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  1. Cell viability is one of the basic properties indicating the physiological state of the cell, thus, it has long been one of the major considerations in biotechnological applications. Conventional methods for e...

    Authors: Ning Wei, Erwin Flaschel, Karl Friehs and Tim Wilhelm Nattkemper
    Citation: BMC Bioinformatics 2008 9:449
    Content type: Research article Published on:

  4. The subcellular localisation of proteins in intact living cells is an important means for gaining information about protein functions. Even dynamic processes can be captured, which can barely be predicted base...

    Authors: Marko Tscherepanow, Nickels Jensen and Franz Kummert
    Citation: BMC Bioinformatics 2008 9:445
    Content type: Research article Published on:

  5. Analysis of large-scale experimental datasets frequently produces one or more sets of proteins that are subsequently mined for functional interpretation and validation. To this end, a number of computational m...

    Authors: Monica Chagoyen, Jose M Carazo and Alberto Pascual-Montano
    Citation: BMC Bioinformatics 2008 9:444
    Content type: Methodology article Published on:

  6. Mass spectrometry is a key technique in proteomics and can be used to analyze complex samples quickly. One key problem with the mass spectrometric analysis of peptides and proteins, however, is the fact that a...

    Authors: Wiebke Timm, Alexandra Scherbart, Sebastian Böcker, Oliver Kohlbacher and Tim W Nattkemper
    Citation: BMC Bioinformatics 2008 9:443
    Content type: Methodology article Published on:

  7. Non-sequence gene data (images, literature, etc.) can be found in many different public databases. Access to these data is mostly by text based methods using gene names; however, gene annotation is neither com...

    Authors: Michael J Gilchrist, Mikkel B Christensen, Richard Harland, Nicolas Pollet, James C Smith, Naoto Ueno and Nancy Papalopulu
    Citation: BMC Bioinformatics 2008 9:442
    Content type: Methodology article Published on:

  8. Modelling proteins with multiple domains is one of the central challenges in Structural Biology. Although homology modelling has successfully been applied for prediction of protein structures, very often domai...

    Authors: Tammy MK Cheng, Tom L Blundell and Juan Fernandez-Recio
    Citation: BMC Bioinformatics 2008 9:441
    Content type: Research article Published on:

  9. Of the 5 484 predicted proteins of Plasmodium falciparum, the main causative agent of malaria, about 60% do not have sufficient sequence similarity with proteins in other organisms to warrant provision of functio...

    Authors: Laurent Bréhélin, Jean-François Dufayard and Olivier Gascuel
    Citation: BMC Bioinformatics 2008 9:440
    Content type: Research article Published on:

  11. Virtual or in silico ligand screening combined with other computational methods is one of the most promising methods to search for new lead compounds, thereby greatly assisting the drug discovery process. Despite...

    Authors: Tania Pencheva, David Lagorce, Ilza Pajeva, Bruno O Villoutreix and Maria A Miteva
    Citation: BMC Bioinformatics 2008 9:438
    Content type: Methodology article Published on:

  12. Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological...

    Authors: Kieran O'Neill, Alexander Garcia, Anita Schwegmann, Rafael C Jimenez, Dan Jacobson and Henning Hermjakob
    Citation: BMC Bioinformatics 2008 9:437
    Content type: Software Published on:

  13. The specific recognition of genomic cis-regulatory elements by transcription factors (TFs) plays an essential role in the regulation of coordinated gene expression. Studying the mechanisms determining binding spe...

    Authors: Vladimir Espinosa Angarica, Abel González Pérez, Ana T Vasconcelos, Julio Collado-Vides and Bruno Contreras-Moreira
    Citation: BMC Bioinformatics 2008 9:436
    Content type: Research article Published on:

  14. Computational biology is often associated with genetic or genomic studies only. However, thanks to the increase of computational resources, computational models are appreciated as useful tools in many other sc...

    Authors: Benjamin Roche, Jean-François Guégan and François Bousquet
    Citation: BMC Bioinformatics 2008 9:435
    Content type: Software Published on:

  15. In cancer research, most clinical variables have already been investigated and are now well established. The use of transcriptomic variables has raised two problems: restricting their number and validating the...

    Authors: Caroline Truntzer, Delphine Maucort-Boulch and Pascal Roy
    Citation: BMC Bioinformatics 2008 9:434
    Content type: Research article Published on:

  16. Most gene finders score candidate gene models with state-based methods, typically HMMs, by combining local properties (coding potential, splice donor and acceptor patterns, etc). Competing models with similar ...

    Authors: Qian Liu, Koby Crammer, Fernando CN Pereira and David S Roos
    Citation: BMC Bioinformatics 2008 9:433
    Content type: Methodology article Published on:

  17. Alternative RNA splicing greatly increases proteome diversity and thereby contribute to species- or tissue-specific functions. The possibility to study alternative splicing (AS) events on a genomic scale using...

