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  1. Content type: Software article

    Investigators often interpret genome-wide data by analyzing the expression levels of genes within pathways. While this within-pathway analysis is routine, the products of any one pathway can affect the activit...

    Authors: Kathleen M. Chen, Jie Tan, Gregory P. Way, Georgia Doing, Deborah A. Hogan and Casey S. Greene

    Citation: BioData Mining 2018 11:14

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  2. Content type: Research

    Human microbiome studies in clinical settings generally focus on distinguishing the microbiota in health from that in disease at a specific point in time. However, microbiome samples may be associated with dis...

    Authors: Laura Tipton, Karen T. Cuenco, Laurence Huang, Ruth M. Greenblatt, Eric Kleerup, Frank Sciurba, Steven R. Duncan, Michael P. Donahoe, Alison Morris and Elodie Ghedin

    Citation: BioData Mining 2018 11:12

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  3. Content type: Methodology

    In text mining, document clustering describes the efforts to assign unstructured documents to clusters, which in turn usually refer to topics. Clustering is widely used in science for data retrieval and organi...

    Authors: Jens Dörpinghaus, Sebastian Schaaf and Marc Jacobs

    Citation: BioData Mining 2018 11:11

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  4. Content type: Research

    The Toxicological Priority Index (ToxPi) is a method for prioritization and profiling of chemicals that integrates data from diverse sources. However, individual data sources (“assays”), such as in vitro bioas...

    Authors: Kimberly T. To, Rebecca C. Fry and David M. Reif

    Citation: BioData Mining 2018 11:10

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  5. Content type: Research

    Gene set analysis is a valuable tool to summarize high-dimensional gene expression data in terms of biologically relevant sets. This is an active area of research and numerous gene set analysis methods have be...

    Authors: Ravi Mathur, Daniel Rotroff, Jun Ma, Ali Shojaie and Alison Motsinger-Reif

    Citation: BioData Mining 2018 11:8

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  6. Content type: Research

    Machine learning methods have gained popularity and practicality in identifying linear and non-linear effects of variants associated with complex disease/traits. Detection of epistatic interactions still remai...

    Authors: Shefali S. Verma, Anastasia Lucas, Xinyuan Zhang, Yogasudha Veturi, Scott Dudek, Binglan Li, Ruowang Li, Ryan Urbanowicz, Jason H. Moore, Dokyoon Kim and Marylyn D. Ritchie

    Citation: BioData Mining 2018 11:5

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  7. Content type: Research

    Biclustering algorithms search for groups of genes that share the same behavior under a subset of samples in gene expression data. Nowadays, the biological knowledge available in public repositories can be use...

    Authors: Juan A. Nepomuceno, Alicia Troncoso, Isabel A. Nepomuceno-Chamorro and Jesús S. Aguilar-Ruiz

    Citation: BioData Mining 2018 11:4

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  8. Content type: Research

    Evolutionary computation (EC) has been widely applied to biological and biomedical data. The practice of EC involves the tuning of many parameters, such as population size, generation count, selection size, an...

    Authors: Moshe Sipper, Weixuan Fu, Karuna Ahuja and Jason H. Moore

    Citation: BioData Mining 2018 11:2

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  9. Content type: Research

    Survival analysis is a statistical technique widely used in many fields of science, in particular in the medical area, and which studies the time until an event of interest occurs. Outlier detection in this co...

    Authors: Eunice Carrasquinha, André Veríssimo, Marta B. Lopes and Susana Vinga

    Citation: BioData Mining 2018 11:1

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  10. Content type: Research

    Matrix factorization is a well established pattern discovery tool that has seen numerous applications in biomedical data analytics, such as gene expression co-clustering, patient stratification, and gene-disea...

    Authors: Andrej Čopar, Marinka žitnik and Blaž Zupan

    Citation: BioData Mining 2017 10:41

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  11. Content type: Research

    In the nervous system, the neurons communicate through synapses. The size, morphology, and connectivity of these synapses are significant in determining the functional properties of the neural network. Therefo...

    Authors: Qiwei Xie, Xi Chen, Hao Deng, Danqian Liu, Yingyu Sun, Xiaojuan Zhou, Yang Yang and Hua Han

    Citation: BioData Mining 2017 10:40

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  12. Content type: Software article

    Recent advances in nucleic acid sequencing technologies have led to a dramatic increase in the number of markers available to generate genetic linkage maps. This increased marker density can be used to improve...

    Authors: J. Grey Monroe, Zachariah A. Allen, Paul Tanger, Jack L. Mullen, John T. Lovell, Brook T. Moyers, Darrell Whitley and John K. McKay

    Citation: BioData Mining 2017 10:38

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  13. Content type: Methodology

    Clustering plays a crucial role in several application domains, such as bioinformatics. In bioinformatics, clustering has been extensively used as an approach for detecting interesting patterns in genetic data...

    Authors: Luluah Alhusain and Alaaeldin M. Hafez

    Citation: BioData Mining 2017 10:37

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  14. Content type: Research

    The selection, development, or comparison of machine learning methods in data mining can be a difficult task based on the target problem and goals of a particular study. Numerous publicly available real-world ...

    Authors: Randal S. Olson, William La Cava, Patryk Orzechowski, Ryan J. Urbanowicz and Jason H. Moore

    Citation: BioData Mining 2017 10:36

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  15. Content type: Research

    Obesity is a medical condition that is known for increased body mass index (BMI). It is also associated with chronic low level inflammation. Obesity disrupts the immune-metabolic homeostasis by changing the se...

    Authors: Indrani Ray, Anindya Bhattacharya and Rajat K. De

    Citation: BioData Mining 2017 10:33

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  16. Content type: Methodology

    Detecting the differences in gene expression data is important for understanding the underlying molecular mechanisms. Although the differentially expressed genes are a large component, differences in correlati...

    Authors: Elpidio-Emmanuel Gonzalez-Valbuena and Víctor Treviño

    Citation: BioData Mining 2017 10:32

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  17. Content type: Review

    The ability of external investigators to reproduce published scientific findings is critical for the evaluation and validation of biomedical research by the wider community. However, a substantial proportion o...

    Authors: Spiros Denaxas, Kenan Direk, Arturo Gonzalez-Izquierdo, Maria Pikoula, Aylin Cakiroglu, Jason Moore, Harry Hemingway and Liam Smeeth

    Citation: BioData Mining 2017 10:31

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