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  1. Natively unfolded proteins lack a well defined three dimensional structure but have important biological functions, suggesting a re-assignment of the structure-function paradigm. To assess that a given protein...

    Authors: Antonio Deiana and Andrea Giansanti
    Citation: BMC Bioinformatics 2010 11:198
    Content type: Methodology article Published on:

  2. Epistatic miniarray profiling (E-MAPs) is a high-throughput approach capable of quantifying aggravating or alleviating genetic interactions between gene pairs. The datasets resulting from E-MAP experiments typ...

    Authors: Colm Ryan, Derek Greene, Gerard Cagney and Pádraig Cunningham
    Citation: BMC Bioinformatics 2010 11:197
    Content type: Research article Published on:

  4. We analysed 48 non-redundant antibiotic target proteins from all bacteria, 22 antibiotic target proteins from E. coli only and 4243 non-drug targets from E. coli to identify differences in their properties and to...

    Authors: Tala M Bakheet and Andrew J Doig
    Citation: BMC Bioinformatics 2010 11:195
    Content type: Research article Published on:

  5. Chromatin immunoprecipitation combined with DNA microarrays (ChIP-chip) is an assay used for investigating DNA-protein-binding or post-translational chromatin/histone modifications. As with all high-throughput...

    Authors: Benedikt Zacher, Pei Fen Kuan and Achim Tresch
    Citation: BMC Bioinformatics 2010 11:194
    Content type: Software Published on:

  8. Extracting protein-protein interactions from biomedical literature is an important task in biomedical text mining. Supervised machine learning methods have been used with great success in this task but they te...

    Authors: Yanpeng Li, Xiaohua Hu, Hongfei Lin and Zhihao Yang
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  9. Finding relevant articles from PubMed is challenging because it is hard to express the user's specific intention in the given query interface, and a keyword query typically retrieves a large number of results....

    Authors: Hwanjo Yu, Taehoon Kim, Jinoh Oh, Ilhwan Ko, Sungchul Kim and Wook-Shin Han
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  10. With the rapid development of genome sequencing techniques, traditional research methods based on the isolation and cultivation of microorganisms are being gradually replaced by metagenomics, which is also kno...

    Authors: Bin Yang, Yu Peng, Henry Chi-Ming Leung, Siu-Ming Yiu, Jing-Chi Chen and Francis Yuk-Lun Chin
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  11. Diagnosis techniques using urine are non-invasive, inexpensive, and easy to perform in clinical settings. The metabolites in urine, as the end products of cellular processes, are closely linked to phenotypes. ...

    Authors: Younghoon Kim, Imhoi Koo, Byung Hwa Jung, Bong Chul Chung and Doheon Lee
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  12. Since Swanson proposed the Undiscovered Public Knowledge (UPK) model, there have been many approaches to uncover UPK by mining the biomedical literature. These earlier works, however, required substantial manu...

    Authors: Ali Z Ijaz, Min Song and Doheon Lee
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  13. Although both conservation and correlated mutation (CM) are important information reflecting the different sorts of context in multiple sequence alignment, most of alignment methods use sequence profiles that ...

    Authors: Chan-seok Jeong and Dongsup Kim
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  14. Drug-drug interactions are frequently reported in the increasing amount of biomedical literature. Information Extraction (IE) techniques have been devised as a useful instrument to manage this knowledge. Never...

    Authors: Isabel Segura-Bedmar, Mario Crespo, César de Pablo-Sánchez and Paloma Martínez
    Citation: BMC Bioinformatics 2010 11(Suppl 2):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 11 Supplement 2

  15. With the rapid development of new genetic measurement methods, several types of genetic alterations can be quantified in a high-throughput manner. While the initial focus has been on investigating each data se...

    Authors: Charlotte Soneson, Henrik Lilljebjörn, Thoas Fioretos and Magnus Fontes
    Citation: BMC Bioinformatics 2010 11:191
    Content type: Research article Published on:

  17. Cancer is caused through a multistep process, in which a succession of genetic changes, each conferring a competitive advantage for growth and proliferation, leads to the progressive conversion of normal human...

    Authors: Felix Sanchez-Garcia, Uri David Akavia, Eyal Mozes and Dana Pe'er
    Citation: BMC Bioinformatics 2010 11:189
    Content type: Software Published on:

  18. The dynamic motions of many proteins are central to their function. It therefore follows that the dynamic requirements of a protein are evolutionary constrained. In order to assess and quantify this, one needs...

