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BioData Mining


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  1. Content type: Methodology

    Several biclustering algorithms have been proposed to identify biclusters, in which genes share similar expression patterns across a number of conditions. However, different algorithms would yield different bi...

    Authors: Li Li, Yang Guo, Wenwu Wu, Youyi Shi, Jian Cheng and Shiheng Tao

    Citation: BioData Mining 2012 5:8

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  2. Content type: Methodology

    The AthaMap database generates a genome-wide map for putative transcription factor binding sites for A. thaliana. When analyzing transcriptional regulation using AthaMap it may be important to learn which genes a...

    Authors: Lorenz Bülow, Julio C Bolívar, Jonas Ruhe, Yuri Brill and Reinhard Hehl

    Citation: BioData Mining 2012 5:7

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  3. Content type: Research

    Next-generation sequencing technologies generate a significant number of short reads that are utilized to address a variety of biological questions. However, quite often, sequencing reads tend to have low qual...

    Authors: Xiaoqing Yu, Kishore Guda, Joseph Willis, Martina Veigl, Zhenghe Wang, Sanford Markowitz, Mark D Adams and Shuying Sun

    Citation: BioData Mining 2012 5:6

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  4. Content type: Software article

    Phenome-Wide Association Studies (PheWAS) can be used to investigate the association between single nucleotide polymorphisms (SNPs) and a wide spectrum of phenotypes. This is a complementary approach to Genome...

    Authors: Sarah A Pendergrass, Scott M Dudek, Dana C Crawford and Marylyn D Ritchie

    Citation: BioData Mining 2012 5:5

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  5. Content type: Review

    With the rapid development of biological technology, measurement of thousands of genes or SNPs can be carried out simultaneously. Improved procedures for multiple hypothesis testing when the number of tests is...

    Authors: Jiang Gui, Tor D Tosteson and Mark Borsuk

    Citation: BioData Mining 2012 5:4

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  6. Content type: Methodology

    Multifactor Dimensionality Reduction (MDR) is a popular and successful data mining method developed to characterize and detect nonlinear complex gene-gene interactions (epistasis) that are associated with dise...

    Authors: Hongying Dai, Madhusudan Bhandary, Mara Becker, J Steven Leeder, Roger Gaedigk and Alison A Motsinger-Reif

    Citation: BioData Mining 2012 5:3

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  7. Content type: Research

    Graph drawing is an integral part of many systems biology studies, enabling visual exploration and mining of large-scale biological networks. While a number of layout algorithms are available in popular networ...

    Authors: Johannes Tuikkala, Heidi Vähämaa, Pekka Salmela, Olli S Nevalainen and Tero Aittokallio

    Citation: BioData Mining 2012 5:2

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  8. Content type: Software article

    Keeping up-to-date with bioscience literature is becoming increasingly challenging. Several recent methods help meet this challenge by allowing literature search to be launched based on lists of abstracts that...

    Authors: Theodoros G Soldatos, Seán I O'Donoghue, Venkata P Satagopam, Adriano Barbosa-Silva, Georgios A Pavlopoulos, Ana Carolina Wanderley-Nogueira, Nina Mota Soares-Cavalcanti and Reinhard Schneider

    Citation: BioData Mining 2012 5:1

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  9. Content type: Research

    Maturation inhibitors such as Bevirimat are a new class of antiretroviral drugs that hamper the cleavage of HIV-1 proteins into their functional active forms. They bind to these preproteins and inhibit their c...

    Authors: J Nikolaj Dybowski, Mona Riemenschneider, Sascha Hauke, Martin Pyka, Jens Verheyen, Daniel Hoffmann and Dominik Heider

    Citation: BioData Mining 2011 4:26

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  10. Content type: Methodology

    A goal of human genetics is to discover genetic factors that influence individuals' susceptibility to common diseases. Most common diseases are thought to result from the joint failure of two or more interacti...

    Authors: Daniel S Himmelstein, Casey S Greene and Jason H Moore

    Citation: BioData Mining 2011 4:21

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    The Erratum to this article has been published in BioData Mining 2016 9:9

  11. Content type: Methodology

    One important concept in traditional Chinese medicine (TCM) is "treating different diseases with the same therapy". In TCM practice, some patients with Rheumatoid Arthritis (RA) and some other patients with Co...

    Authors: Guang Zheng, Miao Jiang, Xiaojuan He, Jing Zhao, Hongtao Guo, Gao Chen, Qinglin Zha and Aiping Lu

    Citation: BioData Mining 2011 4:18

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  12. Content type: Research

    MicroRNAs (miRNAs) mediate posttranscriptional regulation of protein-coding genes by binding to the 3' untranslated region of target mRNAs, leading to translational inhibition, mRNA destabilization or degradat...

    Authors: Jun-ichi Satoh and Hiroko Tabunoki

    Citation: BioData Mining 2011 4:17

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  13. Content type: Research

    To make sense out of gene expression profiles, such analyses must be pushed beyond the mere listing of affected genes. For example, if a group of genes persistently display similar changes in expression levels...

    Authors: Pablo C Echeverría, Fedor Forafonov, Deo P Pandey, Guillaume Mühlebach and Didier Picard

    Citation: BioData Mining 2011 4:15

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  14. Content type: Methodology

    DNA methylation plays a very important role in the silencing of tumor suppressor genes in various tumor types. In order to gain a genome-wide understanding of how changes in methylation affect tumor growth, th...

    Authors: Shuying Sun, Yi-Wen Huang, Pearlly S Yan, Tim HM Huang and Shili Lin

    Citation: BioData Mining 2011 4:13

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  15. Content type: Research

    The ability to accurately classify cancer patients into risk classes, i.e. to predict the outcome of the pathology on an individual basis, is a key ingredient in making therapeutic decisions. In recent years g...

    Authors: Leonardo Vanneschi, Antonella Farinaccio, Giancarlo Mauri, Marco Antoniotti, Paolo Provero and Mario Giacobini

    Citation: BioData Mining 2011 4:12

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  16. Content type: Review

    Understanding complex systems often requires a bottom-up analysis towards a systems biology approach. The need to investigate a system, not only as individual components but as a whole, emerges. This can be do...

    Authors: Georgios A Pavlopoulos, Maria Secrier, Charalampos N Moschopoulos, Theodoros G Soldatos, Sophia Kossida, Jan Aerts, Reinhard Schneider and Pantelis G Bagos

    Citation: BioData Mining 2011 4:10

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