    Authors: Ting-Yu Chang, Yin-Yi Li, Chih-Hung Jen, Tsun-Po Yang, Chi-Hung Lin, Ming-Ta Hsu and Hsei-Wei Wang
    Citation: BMC Bioinformatics 2008 9:432
    Content type: Software Published on:

  18. Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical a...

    Authors: Jacques Rougemont, Arnaud Amzallag, Christian Iseli, Laurent Farinelli, Ioannis Xenarios and Felix Naef
    Citation: BMC Bioinformatics 2008 9:431
    Content type: Methodology article Published on:

  19. β-turn is a secondary protein structure type that plays significant role in protein folding, stability, and molecular recognition. To date, several methods for prediction of β-turns from protein sequences were de...

    Authors: Ce Zheng and Lukasz Kurgan
    Citation: BMC Bioinformatics 2008 9:430
    Content type: Methodology article Published on:

  20. Amino acid sequence probability distributions, or profiles, have been used successfully to predict secondary structure and local structure in proteins. Profile models assume the statistical independence of eac...

    Authors: Christopher Bystroff and Bobbie-Jo Webb-Robertson
    Citation: BMC Bioinformatics 2008 9:429
    Content type: Research article Published on:

  21. In the last five years large online resources of human variability have appeared, notably HapMap, Perlegen and the CEPH foundation. These databases of genotypes with population information act as catalogues of...

    Authors: Jorge Amigo, Antonio Salas, Christopher Phillips and Ángel Carracedo
    Citation: BMC Bioinformatics 2008 9:428
    Content type: Software Published on:

  23. The local connectivity and global position of a protein in a protein interaction network are known to correlate with some of its functional properties, including its essentiality or dispensability. It is there...

    Authors: Sri R Paladugu, Shan Zhao, Animesh Ray and Alpan Raval
    Citation: BMC Bioinformatics 2008 9:426
    Content type: Research article Published on:

  24. The Signal-to-Noise-Ratio (SNR) is often used for identification of biomarkers for two-class problems and no formal and useful generalization of SNR is available for multiclass problems. We propose innovative ...

    Authors: Yu-Shuen Tsai, Chin-Teng Lin, George C Tseng, I-Fang Chung and Nikhil Ranjan Pal
    Citation: BMC Bioinformatics 2008 9:425
    Content type: Research article Published on:

  25. Finding the dominant direction of flow of information in densely interconnected regulatory or signaling networks is required in many applications in computational biology and neuroscience. This is achieved by ...

    Authors: Iaroslav Ispolatov and Sergei Maslov
    Citation: BMC Bioinformatics 2008 9:424
    Content type: Research article Published on:

  26. Mass Spectrometry coupled to Liquid Chromatography (LC-MS) is commonly used to analyze the protein content of biological samples in large scale studies. The data resulting from an LC-MS experiment is huge, hig...

    Authors: Ole Schulz-Trieglaff, Nico Pfeifer, Clemens Gröpl, Oliver Kohlbacher and Knut Reinert
    Citation: BMC Bioinformatics 2008 9:423
    Content type: Software Published on:

  27. High throughput microarray technologies have afforded the investigation of genomes, epigenomes, and transcriptomes at unprecedented resolution. However, software packages to handle, analyze, and visualize data...

    Authors: Raj Chari, Bradley P Coe, Craig Wedseltoft, Marie Benetti, Ian M Wilson, Emily A Vucic, Calum MacAulay, Raymond T Ng and Wan L Lam
    Citation: BMC Bioinformatics 2008 9:422
    Content type: Software Published on:

  28. We consider the discovery of recombinant segments jointly with their origins within multilocus DNA sequences from bacteria representing heterogeneous populations of fairly closely related species. The currentl...

    Authors: Pekka Marttinen, Adam Baldwin, William P Hanage, Chris Dowson, Eshwar Mahenthiralingam and Jukka Corander
    Citation: BMC Bioinformatics 2008 9:421
    Content type: Methodology article Published on:

  30. The process of horizontal gene transfer (HGT) is believed to be widespread in Bacteria and Archaea, but little comparative data is available addressing its occurrence in complete microbial genomes. Collection ...

    Authors: Sheila Podell, Terry Gaasterland and Eric E Allen
    Citation: BMC Bioinformatics 2008 9:419
    Content type: Database Published on:

  33. Many statistical methods have been proposed to identify disease biomarkers from gene expression profiles. However, from gene expression profile data alone, statistical methods often fail to identify biological...

    Authors: Li Chen, Jianhua Xuan, Chen Wang, Ie-Ming Shih, Yue Wang, Zhen Zhang, Eric Hoffman and Robert Clarke
    Citation: BMC Bioinformatics 2008 9:416
    Content type: Methodology article Published on:

  34. Gene expression levels in a given cell can be influenced by different factors, namely pharmacological or medical treatments. The response to a given stimulus is usually different for different genes and may de...