    Authors: Márton Münz, Rune Lyngsø, Jotun Hein and Philip C Biggin
    Citation: BMC Bioinformatics 2010 11:188
    Content type: Methodology article Published on:

  20. Real-time PCR has recently become the technique of choice for absolute and relative nucleic acid quantification. The gold standard quantification method in real-time PCR assumes that the compared samples have ...

    Authors: Davide Sisti, Michele Guescini, Marco BL Rocchi, Pasquale Tibollo, Mario D'Atri and Vilberto Stocchi
    Citation: BMC Bioinformatics 2010 11:186
    Content type: Methodology article Published on:

  23. Microarray technology is a high-throughput method for measuring the expression levels of thousand of genes simultaneously. The observed intensities combine a non-specific binding, which is a major disadvantage...

    Authors: Megu Ohtaki, Keiko Otani, Keiko Hiyama, Naomi Kamei, Kenichi Satoh and Eiso Hiyama
    Citation: BMC Bioinformatics 2010 11:183
    Content type: Research article Published on:

  24. There is an increasing usage of ion mobility-mass spectrometry (IMMS) in proteomics. IMMS combines the features of ion mobility spectrometry (IMS) and mass spectrometry (MS). It separates and detects peptide i...

    Authors: Bing Wang, Steve Valentine, Manolo Plasencia, Sriram Raghuraman and Xiang Zhang
    Citation: BMC Bioinformatics 2010 11:182
    Content type: Research article Published on:

  25. Gene silencing using exogenous small interfering RNAs (siRNAs) is now a widespread molecular tool for gene functional study and new-drug target identification. The key mechanism in this technique is to design ...

    Authors: Qi Liu, Qian Xu, Vincent W Zheng, Hong Xue, Zhiwei Cao and Qiang Yang
    Citation: BMC Bioinformatics 2010 11:181
    Content type: Research article Published on:

  27. Position-specific priors have been shown to be a flexible and elegant way to extend the power of Gibbs sampler-based motif discovery algorithms. Information of many types–including sequence conservation, nucle...

    Authors: Timothy L Bailey, Mikael Bodén, Tom Whitington and Philip Machanick
    Citation: BMC Bioinformatics 2010 11:179
    Content type: Research article Published on:

  28. CellML is an XML based language for representing mathematical models, in a machine-independent form which is suitable for their exchange between different authors, and for archival in a model repository. Allow...

    Authors: Andrew K Miller, Justin Marsh, Adam Reeve, Alan Garny, Randall Britten, Matt Halstead, Jonathan Cooper, David P Nickerson and Poul F Nielsen
    Citation: BMC Bioinformatics 2010 11:178
    Content type: Software Published on:

  29. Time-of-flight mass spectrometry (TOF-MS) has the potential to provide non-invasive, high-throughput screening for cancers and other serious diseases via detection of protein biomarkers in blood or other acces...

    Authors: Karl W Kuschner, Dariya I Malyarenko, William E Cooke, Lisa H Cazares, OJ Semmes and Eugene R Tracy
    Citation: BMC Bioinformatics 2010 11:177
    Content type: Methodology article Published on:

  32. It is well known that most of the binding free energy of protein interaction is contributed by a few key hot spot residues. These residues are crucial for understanding the function of proteins and studying th...

    Authors: Jun-Feng Xia, Xing-Ming Zhao, Jiangning Song and De-Shuang Huang
    Citation: BMC Bioinformatics 2010 11:174
    Content type: Research article Published on:

  34. Ever since the ground-breaking work of Anfinsen et al. in which a denatured protein was found to refold to its native state, it has been frequently stated by the protein fold prediction community that all the ...

    Authors: Jonathan J Ellis, Fabien PE Huard, Charlotte M Deane, Sheenal Srivastava and Graham R Wood
    Citation: BMC Bioinformatics 2010 11:172
    Content type: Research article Published on:

  35. Recent developments of high-density SNP chips across a number of species require accurate genetic maps. Despite rapid advances in genome sequence assembly and availability of a number of tools for creating gen...

