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  1. Over the last two decades a large number of algorithms has been developed for regulatory motif finding. Here we show how many of these algorithms, especially those that model binding specificities of regulator...

    Authors: Erik van Nimwegen
    Citation: BMC Bioinformatics 2007 8(Suppl 6):S4
    Content type: Review Published on:

    This article is part of a Supplement: Volume 8 Supplement 6

  2. Investigators in the biological sciences continue to exploit laboratory automation methods and have dramatically increased the rates at which they can generate data. In many environments, the methods themselve...

    Authors: Michael C Wendl, Scott Smith, Craig S Pohl, David J Dooling, Asif T Chinwalla, Kevin Crouse, Todd Hepler, Shin Leong, Lynn Carmichael, Mike Nhan, Benjamin J Oberkfell, Elaine R Mardis, LaDeana W Hillier and Richard K Wilson
    Citation: BMC Bioinformatics 2007 8:362
    Content type: Methodology article Published on:

  3. In an epitope-based vaccine setting, the use of conserved epitopes would be expected to provide broader protection across multiple strains, or even species, than epitopes derived from highly variable genome re...

    Authors: Huynh-Hoa Bui, John Sidney, Wei Li, Nicolas Fusseder and Alessandro Sette
    Citation: BMC Bioinformatics 2007 8:361
    Content type: Software Published on:

  4. The analysis of microarray experiments requires accurate and up-to-date functional annotation of the microarray reporters to optimize the interpretation of the biological processes involved. Pathway visualizat...

    Authors: Stan Gaj, Arie van Erk, Rachel IM van Haaften and Chris TA Evelo
    Citation: BMC Bioinformatics 2007 8:360
    Content type: Methodology article Published on:

  5. High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ...

    Authors: Srinka Ghosh, Heather A Hirsch, Edward A Sekinger, Philipp Kapranov, Kevin Struhl and Thomas R Gingeras
    Citation: BMC Bioinformatics 2007 8:359
    Content type: Methodology article Published on:

  6. Arabidopsis thaliana is the model species of current plant genomic research with a genome size of 125 Mb and approximately 28,000 genes. The function of half of these genes is currently unknown. The purpose of th...

    Authors: Hui Lan, Rachel Carson, Nicholas J Provart and Anthony J Bonner
    Citation: BMC Bioinformatics 2007 8:358
    Content type: Research article Published on:

  7. The prediction of the secondary structure of proteins is one of the most studied problems in bioinformatics. Despite their success in many problems of biological sequence analysis, Hidden Markov Models (HMMs) ...

    Authors: Kyoung-Jae Won, Thomas Hamelryck, Adam Prügel-Bennett and Anders Krogh
    Citation: BMC Bioinformatics 2007 8:357
    Content type: Research article Published on:

  10. Computational methods to predict transcription factor binding sites (TFBS) based on exhaustive algorithms are guaranteed to find the best patterns but are often limited to short ones or impose some constraints...

    Authors: Fathi Elloumi and Martha Nason
    Citation: BMC Bioinformatics 2007 8:354
    Content type: Methodology article Published on:

  13. Odorant binding proteins (OBPs) are believed to shuttle odorants from the environment to the underlying odorant receptors, for which they could potentially serve as odorant presenters. Although several sequenc...

    Authors: Ganesan Pugalenthi, Ke Tang, PN Suganthan, G Archunan and R Sowdhamini
    Citation: BMC Bioinformatics 2007 8:351
    Content type: Research article Published on:

  14. The design of long oligonucleotides for spotted DNA microarrays requires detailed attention to ensure their optimal performance in the hybridization process. The main challenge is to select an optimal oligonuc...

    Authors: Guangan Hu, Manuel Llinás, Jingguang Li, Peter Rainer Preiser and Zbynek Bozdech
    Citation: BMC Bioinformatics 2007 8:350
    Content type: Methodology article Published on:

  15. The main two sorts of automatic gene annotation frameworks are ab initio and alignment-based, the latter splitting into two sub-groups. The first group is used for intra-species alignments, among which are succes...

    Authors: Heng Li, Liang Guan, Tao Liu, Yiran Guo, Wei-Mou Zheng, Gane Ka-Shu Wong and Jun Wang
    Citation: BMC Bioinformatics 2007 8:349
    Content type: Methodology article Published on:

  16. Although molecular pathway information and the International HapMap Project data can help biomedical researchers to investigate the aetiology of complex diseases more effectively, such information is missing o...

