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  1. The iRefIndex consolidates protein interaction data from ten databases in a rigorous manner using sequence-based hash keys. Working with consolidated interaction data comes with distinct challenges: data are r...

    Authors: Sabry Razick, Antonio Mora, Katerina Michalickova, Paul Boddie and Ian M Donaldson
    Citation: BMC Bioinformatics 2011 12:388
    Content type: Research article Published on:

  2. Uncovering the relationship between the conserved chromosomal segments and the functional relatedness of elements within these segments is an important question in computational genomics. We build upon the ser...

    Authors: Anasua Sarkar, Hayssam Soueidan and Macha Nikolski
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S18
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  3. The identification of functional regions contained in a given multiple sequence alignment constitutes one of the major challenges of comparative genomics. Several studies have focused on the identification of ...

    Authors: Dunarel Badescu, Alix Boc, Abdoulaye Baniré Diallo and Vladimir Makarenkov
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S9
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  4. A gene tree for a gene family is often discordant with the containing species tree because of its complex evolutionary course during which gene duplication, gene loss and incomplete lineage sorting events migh...

    Authors: Taoyang Wu and Louxin Zhang
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S7
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  5. Paralog reduction, the loss of duplicate genes after whole genome duplication (WGD) is a pervasive process. Whether this loss proceeds gene by gene or through deletion of multi-gene DNA segments is controversi...

    Authors: Baoyong Wang, Chunfang Zheng and David Sankoff
    Citation: BMC Bioinformatics 2011 12(Suppl 9):S5
    Content type: Proceedings Published on:

    This article is part of a Supplement: Volume 12 Supplement 9

  6. Linear regression models are used to quantitatively predict drug resistance, the phenotype, from the HIV-1 viral genotype. As new antiretroviral drugs become available, new resistance pathways emerge and the n...

    Authors: Koen Van der Borght, Elke Van Craenenbroeck, Pierre Lecocq, Margriet Van Houtte, Barbara Van Kerckhove, Lee Bacheler, Geert Verbeke and Herman van Vlijmen
    Citation: BMC Bioinformatics 2011 12:386
    Content type: Research article Published on:

  7. This article describes the approaches taken by the OntoGene group at the University of Zurich in dealing with two tasks of the BioCreative III competition: classification of articles which contain curatable pr...

    Authors: Gerold Schneider, Simon Clematide and Fabio Rinaldi
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S13
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  8. We participated, as Team 81, in the Article Classification and the Interaction Method subtasks (ACT and IMT, respectively) of the Protein-Protein Interaction task of the BioCreative III Challenge. For the ACT, we...

    Authors: Anália Lourenço, Michael Conover, Andrew Wong, Azadeh Nematzadeh, Fengxia Pan, Hagit Shatkay and Luis M Rocha
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S12
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

    The Erratum to this article has been published in BMC Bioinformatics 2012 13:180

  9. The selection of relevant articles for curation, and linking those articles to experimental techniques confirming the findings became one of the primary subjects of the recent BioCreative III contest. The cont...

    Authors: Xinglong Wang, Rafal Rak, Angelo Restificar, Chikashi Nobata, CJ Rupp, Riza Theresa B Batista-Navarro, Raheel Nawaz and Sophia Ananiadou
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S11
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  10. Protein-protein interaction (PPI) is an important biomedical phenomenon. Automatically detecting PPI-relevant articles and identifying methods that are used to study PPI are important text mining tasks. In thi...

    Authors: Shashank Agarwal, Feifan Liu and Hong Yu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S10
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  11. Identifying protein-protein interactions (PPIs) from literature is an important step in mining the function of individual proteins as well as their biological network. Since it is known that PPIs have distinct...

    Authors: Sun Kim and W John Wilbur
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S9
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  12. The vast amount of data published in the primary biomedical literature represents a challenge for the automated extraction and codification of individual data elements. Biological databases that rely solely on...

    Authors: Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni and Mike Tyers
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S8
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  13. Gene normalization (GN) is the task of identifying the unique database IDs of genes and proteins in literature. The best-known public competition of GN systems is the GN task of the BioCreative challenge, whic...

    Authors: Richard Tzong-Han Tsai and Po-Ting Lai
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S7
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  14. Previously, gene normalization (GN) systems are mostly focused on disambiguation using contextual information. An effective gene mention tagger is deemed unnecessary because the subsequent steps will filter ou...

    Authors: Cheng-Ju Kuo, Maurice HT Ling and Chun-Nan Hsu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S6
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  16. The BioCreative challenge evaluation is a community-wide effort for evaluating text mining and information extraction systems applied to the biological domain. The biocurator community, as an active user of bi...

    Authors: Cecilia N Arighi, Phoebe M Roberts, Shashank Agarwal, Sanmitra Bhattacharya, Gianni Cesareni, Andrew Chatr-aryamontri, Simon Clematide, Pascale Gaudet, Michelle Gwinn Giglio, Ian Harrow, Eva Huala, Martin Krallinger, Ulf Leser, Donghui Li, Feifan Liu, Zhiyong Lu…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S4
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  17. Determining usefulness of biomedical text mining systems requires realistic task definition and data selection criteria without artificial constraints, measuring performance aspects that go beyond traditional ...

