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  1. 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
    Content type: Methodology Published on:

  2. 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
    Content type: Methodology Published on:

  4. 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
    Content type: Research Published on:

  5. 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
    Content type: Methodology Published on:

  6. 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
    Content type: Research Published on:

  8. 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
    Content type: Short report Published on:

  9. 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
    Content type: Methodology Published on:

  10. 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
    Content type: Methodology Published on:

  11. 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
    Content type: Research Published on:

  12. 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
    Content type: Software article Published on:

  13. 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
    Content type: Review Published on:

  14. 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
    Content type: Methodology Published on:

  15. 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
    Content type: Research Published on:

  16. 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
    Content type: Software article Published on:

  17. 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
    Content type: Research Published on:

  22. 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
    Content type: Methodology Published on:

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

  25. 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
    Content type: Methodology Published on:

  26. 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
    Content type: Research Published on:

  28. 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
    Content type: Research Published on:

  30. 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
    Content type: Methodology Published on:

  31. 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
    Content type: Research Published on:

  33. 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
    Content type: Review Published on:

  35. Copy number variants are >1 kb genomic amplifications or deletions that can be identified using array platforms. However, arrays produce substantial background noise that contributes to high false discovery ra...

    Authors: Britney L Grayson and Thomas M Aune
    Citation: BioData Mining 2011 4:8
    Content type: Methodology Published on:

  38. Gene expression microarray data have been organized and made available as public databases, but the utilization of such highly heterogeneous reference datasets in the interpretation of data from individual tes...

    Authors: Sami K Kilpinen, Kalle A Ojala and Olli P Kallioniemi
    Citation: BioData Mining 2011 4:5
    Content type: Methodology Published on:

  39. Several methods have been presented for the analysis of complex interactions between genetic polymorphisms and/or environmental factors. Despite the available methods, there is still a need for alternative met...

    Authors: Thorsten Lehr, Jing Yuan, Dirk Zeumer, Supriya Jayadev and Marylyn D Ritchie
    Citation: BioData Mining 2011 4:4
    Content type: Research Published on:

  41. Measurements on gene level are widely used to gain new insights in complex diseases e.g. cancer. A promising approach to understand basic biological mechanisms is to combine gene expression profiles and classi...

    Authors: Christian W Martin, Anika Tauchen, Anke Becker and Tim W Nattkemper
    Citation: BioData Mining 2011 4:2
    Content type: Research Published on:

  42. The present knowledge of protein structures at atomic level derives from some 60,000 molecules. Yet the exponential ever growing set of hypothetical protein sequences comprises some 10 million chains and this ...

    Authors: Marco Vassura, Pietro Di Lena, Luciano Margara, Maria Mirto, Giovanni Aloisio, Piero Fariselli and Rita Casadio
    Citation: BioData Mining 2011 4:1
    Content type: Research Published on:

  44. Initial genome-wide association study (GWAS) discoveries are being further explored through the use of large cohorts across multiple and diverse populations involving meta-analyses within large consortia and n...

    Authors: Sarah A Pendergrass, Scott M Dudek, Dana C Crawford and Marylyn D Ritchie
    Citation: BioData Mining 2010 3:10
    Content type: Software article Published on:

  46. A fundamental goal of human genetics is the discovery of polymorphisms that predict common, complex diseases. It is hypothesized that complex diseases are due to a myriad of factors including environmental exp...

    Authors: Alison A Motsinger-Reif, Sushamna Deodhar, Stacey J Winham and Nicholas E Hardison
    Citation: BioData Mining 2010 3:8
    Content type: Methodology Published on:

  49. Growing interest and burgeoning technology for discovering genetic mechanisms that influence disease processes have ushered in a flood of genetic association studies over the last decade, yet little heritabili...

    Authors: Stephen D Turner, Scott M Dudek and Marylyn D Ritchie
    Citation: BioData Mining 2010 3:5
    Content type: Research Published on:

  50. Massively parallel sequencing allows for genome-wide hypothesis-free investigation of for instance transcription factor binding sites or histone modifications. Although nucleotide resolution detailed informati...

    Authors: Stefan Enroth, Robin Andersson, Claes Wadelius and Jan Komorowski
    Citation: BioData Mining 2010 3:4
    Content type: Software article Published on:
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BioData Mining

ISSN: 1756-0381