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Predictive rule inference for epistatic interaction detection in genome-wide association studies

Xiang Wan, Can Yang, Qiang Yang, Hong Xue, Nelson L.S. Tang, Weichuan Yu
<span title="2009-10-30">2009</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
In this work, we propose a novel learning approach (SNPRuler) based on the predictive rule inference to find disease-associated epistatic interactions.  ...  Motivation: Under the current era of genome-wide association study (GWAS), finding epistatic interactions in the large volume of SNP data is a challenging and unsolved issue.  ...  INTRODUCTION In genetic epidemiology, a genome-wide association study (GWAS) is an examination of genetic variations across a given genome, designed to identify genetic associations with observable traits  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp622">doi:10.1093/bioinformatics/btp622</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19880365">pmid:19880365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qvadbwdvx5g2xov2zn3cnt7nw4">fatcat:qvadbwdvx5g2xov2zn3cnt7nw4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180728084013/https://watermark.silverchair.com/btp622.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbwwggG4BgkqhkiG9w0BBwagggGpMIIBpQIBADCCAZ4GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM13TtepMEXxAKrXNLAgEQgIIBbwFpAsKxvbf4R9xIpehGyEohWegeEb3z52LvXqTvr38yzcp5_uTrK_TlqzEpoHJnykRnYVew08Nt2N05pvmh2qsEAZp-omuCi0LzIPBrb-qRgkDb3iHpSxkHHAyT5PepnvCrV9QSqvcAqijWgpkx9vMKnSpg7EDp-Wv2q8EO4bI4qt7nCmU6oTxYhWRM2TcsjSBriQweFOUR50CHSWOjHL2gPhmvjXdwjDgcMjJk1l771PdW3IQ11k7uV_uRAmaLPjtAz3Gwvz8l4-nEjnzoROYkxhcTq3-eXorLhOROBBhjsu_AxfHCru7NlvLNxlLz3gL72PKUWGK3saYg6nu4ImyUH1r4ZxPMZk77ljQaEuUwpV_IhT1_oIzIIgIcwwra3PPDcv1KsXwPcgj5qvdOP5-JEtspnKn3SC3btdoQfTNV9vPR0owJfpHnN8V-9oKmIEddCu--I64Welv64I_rhmfaqmE6LQciFj2lNxs6PBw" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/88/76/88762acc918ee602c7d8f77df58dbd26c1365944.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btp622"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Inferring network interactions within a cell

G. W. Carter
<span title="2005-01-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
These networks involve distinct interaction types detected by a combination of methods, ranging from directly observed physical interactions based in biochemistry to interactions inferred from phenotype  ...  Considering yeast as a model system, recent analytical methods are reviewed here and specific aims are proposed to improve network interaction inference and facilitate predictive biological modelling.  ...  Acknowledgments The author thanks Tim Galitski for contributions to the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.4.380">doi:10.1093/bib/6.4.380</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16420736">pmid:16420736</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dlklcwolsbcxniihijty22kh4u">fatcat:dlklcwolsbcxniihijty22kh4u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190217131117/https://static.aminer.org/pdf/PDF/000/592/503/knowledge_media_and_meme_media_architectures_from_the_viewpoint_of.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/39/07/3907f573a3210ab25ce4e6ee69662983cd8bcdde.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/6.4.380"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

CINOEDV: a co-information based method for detecting and visualizing n-order epistatic interactions

Junliang Shang, Yingxia Sun, Jin-Xing Liu, Junfeng Xia, Junying Zhang, Chun-Hou Zheng
<span title="2016-05-17">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results demonstrate that CINOEDV is promising in detecting and visualizing n-order epistatic interactions.  ...  Detecting and visualizing nonlinear interaction effects of single nucleotide polymorphisms (SNPs) or epistatic interactions are important topics in bioinformatics since they play an important role in unraveling  ...  They also proposed another method SNPRuler [17] based on predictive rule inference.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1076-8">doi:10.1186/s12859-016-1076-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27184783">pmid:27184783</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4869388/">pmcid:PMC4869388</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ganjg56apfbczdurcf4tift3i4">fatcat:ganjg56apfbczdurcf4tift3i4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180718231106/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-016-1076-8?site=bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/2b/16/2b16acddd8abdfdce8efd1eb77b4023acde25b93.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1076-8"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4869388" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DESeeker: detecting epistatic interactions using a two-stage differential evolution algorithm

Boxin Guan, Yuhai Zhao, Yuan Li
<span title="">2019</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q7qi7j4ckfac7ehf3mjbso4hne" style="color: black;">IEEE Access</a> </i> &nbsp;
In large-scale association studies, finding epistatic interactions in the large volume of SNP data is a challenging issue.  ...  In this paper, a novel differential evolution-based algorithm DEseeker is proposed to detect epistatic interactions.  ...  ABBREVIATIONS SNP: single nucleotide polymorphism; DESeeker: twostage differential evolution algorithm; GWAS: genome-wide association studies; SNPRuler: predictive rule inference for epistatic interaction  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/access.2019.2917132">doi:10.1109/access.2019.2917132</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ywudoktbojacpgzd4ubxp3223e">fatcat:ywudoktbojacpgzd4ubxp3223e</a> </span>
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Genome-wide discovery of epistatic loci affecting antibiotic resistance using evolutionary couplings [article]

