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  1. An ever increasing number of techniques are being used to find genes with similar profiles from microarray studies. Visualization of gene expression profiles can aid this process, potentially contributing to t...

    Authors: Yvonne E Pittelkow and Susan R Wilson
    Citation: BMC Bioinformatics 2007 8:486
    Content type: Methodology article Published on:

  2. The quality of cDNA microarray data is crucial for expanding its application to other research areas, such as the study of gene regulatory networks. Despite the fact that a number of algorithms have been sugge...

    Authors: Hye Young Kim, Seo Eun Lee, Min Jung Kim, Jin Il Han, Bo Kyung Kim, Yong Sung Lee, Young Seek Lee and Jin Hyuk Kim
    Citation: BMC Bioinformatics 2007 8:485
    Content type: Research article Published on:

  4. In the "post-genome" era, mass spectrometry (MS) has become an important method for the analysis of proteins and the rapid advancement of this technique, in combination with other proteomics methods, results i...

    Authors: Arnaud Droit, Joanna M Hunter, Michèle Rouleau, Chantal Ethier, Aude Picard-Cloutier, David Bourgais and Guy G Poirier
    Citation: BMC Bioinformatics 2007 8:483
    Content type: Database Published on:

  5. Predicting protein complexes from experimental data remains a challenge due to limited resolution and stochastic errors of high-throughput methods. Current algorithms to reconstruct the complexes typically rel...

    Authors: Wasinee Rungsarityotin, Roland Krause, Arno Schödl and Alexander Schliep
    Citation: BMC Bioinformatics 2007 8:482
    Content type: Research article Published on:

  6. Reliable transcription factor binding site (TFBS) prediction methods are essential for computer annotation of large amount of genome sequence data. However, current methods to predict TFBSs are hampered by the...

    Authors: Victor G Levitsky, Elena V Ignatieva, Elena A Ananko, Igor I Turnaev, Tatyana I Merkulova, Nikolay A Kolchanov and TC Hodgman
    Citation: BMC Bioinformatics 2007 8:481
    Content type: Research article Published on:

  8. Large molecular sequence databases are fundamental resources for modern bioscientists. Whether for project-specific purposes or sharing data with colleagues, it is often advantageous to maintain smaller sequen...

    Authors: Scott A Givan, Christopher M Sullivan and James C Carrington
    Citation: BMC Bioinformatics 2007 8:479
    Content type: Software Published on:

  10. Novel molecular and statistical methods are in rising demand for disease diagnosis and prognosis with the help of recent advanced biotechnology. High-resolution mass spectrometry (MS) is one of those biotechno...

    Authors: Jingjing Ye, Hao Liu, Crystal Kirmiz, Carlito B Lebrilla and David M Rocke
    Citation: BMC Bioinformatics 2007 8:477
    Content type: Methodology article Published on:

  11. The joint analysis of several categorical variables is a common task in many areas of biology, and is becoming central to systems biology investigations whose goal is to identify potentially complex interactio...

    Authors: Corinne Dahinden, Giovanni Parmigiani, Mark C Emerick and Peter Bühlmann
    Citation: BMC Bioinformatics 2007 8:476
    Content type: Methodology article Published on:

  13. The recent availability of new, less expensive high-throughput DNA sequencing technologies has yielded a dramatic increase in the volume of sequence data that must be analyzed. These data are being generated f...

    Authors: Michael C Schatz, Cole Trapnell, Arthur L Delcher and Amitabh Varshney
    Citation: BMC Bioinformatics 2007 8:474
    Content type: Software Published on:

  14. Eukaryotic cells have developed mechanisms to respond to external environmental or physiological changes (stresses). In order to increase the activities of stress-protection functions in response to an environ...

    Authors: Li-Hsieh Lin, Hsiao-Ching Lee, Wen-Hsiung Li and Bor-Sen Chen
    Citation: BMC Bioinformatics 2007 8:473
    Content type: Methodology article Published on:

  15. Maximum parsimony phylogenetic tree reconstruction from genetic variation data is a fundamental problem in computational genetics with many practical applications in population genetics, whole genome analysis,...

    Authors: Srinath Sridhar, Fumei Lam, Guy E Blelloch, R Ravi and Russell Schwartz
    Citation: BMC Bioinformatics 2007 8:472
    Content type: Research article Published on:

  18. Ribozymes are small catalytic RNAs that possess the dual functions of sequence-specific RNA recognition and site-specific cleavage. Trans-cleaving ribozymes can inhibit translation of genes at the messenger RNA (...

