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  1. 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:

  2. 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:

  3. 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:

  4. 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:

  5. 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:

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  12. 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:

  14. 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:

  15. 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:

  18. 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:

  19. 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:

  20. 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:

  21. Serial Analysis of Gene Expression (SAGE) is a powerful tool to determine gene expression profiles. Two types of SAGE libraries, ShortSAGE and LongSAGE, are classified based on the length of the SAGE tag (10 v...

    Authors: Yi-Ju Li, Puting Xu, Xuejun Qin, Donald E Schmechel, Christine M Hulette, Jonathan L Haines, Margaret A Pericak-Vance and John R Gilbert
    Citation: BMC Bioinformatics 2006 7:504
    Content type: Research article Published on:

  23. 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:

  25. Here we describe PathogenMIPer, a software program for designing molecular inversion probe (MIP) oligonucleotides for use in pathogen identification and detection. The software designs unique and specific olig...

    Authors: Sreedevi Thiyagarajan, Miloslav Karhanek, Michael Akhras, Ronald W Davis and Nader Pourmand
    Citation: BMC Bioinformatics 2006 7:500
    Content type: Software Published on:

  26. Accurate multiple sequence alignments of proteins are very important in computational biology today. Despite the numerous efforts made in this field, all alignment strategies have certain shortcomings resultin...

    Authors: Saikat Chakrabarti, Christopher J Lanczycki, Anna R Panchenko, Teresa M Przytycka, Paul A Thiessen and Stephen H Bryant
    Citation: BMC Bioinformatics 2006 7:499
    Content type: Research article Published on:

  27. In sequence analysis the multiple alignment builds the fundament of all proceeding analyses. Errors in an alignment could strongly influence all succeeding analyses and therefore could lead to wrong prediction...

    Authors: Philipp N Seibel, Tobias Müller, Thomas Dandekar, Jörg Schultz and Matthias Wolf
    Citation: BMC Bioinformatics 2006 7:498
    Content type: Software Published on:

  29. DNA methylation plays an important role in development and tumorigenesis by epigenetic modification and silencing of critical genes. The development of PCR-based methylation assays on bisulphite modified DNA h...

    Authors: Filip Pattyn, Jasmien Hoebeeck, Piet Robbrecht, Evi Michels, Anne De Paepe, Guy Bottu, David Coornaert, Robert Herzog, Frank Speleman and Jo Vandesompele
    Citation: BMC Bioinformatics 2006 7:496
    Content type: Research article Published on:

  31. The progress through the eukaryotic cell division cycle is driven by an underlying molecular regulatory network. Cell cycle progression can be considered as a series of irreversible transitions from one steady...

    Authors: Anna Lovrics, Attila Csikász-Nagy, István Gy Zsély, Judit Zádor, Tamás Turányi and Béla Novák
    Citation: BMC Bioinformatics 2006 7:494
    Content type: Research article Published on:

  33. The rapid proliferation of biomedical text makes it increasingly difficult for researchers to identify, synthesize, and utilize developed knowledge in their fields of interest. Automated information extraction...

    Authors: Yang Jin, Ryan T McDonald, Kevin Lerman, Mark A Mandel, Steven Carroll, Mark Y Liberman, Fernando C Pereira, Raymond S Winters and Peter S White
    Citation: BMC Bioinformatics 2006 7:492
    Content type: Research article Published on:

  35. Today, there is a growing need in bioinformatics to combine available software tools into chains, thus building complex applications from existing single-task tools. To create such workflows, the tools involve...

    Authors: Philipp N Seibel, Jan Krüger, Sven Hartmeier, Knut Schwarzer, Kai Löwenthal, Henning Mersch, Thomas Dandekar and Robert Giegerich
    Citation: BMC Bioinformatics 2006 7:490
    Content type: Software Published on:

  36. Sharing of microarray data within the research community has been greatly facilitated by the development of the disclosure and communication standards MIAME and MAGE-ML by the MGED Society. However, the comple...

    Authors: Tim F Rayner, Philippe Rocca-Serra, Paul T Spellman, Helen C Causton, Anna Farne, Ele Holloway, Rafael A Irizarry, Junmin Liu, Donald S Maier, Michael Miller, Kjell Petersen, John Quackenbush, Gavin Sherlock, Christian J Stoeckert Jr, Joseph White, Patricia L Whetzel…
    Citation: BMC Bioinformatics 2006 7:489
    Content type: Commentary Published on:

  45. RNA-dependent gene silencing is becoming a routine tool used in laboratories worldwide. One of the important remaining hurdles in the selection of the target sequence, if not the most important one, is the des...

    Authors: Jean-François Lucier, Lucien Junior Bergeron, Francis P Brière, Rodney Ouellette, Sherif Abou Elela and Jean-Pierre Perreault
    Citation: BMC Bioinformatics 2006 7:480
    Content type: Software Published on:

  46. Protein identification based on mass spectrometry (MS) has previously been performed using peptide mass fingerprinting (PMF) or tandem MS (MS/MS) database searching. However, these methods cannot identify prot...

    Authors: Kosaku Shinoda, Nozomu Yachie, Takeshi Masuda, Naoyuki Sugiyama, Masahiro Sugimoto, Tomoyoshi Soga and Masaru Tomita
    Citation: BMC Bioinformatics 2006 7:479
    Content type: Methodology article Published on:

  47. Signal recognition and information processing is a fundamental cellular function, which in part involves comprehensive transcriptional regulatory (TR) mechanisms carried out in response to complex environmenta...

    Authors: Illés J Farkas, Chuang Wu, Chakra Chennubhotla, Ivet Bahar and Zoltán N Oltvai
    Citation: BMC Bioinformatics 2006 7:478
    Content type: Research article Published on:

  48. A large number of studies on genome sequences have revealed the major role played by repeated sequences in the structure, function, dynamics and evolution of genomes. In-depth repeat analysis requires speciali...

    Authors: Patrick Durand, Frédéric Mahé, Anne-Sophie Valin and Jacques Nicolas
    Citation: BMC Bioinformatics 2006 7:477
    Content type: Methodology article Published on:

  50. Two-Dimensional Difference In Gel Electrophoresis (2D-DIGE) is a powerful tool for measuring differences in protein expression between samples or conditions. However, to remove systematic variability within an...

    Authors: Kim Kultima, Birger Scholz, Henrik Alm, Karl Sköld, Marcus Svensson, Alan R Crossman, Erwan Bezard, Per E Andrén and Ingrid Lönnstedt
    Citation: BMC Bioinformatics 2006 7:475
    Content type: Research article Published on:

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