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  1. An important step in understanding the conditions that specify gene expression is the recognition of gene regulatory elements. Due to high diversity of different types of transcription factors and their DNA bi...

    Authors: Maria Stepanova, Feng Lin and Valerie C-L Lin
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S27
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  2. DNA microarrays are a powerful tool for monitoring the expression of tens of thousands of genes simultaneously. With the advance of microarray technology, the challenge issue becomes how to analyze a large amo...

    Authors: Guoqing Lu, The V Nguyen, Yuannan Xia and Michael Fromm
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S26
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  3. The problem of inferring the evolutionary history and constructing the phylogenetic tree with high performance has become one of the major problems in computational biology.

    Authors: Ling Qin, Yixin Chen, Yi Pan and Ling Chen
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S24
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  4. Quantitative simultaneous monitoring of the expression levels of thousands of genes under various experimental conditions is now possible using microarray experiments. However, there are still gaps toward whol...

    Authors: Xiao-Li Li, Yin-Chet Tan and See-Kiong Ng
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S23
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  5. Cell culture systems are useful in studying toxicological effects of chemicals such as Hexahydro-1,3,5-trinitro-1,3,5-triazine (RDX), however little is known as to how accurately isolated cells reflect respons...

    Authors: Edward J Perkins, Wenjun Bao, Xin Guan, Choo-Yaw Ang, Russell D Wolfinger, Tzu-Ming Chu, Sharon A Meyer and Laura S Inouye
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S22
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  6. Spatio-temporal dynamics within cells can now be visualized at appropriate resolution, due to the advances in molecular imaging technologies. Even single-particle tracking (SPT) and single fluorophore video im...

    Authors: Ryuzo Azuma, Tetsuji Kitagawa, Hiroshi Kobayashi and Akihiko Konagaya
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S20
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  7. Comparative genomics has become an essential approach for identifying homologous gene candidates and their functions, and for studying genome evolution. There are many tools available for genome comparisons. U...

    Authors: Guoqing Lu, Liying Jiang, Resa MK Helikar, Thaine W Rowley, Luwen Zhang, Xianfeng Chen and Etsuko N Moriyama
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S18
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  8. Hydrophobins are fungal proteins that can turn into amphipathic membranes at hydrophilic/hydrophobic interfaces by self-assembly. The assemblages by Class I hydrophobins are extremely stable and possess the re...

    Authors: Kuan Yang, Youping Deng, Chaoyang Zhang and Mohamed Elasri
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S16
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  9. Protein secondary structure prediction is a fundamental and important component in the analytical study of protein structure and functions. The prediction technique has been developed for several decades. The ...

    Authors: Hang Chen, Fei Gu and Zhengge Huang
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S14
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  10. The problem of finding a Shortest Common Supersequence (SCS) of a set of sequences is an important problem with applications in many areas. It is a key problem in biological sequences analysis. The SCS problem...

    Authors: Kang Ning and Hon Wai Leong
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  11. One main research challenge in the post-genomic era is to understand the relationship between protein sequences and their biological functions. In recent years, several automated annotation systems have been d...

    Authors: Zhong-Hui Duan, Brent Hughes, Lothar Reichel, Dianne M Perez and Ting Shi
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  12. Protein sequence clustering has been widely used as a part of the analysis of protein structure and function. In most cases single linkage or graph-based clustering algorithms have been applied. OPTICS (Orderi...

    Authors: Yonghui Chen, Kevin D Reilly, Alan P Sprague and Zhijie Guan
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  13. Recently several statistical methods have been proposed to identify genes with differential expression between two conditions. However, very few studies consider the problem of sample imbalance and there is no...

    Authors: Kun Yang, Jianzhong Li and Hong Gao
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  14. Microarray techniques have revolutionized genomic research by making it possible to monitor the expression of thousands of genes in parallel. As the amount of microarray data being produced is increasing at an...

    Authors: Lily R Liang, Shiyong Lu, Xuena Wang, Yi Lu, Vinay Mandal, Dorrelyn Patacsil and Deepak Kumar
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  15. Structure matching plays an important part in understanding the functional role of biological structures. Bioinformatics assists in this effort by reformulating this process into a problem of finding a maximum...

    Authors: Xiuzhen Huang, Jing Lai and Steven F Jennings
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  16. Haplotype analysis has gained increasing attention in the context of association studies of disease genes and drug responsivities over the last years. The potential use of haplotypes has led to the initiation ...

    Authors: Qiangfeng Zhang, Yuzhong Zhao, Guoliang Chen and Yun Xu
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S5
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  17. Searching for the longest common sequence (LCS) of multiple biosequences is one of the most fundamental tasks in bioinformatics. In this paper, we present a parallel algorithm named FAST_LCS to speedup the com...

