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  1. High-density short oligonucleotide microarrays are useful tools for studying biodiversity, because they can be used to investigate both nucleotide and expression polymorphisms. However, when different strains ...

    Authors: Hironori Fujisawa, Youko Horiuchi, Yoshiaki Harushima, Toyoyuki Takada, Shinto Eguchi, Takako Mochizuki, Takayuki Sakaguchi, Toshihiko Shiroishi and Nori Kurata
    Citation: BMC Bioinformatics 2009 10:131
    Content type: Methodology article Published on:

  2. Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological ...

    Authors: Weijian Xuan, Manhong Dai, Barbara Mirel, Jean Song, Brian Athey, Stanley J Watson and Fan Meng
    Citation: BMC Bioinformatics 2009 10(Suppl 5):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 5

  6. The construction of a whole-genome physical map has been an essential component of numerous genome projects initiated since the inception of the Human Genome Project. Its usefulness has been proved for whole-g...

    Authors: Simone Scalabrin, Michele Morgante and Alberto Policriti
    Citation: BMC Bioinformatics 2009 10:127
    Content type: Software Published on:

  7. Gene expression signatures in the mammalian brain hold the key to understanding neural development and neurological disease. Researchers have previously used voxelation in combination with microarrays for acqu...

    Authors: Li An, Hongbo Xie, Mark H Chin, Zoran Obradovic, Desmond J Smith and Vasileios Megalooikonomou
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  8. High-throughput microarray technologies have generated and accumulated massive amounts of gene expression datasets that contain expression levels of thousands of genes under hundreds of different experimental ...

    Authors: Junwan Liu, Zhoujun Li, Xiaohua Hu and Yiming Chen
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  10. In many cases biomedical data sets contain outliers that make it difficult to achieve reliable knowledge discovery. Data analysis without removing outliers could lead to wrong results and provide misleading in...

    Authors: Jung Hun Oh and Jean Gao
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  11. Transcriptional regulation is a fundamental process in biological systems, where transcription factors (TFs) have been revealed to play crucial roles. In recent years, in addition to TFs, an increasing number ...

    Authors: Rui-Sheng Wang, Guangxu Jin, Xiang-Sun Zhang and Luonan Chen
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  12. Protein-protein interactions play vital roles in nearly all cellular processes and are involved in the construction of biological pathways such as metabolic and signal transduction pathways. Although large-sca...

    Authors: Xiaotong Lin, Mei Liu and Xue-wen Chen
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  13. Identification of functionally important sites in biomolecular sequences has broad applications ranging from rational drug design to the analysis of metabolic and signal transduction networks. Experimental det...

    Authors: Cornelia Caragea, Jivko Sinapov, Drena Dobbs and Vasant Honavar
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  14. Evolutionary trees are family trees that represent the relationships between a group of organisms. Phylogenetic heuristics are used to search stochastically for the best-scoring trees in tree space. Given that...

    Authors: Seung-Jin Sul, Suzanne Matthews and Tiffani L Williams
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  15. Recent studies in computational primary protein sequence analysis have leveraged the power of unlabeled data. For example, predictive models based on string kernels trained on sequences known to belong to part...

    Authors: Pavel Kuksa, Pai-Hsi Huang and Vladimir Pavlovic
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  16. A large amount of computational and experimental work has been devoted to uncovering network motifs in gene regulatory networks. The leading hypothesis is that evolutionary processes independently selected rec...

    Authors: Oscar Harari, Coral del Val, Rocío Romero-Zaliz, Dongwoo Shin, Henry Huang, Eduardo A Groisman and Igor Zwir
    Citation: BMC Bioinformatics 2009 10(Suppl 4):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 4

  17. Recombination has a profound impact on the evolution of viruses, but characterizing recombination patterns in molecular sequences remains a challenging endeavor. Despite its importance in molecular evolutionar...

    Authors: Philippe Lemey, Martin Lott, Darren P Martin and Vincent Moulton
    Citation: BMC Bioinformatics 2009 10:126
    Content type: Research article Published on:

  18. A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring c...

    Authors: Daniel Schober, Barry Smith, Suzanna E Lewis, Waclaw Kusnierczyk, Jane Lomax, Chris Mungall, Chris F Taylor, Philippe Rocca-Serra and Susanna-Assunta Sansone
    Citation: BMC Bioinformatics 2009 10:125
    Content type: Correspondence Published on:

  19. Tilt series are commonly used in electron tomography as a means of collecting three-dimensional information from two-dimensional projections. A common problem encountered is the projection alignment prior to 3...

