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  1. Comfrey (Symphytum officinale) is a perennial plant and has been consumed by humans as a vegetable, a tea and an herbal medicine for more than 2000 years. It, however, is hepatotoxic and carcinogenic in experimen...

    Authors: Lei Guo, Nan Mei, Stacey Dial, James Fuscoe and Tao Chen
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S22
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  2. The UNO/RIC Nanopore Detector provides a new way to study the binding and conformational changes of individual antibodies. Many critical questions regarding antibody function are still unresolved, questions th...

    Authors: Stephen Winters-Hilt, Eric Morales, Iftekhar Amin and Alexander Stoyanov
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  3. Support Vector Machines (SVMs) provide a powerful method for classification (supervised learning). Use of SVMs for clustering (unsupervised learning) is now being considered in a number of different ways.

    Authors: Stephen Winters-Hilt and Sam Merat
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  4. Multiple recent studies have found aberrant expression profiles of microRNAome in human cancers. While several target genes have been experimentally identified for some microRNAs in various tumors, the global ...

    Authors: Yuriy Gusev, Thomas D Schmittgen, Megan Lerner, Russell Postier and Daniel Brackett
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  5. Ionic current blockade signal processing, for use in nanopore detection, offers a promising new way to analyze single molecule properties, with potential implications for DNA sequencing. The alpha-Hemolysin tr...

    Authors: Alexander Churbanov, Carl Baribault and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  6. A nanopore detector has a nanometer-scale trans-membrane channel across which a potential difference is established, resulting in an ionic current through the channel in the pA-nA range. A distinctive channel ...

    Authors: Matthew Landry and Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  7. Synthetic transcription factors (STFs) promise to offer a powerful new therapeutic against Cancer, AIDS, and genetic disease. Currently, 10% of drugs are of this type, including salicylate and tamoxifen. STFs ...

    Authors: Stephen Winters-Hilt, Amanda Davis, Iftekhar Amin and Eric Morales
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  8. Nanopore detection is based on observations of the ionic current threading a single, highly stable, nanometer-scale channel. The dimensions are such that small biomolecules and biopolymers (like DNA and peptid...

    Authors: Stephen Winters-Hilt
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  9. Eisenia fetida, commonly known as red wiggler or compost worm, belongs to the Lumbricidae family of the Annelida phylum. Little is known about its genome sequence although it has been extensively used as a test o...

    Authors: Mehdi Pirooznia, Ping Gong, Xin Guan, Laura S Inouye, Kuan Yang, Edward J Perkins and Youping Deng
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  10. Urine from male Sprague-Dawley rats 25, 40, and 80 days old was analyzed by NMR and UPLC/MS. The effects of data normalization procedures on principal component analysis (PCA) and quantitative analysis of NMR-...

    Authors: Laura K Schnackenberg, Jinchun Sun, Parvaneh Espandiari, Ricky D Holland, Joseph Hanig and Richard D Beger
    Citation: BMC Bioinformatics 2007 8(Suppl 7):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 8 Supplement 7

  12. Reliable predictions of Cytotoxic T lymphocyte (CTL) epitopes are essential for rational vaccine design. Most importantly, they can minimize the experimental effort needed to identify epitopes. NetCTL is a web...

    Authors: Mette V Larsen, Claus Lundegaard, Kasper Lamberth, Soren Buus, Ole Lund and Morten Nielsen
    Citation: BMC Bioinformatics 2007 8:424
    Content type: Research article Published on:

  14. Array comparative genome hybridization (aCGH) provides information about genomic aberrations. Alterations in the DNA copy number may cause the cell to malfunction, leading to cancer. Therefore, the identificat...

    Authors: Carmen Lai, Hugo M Horlings, Marc J van de Vijver, Eric H van Beers, Petra M Nederlof, Lodewyk FA Wessels and Marcel JT Reinders
    Citation: BMC Bioinformatics 2007 8:422
    Content type: Research article Published on:

  15. An indirect approach is usually used to estimate the metabolic fluxes of an organism: couple the available measurements with known biological constraints (e.g. stoichiometry). Typically this estimation is done...

    Authors: Francisco Llaneras and Jesús Picó
    Citation: BMC Bioinformatics 2007 8:421
    Content type: Methodology article Published on:

  16. Knowing the subcellular location of proteins provides clues to their function as well as the interconnectivity of biological processes. Dozens of tools are available for predicting protein location in the euka...

    Authors: Yao Qing Shen and Gertraud Burger
    Citation: BMC Bioinformatics 2007 8:420
    Content type: Methodology article Published on:

  17. Gas chromatography-mass spectrometry (GC-MS) is a robust platform for the profiling of certain classes of small molecules in biological samples. When multiple samples are profiled, including replicates of the ...