    Authors: Yixin Chen, Andrew Wan and Wei Liu
    Citation: BMC Bioinformatics 2006 7(Suppl 4):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 7 Supplement 4

  18. The estimation of the difference between two evolutionary distances within a triplet of homologs is a common operation that is used for example to determine which of two sequences is closer to a third one. The...

    Authors: Christophe Dessimoz, Manuel Gil, Adrian Schneider and Gaston H Gonnet
    Citation: BMC Bioinformatics 2006 7:529
    Content type: Methodology article Published on:

  20. Studies on the distribution of indel sizes have consistently found that they obey a power law. This finding has lead several scientists to propose that logarithmic gap costs, G (k) = a + c ln k, are more biologic...

    Authors: Reed A Cartwright
    Citation: BMC Bioinformatics 2006 7:527
    Content type: Methodology article Published on:

  21. Expression microarrays represent a powerful technique for the simultaneous investigation of thousands of genes. The evidence that genes are not randomly distributed in the genome and that their coordinated exp...

    Authors: Federico E Turkheimer, Federico Roncaroli, Benoit Hennuy, Christian Herens, Minh Nguyen, Didier Martin, Annick Evrard, Vincent Bours, Jacques Boniver and Manuel Deprez
    Citation: BMC Bioinformatics 2006 7:526
    Content type: Research article Published on:

  22. The advent of genotype data from large-scale efforts that catalog the genetic variants of different populations have given rise to new avenues for multifactorial disease association studies. Recent work shows ...

    Authors: Chun Meng Song, Boon Huat Yeo, Erwin Tantoso, Yuchen Yang, Yun Ping Lim, Kuo-Bin Li and Gunaretnam Rajagopal
    Citation: BMC Bioinformatics 2006 7:525
    Content type: Software Published on:

  23. Multiple sequence alignment (MSA) is a useful tool in bioinformatics. Although many MSA algorithms have been developed, there is still room for improvement in accuracy and speed. In the alignment of a family o...

    Authors: Shinsuke Yamada, Osamu Gotoh and Hayato Yamana
    Citation: BMC Bioinformatics 2006 7:524
    Content type: Research article Published on:

  25. The discovery of cis-regulatory motifs still remains a challenging task even though the number of sequenced genomes is constantly growing. Computational analyses using pattern search algorithms have been valua...

    Authors: Kenneth W Berendzen, Kurt Stüber, Klaus Harter and Dierk Wanke
    Citation: BMC Bioinformatics 2006 7:522
    Content type: Research article Published on:

  26. Single nucleotide polymorphisms (SNPs) are DNA sequence variations, occurring when a single nucleotide – adenine (A), thymine (T), cytosine (C) or guanine (G) – is altered. Arguably, SNPs account for more than...

    Authors: Mohua Podder, William J Welch, Ruben H Zamar and Scott J Tebbutt
    Citation: BMC Bioinformatics 2006 7:521
    Content type: Research article Published on:

  27. The use of exogenous small interfering RNAs (siRNAs) for gene silencing has quickly become a widespread molecular tool providing a powerful means for gene functional study and new drug target identification. A...

    Authors: Jean-Philippe Vert, Nicolas Foveau, Christian Lajaunie and Yves Vandenbrouck
    Citation: BMC Bioinformatics 2006 7:520
    Content type: Methodology article Published on:

  29. Knowing the submitochondria localization of a mitochondria protein is an important step to understand its function. We develop a method which is based on an extended version of pseudo-amino acid composition to...

    Authors: Pufeng Du and Yanda Li
    Citation: BMC Bioinformatics 2006 7:518
    Content type: Methodology article Published on:

  30. A wide range of research areas in bioinformatics, molecular biology and medicinal chemistry require precise chemical structure information about molecules and reactions, e.g. drug design, ligand docking, metaboli...

    Authors: Martin A Ott and Gert Vriend
    Citation: BMC Bioinformatics 2006 7:517
    Content type: Database Published on:

  31. Short interfering RNAs have allowed the development of clean and easily regulated methods for disruption of gene expression. However, while these methods continue to grow in popularity, designing effective siR...

    Authors: Wuming Gong, Yongliang Ren, Qiqi Xu, Yejun Wang, Dong Lin, Haiyan Zhou and Tongbin Li
    Citation: BMC Bioinformatics 2006 7:516
    Content type: Research article Published on:

  32. Measuring each protein's importance in signaling networks helps to identify the crucial proteins in a cellular process, find the fragile portion of the biology system and further assist for disease therapy. Ho...

    Authors: Wei Liu, Dong Li, Jiyang Zhang, Yunping Zhu and Fuchu He
    Citation: BMC Bioinformatics 2006 7:515
    Content type: Research article Published on:

  33. Uncertainty often affects molecular biology experiments and data for different reasons. Heterogeneity of gene or protein expression within the same tumor tissue is an example of biological uncertainty which sh...

