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  1. The Comparative Toxicogenomics Database (CTD) is a publicly available resource that promotes understanding about the etiology of environmental diseases. It provides manually curated chemical-gene/protein inter...

    Authors: Thomas C Wiegers, Allan Peter Davis, K Bretonnel Cohen, Lynette Hirschman and Carolyn J Mattingly
    Citation: BMC Bioinformatics 2009 10:326
    Content type: Research article Published on:

  2. Riboswitches are a type of noncoding RNA that regulate gene expression by switching from one structural conformation to another on ligand binding. The various classes of riboswitches discovered so far are diff...

    Authors: Payal Singh, Pradipta Bandyopadhyay, Sudha Bhattacharya, A Krishnamachari and Supratim Sengupta
    Citation: BMC Bioinformatics 2009 10:325
    Content type: Methodology article Published on:

  3. The KEGG Pathway database is a valuable collection of metabolic pathway maps. Nevertheless, the production of simulation capable metabolic networks from KEGG Pathway data is a challenging complicated work, reg...

    Authors: Konstantinos Moutselos, Ioannis Kanaris, Aristotelis Chatziioannou, Ilias Maglogiannis and Fragiskos N Kolisis
    Citation: BMC Bioinformatics 2009 10:324
    Content type: Software Published on:

  5. This paper presents a framework for integrating disparate data sets to predict gene function. The algorithm constructs a graph, called an integrated similarity graph, by computing similarities based upon both ...

    Authors: Brandon M Malone, Andy D Perkins and Susan M Bridges
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S20
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  6. Microarray technology has made it possible to simultaneously monitor the expression levels of thousands of genes in a single experiment. However, the large number of genes greatly increases the challenges of a...

    Authors: Cuilan Gao, Xin Dang, Yixin Chen and Dawn Wilkins
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S19
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  7. The increasingly large amount of free, online biological text makes automatic interaction extraction correspondingly attractive. Machine learning is one strategy that works by uncovering and using useful prope...

    Authors: Lifeng Zhang, Daniel Berleant, Jing Ding, Tuan Cao and Eve Syrkin Wurtele
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  8. To grow beyond certain size and reach oxygen and other essential nutrients, solid tumors trigger angiogenesis (neovascularization) by secreting various growth factors. Based on this fact, several researches pr...

    Authors: Mutlu Mete, Leah Hennings, Horace J Spencer and Umit Topaloglu
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  9. Environmental monitoring for pharmaceuticals and endocrine disruptors in the aquatic environment traditionally employs a variety of methods including analytical chemistry, as well as a variety of histological ...

    Authors: Natàlia Garcia-Reyero, Ira R Adelman, Dalma Martinović, Li Liu and Nancy D Denslow
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  10. Nanomaterials are being manufactured on a commercial scale for use in medical, diagnostic, energy, component and communications industries. However, concerns over the safety of engineered nanomaterials have su...

    Authors: Amin Zollanvari, Mary Jane Cunningham, Ulisses Braga-Neto and Edward R Dougherty
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  11. The widespread availability of microarray technology has driven functional genomics to the forefront as scientists seek to draw meaningful biological conclusions from their microarray results. Gene annotation ...

    Authors: Bart HJ van den Berg, Chamali Thanthiriwatte, Prashanti Manda and Susan M Bridges
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  12. Pathway-oriented experimental and computational studies have led to a significant accumulation of biological knowledge concerning three major types of biological pathway events: molecular signaling events, gen...

    Authors: Sudhir R Chowbina, Xiaogang Wu, Fan Zhang, Peter M Li, Ragini Pandey, Harini N Kasamsetty and Jake Y Chen
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  13. Gene co-expression networks are often constructed by computing some measure of similarity between expression levels of gene transcripts and subsequently applying a high-pass filter to remove all but the most l...

    Authors: Andy D Perkins and Michael A Langston
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  14. As a major component of plant cell wall, lignin plays important roles in mechanical support, water transport, and stress responses. As the main cause for the recalcitrance of plant cell wall, lignin modificati...

    Authors: Zhanyou Xu, Dandan Zhang, Jun Hu, Xin Zhou, Xia Ye, Kristen L Reichel, Nathan R Stewart, Ryan D Syrenne, Xiaohan Yang, Peng Gao, Weibing Shi, Crissa Doeppke, Robert W Sykes, Jason N Burris, Joseph J Bozell, Max Zong-Ming Cheng…
    Citation: BMC Bioinformatics 2009 10(Suppl 11):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 11

  16. The rapid evolution of Internet technologies and the collaborative approaches that dominate the field have stimulated the development of numerous bioinformatics resources. To address this new framework, severa...

