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  1. The statistical genetics phenomenon of epistasis is widely acknowledged to confound disease etiology. In order to evaluate strategies for detecting these complex multi-locus disease associations, simulation st...

    Authors: Ryan J Urbanowicz, Ambrose LS Granizo-Mackenzie, Jeff Kiralis and Jason H Moore

    Citation: BioData Mining 2014 7:8

    Content type: Research

    Published on:

  2. In silco Biology is increasingly important and is often based on public data. While the problem of contamination is well recognised in microbiology labs the corresponding problem of database corruption has recei...

    Authors: William B Langdon

    Citation: BioData Mining 2014 7:3

    Content type: Research

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  3. Mitochondria play a critical role in the cell and have DNA independent of the nuclear genome. There is much evidence that mitochondrial DNA (mtDNA) variation plays a role in human health and disease, however, ...

    Authors: Sabrina L Mitchell, Jacob B Hall, Robert J Goodloe, Jonathan Boston, Eric Farber-Eger, Sarah A Pendergrass, William S Bush and Dana C Crawford

    Citation: BioData Mining 2014 7:6

    Content type: Research

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  4. Several different genetic and environmental factors have been identified as independent risk factors for bladder cancer in population-based studies. Recent studies have turned to understanding the role of gene...

    Authors: Ting Hu, Qinxin Pan, Angeline S Andrew, Jillian M Langer, Michael D Cole, Craig R Tomlinson, Margaret R Karagas and Jason H Moore

    Citation: BioData Mining 2014 7:5

    Content type: Short report

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  5. Logistic regression has been the de facto, and often the only, model used in the description and analysis of relationships between a binary outcome and observed features. It is widely used to obtain the condition...

    Authors: Abhijit Dasgupta, Silke Szymczak, Jason H Moore, Joan E Bailey-Wilson and James D Malley

    Citation: BioData Mining 2014 7:2

    Content type: Methodology

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  6. Networks are commonly used to represent and analyze large and complex systems of interacting elements. In systems biology, human disease networks show interactions between disorders sharing common genetic back...

    Authors: Christian Darabos, Marquitta J White, Britney E Graham, Derek N Leung, Scott M Williams and Jason H Moore

    Citation: BioData Mining 2014 7:1

    Content type: Research

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  7. The ever-growing wealth of biological information available through multiple comprehensive database repositories can be leveraged for advanced analysis of data. We have now extensively revised and updated the ...

    Authors: Sarah A Pendergrass, Alex Frase, John Wallace, Daniel Wolfe, Neerja Katiyar, Carrie Moore and Marylyn D Ritchie

    Citation: BioData Mining 2013 6:25

    Content type: Software article

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  8. Personal genome analysis is now being considered for evaluation of disease risk in healthy individuals, utilizing both rare and common variants. Multiple scores have been developed to predict the deleteriousne...

    Authors: Thanawadee Preeprem and Greg Gibson

    Citation: BioData Mining 2013 6:24

    Content type: Research

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  9. Gene expression profiles have been broadly used in cancer research as a diagnostic or prognostic signature for the clinical outcome prediction such as stage, grade, metastatic status, recurrence, and patient s...

    Authors: Dokyoon Kim, Ruowang Li, Scott M Dudek and Marylyn D Ritchie

    Citation: BioData Mining 2013 6:23

    Content type: Research

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  10. Influx of newly determined crystal structures into primary structural databases is increasing at a rapid pace. This leads to updation of primary and their dependent secondary databases which makes large scale ...

    Authors: Eshita Mutt, Sudha Sane Rani and Ramanathan Sowdhamini

    Citation: BioData Mining 2013 6:20

    Content type: Research

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  11. Currently there are definitions from many agencies and research societies defining “bioinformatics” as deriving knowledge from computational analysis of large volumes of biological and biomedical data. Should thi...

    Authors: Xiuzhen Huang, Barry Bruce, Alison Buchan, Clare Bates Congdon, Carole L Cramer, Steven F Jennings, Hongmei Jiang, Zenglu Li, Gail McClure, Rick McMullen, Jason H Moore, Bindu Nanduri, Joan Peckham, Andy Perkins, Shawn W Polson, Bhanu Rekepalli…

    Citation: BioData Mining 2013 6:19

    Content type: Review

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  12. With the abundance of information and analysis results being collected for genetic loci, user-friendly and flexible data visualization approaches can inform and improve the analysis and dissemination of these ...

