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  2. 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:

  4. 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:

  6. 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:

  7. 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:

  8. 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:

  10. 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:

  12. High-throughput sequencing technology has become popular and widely used to study protein and DNA interactions. Chromatin immunoprecipitation, followed by sequencing of the resulting samples, produces large am...

    Authors: Christiana Spyrou, Rory Stark, Andy G Lynch and Simon Tavaré
    Citation: BMC Bioinformatics 2009 10:299
    Content type: Research article Published on:

  14. Protein-protein interactions (PPIs) play fundamental roles in nearly all biological processes, and provide major insights into the inner workings of cells. A vast amount of PPI data for various organisms is av...

    Authors: Konstantin Voevodski, Shang-Hua Teng and Yu Xia
    Citation: BMC Bioinformatics 2009 10:297
    Content type: Methodology article Published on:

  16. MicroRNAs are small endogenously expressed non-coding RNA molecules that regulate target gene expression through translation repression or messenger RNA degradation. MicroRNA regulation is performed through pa...

    Authors: Manolis Maragkakis, Panagiotis Alexiou, Giorgio L Papadopoulos, Martin Reczko, Theodore Dalamagas, George Giannopoulos, George Goumas, Evangelos Koukis, Kornilios Kourtis, Victor A Simossis, Praveen Sethupathy, Thanasis Vergoulis, Nectarios Koziris, Timos Sellis, Panagiotis Tsanakas and Artemis G Hatzigeorgiou
    Citation: BMC Bioinformatics 2009 10:295
    Content type: Research article Published on:

  17. Purely epistatic multi-locus interactions cannot generally be detected via single-locus analysis in case-control studies of complex diseases. Recently, many two-locus and multi-locus analysis techniques have b...

    Authors: Waranyu Wongseree, Anunchai Assawamakin, Theera Piroonratana, Saravudh Sinsomros, Chanin Limwongse and Nachol Chaiyaratana
    Citation: BMC Bioinformatics 2009 10:294
    Content type: Methodology article Published on:

  18. The ability to predict drug sensitivity in cancer is one of the exciting promises of pharmacogenomic research. Several groups have demonstrated the ability to predict drug sensitivity by integrating chemo-sens...

    Authors: Pavithra Shivakumar and Michael Krauthammer
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S17
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  19. The incorporation of biological knowledge can enhance the analysis of biomedical data. We present a novel method that uses a proteomic knowledge base to enhance the performance of a rule-learning algorithm in ...

    Authors: Jonathan L Lustgarten, Shyam Visweswaran, Robert P Bowser, William R Hogan and Vanathi Gopalakrishnan
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S16
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  20. Functional magnetic resonance imaging (fMRI) is a technology used to detect brain activity. Patterns of brain activation have been utilized as biomarkers for various neuropsychiatric applications. Detecting de...

    Authors: Bo Jin, Alvin Strasburger, Steven J Laken, F Andrew Kozel, Kevin A Johnson, Mark S George and Xinghua Lu
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S15
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  21. The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources. The system's indexing workflow processes the text metadata of dive...

    Authors: Nigam H Shah, Nipun Bhatia, Clement Jonquet, Daniel Rubin, Annie P Chiang and Mark A Musen
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S14
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  22. The availability of up-to-date, executable, evidence-based medical knowledge is essential for many clinical applications, such as pharmacovigilance, but executable knowledge is costly to obtain and update. Aut...

    Authors: Xiaoyan Wang, George Hripcsak and Carol Friedman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S13
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  23. Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for trans...

    Authors: Brett R South, Shuying Shen, Makoto Jones, Jennifer Garvin, Matthew H Samore, Wendy W Chapman and Adi V Gundlapalli
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S12
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  24. Many common and chronic diseases are influenced at some level by genetic variation. Research done in population genetics, specifically in the area of single nucleotide polymorphisms (SNPs) is critical to under...

    Authors: Terry H Shen, Christopher S Carlson and Peter Tarczy-Hornoch
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S11
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  25. This study describes a large-scale manual re-annotation of data samples in the Gene Expression Omnibus (GEO), using variables and values derived from the National Cancer Institute thesaurus. A framework is des...

    Authors: Ronilda Lacson, Erik Pitzer, Christian Hinske, Pedro Galante and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S10
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  26. Large repositories of biomedical research data are most useful to translational researchers if their data can be aggregated for efficient queries and analyses. However, inconsistent or non-existent annotations...

    Authors: Erik Pitzer, Ronilda Lacson, Christian Hinske, Jihoon Kim, Pedro AF Galante and Lucila Ohno-Machado
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  27. Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to ...

    Authors: Casey Lynnette Overby, Peter Tarczy-Hornoch and Dina Demner-Fushman
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S8
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  28. The decision environment for cancer care is becoming increasingly complex due to the discovery and development of novel genomic tests that offer information regarding therapy response, prognosis and monitoring...

    Authors: Angel Janevski, Sitharthan Kamalakaran, Nilanjana Banerjee, Vinay Varadan and Nevenka Dimitrova
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  29. Current outcome predictors based on "molecular profiling" rely on gene lists selected without consideration for their molecular mechanisms. This study was designed to demonstrate that we could learn about gene...

    Authors: Xinan Yang, Yong Huang, James L Chen, Jianming Xie, Xiao Sun and Yves A Lussier
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S6
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  30. The osteocyte is a type of cell that appears to be one of the key endocrine regulators of bone metabolism and a key responder to initiate bone formation and remodeling. Identifying the regulatory networks in o...