    Authors: Guillermo de la Calle, Miguel García-Remesal, Stefano Chiesa, Diana de la Iglesia and Victor Maojo
    Citation: BMC Bioinformatics 2009 10:320
    Content type: Methodology article Published on:

  18. Complex networks are studied across many fields of science and are particularly important to understand biological processes. Motifs in networks are small connected sub-graphs that occur significantly in highe...

    Authors: Zahra Razaghi Moghadam Kashani, Hayedeh Ahrabian, Elahe Elahi, Abbas Nowzari-Dalini, Elnaz Saberi Ansari, Sahar Asadi, Shahin Mohammadi, Falk Schreiber and Ali Masoudi-Nejad
    Citation: BMC Bioinformatics 2009 10:318
    Content type: Methodology article Published on:

  19. The breadth of biological databases and their information content continues to increase exponentially. Unfortunately, our ability to query such sources is still often suboptimal. Here, we introduce and apply c...

    Authors: Timo Duchrow, Timur Shtatland, Daniel Guettler, Misha Pivovarov, Stefan Kramer and Ralph Weissleder
    Citation: BMC Bioinformatics 2009 10:317
    Content type: Research article Published on:

  20. The development of effective environmental shotgun sequence binning methods remains an ongoing challenge in algorithmic analysis of metagenomic data. While previous methods have focused primarily on supervised...

    Authors: Andrey Kislyuk, Srijak Bhatnagar, Jonathan Dushoff and Joshua S Weitz
    Citation: BMC Bioinformatics 2009 10:316
    Content type: Methodology article Published on:

  21. Semantically-enriched browsing has enhanced the browsing experience by providing contextualised dynamically generated Web content, and quicker access to searched-for information. However, adoption of Semantic ...

    Authors: Helen Oliver, Gayo Diallo, Ed de Quincey, Dimitra Alexopoulou, Bianca Habermann, Patty Kostkova, Michael Schroeder, Simon Jupp, Khaled Khelif, Robert Stevens, Gawesh Jawaheer and Gemma Madle
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S14
    Content type: Research Published on:

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

  22. There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include l...

    Authors: Jose Antonio Miñarro-Gimenez, Marisa Madrid and Jesualdo Tomas Fernandez-Breis
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S13
    Content type: Research Published on:

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

  23. A key application area of semantic technologies is the fast-developing field of bioinformatics. Sealife was a project within this field with the aim of creating semantics-based web browsing capabilities for th...

    Authors: Karen Sutherland, Kenneth McLeod, Gus Ferguson and Albert Burger
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S12
    Content type: Research Published on:

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

  24. Life scientists need help in coping with the plethora of fast growing and scattered knowledge resources. Ideally, this knowledge should be integrated in a form that allows them to pose complex questions that a...

    Authors: Erick Antezana, Ward Blondé, Mikel Egaña, Alistair Rutherford, Robert Stevens, Bernard De Baets, Vladimir Mironov and Martin Kuiper
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S11
    Content type: Research Published on:

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

  25. As interest in adopting the Semantic Web in the biomedical domain continues to grow, Semantic Web technology has been evolving and maturing. A variety of technological approaches including triplestore technolo...

    Authors: Kei-Hoi Cheung, H Robert Frost, M Scott Marshall, Eric Prud'hommeaux, Matthias Samwald, Jun Zhao and Adrian Paschke
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S10
    Content type: Research Published on:

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

  26. Hypothesis generation in molecular and cellular biology is an empirical process in which knowledge derived from prior experiments is distilled into a comprehensible model. The requirement of automated support ...

    Authors: Marco Roos, M Scott Marshall, Andrew P Gibson, Martijn Schuemie, Edgar Meij, Sophia Katrenko, Willem Robert van Hage, Konstantinos Krommydas and Pieter W Adriaans
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S9
    Content type: Research Published on:

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

  27. The development of bioinformatics databases, algorithms, and tools throughout the last years has lead to a highly distributed world of bioinformatics services. Without adequate management and development suppo...

    Authors: Anna-Lena Lamprecht, Tiziana Margaria and Bernhard Steffen
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S8
    Content type: Research Published on:

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

  28. Current search engines are keyword-based. Semantic technologies promise a next generation of semantic search engines, which will be able to answer questions. Current approaches either apply natural language pr...

