: Research article Published on:

  14. The propensity of oligonucleotide strands to form stable duplexes with complementary sequences is fundamental to a variety of biological and biotechnological processes as various as microRNA signalling, microa...

    Authors: Thomas Naiser, Jona Kayser, Timo Mai, Wolfgang Michel and Albrecht Ott
    Citation: BMC Bioinformatics 2008 9:509
    Content type: Research article Published on:

  15. Large biological data sets, such as expression profiles, benefit from reduction of random noise. Principal component (PC) analysis has been used for this purpose, but it tends to remove small features as well ...

    Authors: Joseph W Foley and Fumiaki Katagiri
    Citation: BMC Bioinformatics 2008 9:508
    Content type: Methodology article Published on:

  16. One-dimensional (1D) 1H nuclear magnetic resonance (NMR) spectroscopy is widely used in metabolomic studies involving biofluids and tissue extracts. There are several software packages that support compound ident...

    Authors: Jianguo Xia, Trent C Bjorndahl, Peter Tang and David S Wishart
    Citation: BMC Bioinformatics 2008 9:507
    Content type: Research article Published on:

  18. High-throughput microarrays are widely used to study gene expression across tissues and developmental stages. Analysis of gene expression data is challenging in these experiments due to the presence of signifi...

    Authors: Terri T Ni, William J Lemon, Yu Shyr and Tao P Zhong
    Citation: BMC Bioinformatics 2008 9:505
    Content type: Methodology article Published on:

  19. Liquid chromatography coupled to mass spectrometry (LC/MS) is an important analytical technology for e.g. metabolomics experiments. Determining the boundaries, centres and intensities of the two-dimensional si...

    Authors: Ralf Tautenhahn, Christoph Böttcher and Steffen Neumann
    Citation: BMC Bioinformatics 2008 9:504
    Content type: Research article Published on:

  22. There is accumulating evidence that the milieu of repeat elements and other non-genic sequence features at a given chromosomal locus, here defined as the genome environment, can play an important role in regul...

    Authors: Derek Huntley, Y Amy Tang, Tatyana B Nesterova, Sarah Butcher and Neil Brockdorff
    Citation: BMC Bioinformatics 2008 9:501
    Content type: Software Published on:

  23. Post translational modifications (PTMs) occur in the vast majority of proteins and are essential for function. Prediction of the sequence location of PTMs enhances the functional characterisation of proteins. ...

    Authors: Stephen E Hamby and Jonathan D Hirst
    Citation: BMC Bioinformatics 2008 9:500
    Content type: Research article Published on:

  24. One of the greatest challenges in Metabolic Engineering is to develop quantitative models and algorithms to identify a set of genetic manipulations that will result in a microbial strain with a desirable metab...

    Authors: Miguel Rocha, Paulo Maia, Rui Mendes, José P Pinto, Eugénio C Ferreira, Jens Nielsen, Kiran Raosaheb Patil and Isabel Rocha
    Citation: BMC Bioinformatics 2008 9:499
    Content type: Research article Published on:

  25. The recent availability of complete sequences for numerous closely related bacterial genomes opens up new challenges in comparative genomics. Several methods have been developed to align complete genomes at th...

    Authors: Hélène Chiapello, Annie Gendrault, Christophe Caron, Jérome Blum, Marie-Agnès Petit and Meriem El Karoui
    Citation: BMC Bioinformatics 2008 9:498
    Content type: Database Published on:

  26. The use of clustering methods for the discovery of cancer subtypes has drawn a great deal of attention in the scientific community. While bioinformaticians have proposed new clustering methods that take advant...

    Authors: Marcilio CP de Souto, Ivan G Costa, Daniel SA de Araujo, Teresa B Ludermir and Alexander Schliep
    Citation: BMC Bioinformatics 2008 9:497
    Content type: Research article Published on:

  27. Molecular typing methods are commonly used to study genetic relationships among bacterial isolates. Many of these methods have become standardized and produce portable data. A popular approach for analyzing su...

    Authors: Josephine F Reyes, Andrew R Francis and Mark M Tanaka
    Citation: BMC Bioinformatics 2008 9:496
    Content type: Research article Published on:

  28. The identification of transcription factor binding sites is difficult since they are only a small number of nucleotides in size, resulting in large numbers of false positives and false negatives in current app...

    Authors: Matthew S Hestand, Michiel van Galen, Michel P Villerius, Gert-Jan B van Ommen, Johan T den Dunnen and Peter AC 't Hoen
    Citation: BMC Bioinformatics 2008 9:495
    Content type: Software Published on:

  29. Some splicing isoform-specific transcriptional regulations are related to disease. Therefore, detection of disease specific splice variations is the first step for finding disease specific transcriptional regu...

