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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  6. 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:

  7. 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:

  9. 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:

  10. 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:

  11. 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:

  13. 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:

  14. 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:

  16. 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:

  17. 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:

  18. 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:

  19. 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:

  21. 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:

  23. Modeling of metabolic networks includes tasks such as network assembly, network overview, calculation of metabolic fluxes and testing the robustness of the network.

    Authors: Roland Schwarz, Chunguang Liang, Christoph Kaleta, Mark Kühnel, Eik Hoffmann, Sergei Kuznetsov, Michael Hecker, Gareth Griffiths, Stefan Schuster and Thomas Dandekar
    Citation: BMC Bioinformatics 2007 8:313
    Content type: Software Published on:

  24. 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:

  25. The architecture of biological networks has been reported to exhibit high level of modularity, and to some extent, topological modules of networks overlap with known functional modules. However, how the modula...

    Authors: Jing Zhao, Guo-Hui Ding, Lin Tao, Hong Yu, Zhong-Hao Yu, Jian-Hua Luo, Zhi-Wei Cao and Yi-Xue Li
    Citation: BMC Bioinformatics 2007 8:311
    Content type: Research article Published on:

  26. The number of algorithms available to predict ligand-protein interactions is large and ever-increasing. The number of test cases used to validate these methods is usually small and problem dependent. Recently,...

    Authors: Luis A Diago, Persy Morell, Longendri Aguilera and Ernesto Moreno
    Citation: BMC Bioinformatics 2007 8:310
    Content type: Research article Published on:

  29. Protein structural data has increased exponentially, such that fast and accurate tools are necessary to access structure similarity search. To improve the search speed, several methods have been designed to re...

    Authors: Wei-Cheng Lo, Po-Jung Huang, Chih-Hung Chang and Ping-Chiang Lyu
    Citation: BMC Bioinformatics 2007 8:307
    Content type: Methodology article Published on:

  30. Many algorithms exist for protein structural alignment, based on internal protein coordinates or on explicit superposition of the structures. These methods are usually successful for detecting structural simil...

    Authors: Leandro Martínez, Roberto Andreani and José Mario Martínez
    Citation: BMC Bioinformatics 2007 8:306
    Content type: Methodology article Published on:

  31. Structure identification of dynamic models for complex biological systems is the cornerstone of their reverse engineering. Biochemical Systems Theory (BST) offers a particularly convenient solution because its...

    Authors: Marco Vilela, Carlos CH Borges, Susana Vinga, Ana Tereza R Vasconcelos, Helena Santos, Eberhard O Voit and Jonas S Almeida
    Citation: BMC Bioinformatics 2007 8:305
    Content type: Research article Published on:

  35. Genome-wide association studies of common diseases for common, low penetrance causal variants are underway. A proportion of these will alter protein sequences, the most common of which is the non-synonymous si...

    Authors: David F Burke, Catherine L Worth, Eva-Maria Priego, Tammy Cheng, Luc J Smink, John A Todd and Tom L Blundell
    Citation: BMC Bioinformatics 2007 8:301
    Content type: Methodology article Published on:

  36. Sequence-derived structural and physicochemical descriptors have frequently been used in machine learning prediction of protein functional families, thus there is a need to comparatively evaluate the effective...

    Authors: Serene AK Ong, Hong Huang Lin, Yu Zong Chen, Ze Rong Li and Zhiwei Cao
    Citation: BMC Bioinformatics 2007 8:300
    Content type: Research article Published on:

  37. Large-scale sequencing of entire genomes has ushered in a new age in biology. One of the next grand challenges is to dissect the cellular networks consisting of many individual functional modules. Defining co-...

    Authors: Feng Luo, Yunfeng Yang, Jianxin Zhong, Haichun Gao, Latifur Khan, Dorothea K Thompson and Jizhong Zhou
    Citation: BMC Bioinformatics 2007 8:299
    Content type: Research article Published on:

  38. Approximately 5% of Pfam families are enzymatic, but only a small fraction of the sequences within these families (<0.5%) have had the residues responsible for catalysis determined. To increase the active site...