    Authors: Carlos Oscar Sanchez Sorzano, Cédric Messaoudi, Matthias Eibauer, JR Bilbao-Castro, R Hegerl, S Nickell, S Marco and JM Carazo
    Citation: BMC Bioinformatics 2009 10:124
    Content type: Methodology article Published on:

  20. The availability of 12 fully sequenced Drosophila species genomes provides an excellent opportunity to explore the evolutionary mechanism, structure and function of gene families in Drosophila. Currently, several...

    Authors: Jinyu Wu, Xiang Xu, Jian Xiao, Long Xu, Huiguang Yi, Shengjie Gao, Jing Liu, Qiyu Bao, Fangqing Zhao and Xiaokun Li
    Citation: BMC Bioinformatics 2009 10:123
    Content type: Database Published on:

  22. During this recent decade, microarray-based single nucleotide polymorphism (SNP) data are becoming more widely used as markers for linkage analysis in the identification of loci for disease-associated genes. A...

    Authors: Yoko Fukuda, Yasuo Nakahara, Hidetoshi Date, Yuji Takahashi, Jun Goto, Akinori Miyashita, Ryozo Kuwano, Hiroki Adachi, Eiji Nakamura and Shoji Tsuji
    Citation: BMC Bioinformatics 2009 10:121
    Content type: Software Published on:

  24. Drosophila gene expression pattern images document the spatiotemporal dynamics of gene expression during embryogenesis. A comparative analysis of these images could provide a fundamentally important way for study...

    Authors: Shuiwang Ji, Ying-Xin Li, Zhi-Hua Zhou, Sudhir Kumar and Jieping Ye
    Citation: BMC Bioinformatics 2009 10:119
    Content type: Methodology article Published on:

  25. Although integrons and their associated gene cassettes are present in ~10% of bacteria and can represent up to 3% of the genome in which they are found, very few have been properly identified and annotated in ...

    Authors: Michael J Joss, Jeremy E Koenig, Maurizio Labbate, Martin F Polz, Michael R Gillings, Harold W Stokes, W Ford Doolittle and Yan Boucher
    Citation: BMC Bioinformatics 2009 10:118
    Content type: Database Published on:

  26. Phosphorylation of proteins plays a crucial role in the regulation and activation of metabolic and signaling pathways and constitutes an important target for pharmaceutical intervention. Central to the phospho...

    Authors: Pawel Durek, Christian Schudoma, Wolfram Weckwerth, Joachim Selbig and Dirk Walther
    Citation: BMC Bioinformatics 2009 10:117
    Content type: Research article Published on:

  28. The "common disease – common variant" hypothesis and genome-wide association studies have achieved numerous successes in the last three years, particularly in genetic mapping in human diseases. Nevertheless, t...

    Authors: Zhipeng Cai, Hadi Sabaa, Yining Wang, Randy Goebel, Zhiquan Wang, Jiaofen Xu, Paul Stothard and Guohui Lin
    Citation: BMC Bioinformatics 2009 10:115
    Content type: Research article Published on:

  29. Protein-protein interactions (PPIs) are critical to every aspect of biological processes. Expansion of all PPIs from a set of given queries often results in a complex PPI network lacking spatiotemporal conside...

    Authors: Sheng-An Lee, Chen-Hsiung Chan, Tzu-Chi Chen, Chia-Ying Yang, Kuo-Chuan Huang, Chi-Hung Tsai, Jin-Mei Lai, Feng-Sheng Wang, Cheng-Yan Kao and Chi-Ying F Huang
    Citation: BMC Bioinformatics 2009 10:114
    Content type: Software Published on:

  30. Polypeptides are composed of amino acids covalently bonded via a peptide bond. The majority of peptide bonds in proteins is found to occur in the trans conformation. In spite of their infrequent occurrence, cis p...

    Authors: Konstantinos P Exarchos, Themis P Exarchos, Costas Papaloukas, Anastassios N Troganis and Dimitrios I Fotiadis
    Citation: BMC Bioinformatics 2009 10:113
    Content type: Research article Published on:

  33. High-throughput real-time quantitative reverse transcriptase polymerase chain reaction (qPCR) is a widely used technique in experiments where expression patterns of genes are to be profiled. Current stage tech...

