Literature DB >> 25053743

Kernel methods for large-scale genomic data analysis.

Xuefeng Wang, Eric P Xing, Daniel J Schaid.   

Abstract

Machine learning, particularly kernel methods, has been demonstrated as a promising new tool to tackle the challenges imposed by today's explosive data growth in genomics. They provide a practical and principled approach to learning how a large number of genetic variants are associated with complex phenotypes, to help reveal the complexity in the relationship between the genetic markers and the outcome of interest. In this review, we highlight the potential key role it will have in modern genomic data processing, especially with regard to integration with classical methods for gene prioritizing, prediction and data fusion.
© The Author 2014. Published by Oxford University Press. For Permissions, please email: journals.permissions@oup.com.

Keywords:  association test; kernel logistic regression; kernel methods; lasso; machine learning; prediction; structured mapping

Mesh:

Year:  2014        PMID: 25053743      PMCID: PMC4375394          DOI: 10.1093/bib/bbu024

Source DB:  PubMed          Journal:  Brief Bioinform        ISSN: 1467-5463            Impact factor:   11.622


  32 in total

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2.  Semiparametric regression of multidimensional genetic pathway data: least-squares kernel machines and linear mixed models.

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Journal:  Biometrics       Date:  2007-12       Impact factor: 2.571

3.  Ensemble learning prediction of protein-protein interactions using proteins functional annotations.

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4.  A kernel regression approach to gene-gene interaction detection for case-control studies.

Authors:  Nicholas B Larson; Daniel J Schaid
Journal:  Genet Epidemiol       Date:  2013-07-19       Impact factor: 2.135

5.  Population structure and eigenanalysis.

Authors:  Nick Patterson; Alkes L Price; David Reich
Journal:  PLoS Genet       Date:  2006-12       Impact factor: 5.917

6.  Statistical estimation of correlated genome associations to a quantitative trait network.

Authors:  Seyoung Kim; Eric P Xing
Journal:  PLoS Genet       Date:  2009-08-14       Impact factor: 5.917

7.  Estimation and testing for the effect of a genetic pathway on a disease outcome using logistic kernel machine regression via logistic mixed models.

Authors:  Dawei Liu; Debashis Ghosh; Xihong Lin
Journal:  BMC Bioinformatics       Date:  2008-06-24       Impact factor: 3.169

8.  Predicting complex traits using a diffusion kernel on genetic markers with an application to dairy cattle and wheat data.

Authors:  Gota Morota; Masanori Koyama; Guilherme J M Rosa; Kent A Weigel; Daniel Gianola
Journal:  Genet Sel Evol       Date:  2013-06-13       Impact factor: 4.297

9.  Prediction of complex human traits using the genomic best linear unbiased predictor.

Authors:  Gustavo de Los Campos; Ana I Vazquez; Rohan Fernando; Yann C Klimentidis; Daniel Sorensen
Journal:  PLoS Genet       Date:  2013-07-11       Impact factor: 5.917

10.  A pathway-based data integration framework for prediction of disease progression.

Authors:  José A Seoane; Ian N M Day; Tom R Gaunt; Colin Campbell
Journal:  Bioinformatics       Date:  2013-10-24       Impact factor: 6.937

View more
  9 in total

Review 1.  Methods for biological data integration: perspectives and challenges.

Authors:  Vladimir Gligorijević; Nataša Pržulj
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2.  Bayesian varying coefficient kernel machine regression to assess neurodevelopmental trajectories associated with exposure to complex mixtures.

Authors:  Shelley H Liu; Jennifer F Bobb; Birgit Claus Henn; Chris Gennings; Lourdes Schnaas; Martha Tellez-Rojo; David Bellinger; Manish Arora; Robert O Wright; Brent A Coull
Journal:  Stat Med       Date:  2018-09-12       Impact factor: 2.373

3.  On Sample Size and Power Calculation for Variant Set-Based Association Tests.

Authors:  Baolin Wu; James S Pankow
Journal:  Ann Hum Genet       Date:  2016-02-01       Impact factor: 1.670

4.  Machine learning workflows to estimate class probabilities for precision cancer diagnostics on DNA methylation microarray data.

Authors:  Máté E Maros; David Capper; David T W Jones; Volker Hovestadt; Andreas von Deimling; Stefan M Pfister; Axel Benner; Manuela Zucknick; Martin Sill
Journal:  Nat Protoc       Date:  2020-01-13       Impact factor: 13.491

5.  Fenchel duality of Cox partial likelihood with an application in survival kernel learning.

Authors:  Christopher M Wilson; Kaiqiao Li; Qiang Sun; Pei Fen Kuan; Xuefeng Wang
Journal:  Artif Intell Med       Date:  2021-04-24       Impact factor: 7.011

Review 6.  Machine and deep learning meet genome-scale metabolic modeling.

Authors:  Guido Zampieri; Supreeta Vijayakumar; Elisabeth Yaneske; Claudio Angione
Journal:  PLoS Comput Biol       Date:  2019-07-11       Impact factor: 4.475

7.  Semblance: An empirical similarity kernel on probability spaces.

Authors:  Divyansh Agarwal; Nancy R Zhang
Journal:  Sci Adv       Date:  2019-12-04       Impact factor: 14.136

8.  Approximate Genome-Based Kernel Models for Large Data Sets Including Main Effects and Interactions.

Authors:  Jaime Cuevas; Osval A Montesinos-López; J W R Martini; Paulino Pérez-Rodríguez; Morten Lillemo; Jose Crossa
Journal:  Front Genet       Date:  2020-10-15       Impact factor: 4.599

9.  Scuba: scalable kernel-based gene prioritization.

Authors:  Guido Zampieri; Dinh Van Tran; Michele Donini; Nicolò Navarin; Fabio Aiolli; Alessandro Sperduti; Giorgio Valle
Journal:  BMC Bioinformatics       Date:  2018-01-25       Impact factor: 3.169

  9 in total

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