    Authors: Francesca Demichelis, Paolo Magni, Paolo Piergiorgi, Mark A Rubin and Riccardo Bellazzi
    Citation: BMC Bioinformatics 2006 7:514
    Content type: Research article Published on:

  34. Data integration is a crucial task in the biomedical domain and integrating data sources is one approach to integrating data. Data elements (DEs) in particular play an important role in data integration. We co...

    Authors: Fleur Mougin, Anita Burgun and Olivier Bodenreider
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 3

  35. Propositional representations of biomedical knowledge are a critical component of most aspects of semantic mining in biomedicine. However, the proper set of propositions has yet to be determined. Recently, the...

    Authors: K Bretonnel Cohen and Lawrence Hunter
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 3

  36. Automatic recognition of relations between a specific disease term and its relevant genes or protein terms is an important practice of bioinformatics. Considering the utility of the results of this approach, w...

    Authors: Hong-Woo Chun, Yoshimasa Tsuruoka, Jin-Dong Kim, Rie Shiba, Naoki Nagata, Teruyoshi Hishiki and Jun'ichi Tsujii
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 3

  37. The biomedical domain is witnessing a rapid growth of the amount of published scientific results, which makes it increasingly difficult to filter the core information. There is a real need for support tools th...

    Authors: Fabio Rinaldi, Gerold Schneider, Kaarel Kaljurand, Michael Hess and Martin Romacker
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 3

  38. We study the adaptation of Link Grammar Parser to the biomedical sublanguage with a focus on domain terms not found in a general parser lexicon. Using two biomedical corpora, we implement and evaluate three ap...

    Authors: Sampo Pyysalo, Tapio Salakoski, Sophie Aubin and Adeline Nazarenko
    Citation: BMC Bioinformatics 2006 7(Suppl 3):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 7 Supplement 3

  40. Expressed sequence tag (EST) analyses provide a rapid and economical means to identify candidate genes that may be involved in a particular biological process. These ESTs are useful in many Functional Genomics...

    Authors: Mariano Latorre, Herman Silva, Juan Saba, Carito Guziolowski, Paula Vizoso, Veronica Martinez, Jonathan Maldonado, Andrea Morales, Rodrigo Caroca, Veronica Cambiazo, Reinaldo Campos-Vargas, Mauricio Gonzalez, Ariel Orellana, Julio Retamales and Lee A Meisel
    Citation: BMC Bioinformatics 2006 7:513
    Content type: Software Published on:

  42. Concerns are often raised about the accuracy of microarray technologies and the degree of cross-platform agreement, but there are yet no methods which can unambiguously evaluate precision and sensitivity for t...

    Authors: Andrew J Holloway, Alicia Oshlack, Dileepa S Diyagama, David DL Bowtell and Gordon K Smyth
    Citation: BMC Bioinformatics 2006 7:511
    Content type: Methodology article Published on:

  43. Protein-structure alignment is a fundamental tool to study protein function, evolution and model building. In the last decade several methods for structure alignment were introduced, but most of them ignore th...

    Authors: Bjoern Kolbeck, Patrick May, Tobias Schmidt-Goenner, Thomas Steinke and Ernst-Walter Knapp
    Citation: BMC Bioinformatics 2006 7:510
    Content type: Methodology article Published on:

  46. Circular Dichroism (CD) spectroscopy is a widely used method for studying protein structures in solution. Modern synchrotron radiation CD (SRCD) instruments have considerably higher photon fluxes than do conve...

    Authors: Jonathan G Lees, Andrew J Miles, Robert W Janes and B A Wallace
    Citation: BMC Bioinformatics 2006 7:507
    Content type: Research article Published on:

  47. The analysis of biochemical networks using a logical (Boolean) description is an important approach in Systems Biology. Recently, new methods have been proposed to analyze large signaling and regulatory networ...

    Authors: Julio Saez-Rodriguez, Sebastian Mirschel, Rebecca Hemenway, Steffen Klamt, Ernst Dieter Gilles and Martin Ginkel
    Citation: BMC Bioinformatics 2006 7:506
    Content type: Software Published on:

  48. We present an approach designed to identify gene regulation patterns using sequence and expression data collected for Saccharomyces cerevisae. Our main goal is to relate the combinations of transcription factor b...

    Authors: Bartek Wilczyński, Torgeir R Hvidsten, Andriy Kryshtafovych, Jerzy Tiuryn, Jan Komorowski and Krzysztof Fidelis
    Citation: BMC Bioinformatics 2006 7:505
    Content type: Methodology article Published on:

  50. An important class of interaction switches for biological circuits and disease pathways are short binding motifs. However, the biological experiments to find these binding motifs are often laborious and expens...

    Authors: Soon-Heng Tan, Willy Hugo, Wing-Kin Sung and See-Kiong Ng
    Citation: BMC Bioinformatics 2006 7:502
    Content type: Methodology article Published on:

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