    Authors: Angela K Dean, Stephen E Harris, Ivo Kalajzic and Jianhua Ruan
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  31. Physicians use clinical and physiological data to treat patients every day, and it is essential for treating a patient appropriately. However, medical sources of clinical physiological data are only now starti...

    Authors: Adam D Grossman, Mitchell J Cohen, Geoffrey T Manley and Atul J Butte
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S4
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  32. Chronic renal diseases are currently classified based on morphological similarities such as whether they produce predominantly inflammatory or non-inflammatory responses. However, such classifications do not r...

    Authors: Suresh K Bhavnani, Felix Eichinger, Sebastian Martini, Paul Saxman, HV Jagadish and Matthias Kretzler
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S3
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  33. Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate...

    Authors: Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim and Doheon Lee
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S2
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  34. Gene interactions play a central role in transcriptional networks. Many studies have performed genome-wide expression analysis to reconstruct regulatory networks to investigate disease processes. Since biologi...

    Authors: Hsun-Hsien Chang and Marco F Ramoni
    Citation: BMC Bioinformatics 2009 10(Suppl 9):S1
    Content type: Introduction Published on:

    This article is part of a Supplement: Volume 10 Supplement 9

  36. Array comparative genomic hybridization is a fast and cost-effective method for detecting, genotyping, and comparing the genomic sequence of unknown bacterial isolates. This method, as with all microarray appl...

    Authors: Adam M Phillippy, Xiangyu Deng, Wei Zhang and Steven L Salzberg
    Citation: BMC Bioinformatics 2009 10:293
    Content type: Methodology article Published on:

  38. Wiki technology has become a ubiquitous mechanism for dissemination of information, and places strong emphasis on collaboration. We aimed to leverage wiki technology to allow small groups of researchers to col...

    Authors: Jonathan R Manning, Ann Hedley, John J Mullins and Donald R Dunbar
    Citation: BMC Bioinformatics 2009 10:291
    Content type: Software Published on:

  39. The identification of essential genes is important for the understanding of the minimal requirements for cellular life and for practical purposes, such as drug design. However, the experimental techniques for ...

    Authors: Marcio L Acencio and Ney Lemke
    Citation: BMC Bioinformatics 2009 10:290
    Content type: Methodology article Published on:

  40. The definition of a hypothetical protein is a protein that is predicted to be expressed from an open reading frame, but for which there is no experimental evidence of translation. Hypothetical proteins constit...

    Authors: Claus Desler, Prashanth Suravajhala, May Sanderhoff, Merete Rasmussen and Lene Juel Rasmussen
    Citation: BMC Bioinformatics 2009 10:289
    Content type: Methodology article Published on:

  42. Detecting candidate B-cell epitopes in a protein is a basic and fundamental step in many immunological applications. Due to the impracticality of experimental approaches to systematically scan the entire prote...

    Authors: Nimrod D Rubinstein, Itay Mayrose, Eric Martz and Tal Pupko
    Citation: BMC Bioinformatics 2009 10:287
    Content type: Software Published on:

  43. Restriction enzymes can produce easily definable segments from DNA sequences by using a variety of cut patterns. There are, however, no software tools that can aid in gene building -- that is, modifying wild-t...

    Authors: Chao Li, Yuhua Li, Xiangmin Zhang, Phillip Stafford and Valentin Dinu
    Citation: BMC Bioinformatics 2009 10:286
    Content type: Software Published on:

  45. Understanding genome evolution provides insight into biological mechanisms. For many years comparative genomics and analysis of conserved chromosomal regions have helped to unravel the mechanisms involved in g...

    Authors: Virginie Lopez Rascol, Anthony Levasseur, Olivier Chabrol, Simona Grusea, Philippe Gouret, Etienne GJ Danchin and Pierre Pontarotti
    Citation: BMC Bioinformatics 2009 10:284
    Content type: Research article Published on:

  47. The conservation of sequences between related genomes has long been recognised as an indication of functional significance and recognition of sequence homology is one of the principal approaches used in the an...

    Authors: Matteo Rè, Graziano Pesole and David S Horner
    Citation: BMC Bioinformatics 2009 10:282
    Content type: Methodology article Published on:

  48. Gene discovery algorithms typically examine sequence data for low level patterns. A novel method to computationally discover higher order DNA structures is presented, using a context sensitive grammar. The alg...

    Authors: Guy Tsafnat, Enrico Coiera, Sally R Partridge, Jaron Schaeffer and Jon R Iredell
    Citation: BMC Bioinformatics 2009 10:281
    Content type: Methodology article Published on:

  49. The ability to generate transcriptional data on the scale of entire genomes has been a boon both in the improvement of biological understanding and in the amount of data generated. The latter, the amount of da...

    Authors: Aaron L Vollrath, Adam A Smith, Mark Craven and Christopher A Bradfield
    Citation: BMC Bioinformatics 2009 10:280
    Content type: Software Published on:

  50. Life sciences make heavily use of the web for both data provision and analysis. However, the increasing amount of available data and the diversity of analysis tools call for machine accessible interfaces in or...

    Authors: Johannes Wagener, Ola Spjuth, Egon L Willighagen and Jarl ES Wikberg
    Citation: BMC Bioinformatics 2009 10:279
    Content type: Methodology article Published on:

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