    Authors: Mark D Robinson, David P De Souza, Woon Wai Keen, Eleanor C Saunders, Malcolm J McConville, Terence P Speed and Vladimir A Likić
    Citation: BMC Bioinformatics 2007 8:419
    Content type: Methodology article Published on:

  20. We introduce the decision support system for Protein (Structure) Comparison, Knowledge, Similarity and Information (ProCKSI). ProCKSI integrates various protein similarity measures through an easy to use interfac...

    Authors: Daniel Barthel, Jonathan D Hirst, Jacek Błażewicz, Edmund K Burke and Natalio Krasnogor
    Citation: BMC Bioinformatics 2007 8:416
    Content type: Research article Published on:

  21. Independently derived expression profiles of the same biological condition often have few genes in common. In this study, we created populations of expression profiles from publicly available microarray datase...

    Authors: Michael Gormley, William Dampier, Adam Ertel, Bilge Karacali and Aydin Tozeren
    Citation: BMC Bioinformatics 2007 8:415
    Content type: Research article Published on:

  22. Although many genomic features have been used in the prediction of protein-protein interactions (PPIs), frequently only one is used in a computational method. After realizing the limited power in the predictio...

    Authors: Jingchun Sun, Yan Sun, Guohui Ding, Qi Liu, Chuan Wang, Youyu He, Tieliu Shi, Yixue Li and Zhongming Zhao
    Citation: BMC Bioinformatics 2007 8:414
    Content type: Methodology article Published on:

  24. Many researchers are concerned with the comparability and reliability of microarray gene expression data. Recent completion of the MicroArray Quality Control (MAQC) project provides a unique opportunity to ass...

    Authors: James J Chen, Huey-Miin Hsueh, Robert R Delongchamp, Chien-Ju Lin and Chen-An Tsai
    Citation: BMC Bioinformatics 2007 8:412
    Content type: Correspondence Published on:

  25. Answers to several fundamental questions in statistical genetics would ideally require knowledge of the ancestral pedigree and of the gene flow therein. A few examples of such questions are haplotype estimatio...

    Authors: Dario Gasbarra, Matti Pirinen, Mikko J Sillanpää and Elja Arjas
    Citation: BMC Bioinformatics 2007 8:411
    Content type: Methodology article Published on:

  26. Accurate selection of splice sites during the splicing of precursors to messenger RNA requires both relatively well-characterized signals at the splice sites and auxiliary signals in the adjacent exons and int...

    Authors: Rezarta Islamaj Dogan, Lise Getoor, W John Wilbur and Stephen M Mount
    Citation: BMC Bioinformatics 2007 8:410
    Content type: Research article Published on:

  27. Since real time PCR was first developed, several approaches to estimating the initial quantity of template in an RT-PCR reaction have been tried. While initially only the early thermal cycles corresponding to ...

    Authors: Marjo V Smith, Chris R Miller, Michael Kohn, Nigel J Walker and Chris J Portier
    Citation: BMC Bioinformatics 2007 8:409
    Content type: Methodology article Published on:

  28. Nowadays modern biology aims at unravelling the strands of complex biological structures such as the protein-protein interaction (PPI) networks. A key concept in the organization of PPI networks is the existen...

    Authors: Ioannis A Maraziotis, Konstantina Dimitrakopoulou and Anastasios Bezerianos
    Citation: BMC Bioinformatics 2007 8:408
    Content type: Research article Published on:

  29. Cell specific gene expression is largely regulated by different combinations of transcription factors that bind cis-elements in the upstream promoter sequence. However, experimental detection of cis-elements is d...

    Authors: Charles G Danko, Vera A McIlvain, Maochun Qin, Barry E Knox and Arkady M Pertsov
    Citation: BMC Bioinformatics 2007 8:407
    Content type: Research article Published on:

  30. Marine ecological genomics can be defined as the application of genomic sciences to understand the structure and function of marine ecosystems. In this field of research, the analysis of genomes and metagenome...

    Authors: Thierry Lombardot, Renzo Kottmann, Gregory Giuliani, Andrea de Bono, Nans Addor and Frank Oliver Glöckner
    Citation: BMC Bioinformatics 2007 8:406
    Content type: Software Published on:

  31. Current tools for Co-phylogenetic analyses are not able to cope with the continuous accumulation of phylogenetic data. The sophisticated statistical test for host-parasite co-phylogenetic analyses implemented ...

    Authors: Alexandros Stamatakis, Alexander F Auch, Jan Meier-Kolthoff and Markus Göker
    Citation: BMC Bioinformatics 2007 8:405
    Content type: Software Published on:

  34. Accurate taxonomy is best maintained if species are arranged as hierarchical groups in phylogenetic trees. This is especially important as trees grow larger as a consequence of a rapidly expanding sequence dat...

