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  1. Content type: Research

    Microbial communities adapt to environmental conditions for optimizing metabolic flux. Such adaption may include cooperative mechanisms eventually resulting in phenotypic observables as emergent properties tha...

    Authors: Magnus Bosse, Alexander Heuwieser, Andreas Heinzel, Ivan Nancucheo, Hivana Melo Barbosa Dall’Agnol, Arno Lukas, George Tzotzos and Bernd Mayer

    Citation: BioData Mining 2015 8:21

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  2. Content type: Methodology

    Taxanes are naturally occurring compounds which belong to a powerful group of chemotherapeutic drugs with anticancer properties. Their current use, clinical efficacy, and unique mechanism of action indicate th...

    Authors: Kasi Murugan, Sangeetha Shanmugasamy, Saleh Al-Sohaibani, Naga Vignesh, Kandavel Palanikannan, Antonydhason Vimala and Gopal Ramesh Kumar

    Citation: BioData Mining 2015 8:19

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  3. Content type: Software article

    The study of interactions between molecules belonging to different biochemical families (such as lipids and nucleic acids) requires specialized data analysis methods. This article describes the DNA Microarray ...

    Authors: Tomasz Waller, Tomasz Gubała, Krzysztof Sarapata, Monika Piwowar and Wiktor Jurkowski

    Citation: BioData Mining 2015 8:18

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  4. Content type: Methodology

    In genome-wide studies, hundreds of thousands of hypothesis tests are performed simultaneously. Bonferroni correction and False Discovery Rate (FDR) can effectively control type I error but often yield a high ...

    Authors: Jiang Gui, Casey S. Greene, Con Sullivan, Walter Taylor, Jason H. Moore and Carol Kim

    Citation: BioData Mining 2015 8:17

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  5. Content type: Research

    Biorepositories linked to de-identified electronic medical records (EMRs) have the potential to complement traditional epidemiologic studies in genotype-phenotype studies of complex human diseases and traits. ...

    Authors: Logan Dumitrescu, Robert Goodloe, Yukiko Bradford, Eric Farber-Eger, Jonathan Boston and Dana C Crawford

    Citation: BioData Mining 2015 8:15

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  6. Content type: Research

    Accurate identification of linear B-cell epitopes plays an important role in peptide vaccine designs, immunodiagnosis, and antibody productions. Although several prediction methods have been reported, unsatisf...

    Authors: Weike Shen, Yuan Cao, Lei Cha, Xufei Zhang, Xiaomin Ying, Wei Zhang, Kun Ge, Wuju Li and Li Zhong

    Citation: BioData Mining 2015 8:14

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  7. Content type: Research

    To facilitate the implementation of the Family Smoking Prevention and Tobacco Control Act of 2009, the Federal Drug Agency (FDA) Center for Tobacco Products (CTP) has identified research priorities under the u...

    Authors: Dingcheng Li, Janet Okamoto, Hongfang Liu and Scott Leischow

    Citation: BioData Mining 2015 8:11

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  8. Content type: Methodology

    One of the most challenging tasks in genomic analysis nowadays is metagenomics. Biomedical applications of metagenomics give rise to datasets containing hundreds and thousands of samples from various body site...

    Authors: Dmitry Alexeev, Tanya Bibikova, Boris Kovarsky, Damir Melnikov, Alexander Tyakht and Vadim Govorun

    Citation: BioData Mining 2015 8:10

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  9. Content type: Research

    Pharmacogenomics (PGx) as an emerging field, is poised to change the way we practice medicine and deliver health care by customizing drug therapies on the basis of each patient’s genetic makeup. A large volume...

    Authors: Liwei Wang, Hongfang Liu, Christopher G Chute and Qian Zhu

    Citation: BioData Mining 2015 8:9

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  10. Content type: Editorial

    Whether your interests lie in scientific arenas, the corporate world, or in government, you have certainly heard the praises of big data: Big data will give you new insights, allow you to become more efficient...

    Authors: Xiuzhen Huang, Steven F Jennings, Barry Bruce, Alison Buchan, Liming Cai, Pengyin Chen, Carole L Cramer, Weihua Guan, Uwe KK Hilgert, Hongmei Jiang, Zenglu Li, Gail McClure, Donald F McMullen, Bindu Nanduri, Andy Perkins, Bhanu Rekepalli…

    Citation: BioData Mining 2015 8:7

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  11. Content type: Research

    Biological insights into group differences, such as disease status, have been achieved through differential co-expression analysis of microarray data. Additional understanding of group differences may be achie...

    Authors: Caleb A Lareau, Bill C White, Ann L Oberg and Brett A McKinney

    Citation: BioData Mining 2015 8:5

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  12. Content type: Research

    The prediction of solvent accessibility could provide valuable clues for analyzing protein structure and functions, such as protein 3-Dimensional structure and B-cell epitope prediction. To fully decipher the ...

    Authors: Jian Zhang, Wenhan Chen, Pingping Sun, Xiaowei Zhao and Zhiqiang Ma

    Citation: BioData Mining 2015 8:3

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  13. Content type: Research

    We develop a new concept that reflects how genes are connected based on microarray data using the coefficient of determination (the squared Pearson correlation coefficient). Our gene rank combines a priori kno...

    Authors: Eugene Demidenko

    Citation: BioData Mining 2015 8:2

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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. 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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  23. 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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  24. 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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  25. 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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  26. 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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  27. 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

  28. 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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  29. 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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  30. 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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  31. 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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  32. 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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  33. 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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