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  1. Content type: Methodology

    Geneticists who look beyond single locus disease associations require additional strategies for the detection of complex multi-locus effects. Epistasis, a multi-locus masking effect, presents a particular chal...

    Authors: Ryan J Urbanowicz, Jeff Kiralis, Nicholas A Sinnott-Armstrong, Tamra Heberling, Jonathan M Fisher and Jason H Moore

    Citation: BioData Mining 2012 5:16

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  2. Content type: Methodology

    Algorithms designed to detect complex genetic disease associations are initially evaluated using simulated datasets. Typical evaluations vary constraints that influence the correct detection of underlying mode...

    Authors: Ryan J Urbanowicz, Jeff Kiralis, Jonathan M Fisher and Jason H Moore

    Citation: BioData Mining 2012 5:15

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  3. Content type: Research

    In bio-medicine, exploratory studies and hypothesis generation often begin with researching existing literature to identify a set of factors and their association with diseases, phenotypes, or biological proce...

    Authors: Vida Abedi, Ramin Zand, Mohammed Yeasin and Fazle Elahi Faisal

    Citation: BioData Mining 2012 5:13

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  4. Content type: Methodology

    Since processes in well-known model organisms have specific features different from those in Bos taurus, the organism under study, a good way to describe gene regulation in ruminant embryos would be a species-spe...

    Authors: Nicolas Turenne, Evgeniy Tiys, Vladimir Ivanisenko, Nikolay Yudin, Elena Ignatieva, Damien Valour, Séverine A Degrelle and Isabelle Hue

    Citation: BioData Mining 2012 5:12

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  5. Content type: Research

    Most of the current proteomic researches focus on proteome alteration due to pathological disorders (i.e.: colorectal cancer) rather than normal healthy state when mentioning colon. As a result, there are lacks o...

    Authors: Sameh Magdeldin, Yutaka Yoshida, Huiping Li, Yoshitaka Maeda, Munesuke Yokoyama, Shymaa Enany, Ying Zhang, Bo Xu, Hidehiko Fujinaka, Eishin Yaoita, Sei Sasaki and Tadashi Yamamoto

    Citation: BioData Mining 2012 5:11

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  6. Content type: Short report

    It is increasingly clear that common human diseases have a complex genetic architecture characterized by both additive and nonadditive genetic effects. The goal of the present study was to determine whether pa...

    Authors: Nora Chung Kim, Peter C Andrews, Folkert W Asselbergs, H Robert Frost, Scott M Williams, Brent T Harris, Cynthia Read, Kathleen D Askland and Jason H Moore

    Citation: BioData Mining 2012 5:9

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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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

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