    Authors: Yu Shao, Susan Wu, Chi Yu Chan, Jessie R Klapper, Erasmus Schneider and Ye Ding
    Citation: BMC Bioinformatics 2007 8:469
    Content type: Research article Published on:

  19. High-throughput peptide and protein identification technologies have benefited tremendously from strategies based on tandem mass spectrometry (MS/MS) in combination with database searching algorithms. A major ...

    Authors: Nico Pfeifer, Andreas Leinenbach, Christian G Huber and Oliver Kohlbacher
    Citation: BMC Bioinformatics 2007 8:468
    Content type: Research article Published on:

  20. In the analysis of networks we frequently require the statistical significance of some network statistic, such as measures of similarity for the properties of interacting nodes. The structure of the network ma...

    Authors: Thomas Thorne and Michael PH Stumpf
    Citation: BMC Bioinformatics 2007 8:467
    Content type: Methodology article Published on:

  21. Subcellular location prediction of proteins is an important and well-studied problem in bioinformatics. This is a problem of predicting which part in a cell a given protein is transported to, where an amino ac...

    Authors: Takeyuki Tamura and Tatsuya Akutsu
    Citation: BMC Bioinformatics 2007 8:466
    Content type: Research article Published on:

  22. Simple Sequence Repeats (SSRs), or microsatellites, are among the most powerful genetic markers known. A common method for the development of SSR markers is the construction of genomic DNA libraries enriched f...

    Authors: Alexis Dereeper, Xavier Argout, Claire Billot, Jean-François Rami and Manuel Ruiz
    Citation: BMC Bioinformatics 2007 8:465
    Content type: Software Published on:

  25. The construction of literature-based networks of gene-gene interactions is one of the most important applications of text mining in bioinformatics. Extracting potential gene relationships from the biomedical l...

    Authors: Hyunsoo Kim, Haesun Park and Barry L Drake
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  26. With more and more research dedicated to literature mining in the biomedical domain, more and more systems are available for people to choose from when building literature mining applications. In this study, w...

    Authors: Manabu Torii, Zhang-zhi Hu, Min Song, Cathy H Wu and Hongfang Liu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  27. A huge amount of biomedical textual information has been produced and collected in MEDLINE for decades. In order to easily utilize biomedical information in the free text, document clustering and text summariz...

    Authors: Illhoi Yoo, Xiaohua Hu and Il-Yeol Song
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  28. Annotating genes and their products with Gene Ontology codes is an important area of research. One approach is to use the information available about these genes in the biomedical literature. The goal in this ...

    Authors: Padmini Srinivasan and Xin Ying Qiu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  29. As systems biology has begun to draw growing attention, bio-network inference and analysis have become more and more important. Though there have been many efforts for bio-network inference, they are still far...

    Authors: Doheon Lee, Sangwoo Kim and Younghoon Kim
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  30. Biomedical ontologies are emerging as critical tools in genomic and proteomic research, where complex data in disparate resources need to be integrated. A number of ontologies describe properties that can be a...

    Authors: Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith and Cathy H Wu
    Citation: BMC Bioinformatics 2007 8(Suppl 9):S1
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 9

  31. The ambition of most molecular biologists is the understanding of the intricate network of molecular interactions that control biological systems. As scientists uncover the components and the connectivity of t...

    Authors: Alessandro Di Cara, Abhishek Garg, Giovanni De Micheli, Ioannis Xenarios and Luis Mendoza
    Citation: BMC Bioinformatics 2007 8:462
    Content type: Software Published on:

  33. Research in evolution requires software for visualizing and editing phylogenetic trees, for increasingly very large datasets, such as arise in expression analysis or metagenomics, for example. It would be desi...

    Authors: Daniel H Huson, Daniel C Richter, Christian Rausch, Tobias Dezulian, Markus Franz and Regula Rupp
    Citation: BMC Bioinformatics 2007 8:460
    Content type: Software Published on:

  34. Peptides binding to Major Histocompatibility Complex (MHC) class II molecules are crucial for initiation and regulation of immune responses. Predicting peptides that bind to a specific MHC molecule plays an im...

    Authors: Menaka Rajapakse, Bertil Schmidt, Lin Feng and Vladimir Brusic
    Citation: BMC Bioinformatics 2007 8:459
    Content type: Research article Published on:

  49. In this meeting report we give an overview of the 3rd International Society for Computational Biology Student Council Symposium. Furthermore, we explain the role of the Student Council and the symposium series...

    Authors: Nils Gehlenborg, Manuel Corpas and Sarath Chandra Janga
    Citation: BMC Bioinformatics 2007 8(Suppl 8):I1
    Content type: Meeting report Published on:

    This article is part of a Supplement: Volume 8 Supplement 8

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