    Authors: Heiko Dietze and Michael Schroeder
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S7
    Content type: Research Published on:

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

  29. Computer-based pathway discovery is concerned with two important objectives: pathway identification and analysis. Conventional mining and modeling approaches aimed at pathway discovery are often effective at a...

    Authors: George Zheng and Athman Bouguettaya
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S6
    Content type: Research Published on:

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

  30. The analysis of information in the biological domain is usually focused on the analysis of data from single on-line data sources. Unfortunately, studying a biological process requires having access to disperse...

    Authors: María del Mar Roldán-García, Ismael Navas-Delgado, Amine Kerzazi, Othmane Chniber, Joaquín Molina-Castro and José F Aldana-Montes
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S5
    Content type: Research Published on:

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

  31. This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear corresp...

    Authors: Antonio Jimeno-Yepes, Ernesto Jiménez-Ruiz, Rafael Berlanga-Llavori and Dietrich Rebholz-Schuhmann
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S4
    Content type: Research Published on:

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

  32. This paper summarises the lessons and experiences gained from a case study of the application of semantic web technologies to the integration of data from the bacterial species Francisella tularensis novicida (Fn

    Authors: Nadia Anwar and Ela Hunt
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S3
    Content type: Research Published on:

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

  33. The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrati...

    Authors: Jamie P McCusker, Joshua A Phillips, Alejandra González Beltrán, Anthony Finkelstein and Michael Krauthammer
    Citation: BMC Bioinformatics 2009 10(Suppl 10):S2
    Content type: Research Published on:

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

  35. We generalized penalized canonical correlation analysis for analyzing microarray gene-expression measurements for checking completeness of known metabolic pathways and identifying candidate genes for incorpora...

    Authors: Sandra Waaijenborg and Aeilko H Zwinderman
    Citation: BMC Bioinformatics 2009 10:315
    Content type: Methodology article Published on:

  36. Transmembrane (TM) proteins are proteins that span a biological membrane one or more times. As their 3-D structures are hard to determine, experiments focus on identifying their topology (i. e. which parts of ...

    Authors: Martin Klammer, David N Messina, Thomas Schmitt and Erik LL Sonnhammer
    Citation: BMC Bioinformatics 2009 10:314
    Content type: Methodology article Published on:

  41. SSWAP (S imple S emantic W eb A rchitecture and P rotocol; pronounced "swap") is an architecture, protocol, and platform for using reasoning to semantically integrate heterogeneous disparate data and services on ...

    Authors: Damian DG Gessler, Gary S Schiltz, Greg D May, Shulamit Avraham, Christopher D Town, David Grant and Rex T Nelson
    Citation: BMC Bioinformatics 2009 10:309
    Content type: Software Published on:

  43. A central task in contemporary biosciences is the identification of biological processes showing response in genome-wide differential gene expression experiments. Two types of analysis are common. Either, one ...

    Authors: Petri Törönen, Pauli J Ojala, Pekka Marttinen and Liisa Holm
    Citation: BMC Bioinformatics 2009 10:307
    Content type: Research article Published on:

  45. Chromatin immunoprecipitation on tiling arrays (ChIP-chip) has been employed to examine features such as protein binding and histone modifications on a genome-wide scale in a variety of cell types. Array data ...

    Authors: Simon RV Knott, Christopher J Viggiani, Oscar M Aparicio and Simon Tavaré
    Citation: BMC Bioinformatics 2009 10:305
    Content type: Methodology article Published on:

  46. Dual-channel microarray experiments are commonly employed for inference of differential gene expressions across varying organisms and experimental conditions. The design of dual-channel microarray experiments ...

    Authors: Ahmet Sacan, Nilgun Ferhatosmanoglu and Hakan Ferhatosmanoglu
    Citation: BMC Bioinformatics 2009 10:304
    Content type: Database Published on:

  47. One of the most neglected areas of biomedical Text Mining (TM) is the development of systems based on carefully assessed user needs. We have recently investigated the user needs of an important task yet to be ...

    Authors: Anna Korhonen, Ilona Silins, Lin Sun and Ulla Stenius
    Citation: BMC Bioinformatics 2009 10:303
    Content type: Research article Published on:

  49. Stagonospora nodorum, a fungal ascomycete in the class dothideomycetes, is a damaging pathogen of wheat. It is a model for necrotrophic fungi that cause necrotic symptoms via the interaction of multiple effector ...

    Authors: Scott Bringans, James K Hane, Tammy Casey, Kar-Chun Tan, Richard Lipscombe, Peter S Solomon and Richard P Oliver
    Citation: BMC Bioinformatics 2009 10:301
    Content type: Research article Published on:

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