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  1. A mathematical model to understand, predict, control, or even design a real biological system is a central theme in systems biology. A dynamic biological system is always modeled as a nonlinear ordinary differ...

    Authors: Wu Hsiung Wu, Feng Sheng Wang and Maw Shang Chang
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S17
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  2. Signal peptides (SPs) mediate the targeting of secretory precursor proteins to the correct subcellular compartments in prokaryotes and eukaryotes. Identifying these transient peptides is crucial to the medical...

    Authors: Khar Heng Choo and Shoba Ranganathan
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S15
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  3. The rapid growth of protein-protein interaction (PPI) data has led to the emergence of PPI network analysis. Despite advances in high-throughput techniques, the interactomes of several model organisms are stil...

    Authors: Sheng-An Lee, Cheng-hsiung Chan, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao and Chi-Ying F Huang
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  4. Single nucleotide polymorphisms (SNPs) are the most commonly studied units of genetic variation. The discovery of such variation may help to identify causative gene mutations in monogenic diseases and SNPs ass...

    Authors: Chumpol Ngamphiw, Supasak Kulawonganunchai, Anunchai Assawamakin, Ekachai Jenwitheesuk and Sissades Tongsima
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  5. Transcription factor binding sites (TFBSs) are crucial in the regulation of gene transcription. Recently, chromatin immunoprecipitation followed by cDNA microarray hybridization (ChIP-chip array) has been used...

    Authors: Chung-Chin Lu, Wei-Hao Yuan and Te-Ming Chen
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  6. MicroRNAs (miRNAs) are a class of small non-coding RNA molecules (20–24 nt), which are believed to participate in repression of gene expression. They play important roles in several biological processes (e.g. ...

    Authors: Dang Hung Tran, Kenji Satou and Tu Bao Ho
    Citation: BMC Bioinformatics 2008 9(Suppl 12):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 9 Supplement 12

  7. Eukaryotic DNA replication is regulated at the level of large chromosomal domains (0.5–5 megabases in mammals) within which replicons are activated relatively synchronously. These domains replicate in a specif...

    Authors: Nodin Weddington, Alexander Stuy, Ichiro Hiratani, Tyrone Ryba, Tomoki Yokochi and David M Gilbert
    Citation: BMC Bioinformatics 2008 9:530
    Content type: Database Published on:

  8. Mass spectrometry (MS) based label-free protein quantitation has mainly focused on analysis of ion peak heights and peptide spectral counts. Most analyses of tandem mass spectrometry (MS/MS) data begin with an...

    Authors: John C Braisted, Srilatha Kuntumalla, Christine Vogel, Edward M Marcotte, Alan R Rodrigues, Rong Wang, Shih-Ting Huang, Erik S Ferlanti, Alexander I Saeed, Robert D Fleischmann, Scott N Peterson and Rembert Pieper
    Citation: BMC Bioinformatics 2008 9:529
    Content type: Software Published on:

  9. Millions of single nucleotide polymorphisms have been identified as a result of the human genome project and the rapid advance of high throughput genotyping technology. Genetic association studies, such as rec...

    Authors: Wei Yu, Anja Wulf, Tiebin Liu, Muin J Khoury and Marta Gwinn
    Citation: BMC Bioinformatics 2008 9:528
    Content type: Software Published on:

  10. Computational discovery of motifs in biomolecular sequences is an established field, with applications both in the discovery of functional sites in proteins and regulatory sites in DNA. In recent years there h...

    Authors: Geir Kjetil Sandve, Osman Abul and Finn Drabløs
    Citation: BMC Bioinformatics 2008 9:527
    Content type: Methodology article Published on:

  13. The availability of complete genomic sequences for hundreds of organisms promises to make obtaining genome-wide estimates of substitution rates, selective constraints and other molecular evolution variables of...

    Authors: Rain Simons, Anup Mahurkar, Jonathan Crabtree, Jonathan H Badger, Jane M Carlton and Joana C Silva
    Citation: BMC Bioinformatics 2008 9:524
    Content type: Software Published on:

  17. 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:

  18. 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:

  19. 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:

  21. 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:

  22. 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:

  23. 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:

  24. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  32. 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:

  33. 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:

  36. 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:

  37. 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:

  38. 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:

  39. 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:

  40. 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:

  41. 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:

  42. 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:

  43. 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:

  44. 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:

  47. 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:

  48. 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:

  49. 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

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