    Authors: Claudia Angelini, Luisa Cutillo, Daniela De Canditiis, Margherita Mutarelli and Marianna Pensky
    Citation: BMC Bioinformatics 2008 9:415
    Content type: Software Published on:

  35. Eukaryotic promoter prediction using computational analysis techniques is one of the most difficult jobs in computational genomics that is essential for constructing and understanding genetic regulatory networ...

    Authors: Firoz Anwar, Syed Murtuza Baker, Taskeed Jabid, Md Mehedi Hasan, Mohammad Shoyaib, Haseena Khan and Ray Walshe
    Citation: BMC Bioinformatics 2008 9:414
    Content type: Research article Published on:

  36. Supertree methods combine phylogenies with overlapping sets of taxa into a larger one. Topological conflicts frequently arise among source trees for methodological or biological reasons, such as long branch at...

    Authors: Celine Scornavacca, Vincent Berry, Vincent Lefort, Emmanuel JP Douzery and Vincent Ranwez
    Citation: BMC Bioinformatics 2008 9:413
    Content type: Research article Published on:

  37. Identifying genes and pathways associated with diseases such as cancer has been a subject of considerable research in recent years in the area of bioinformatics and computational biology. It has been demonstra...

    Authors: Zhenqiu Liu, Ronald B Gartenhaus, Ming Tan, Feng Jiang and Xiaoli Jiao
    Citation: BMC Bioinformatics 2008 9:412
    Content type: Methodology article Published on:

  38. A priori analysis of the activity of drugs on the target protein by computational approaches can be useful in narrowing down drug candidates for further experimental tests. Currently, there are a large number ...

    Authors: Pelin Armutlu, Muhittin E Ozdemir, Fadime Uney-Yuksektepe, I Halil Kavakli and Metin Turkay
    Citation: BMC Bioinformatics 2008 9:411
    Content type: Research article Published on:

  39. Most microarray experiments are carried out with the purpose of identifying genes whose expression varies in relation with specific conditions or in response to environmental stimuli. In such studies, genes sh...

    Authors: Stefano Parodi, Vito Pistoia and Marco Muselli
    Citation: BMC Bioinformatics 2008 9:410
    Content type: Methodology article Published on:

  40. Illumina Infinium whole genome genotyping (WGG) arrays are increasingly being applied in cancer genomics to study gene copy number alterations and allele-specific aberrations such as loss-of-heterozygosity (LO...

    Authors: Johan Staaf, Johan Vallon-Christersson, David Lindgren, Gunnar Juliusson, Richard Rosenquist, Mattias Höglund, Åke Borg and Markus Ringnér
    Citation: BMC Bioinformatics 2008 9:409
    Content type: Methodology article Published on:

  41. Nucleotides are trimmed from the ends of variable (V), diversity (D) and joining (J) genes during immunoglobulin (IG) and T cell receptor (TR) rearrangements in B cells and T cells of the immune system. This t...

    Authors: Kevin Bleakley, Marie-Paule Lefranc and Gérard Biau
    Citation: BMC Bioinformatics 2008 9:408
    Content type: Research article Published on:

  45. Microarray technology has unveiled transcriptomic differences among tumors of various phenotypes, and, especially, brought great progress in molecular understanding of phenotypic diversity of breast tumors. Ho...

    Authors: Atsushi Niida, Andrew D Smith, Seiya Imoto, Shuichi Tsutsumi, Hiroyuki Aburatani, Michael Q Zhang and Tetsu Akiyama
    Citation: BMC Bioinformatics 2008 9:404
    Content type: Research article Published on:

  46. Computational models of protein structure are usually inaccurate and exhibit significant deviations from the true structure. The utility of models depends on the degree of these deviations. A number of predict...

    Authors: Marcin Pawlowski, Michal J Gajda, Ryszard Matlak and Janusz M Bujnicki
    Citation: BMC Bioinformatics 2008 9:403
    Content type: Software Published on:

  48. Recent advances in high-throughput screening (HTS) techniques and readily available compound libraries generated using combinatorial chemistry or derived from natural products enable the testing of millions of...

    Authors: Lianyi Han, Yanli Wang and Stephen H Bryant
    Citation: BMC Bioinformatics 2008 9:401
    Content type: Research article Published on:

  49. Current efforts in Metabolomics, such as the Human Metabolome Project, collect structures of biological metabolites as well as data for their characterisation, such as spectra for identification of substances ...

    Authors: Stefan Kuhn, Björn Egert, Steffen Neumann and Christoph Steinbeck
    Citation: BMC Bioinformatics 2008 9:400
    Content type: Methodology article Published on:

  50. Biological pathways are a useful abstraction of biological concepts, and software tools to deal with pathway diagrams can help biological research. PathVisio is a new visualization tool for biological pathways...

    Authors: Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin and Chris Evelo
    Citation: BMC Bioinformatics 2008 9:399
    Content type: Software Published on:

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