    Authors: Hwanseok Rhee and Jin-Sung Lee
    Citation: BMC Bioinformatics 2007 8:348
    Content type: Database Published on:

  18. The most popular methods for significance analysis on microarray data are well suited to find genes differentially expressed across predefined categories. However, identification of features that correlate wit...

    Authors: Lars Gidskehaug, Endre Anderssen, Arnar Flatberg and Bjørn K Alsberg
    Citation: BMC Bioinformatics 2007 8:346
    Content type: Research article Published on:

  20. Lightweight genome viewer (lwgv) is a web-based tool for visualization of sequence annotations in their chromosomal context. It performs most of the functions of larger genome browsers, while relying on standa...

    Authors: Jeremiah J Faith, Andrew J Olson, Timothy S Gardner and Ravi Sachidanandam
    Citation: BMC Bioinformatics 2007 8:344
    Content type: Software Published on:

  21. Modelling of time series data should not be an approximation of input data profiles, but rather be able to detect and evaluate dynamical changes in the time series data. Objective criteria that can be used to ...

    Authors: Ryoko Morioka, Shigehiko Kanaya, Masami Y Hirai, Mitsuru Yano, Naotake Ogasawara and Kazuki Saito
    Citation: BMC Bioinformatics 2007 8:343
    Content type: Research article Published on:

  23. MicroRNAs (miRNAs) are recognized as one of the most important families of non-coding RNAs that serve as important sequence-specific post-transcriptional regulators of gene expression. Identification of miRNAs...

    Authors: Ting-Hua Huang, Bin Fan, Max F Rothschild, Zhi-Liang Hu, Kui Li and Shu-Hong Zhao
    Citation: BMC Bioinformatics 2007 8:341
    Content type: Software Published on:

  25. Expressed sequence tags (ESTs) analyses are a fundamental tool for gene identification in organisms. Given a preliminary EST sample from a certain library, several statistical prediction problems arise. In par...

    Authors: Antonio Lijoi, Ramsés H Mena and Igor Prünster
    Citation: BMC Bioinformatics 2007 8:339
    Content type: Methodology article Published on:

  26. Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate...

    Authors: Catherine C Beauheim, Farrell Wymore, Michael Nitzberg, Zachariah K Zachariah, Heng Jin, JH Pate Skene, Catherine A Ball and Gavin Sherlock
    Citation: BMC Bioinformatics 2007 8:338
    Content type: Software Published on:

  27. In past number of methods have been developed for predicting subcellular location of eukaryotic, prokaryotic (Gram-negative and Gram-positive bacteria) and human proteins but no method has been developed for m...

    Authors: Mamoon Rashid, Sudipto Saha and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2007 8:337
    Content type: Research article Published on:

  28. Combinatorial complexity is a challenging problem in detailed and mechanistic mathematical modeling of signal transduction. This subject has been discussed intensively and a lot of progress has been made withi...

    Authors: Markus Koschorreck, Holger Conzelmann, Sybille Ebert, Michael Ederer and Ernst Dieter Gilles
    Citation: BMC Bioinformatics 2007 8:336
    Content type: Research article Published on:

  30. Cells dynamically adapt their gene expression patterns in response to various stimuli. This response is orchestrated into a number of gene expression modules consisting of co-regulated genes. A growing pool of...

    Authors: Jochen Supper, Martin Strauch, Dierk Wanke, Klaus Harter and Andreas Zell
    Citation: BMC Bioinformatics 2007 8:334
    Content type: Methodology article Published on:

  31. The Distributed Annotation System (DAS) is a network protocol for exchanging biological data. It is frequently used to share annotations of genomes and protein sequence.

    Authors: Andreas Prlić, Thomas A Down, Eugene Kulesha, Robert D Finn, Andreas Kähäri and Tim JP Hubbard
    Citation: BMC Bioinformatics 2007 8:333
    Content type: Research article Published on:

  32. The search for enriched features has become widely used to characterize a set of genes or proteins. A key aspect of this technique is its ability to identify correlations amongst heterogeneous data such as Gen...

    Authors: Roland Barriot, David J Sherman and Isabelle Dutour
    Citation: BMC Bioinformatics 2007 8:332
    Content type: Methodology article Published on:

  34. Protein subcellular localization is crucial for genome annotation, protein function prediction, and drug discovery. Determination of subcellular localization using experimental approaches is time-consuming; th...

    Authors: Emily Chia-Yu Su, Hua-Sheng Chiu, Allan Lo, Jenn-Kang Hwang, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2007 8:330
    Content type: Research article Published on:

  35. To date more than 2,1 million gene products from more than 100000 different species have been described specifying their function, the processes they are involved in and their cellular localization using a ver...