    Authors: Martin Krallinger, Miguel Vazquez, Florian Leitner, David Salgado, Andrew Chatr-aryamontri, Andrew Winter, Livia Perfetto, Leonardo Briganti, Luana Licata, Marta Iannuccelli, Luisa Castagnoli, Gianni Cesareni, Mike Tyers, Gerold Schneider, Fabio Rinaldi, Robert Leaman…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S3
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  18. We report the Gene Normalization (GN) challenge in BioCreative III where participating teams were asked to return a ranked list of identifiers of the genes detected in full-text articles. For training, 32 full...

    Authors: Zhiyong Lu, Hung-Yu Kao, Chih-Hsuan Wei, Minlie Huang, Jingchen Liu, Cheng-Ju Kuo, Chun-Nan Hsu, Richard Tzong-Han Tsai, Hong-Jie Dai, Naoaki Okazaki, Han-Cheol Cho, Martin Gerner, Illes Solt, Shashank Agarwal, Feifan Liu, Dina Vishnyakova…
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S2
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  19. The overall goal of the BioCreative Workshops is to promote the development of text mining and text processing tools which are useful to the communities of researchers and database curators in the biological s...

    Authors: Cecilia N Arighi, Zhiyong Lu, Martin Krallinger, Kevin B Cohen, W John Wilbur, Alfonso Valencia, Lynette Hirschman and Cathy H Wu
    Citation: BMC Bioinformatics 2011 12(Suppl 8):S1
    Content type: Research Published on:

    This article is part of a Supplement: Volume 12 Supplement 8

  20. A critical output of metagenomic studies is the estimation of abundances of taxonomical or functional groups. The inherent uncertainty in assignments to these groups makes it important to consider both their h...

    Authors: Brian D Ondov, Nicholas H Bergman and Adam M Phillippy
    Citation: BMC Bioinformatics 2011 12:385
    Content type: Software Published on:

  22. In previous work, we reported the development of caCORRECT, a novel microarray quality control system built to identify and correct spatial artifacts commonly found on Affymetrix arrays. We have made recent im...

    Authors: Richard A Moffitt, Qiqin Yin-Goen, Todd H Stokes, R Mitchell Parry, James H Torrance, John H Phan, Andrew N Young and May D Wang
    Citation: BMC Bioinformatics 2011 12:383
    Content type: Research article Published on:

  24. Identifying similarities between patterns of differential gene expression provides an opportunity to identify similarities between the experimental and biological conditions that give rise to these gene expres...

    Authors: Adam C Gower, Avrum Spira and Marc E Lenburg
    Citation: BMC Bioinformatics 2011 12:381
    Content type: Methodology article Published on:

  28. Many gene-set analysis methods have been previously proposed and compared through simulation studies and analysis of real datasets for binary phenotypes. We focused on the survival phenotype and compared the p...

    Authors: Seungyeoun Lee, Jinheum Kim and Sunho Lee
    Citation: BMC Bioinformatics 2011 12:377
    Content type: Methodology article Published on:

  30. The widely used k top scoring pair (k-TSP) algorithm is a simple yet powerful parameter-free classifier. It owes its success in many cancer microarray datasets to an effective feature selection algorithm that is ...

    Authors: Ping Shi, Surajit Ray, Qifu Zhu and Mark A Kon
    Citation: BMC Bioinformatics 2011 12:375
    Content type: Research article Published on:

  32. Genomics and proteomics experiments produce a large amount of data that are awaiting functional elucidation. An important step in analyzing such data is to identify functional units, which consist of proteins ...

    Authors: Meghana Chitale, Shriphani Palakodety and Daisuke Kihara
    Citation: BMC Bioinformatics 2011 12:373
    Content type: Research article Published on:

  33. Technological developments have increased the feasibility of large scale genetic association studies. Densely typed genetic markers are obtained using SNP arrays, next-generation sequencing technologies and im...

    Authors: Erika Cule, Paolo Vineis and Maria De Iorio
    Citation: BMC Bioinformatics 2011 12:372
    Content type: Research article Published on:

  34. Representing species-specific proteins and protein complexes in ontologies that are both human- and machine-readable facilitates the retrieval, analysis, and interpretation of genome-scale data sets. Although ...

    Authors: Carol J Bult, Harold J Drabkin, Alexei Evsikov, Darren Natale, Cecilia Arighi, Natalia Roberts, Alan Ruttenberg, Peter D'Eustachio, Barry Smith, Judith A Blake and Cathy Wu
    Citation: BMC Bioinformatics 2011 12:371
    Content type: Database Published on:

  35. Intra-cellular and inter-cellular protein translocation can be observed by microscopic imaging of tissue sections prepared immunohistochemically. A manual densitometric analysis is time-consuming, subjective a...

