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  1. Content type: Research

    The redundancy of information is becoming a critical issue for epidemiologists. High-dimensional datasets require new effective variable selection methods to be developed. This study implements an advanced evo...

    Authors: Christina Brester, Jussi Kauhanen, Tomi-Pekka Tuomainen, Sari Voutilainen, Mauno Rönkkö, Kimmo Ronkainen, Eugene Semenkin and Mikko Kolehmainen

    Citation: BioData Mining 2018 11:18

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  2. Content type: Methodology

    The function of a protein is determined by its native protein structure. Among many protein prediction methods, the Hydrophobic-Polar (HP) model, an ab initio method, simplifies the protein folding prediction ...

    Authors: Cheng-Hong Yang, Kuo-Chuan Wu, Yu-Shiun Lin, Li-Yeh Chuang and Hsueh-Wei Chang

    Citation: BioData Mining 2018 11:17

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  3. Content type: Methodology

    Biologists aim to understand the genetic background of diseases, metabolic disorders or any other genetic condition. Microarrays are one of the main high-throughput technologies for collecting information abou...

    Authors: Jorge Parraga-Alava, Marcio Dorn and Mario Inostroza-Ponta

    Citation: BioData Mining 2018 11:16

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  4. Content type: Research

    Triclustering has shown to be a valuable tool for the analysis of microarray data since its appearance as an improvement of classical clustering and biclustering techniques. The standard for validation of tric...

    Authors: David Gutiérrez-Avilés, Raúl Giráldez, Francisco Javier Gil-Cumbreras and Cristina Rubio-Escudero

    Citation: BioData Mining 2018 11:15

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  5. 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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  6. 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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  7. 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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  8. 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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  9. 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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  10. 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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  11. 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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  12. 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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  13. 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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  14. 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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  15. 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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  16. 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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  17. 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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  18. 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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  19. 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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  20. 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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  21. 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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  22. Content type: Research

    Measuring how gene expression changes in the course of an experiment assesses how an organism responds on a molecular level. Sequencing of RNA molecules, and their subsequent quantification, aims to assess glo...

    Authors: Bork A. Berghoff, Torgny Karlsson, Thomas Källman, E. Gerhart H. Wagner and Manfred G. Grabherr

    Citation: BioData Mining 2017 10:30

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  23. Content type: Methodology

    The modeling of genetic interactions within a cell is crucial for a basic understanding of physiology and for applied areas such as drug design. Interactions in gene regulatory networks (GRNs) include effects ...

    Authors: Mina Moradi Kordmahalleh, Mohammad Gorji Sefidmazgi, Scott H. Harrison and Abdollah Homaifar

    Citation: BioData Mining 2017 10:29

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  24. Content type: Short Report

    BarraCUDA is an open source C program which uses the BWA algorithm in parallel with nVidia CUDA to align short next generation DNA sequences against a reference genome. Recently its source code was optimised u...

    Authors: W. B. Langdon and Brian Yee Hong Lam

    Citation: BioData Mining 2017 10:28

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  25. Content type: Research

    Non-coding RNA (ncRNA) are small non-coding sequences involved in gene expression regulation of many biological processes and diseases. The recent discovery of a large set of different ncRNAs with biologically...

    Authors: Antonino Fiannaca, Massimo La Rosa, Laura La Paglia, Riccardo Rizzo and Alfonso Urso

    Citation: BioData Mining 2017 10:27

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  26. Content type: Research

    The genetic etiology of human lipid quantitative traits is not fully elucidated, and interactions between variants may play a role. We performed a gene-centric interaction study for four different lipid traits...

    Authors: Emily R. Holzinger, Shefali S. Verma, Carrie B. Moore, Molly Hall, Rishika De, Diane Gilbert-Diamond, Matthew B. Lanktree, Nathan Pankratz, Antoinette Amuzu, Amber Burt, Caroline Dale, Scott Dudek, Clement E. Furlong, Tom R. Gaunt, Daniel Seung Kim, Helene Riess…

    Citation: BioData Mining 2017 10:25

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  27. Content type: Software article

    Recently we surveyed the dark-proteome, i.e., regions of proteins never observed by experimental structure determination and inaccessible to homology modelling. Surprisingly, we found that most of the dark pro...

    Authors: Nelson Perdigão, Agostinho C. Rosa and Seán I. O’Donoghue

    Citation: BioData Mining 2017 10:24

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  28. Content type: Software article

    Refinement of candidate gene lists to select the most promising candidates for further experimental verification remains an essential step between high-throughput exploratory analysis and the discovery of spec...

    Authors: Artem Lysenko, Keith Anthony Boroevich and Tatsuhiko Tsunoda

    Citation: BioData Mining 2017 10:22

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  29. Content type: Methodology

    Large-scale genetic studies of common human diseases have focused almost exclusively on the independent main effects of single-nucleotide polymorphisms (SNPs) on disease susceptibility. These studies have had ...

    Authors: Jason H. Moore, Peter C. Andrews, Randal S. Olson, Sarah E. Carlson, Curt R. Larock, Mario J. Bulhoes, James P. O’Connor, Ellen M. Greytak and Steven L. Armentrout

    Citation: BioData Mining 2017 10:19

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  30. Content type: Methodology

    Genetic studies for complex diseases have predominantly discovered main effects at individual loci, but have not focused on genomic and environmental contexts important for a phenotype. Gene Set Enrichment Ana...

    Authors: Vinicius Tragante, Johannes M. I. H. Gho, Janine F. Felix, Ramachandran S. Vasan, Nicholas L. Smith, Benjamin F. Voight, Colin Palmer, Pim van der Harst, Jason H. Moore and Folkert W. Asselbergs

    Citation: BioData Mining 2017 10:18

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  31. Content type: Short report

    Every year around 300 Gl of vinasse, a by-product of ethanol distillation in sugarcane mills, are flushed into more than 9 Mha of sugarcane cropland in Brazil. This practice links fermentation waste management...

    Authors: Lucas P. P. Braga, Rafael F. Alves, Marina T. F. Dellias, Acacio A. Navarrete, Thiago O. Basso and Siu M. Tsai

    Citation: BioData Mining 2017 10:17

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  32. Content type: Research

    Any family of learning machines can be combined into a single learning machine using various methods with myriad degrees of usefulness.

    Authors: Bilguunzaya Battogtokh, Majid Mojirsheibani and James Malley

    Citation: BioData Mining 2017 10:16

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  33. Content type: Methodology

    Reverse engineering of gene regulatory networks (GRNs) from gene expression data is a classical challenge in systems biology. Thanks to high-throughput technologies, a massive amount of gene-expression data ha...

    Authors: Ngoc C. Pham, Benjamin Haibe-Kains, Pau Bellot, Gianluca Bontempi and Patrick E. Meyer

    Citation: BioData Mining 2017 10:15

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  34. Content type: Research

    Large number of features are extracted from protein crystallization trial images to improve the accuracy of classifiers for predicting the presence of crystals or phases of the crystallization process. The exc...

    Authors: Madhav Sigdel, Imren Dinc, Madhu S. Sigdel, Semih Dinc, Marc L. Pusey and Ramazan S. Aygun

    Citation: BioData Mining 2017 10:14

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  35. Content type: Methodology

    A computational evolution system (CES) is a knowledge discovery engine that can identify subtle, synergistic relationships in large datasets. Pareto optimization allows CESs to balance accuracy with model comp...

    Authors: Nathaniel M. Crabtree, Jason H. Moore, John F. Bowyer and Nysia I. George

    Citation: BioData Mining 2017 10:13

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