    Authors: Angelica Tulipano, Giacinto Donvito, Flavio Licciulli, Giorgio Maggi and Andreas Gisel
    Citation: BMC Bioinformatics 2007 8:329
    Content type: Research article Published on:

  37. Polyketides are secondary metabolites of microorganisms with diverse biological activities, including pharmacological functions such as antibiotic, antitumor and agrochemical properties. Polyketides are synthe...

    Authors: Hongseok Tae, Eun-Bae Kong and Kiejung Park
    Citation: BMC Bioinformatics 2007 8:327
    Content type: Software Published on:

  38. When analysing microarray and other small sample size biological datasets, care is needed to avoid various biases. We analyse a form of bias, stratification bias, that can substantially affect analyses using s...

    Authors: Brian J Parker, Simon Günter and Justin Bedo
    Citation: BMC Bioinformatics 2007 8:326
    Content type: Research article Published on:

  39. Bioinformatics tools for automatic processing of biomedical literature are invaluable for both the design and interpretation of large-scale experiments. Many information extraction (IE) systems that incorporat...

    Authors: Richard Tzong-Han Tsai, Wen-Chi Chou, Ying-Shan Su, Yu-Chun Lin, Cheng-Lung Sung, Hong-Jie Dai, Irene Tzu-Hsuan Yeh, Wei Ku, Ting-Yi Sung and Wen-Lian Hsu
    Citation: BMC Bioinformatics 2007 8:325
    Content type: Research article Published on:

  41. In proteomic analysis, MS/MS spectra acquired by mass spectrometer are assigned to peptides by database searching algorithms such as SEQUEST. The assignations of peptides to MS/MS spectra by SEQUEST searching ...

    Authors: Xinning Jiang, Xiaogang Jiang, Guanghui Han, Mingliang Ye and Hanfa Zou
    Citation: BMC Bioinformatics 2007 8:323
    Content type: Research article Published on:

  42. Innovative extensions of (M) ANOVA gain common ground for the analysis of designed metabolomics experiments. ASCA is such a multivariate analysis method; it has successfully estimated effects in megavariate me...

    Authors: Daniel J Vis, Johan A Westerhuis, Age K Smilde and Jan van der Greef
    Citation: BMC Bioinformatics 2007 8:322
    Content type: Research article Published on:

  44. Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates a...

    Authors: Kathrin Klee, Rebecca Ernst, Manuel Spannagl and Klaus FX Mayer
    Citation: BMC Bioinformatics 2007 8:320
    Content type: Software Published on:

  45. Natural antisense transcripts (NATs) are endogenous RNA molecules that exhibit partial or complete complementarity to other RNAs, and that may contribute to the regulation of molecular functions at various lev...

    Authors: Yifei Yin, Yi Zhao, Jie Wang, Changning Liu, Shuguang Chen, Runsheng Chen and Haitao Zhao
    Citation: BMC Bioinformatics 2007 8:319
    Content type: Database Published on:

  46. The translation start site plays an important role in the control of translation efficiency of eukaryotic mRNAs. The recognition of the start AUG codon by eukaryotic ribosomes is considered to depend on its nu...

    Authors: Alex V Kochetov, Andrey Palyanov, Igor I Titov, Dmitry Grigorovich, Akinori Sarai and Nikolay A Kolchanov
    Citation: BMC Bioinformatics 2007 8:318
    Content type: Software Published on:

  47. The incorporation of prior biological knowledge in the analysis of microarray data has become important in the reconstruction of transcription regulatory networks in a cell. Most of the current research has be...

    Authors: Peter Larsen, Eyad Almasri, Guanrao Chen and Yang Dai
    Citation: BMC Bioinformatics 2007 8:317
    Content type: Methodology article Published on:

  49. Metabolic Flux Analysis (MFA) based on isotope labeling experiments (ILEs) is a widely established tool for determining fluxes in metabolic pathways. Isotope labeling networks (ILNs) contain all essential info...

    Authors: Michael Weitzel, Wolfgang Wiechert and Katharina Nöh
    Citation: BMC Bioinformatics 2007 8:315
    Content type: Research article Published on:

  50. The presence of gaps in an alignment of nucleotide or protein sequences is often an inconvenience for bioinformatical studies. In phylogenetic and other analyses, for instance, gapped columns are often discard...

    Authors: Rodrigo Gouveia-Oliveira, Peter W Sackett and Anders G Pedersen
    Citation: BMC Bioinformatics 2007 8:312
    Content type: Methodology article Published on:

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