    Authors: Olga Domanova, Stefan Borbe, Stefanie Mühlfeld, Martin Becker, Ralf Kubitz, Dieter Häussinger and Thomas Berlage
    Citation: BMC Bioinformatics 2011 12:370
    Content type: Methodology article Published on:

  36. A novel method of microarray preprocessing - Frozen Robust Multi-array Analysis (fRMA) - has recently been developed. This algorithm allows the user to preprocess arrays individually while retaining the advant...

    Authors: Matthew N McCall and Rafael A Irizarry
    Citation: BMC Bioinformatics 2011 12:369
    Content type: Software Published on:

  38. Modern gene therapy methods have limited control over where a therapeutic viral vector inserts into the host genome. Vector integration can activate local gene expression, which can cause cancer if the vector ...

    Authors: Angela P Presson, Namshin Kim, Yan Xiaofei, Irvin SY Chen and Sanggu Kim
    Citation: BMC Bioinformatics 2011 12:367
    Content type: Research article Published on:

  40. Regulation of gene expression plays a pivotal role in cellular functions. However, understanding the dynamics of transcription remains a challenging task. A host of computational approaches have been developed...

    Authors: Jérémy Gruel, Michel LeBorgne, Nolwenn LeMeur and Nathalie Théret
    Citation: BMC Bioinformatics 2011 12:365
    Content type: Research article Published on:

  41. Epistasis is recognized ubiquitous in the genetic architecture of complex traits such as disease susceptibility. Experimental studies in model organisms have revealed extensive evidence of biological interacti...

    Authors: Ting Hu, Nicholas A Sinnott-Armstrong, Jeff W Kiralis, Angeline S Andrew, Margaret R Karagas and Jason H Moore
    Citation: BMC Bioinformatics 2011 12:364
    Content type: Research article Published on:

  42. The prediction and study of protein interactions and functional relationships based on similarity of phylogenetic trees, exemplified by the mirrortree and related methodologies, is being widely used. Although dep...

    Authors: Dorota Herman, David Ochoa, David Juan, Daniel Lopez, Alfonso Valencia and Florencio Pazos
    Citation: BMC Bioinformatics 2011 12:363
    Content type: Research article Published on:

  43. With the continued growth in the volume both of experimental G protein-coupled receptor (GPCR) data and of the related peer-reviewed literature, the ability of GPCR researchers to keep up-to-date is becoming i...

    Authors: Bas Vroling, David Thorne, Philip McDermott, Teresa K Attwood, Gert Vriend and Steve Pettifer
    Citation: BMC Bioinformatics 2011 12:362
    Content type: Software Published on:

  44. Increasingly large amounts of DNA sequencing data are being generated within the Wellcome Trust Sanger Institute (WTSI). The traditional file system struggles to handle these increasing amounts of sequence dat...

    Authors: Gen-Tao Chiang, Peter Clapham, Guoying Qi, Kevin Sale and Guy Coates
    Citation: BMC Bioinformatics 2011 12:361
    Content type: Correspondence Published on:

  45. The Gene Ontology (GO) provides a controlled vocabulary for describing the functions of genes and can be used to evaluate the functional coherence of gene sets. Many functional coherence measures consider each...

    Authors: Norberto Díaz-Díaz and Jesús S Aguilar-Ruiz
    Citation: BMC Bioinformatics 2011 12:360
    Content type: Methodology article Published on:

  47. Clustering is a widely applicable pattern recognition method for discovering groups of similar observations in data. While there are a large variety of clustering algorithms, very few of these can enforce cons...

    Authors: Rudolf Frühwirth, D R Mani and Saumyadipta Pyne
    Citation: BMC Bioinformatics 2011 12:358
    Content type: Research article Published on:

  48. Mapping of orthologous genes among species serves an important role in functional genomics by allowing researchers to develop hypotheses about gene function in one species based on what is known about the func...

    Authors: Yanhui Hu, Ian Flockhart, Arunachalam Vinayagam, Clemens Bergwitz, Bonnie Berger, Norbert Perrimon and Stephanie E Mohr
    Citation: BMC Bioinformatics 2011 12:357
    Content type: Research article Published on:

  49. Next-generation sequencing technologies have decentralized sequence acquisition, increasing the demand for new bioinformatics tools that are easy to use, portable across multiple platforms, and scalable for hi...

    Authors: Samuel V Angiuoli, Malcolm Matalka, Aaron Gussman, Kevin Galens, Mahesh Vangala, David R Riley, Cesar Arze, James R White, Owen White and W Florian Fricke
    Citation: BMC Bioinformatics 2011 12:356
    Content type: Software Published on:

  50. Word sense disambiguation (WSD) attempts to solve lexical ambiguities by identifying the correct meaning of a word based on its context. WSD has been demonstrated to be an important step in knowledge-based app...

    Authors: Laura Plaza, Antonio J Jimeno-Yepes, Alberto Díaz and Alan R Aronson
    Citation: BMC Bioinformatics 2011 12:355
    Content type: Research article Published on:

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