    Authors: Jaina Mistry, Alex Bateman and Robert D Finn
    Citation: BMC Bioinformatics 2007 8:298
    Content type: Database Published on:

  40. The Stanford Tissue Microarray Database (TMAD) is a repository of data serving a consortium of pathologists and biomedical researchers. The tissue samples in TMAD are annotated with multiple free-text fields, ...

    Authors: Nigam H Shah, Daniel L Rubin, Inigo Espinosa, Kelli Montgomery and Mark A Musen
    Citation: BMC Bioinformatics 2007 8:296
    Content type: Software Published on:

  41. The translational efficiency of an mRNA can be modulated by upstream open reading frames (uORFs) present in certain genes. A uORF can attenuate translation of the main ORF by interfering with translational rei...

    Authors: Marija Cvijović, Daniel Dalevi, Elizabeth Bilsland, Graham JL Kemp and Per Sunnerhagen
    Citation: BMC Bioinformatics 2007 8:295
    Content type: Research article Published on:

  42. The relationship between divergence of amino-acid sequence and divergence of function among homologous proteins is complex. The assumption that homologs share function – the basis of transfer of annotations in...

    Authors: Vineet Sangar, Daniel J Blankenberg, Naomi Altman and Arthur M Lesk
    Citation: BMC Bioinformatics 2007 8:294
    Content type: Research article Published on:

  43. Manual curation of biological databases, an expensive and labor-intensive process, is essential for high quality integrated data. In this paper we report the implementation of a state-of-the-art Natural Langua...

    Authors: Carlos Rodríguez-Penagos, Heladia Salgado, Irma Martínez-Flores and Julio Collado-Vides
    Citation: BMC Bioinformatics 2007 8:293
    Content type: Methodology article Published on:

  45. Clustering analysis of microarray data is often criticized for giving ambiguous results because of sensitivity to data perturbation or clustering techniques used. In this paper, we describe a new method based ...

    Authors: Gul S Dalgin, Gabriela Alexe, Daniel Scanfeld, Pablo Tamayo, Jill P Mesirov, Shridar Ganesan, Charles DeLisi and Gyan Bhanot
    Citation: BMC Bioinformatics 2007 8:291
    Content type: Research article Published on:

  47. Alternative representations of biochemical networks emphasise different aspects of the data and contribute to the understanding of complex biological systems. In this study we present a variety of automated me...

    Authors: Brian J Holden, John W Pinney, Simon C Lovell, Grigoris D Amoutzias and David L Robertson
    Citation: BMC Bioinformatics 2007 8:289
    Content type: Methodology article Published on:

  48. Transmission electron tomography is an increasingly common three-dimensional electron microscopy approach that can provide new insights into the structure of subcellular components. Transmission electron tomog...

    Authors: Cédric MessaoudiI, Thomas Boudier, Carlos Oscar Sanchez Sorzano and Sergio Marco
    Citation: BMC Bioinformatics 2007 8:288
    Content type: Software Published on:

  49. Many online resources for the life sciences have been developed and introduced in peer-reviewed papers recently, ranging from databases and web applications to data-analysis software. Some have been introduced...

    Authors: Yasunori Yamamoto and Toshihisa Takagi
    Citation: BMC Bioinformatics 2007 8:287
    Content type: Database Published on:

  50. The study of microRNAs (miRNAs) is attracting great considerations. Recent studies revealed that miRNAs play as important regulators of gene expression and some even as cancer players or inhibitors. Many studi...

    Authors: Feng Tian, Huayue Zhang, Xinyu Zhang, Chi Song, Yongjing Xia, Yiqing Wu and Xiangjun Liu
    Citation: BMC Bioinformatics 2007 8:285
    Content type: Methodology article Published on:

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