    Authors: Daniel Wolfe, Scott Dudek, Marylyn D Ritchie and Sarah A Pendergrass

    Citation: BioData Mining 2013 6:18

    Content type: Software article

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  13. Over-sampling methods based on Synthetic Minority Over-sampling Technique (SMOTE) have been proposed for classification problems of imbalanced biomedical data. However, the existing over-sampling methods achie...

    Authors: Munehiro Nakamura, Yusuke Kajiwara, Atsushi Otsuka and Haruhiko Kimura

    Citation: BioData Mining 2013 6:16

    Content type: Research

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  14. Elucidating the content of a DNA sequence is critical to deeper understand and decode the genetic information for any biological system. As next generation sequencing (NGS) techniques have become cheaper and m...

    Authors: Georgios A Pavlopoulos, Anastasis Oulas, Ernesto Iacucci, Alejandro Sifrim, Yves Moreau, Reinhard Schneider, Jan Aerts and Ioannis Iliopoulos

    Citation: BioData Mining 2013 6:13

    Content type: Review

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  15. Public domain databases nowadays provide multiple layers of genome-wide data e.g., promoter methylation, mRNA expression, and miRNA expression and should enable integrative modeling of the mechanisms of regula...

    Authors: Y-h Taguchi

    Citation: BioData Mining 2013 6:11

    Content type: Research

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  16. Applying a statistical method implies identifying underlying (model) assumptions and checking their validity in the particular context. One of these contexts is association modeling for epistasis detection. He...

    Authors: Jestinah M Mahachie John, François Van Lishout, Elena S Gusareva and Kristel Van Steen

    Citation: BioData Mining 2013 6:9

    Content type: Methodology

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  17. Identifying high-order genetics associations with non-additive (i.e. epistatic) effects in population-based studies of common human diseases is a computational challenge. Multifactor dimensionality reduction (...

    Authors: Ryan L Collins, Ting Hu, Christian Wejse, Giorgio Sirugo, Scott M Williams and Jason H Moore

    Citation: BioData Mining 2013 6:4

    Content type: Short report

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  18. Decades after the eradication of smallpox, its etiological agent, variola virus (VARV), remains a threat as a potential bioweapon. Outbreaks of smallpox around the time of the global eradication effort exhibit...

    Authors: Anne Gatewood Hoen, Shea N Gardner and Jason H Moore

    Citation: BioData Mining 2013 6:3

    Content type: Short report

    Published on:

  19. Glucocorticoids are potent anti-inflammatory agents used for the treatment of diseases such as rheumatoid arthritis, asthma, inflammatory bowel disease and psoriasis. Unfortunately, usage is limited because of...

    Authors: Wilco WM Fleuren, Erik JM Toonen, Stefan Verhoeven, Raoul Frijters, Tim Hulsen, Ton Rullmann, René van Schaik, Jacob de Vlieg and Wynand Alkema

    Citation: BioData Mining 2013 6:2

    Content type: Research

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  20. Multifactor Dimensionality Reduction (MDR) has been widely applied to detect gene-gene (GxG) interactions associated with complex diseases. Existing MDR methods summarize disease risk by a dichotomous predispo...

    Authors: Hongying Dai, Richard J Charnigo, Mara L Becker, J Steven Leeder and Alison A Motsinger-Reif

    Citation: BioData Mining 2013 6:1

    Content type: Methodology

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  21. The large sample sizes, freedom of ethical restrictions and ease of repeated measurements make cytotoxicity assays of immortalized lymphoblastoid cell lines a powerful new in vitro method in pharmacogenomics rese...

    Authors: Chad C Brown, Tammy M Havener, Marisa Wong Medina, Ronald M Krauss, Howard L McLeod and Alison A Motsinger‐Reif

    Citation: BioData Mining 2012 5:21

    Content type: Short report

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  22. Each omics platform is now able to generate a large amount of data. Genomics, proteomics, metabolomics, interactomics are compiled at an ever increasing pace and now form a core part of the fundamental systems...

    Authors: Ignacio González, Kim-Anh Lê Cao, Melissa J Davis and Sébastien Déjean

    Citation: BioData Mining 2012 5:19

    Content type: Methodology

    Published on:

  23. 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

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  24. 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

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  25. 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:

  26. 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:

  27. 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:

  28. 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:

  29. 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:

  30. 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:

  31. 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:

  32. 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:

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