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  1. Review

    Methods for enhancing the reproducibility of biomedical research findings using electronic health records

    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...

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

    BioData Mining 2017 10:31

    Published on: 11 September 2017

  2. Research

    RNA-sequence data normalization through in silico prediction of reference genes: the bacterial response to DNA damage as case study

    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...

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

    BioData Mining 2017 10:30

    Published on: 5 September 2017

  3. Short Report

    Genetically improved BarraCUDA

    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...

    W. B. Langdon and Brian Yee Hong Lam

    BioData Mining 2017 10:28

    Published on: 2 August 2017

  4. Research

    nRC: non-coding RNA Classifier based on structural features

    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...

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

    BioData Mining 2017 10:27

    Published on: 1 August 2017

  5. Research

    Discovery and replication of SNP-SNP interactions for quantitative lipid traits in over 60,000 individuals

    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...

    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…

    BioData Mining 2017 10:25

    Published on: 24 July 2017

  6. Software article

    The Dark Proteome Database

    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...

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

    BioData Mining 2017 10:24

    Published on: 20 July 2017

  7. Methodology

    Grid-based stochastic search for hierarchical gene-gene interactions in population-based genetic studies of common human diseases

    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 ...

    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

    BioData Mining 2017 10:19

    Published on: 30 May 2017

  8. Methodology

    Gene Set Enrichment Analyses: lessons learned from the heart failure phenotype

    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...

    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

    BioData Mining 2017 10:18

    Published on: 26 May 2017

  9. Short report

    Vinasse fertirrigation alters soil resistome dynamics: an analysis based on metagenomic profiles

    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...

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

    BioData Mining 2017 10:17

    Published on: 23 May 2017

  10. Research

    The optimal crowd learning machine

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

    Bilguunzaya Battogtokh, Majid Mojirsheibani and James Malley

    BioData Mining 2017 10:16

    Published on: 19 May 2017

  11. Methodology

    Label-free data standardization for clinical metabolomics

    In metabolomics, thousands of substances can be detected in a single assay. This capacity motivates the development of metabolomics testing, which is currently a very promising option for improving laboratory ...

    Petr G. Lokhov, Dmitri L. Maslov, Oleg N. Kharibin, Elena E. Balashova and Alexander I. Archakov

    BioData Mining 2017 10:10

    Published on: 28 February 2017

  12. Methodology

    Semantics-based plausible reasoning to extend the knowledge coverage of medical knowledge bases for improved clinical decision support

    Capturing complete medical knowledge is challenging-often due to incomplete patient Electronic Health Records (EHR), but also because of valuable, tacit medical knowledge hidden away in physicians’ experiences...

    Hossein Mohammadhassanzadeh, William Van Woensel, Samina Raza Abidi and Syed Sibte Raza Abidi

    BioData Mining 2017 10:7

    Published on: 10 February 2017

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