    Authors: Jessica C Mar, Yasumasa Kimura, Kate Schroder, Katharine M Irvine, Yoshihide Hayashizaki, Harukazu Suzuki, David Hume and John Quackenbush
    Citation: BMC Bioinformatics 2009 10:110
    Content type: Methodology article Published on:

  37. Recent advances in automation technologies have enabled the use of flow cytometry for high throughput screening, generating large complex data sets often in clinical trials or drug discovery settings. However,...

    Authors: Florian Hahne, Nolwenn LeMeur, Ryan R Brinkman, Byron Ellis, Perry Haaland, Deepayan Sarkar, Josef Spidlen, Errol Strain and Robert Gentleman
    Citation: BMC Bioinformatics 2009 10:106
    Content type: Software Published on:

  39. The stability of proteins is governed by the heat capacity, enthalpy and entropy changes of folding, which are strongly correlated to the change in solvent accessible surface area experienced by the polypeptid...

    Authors: Jorge Estrada, Pau Bernadó, Martin Blackledge and Javier Sancho
    Citation: BMC Bioinformatics 2009 10:104
    Content type: Software Published on:

  40. Depending on chemical features residues have preferred locations – interior or exterior – in protein structures, which also determine how many other residues are found around them. The close packing of residue...

    Authors: Arumay Pal, Ranjit Prasad Bahadur, Partha Sarathi Ray and Pinak Chakrabarti
    Citation: BMC Bioinformatics 2009 10:103
    Content type: Research article Published on:

  41. The developments of high-throughput genotyping technologies, which enable the simultaneous genotyping of hundreds of thousands of single nucleotide polymorphisms (SNP) have the potential to increase the benefi...

    Authors: High-Seng Chai, Hugues Sicotte, Kent R Bailey, Stephen T Turner, Yan W Asmann and Jean-Pierre A Kocher
    Citation: BMC Bioinformatics 2009 10:102
    Content type: Methodology article Published on:

  42. Conformation generation is a ubiquitous problem in molecule modelling. Many applications require sampling the broad molecular conformational space or perceiving the bioactive conformers to ensure success. Nume...

    Authors: Xiaofeng Liu, Fang Bai, Sisheng Ouyang, Xicheng Wang, Honglin Li and Hualiang Jiang
    Citation: BMC Bioinformatics 2009 10:101
    Content type: Methodology article Published on:

  45. There are many sources of variation in dual labelled microarray experiments, including data acquisition and image processing. The final interpretation of experiments strongly relies on the accuracy of the meas...

    Authors: Annie Glatigny, Hervé Delacroix, Thomas Tang, Nicolas François, Lawrence Aggerbeck and Marie-Hélène Mucchielli-Giorgi
    Citation: BMC Bioinformatics 2009 10:98
    Content type: Methodology article Published on:

  47. An important component of time course microarray studies is the identification of genes that demonstrate significant time-dependent variation in their expression levels. Until recently, available methods for p...

    Authors: Stephen C Billups, Margaret C Neville, Michael Rudolph, Weston Porter and Pepper Schedin
    Citation: BMC Bioinformatics 2009 10:96
    Content type: Research article Published on:

  48. A common method for presenting and studying biological interaction networks is visualization. Software tools can enhance our ability to explore network visualizations and improve our understanding of biologica...

    Authors: Jamie I MacPherson, John W Pinney and David L Robertson
    Citation: BMC Bioinformatics 2009 10:95
    Content type: Software Published on:

  49. Automated microscopy technologies have led to a rapid growth in imaging data on a scale comparable to that of the genomic revolution. High throughput screens are now being performed to determine the localisati...

    Authors: Nicholas A Hamilton, Jack TH Wang, Markus C Kerr and Rohan D Teasdale
    Citation: BMC Bioinformatics 2009 10:94
    Content type: Methodology article Published on:

  50. A central goal of experimental studies in systems biology is to identify meaningful markers that are hidden within a diffuse background of data originating from large-scale analytical intensity measurements as...

    Authors: Alexander Kaever, Thomas Lingner, Kirstin Feussner, Cornelia Göbel, Ivo Feussner and Peter Meinicke
    Citation: BMC Bioinformatics 2009 10:92
    Content type: Software Published on:

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