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BioData Mining

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  1. Content type: Research

    The discovery of breast cancer subtypes and subsequent development of treatments aimed at them has allowed for a great reduction in the mortality of breast cancer. But despite this progress, tumors with simila...

    Authors: Nima Pouladi, Richard Cowper-Sallari and Jason H Moore

    Citation: BioData Mining 2014 7:27

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  2. Content type: Methodology

    Identifying genetic interactions in data obtained from genome-wide association studies (GWASs) can help in understanding the genetic basis of complex diseases. The large number of single nucleotide polymorphis...

    Authors: Charalampos S Floudas, Nara Um, M Ilyas Kamboh, Michael M Barmada and Shyam Visweswaran

    Citation: BioData Mining 2014 7:35

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  3. Content type: Methodology

    Using a collection of different terminal nodesize constructed random forests, each generating a synthetic feature, a synthetic random forest is defined as a kind of hyperforest, calculated using the new input ...

    Authors: Hemant Ishwaran and James D Malley

    Citation: BioData Mining 2014 7:28

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  4. 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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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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

  15. 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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  16. 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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