    Authors: Kazuyuki Numata, Ryo Yoshida, Masao Nagasaki, Ayumu Saito, Seiya Imoto and Satoru Miyano
    Citation: BMC Bioinformatics 2008 9:494
    Content type: Software Published on:

  30. Microarray experimentation requires the application of complex analysis methods as well as the use of non-trivial computer technologies to manage the resultant large data sets. This, together with the prolifer...

    Authors: G Barton, J Abbott, N Chiba, DW Huang, Y Huang, M Krznaric, J Mack-Smith, A Saleem, BT Sherman, B Tiwari, C Tomlinson, T Aitman, J Darlington, L Game, MJE Sternberg and SA Butcher
    Citation: BMC Bioinformatics 2008 9:493
    Content type: Software Published on:

  33. DNA microarrays, which determine the expression levels of tens of thousands of genes from a sample, are an important research tool. However, the volume of data they produce can be an obstacle to interpretation...

    Authors: Alexander L Richards, Peter Holmans, Michael C O'Donovan, Michael J Owen and Lesley Jones
    Citation: BMC Bioinformatics 2008 9:490
    Content type: Research article Published on:

  34. In microarray experiments the numbers of replicates are often limited due to factors such as cost, availability of sample or poor hybridization. There are currently few choices for the analysis of a pair of mi...

    Authors: Robert W Reid and Anthony A Fodor
    Citation: BMC Bioinformatics 2008 9:489
    Content type: Methodology article Published on:

  35. Indexing is a crucial step in any information retrieval system. In MEDLINE, a widely used database of the biomedical literature, the indexing process involves the selection of Medical Subject Headings in order to...

    Authors: Aurélie Névéol, Sonya E Shooshan and Vincent Claveau
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  36. Due to the nature of scientific methodology, research articles are rich in speculative and tentative statements, also known as hedges. We explore a linguistically motivated approach to the problem of recognizi...

    Authors: Halil Kilicoglu and Sabine Bergler
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  37. Detecting uncertain and negative assertions is essential in most BioMedical Text Mining tasks where, in general, the aim is to derive factual knowledge from textual data. This article reports on a corpus annot...

    Authors: Veronika Vincze, György Szarvas, Richárd Farkas, György Móra and János Csirik
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  38. Previous studies of named entity recognition have shown that a reasonable level of recognition accuracy can be achieved by using machine learning models such as conditional random fields or support vector mach...

    Authors: Yoshimasa Tsuruoka, Jun'ichi Tsujii and Sophia Ananiadou
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  39. Like text in other domains, biomedical documents contain a range of terms with more than one possible meaning. These ambiguities form a significant obstacle to the automatic processing of biomedical texts. Pre...

    Authors: Mark Stevenson, Yikun Guo, Robert Gaizauskas and David Martinez
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  40. Term identification is the task of grounding ambiguous mentions of biomedical named entities in text to unique database identifiers. Previous work on term identification has focused on studying species-specifi...

    Authors: Xinglong Wang and Michael Matthews
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  41. When term ambiguity and variability are very high, dictionary-based Named Entity Recognition (NER) is not an ideal solution even though large-scale terminological resources are available. Many researches on stati...

    Authors: Yutaka Sasaki, Yoshimasa Tsuruoka, John McNaught and Sophia Ananiadou
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  43. The Clinical E-Science Framework (CLEF) project has built a system to extract clinically significant information from the textual component of medical records in order to support clinical research, evidence-ba...

    Authors: Angus Roberts, Robert Gaizauskas, Mark Hepple and Yikun Guo
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  44. Automated extraction of protein-protein interactions (PPI) is an important and widely studied task in biomedical text mining. We propose a graph kernel based approach for this task. In contrast to earlier appr...

    Authors: Antti Airola, Sampo Pyysalo, Jari Björne, Tapio Pahikkala, Filip Ginter and Tapio Salakoski
    Citation: BMC Bioinformatics 2008 9(Suppl 11):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 11

  46. An important emerging trend in the analysis of microarray data is to incorporate known pathway information a priori. Expression level "summaries" for pathways, obtained from the expression data for the genes c...

    Authors: Rosemary Braun, Leslie Cope and Giovanni Parmigiani
    Citation: BMC Bioinformatics 2008 9:488
    Content type: Methodology article Published on:

  47. By using a standard Support Vector Machine (SVM) with a Sequential Minimal Optimization (SMO) method of training, Naïve Bayes and other machine learning algorithms we are able to distinguish between two classe...

    Authors: Myron Peto, Andrzej Kloczkowski, Vasant Honavar and Robert L Jernigan
    Citation: BMC Bioinformatics 2008 9:487
    Content type: Research article Published on:

  48. 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:

  50. The rate of mRNA transcription is controlled by transcription factors that bind to specific DNA motifs in promoter regions upstream of protein coding genes. Recent results indicate that not only the presence o...

    Authors: Jakub Orzechowski Westholm, Feifei Xu, Hans Ronne and Jan Komorowski
    Citation: BMC Bioinformatics 2008 9:484
    Content type: Research article Published on:

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