    Authors: Mehar S Khatkar, Matthew Hobbs, Markus Neuditschko, Johann Sölkner, Frank W Nicholas and Herman W Raadsma
    Citation: BMC Bioinformatics 2010 11:171
    Content type: Methodology article Published on:

  36. The recent emergence of the H5N1 influenza virus from avian reservoirs has raised concern about future influenza strains of high virulence emerging that could easily infect humans. We analyzed differential gen...

    Authors: Ken Tatebe, Ahmet Zeytun, Ruy M Ribeiro, Robert Hoffmann, Kevin S Harrod and Christian V Forst
    Citation: BMC Bioinformatics 2010 11:170
    Content type: Research article Published on:

  38. In recent years, gene order data has attracted increasing attention from both biologists and computer scientists as a new type of data for phylogenetic analysis. If gene orders are viewed as one character with...

    Authors: Jian Shi, Yiwei Zhang, Haiwei Luo and Jijun Tang
    Citation: BMC Bioinformatics 2010 11:168
    Content type: Research article Published on:

  40. An important objective of DNA microarray-based gene expression experimentation is determining inter-relationships that exist between differentially expressed genes and biological processes, molecular functions...

    Authors: Saurin D Jani, Gary L Argraves, Jeremy L Barth and W Scott Argraves
    Citation: BMC Bioinformatics 2010 11:166
    Content type: Software Published on:

  42. Gene clustering for annotating gene functions is one of the fundamental issues in bioinformatics. The best clustering solution is often regularized by multiple constraints such as gene expressions, Gene Ontolo...

    Authors: Jia Zeng, Shanfeng Zhu, Alan Wee-Chung Liew and Hong Yan
    Citation: BMC Bioinformatics 2010 11:164
    Content type: Methodology article Published on:

  43. Identifying candidate genes in genetic networks is important for understanding regulation and biological function. Large gene expression datasets contain relevant information about genetic networks, but mining...

    Authors: Anup Parikh, Eryong Huang, Christopher Dinh, Blaz Zupan, Adam Kuspa, Devika Subramanian and Gad Shaulsky
    Citation: BMC Bioinformatics 2010 11:163
    Content type: Research article Published on:

  44. In cancer, gene networks and pathways often exhibit dynamic behavior, particularly during the process of carcinogenesis. Thus, it is important to prioritize those genes that are strongly associated with the fu...

    Authors: Chen Wang, Jianhua Xuan, Huai Li, Yue Wang, Ming Zhan, Eric P Hoffman and Robert Clarke
    Citation: BMC Bioinformatics 2010 11:162
    Content type: Methodology article Published on:

  45. The post-genomic era has brought new challenges regarding the understanding of the organization and function of the human genome. Many of these challenges are centered on the meaning of differential gene regul...

    Authors: Israel T Silva, Ricardo ZN Vêncio, Thiago YK Oliveira, Greice A Molfetta and Wilson A Silva Jr
    Citation: BMC Bioinformatics 2010 11:161
    Content type: Software Published on:

  46. Small molecular cofactors or ligands play a crucial role in the proper functioning of cells. Accurate annotation of their target proteins and binding sites is required for the complete understanding of reactio...

    Authors: Hifzur R Ansari and Gajendra PS Raghava
    Citation: BMC Bioinformatics 2010 11:160
    Content type: Research article Published on:

  47. Small molecules are of increasing interest for bioinformatics in areas such as metabolomics and drug discovery. The recent release of large open access chemistry databases generates a demand for flexible tools...

    Authors: Thomas Kuhn, Egon L Willighagen, Achim Zielesny and Christoph Steinbeck
    Citation: BMC Bioinformatics 2010 11:159
    Content type: Software Published on:

  49. Oligonucleotide arrays have become one of the most widely used high-throughput tools in biology. Due to their sensitivity to experimental conditions, normalization is a crucial step when comparing measurements...

    Authors: Marc Hulsman, Anouk Mentink, Eugene P van Someren, Koen J Dechering, Jan de Boer and Marcel JT Reinders
    Citation: BMC Bioinformatics 2010 11:156
    Content type: Methodology article Published on:

  50. Computational comparison of two protein structures is the starting point of many methods that build on existing knowledge, such as structure modeling (including modeling of protein complexes and conformational...

    Authors: Zong Hong Zhang, Hwee Kuan Lee and Ivana Mihalek
    Citation: BMC Bioinformatics 2010 11:155
    Content type: Research article Published on:

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