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  1. Content type: Research

    Human genomic variations, including single nucleotide polymorphisms (SNPs) and copy number variations (CNVs), are associated with several phenotypic traits varying from mild features to hereditary diseases. Se...

    Authors: Kirsti Laurila, Reija Autio, Lingjia Kong, Elisa Närvä, Samer Hussein, Timo Otonkoski, Riitta Lahesmaa and Harri Lähdesmäki

    Citation: BioData Mining 2014 7:32

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  2. Content type: Methodology

    A network motif is a recurring subnetwork within a network, and it takes on certain functions in practical biological macromolecule applications. Previous algorithms have focused on the computational efficienc...

    Authors: Qiang Zhang and Yuan Xu

    Citation: BioData Mining 2014 8:29

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  3. Content type: Short report

    PGxClean is a new web application that performs quality control analyses for data produced by the Affymetrix DMET chip or other candidate gene technologies. Importantly, the software does not assume that varia...

    Authors: Daniel Rotroff, John Jack, Nathan Campbell, Scott Clark and Alison A Motsinger-Reif

    Citation: BioData Mining 2014 7:24

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  4. Content type: Research

    The major histocompatibility complex (MHC) is responsible for presenting antigens (epitopes) on the surface of antigen-presenting cells (APCs). When pathogen-derived epitopes are presented by MHC class II on a...

    Authors: Clemente Aguilar-Bonavides, Reinaldo Sanchez-Arias and Cristina Lanzas

    Citation: BioData Mining 2014 7:23

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  5. Content type: Review

    The emergence of massive datasets in a clinical setting presents both challenges and opportunities in data storage and analysis. This so called “big data” challenges traditional analytic tools and will increas...

    Authors: Emad A Mohammed, Behrouz H Far and Christopher Naugler

    Citation: BioData Mining 2014 7:22

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  6. Content type: Research

    Genetic understanding of complex traits has developed immensely over the past decade but remains hampered by incomplete descriptions of contribution to phenotypic variance. Gene-environment (GxE) interactions ...

    Authors: Laurence D Parnell, Britt A Blokker, Hassan S Dashti, Paula-Dene Nesbeth, Brittany Elle Cooper, Yiyi Ma, Yu-Chi Lee, Ruixue Hou, Chao-Qiang Lai, Kris Richardson and José M Ordovás

    Citation: BioData Mining 2014 7:21

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  7. Content type: Research

    Genetic contributions to major depressive disorder (MDD) are thought to result from multiple genes interacting with each other. Different procedures have been proposed to detect such interactions. Which approa...

    Authors: Magnus Lekman, Ola Hössjer, Peter Andrews, Henrik Källberg, Daniel Uvehag, Dennis Charney, Husseini Manji, John A Rush, Francis J McMahon, Jason H Moore and Ingrid Kockum

    Citation: BioData Mining 2014 7:19

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  8. Content type: Research

    Effective cancer clinical outcome prediction for understanding of the mechanism of various types of cancer has been pursued using molecular-based data such as gene expression profiles, an approach that has pro...

    Authors: Dokyoon Kim, Ruowang Li, Scott M Dudek, Alex T Frase, Sarah A Pendergrass and Marylyn D Ritchie

    Citation: BioData Mining 2014 7:20

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  9. Content type: Software article

    Reference datasets are often used to compare, interpret or validate experimental data and analytical methods. In the field of gene expression, several reference datasets have been published. Typically, they co...

    Authors: Philip Zimmermann, Stefan Bleuler, Oliver Laule, Florian Martin, Nikolai V Ivanov, Prisca Campanoni, Karen Oishi, Nicolas Lugon-Moulin, Markus Wyss, Tomas Hruz and Wilhelm Gruissem

    Citation: BioData Mining 2014 7:18

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  10. Content type: Software article

    Alzheimer’s disease is the most common form of progressive dementia and there is currently no known cure. The cause of onset is not fully understood but genetic factors are expected to play a significant role....

    Authors: Amanda L Zieselman, Jonathan M Fisher, Ting Hu, Peter C Andrews, Casey S Greene, Li Shen, Andrew J Saykin and Jason H Moore

    Citation: BioData Mining 2014 7:17

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  11. Content type: Methodology

    Next generation sequencing technologies are powerful new tools for investigating a wide range of biological and medical questions. Statistical and computational methods are key to analyzing massive and complex...

    Authors: Yan Zhou, Nan Lin and Baoxue Zhang

    Citation: BioData Mining 2014 7:15

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    The Erratum to this article has been published in BioData Mining 2014 7:30

  12. Content type: Methodology

    The Consortium for Neuropsychiatric Phenomics (CNP) at UCLA was an investigation into the biological bases of traits such as memory and response inhibition phenotypes—to explore whether they are linked to synd...

    Authors: Douglass Stott Parker, Eliza Congdon and Robert M Bilder

    Citation: BioData Mining 2014 7:11

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  13. Content type: Methodology

    In omic research, such as genome wide association studies, researchers seek to repeat their results in other datasets to reduce false positive findings and thus provide evidence for the existence of true assoc...

    Authors: Timothy H Ciesielski, Sarah A Pendergrass, Marquitta J White, Nuri Kodaman, Rafal S Sobota, Minjun Huang, Jacquelaine Bartlett, Jing Li, Qinxin Pan, Jiang Gui, Scott B Selleck, Christopher I Amos, Marylyn D Ritchie, Jason H Moore and Scott M Williams

    Citation: BioData Mining 2014 7:10

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  14. Content type: Research

    Permutation testing is a robust and popular approach for significance testing in genomic research, which has the broad advantage of estimating significance non-parametrically, thereby safe guarding against inf...

    Authors: Ronglin Che, John R Jack, Alison A Motsinger-Reif and Chad C Brown

    Citation: BioData Mining 2014 7:9

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  15. Content type: Research

    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

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  16. Content type: Research

    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

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  17. Content type: Research

    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

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  18. Content type: Short report

    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

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  19. Content type: Methodology

    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

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  20. Content type: Research

    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

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  21. Content type: Software article

    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

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  22. Content type: Research

    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

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  23. Content type: Research

    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

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  24. Content type: Research

    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

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  25. Content type: Review

    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

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  26. Content type: Software article

    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

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  27. Content type: Research

    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

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  28. Content type: Review

    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

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  29. Content type: Research

    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

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  30. Content type: Methodology

    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

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