    Authors: Daniel Dalevi, Todd Z DeSantis, Jakob Fredslund, Gary L Andersen, Victor M Markowitz and Philip Hugenholtz
    Citation: BMC Bioinformatics 2007 8:402
    Content type: Software Published on:

  35. Each major protein database uses its own conventions when assigning protein identifiers. Resolving the various, potentially unstable, identifiers that refer to identical proteins is a major challenge. This is ...

    Authors: Richard G Côté, Philip Jones, Lennart Martens, Samuel Kerrien, Florian Reisinger, Quan Lin, Rasko Leinonen, Rolf Apweiler and Henning Hermjakob
    Citation: BMC Bioinformatics 2007 8:401
    Content type: Software Published on:

  36. The Complete Arabidopsis Transcript MicroArray (CATMA) initiative combines the efforts of laboratories in eight European countries [1] to deliver gene-specific sequence tags (GSTs) for the Arabidopsis research co...

    Authors: Gert Sclep, Joke Allemeersch, Robin Liechti, Björn De Meyer, Jim Beynon, Rishikesh Bhalerao, Yves Moreau, Wilfried Nietfeld, Jean-Pierre Renou, Philippe Reymond, Martin TR Kuiper and Pierre Hilson
    Citation: BMC Bioinformatics 2007 8:400
    Content type: Research article Published on:

  37. The precision of transcriptional regulation is made possible by the specificity of physical interactions between transcription factors and their cognate binding sites on DNA. A major challenge is to decipher t...

    Authors: Randy Z Wu, Christina Chaivorapol, Jiashun Zheng, Hao Li and Shoudan Liang
    Citation: BMC Bioinformatics 2007 8:399
    Content type: Methodology article Published on:

  39. Efforts to predict functional sites from globular proteins is increasingly common; however, the most successful of these methods generally require structural insight. Unfortunately, despite several recent tech...

    Authors: Dennis R Livesay, Patrick D Kidd, Sepehr Eskandari and Usman Roshan
    Citation: BMC Bioinformatics 2007 8:397
    Content type: Research article Published on:

  40. Detecting groups of functionally related proteins from their amino acid sequence alone has been a long-standing challenge in computational genome research. Several clustering approaches, following different st...

    Authors: Tobias Wittkop, Jan Baumbach, Francisco P Lobo and Sven Rahmann
    Citation: BMC Bioinformatics 2007 8:396
    Content type: Research article Published on:

  42. Yu et al. (BMC Bioinformatics 2007,8: 145+) have recently compared the performance of several methods for the detection of genomic amplification and deletion breakpoints using data from high-density single nuc...

    Authors: Oscar M Rueda and Ramon Diaz-Uriarte
    Citation: BMC Bioinformatics 2007 8:394
    Content type: Correspondence Published on:

  43. In a recent report the authors presented a new measure of continuous entropy for DNA sequences, which allows the estimation of their randomness level. The definition therein explored was based on the Rényi ent...

    Authors: Susana Vinga and Jonas S Almeida
    Citation: BMC Bioinformatics 2007 8:393
    Content type: Research article Published on:

  45. Domains are the basic functional units of proteins. It is believed that protein-protein interactions are realized through domain interactions. Revealing multi-domain cooperation can provide deep insights into ...

    Authors: Rui-Sheng Wang, Yong Wang, Ling-Yun Wu, Xiang-Sun Zhang and Luonan Chen
    Citation: BMC Bioinformatics 2007 8:391
    Content type: Research article Published on:

  46. Protein domains coordinate to perform multifaceted cellular functions, and domain combinations serve as the functional building blocks of the cell. The available methods to identify functional domain combinati...

    Authors: William A McLaughlin, Ken Chen, Tingjun Hou and Wei Wang
    Citation: BMC Bioinformatics 2007 8:390
    Content type: Research article Published on:

  47. Three-dimensional (3-D) visualization of multimodality neuroimaging data provides a powerful technique for viewing the relationship between structure and function. A number of applications are available that i...

    Authors: Eider B Moore, Andrew V Poliakov, Peter Lincoln and James F Brinkley
    Citation: BMC Bioinformatics 2007 8:389
    Content type: Software Published on:

  48. In DNA microarray experiments, measurements from different biological samples are often assumed to be independent and to have identical variance. For many datasets these assumptions have been shown to be inval...

    Authors: Anders Sjögren, Erik Kristiansson, Mats Rudemo and Olle Nerman
    Citation: BMC Bioinformatics 2007 8:387
    Content type: Methodology article Published on:

  50. A number of studies on biological networks have been carried out to unravel the topological characteristics that can explain the functional importance of network nodes. For instance, connectivity, clustering c...

    Authors: Yung-Keun Kwon, Sun Shim Choi and Kwang-Hyun Cho
    Citation: BMC Bioinformatics 2007 8:384
    Content type: Research article Published on:

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