Benjamin Schubert, Rohan Maddamsetti, Jackson Nyman, Maha R. Farhat, Debora S. Marks
<span title="2018-05-18">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Our method reduces the number of tests required for an epistatic genome-wide association study and increases the likelihood of identifying causal epistasis.  ...  To solve this problem, we extend a method that has been successfully used to identify epistatic residues in proteins to infer genomic loci that are strongly coupled and associated with antibiotic resistance  ...  ACKNOWLEDGEMENTS We thank members of the Marks lab and Chris Sander for his support during this research project. The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/325993">doi:10.1101/325993</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/577blvtuezg7veu3bwbzp5cfce">fatcat:577blvtuezg7veu3bwbzp5cfce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502183425/https://www.biorxiv.org/content/biorxiv/early/2018/06/05/325993.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/325993"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

eQTL Epistasis – Challenges and Computational Approaches

Yang Huang, Stefan Wuchty, Teresa M. Przytycka
<span title="2013-05-31">2013</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
In this review, we discuss recent algorithmic approaches for the detection of eQTL epistasis and highlight lessons that can be learned from current methods.  ...  This problem is aggravated, when epistatic effects between eQTLs are analyzed.  ...  For example, SNP Ruler is based on a predictive, non-model-fitting rule inference algorithm to find disease-associated epistatic effects (Wan et al., 2010b) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2013.00051">doi:10.3389/fgene.2013.00051</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23755066">pmid:23755066</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3668133/">pmcid:PMC3668133</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3c75cyzoqzgtvmjbiwbcgd2f3q">fatcat:3c75cyzoqzgtvmjbiwbcgd2f3q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171006140210/http://publisher-connector.core.ac.uk/resourcesync/data/Frontiers/pdf/3db/aHR0cDovL2pvdXJuYWwuZnJvbnRpZXJzaW4ub3JnL2FydGljbGUvMTAuMzM4OS9mZ2VuZS4yMDEzLjAwMDUxL3BkZg%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/6f/b1/6fb153bcb03c41f3cbff6fa016cadbca24c55b0f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2013.00051"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3668133" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Random Forest-Based Genome-Wide Scan Reveals Fertility-Related Candidate Genes and Potential Inter-Chromosomal Epistatic Regions Associated With Age at First Calving in Nellore Cattle

Anderson Antonio Carvalho Alves, Rebeka Magalhães da Costa, Larissa Fernanda Simielli Fonseca, Roberto Carvalheiro, Ricardo Vieira Ventura, Guilherme Jordão de Magalhães Rosa, Lucia Galvão Albuquerque
<span title="2022-05-18">2022</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
This study aimed to perform a genome-wide association analysis (GWAS) using the Random Forest (RF) approach for scanning candidate genes for age at first calving (AFC) in Nellore cattle.  ...  Furthermore, some genomic regions previously associated with fertility and growth traits in Nellore cattle were also detected in the present study, reinforcing the effectiveness of RF for pre-screening  ...  response variables in the RF-based genome-wide association study for AFC.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2022.834724">doi:10.3389/fgene.2022.834724</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/35692843">pmid:35692843</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC9178659/">pmcid:PMC9178659</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dt63vgpfmjbshg6ce4nz7z2zua">fatcat:dt63vgpfmjbshg6ce4nz7z2zua</a> </span>
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Full genetic analysis for genome-wide association study of Fangji: a powerful approach for effectively dissecting the molecular architecture of personalized traditional Chinese medicine

Gang Chen, Wen-da Xue, Jun Zhu
<span title="2018-02-08">2018</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zafquc7twvcifjael6np7ukmuy" style="color: black;">Acta Pharmacologica Sinica</a> </i> &nbsp;
Genome-wide association study (GWAS) is an unbiased approach for dissecting the genetic variants underlying complex diseases and individual response to a given treatment.  ...  Furthermore, this analysis can integrate other omic information and allow for variations of Fangji, which is very promising for Fangjiomic study and detection of the sophisticated molecular architecture  ...  Figure 1 . 1 Dissection of the molecular architecture of Fangjiomics using the full genetic analysis of genome-wide association study. (A) The multiherbal Fangji and the rule of compatibility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/aps.2017.137">doi:10.1038/aps.2017.137</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29417942">pmid:29417942</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/spmchg7hn5fg7cz7cge3kiseay">fatcat:spmchg7hn5fg7cz7cge3kiseay</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200313160240/https://www.nature.com/articles/aps2017137.pdf?error=cookies_not_supported&amp;code=94996ccc-e8fb-48bc-97ea-9cd810c55ef8" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/12/bb/12bbbacfbbf717254c42426570fb1214a98e1271.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/aps.2017.137"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Travelling the world of gene-gene interactions

K. Van Steen
<span title="2011-03-26">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
The search for epistasis or gene^gene interaction effects on traits of interest is marked by an exponential growth, not only in terms of methodological development, but also in terms of practical applications  ...  In the quest for disease susceptibility factors and the search for the 'missing heritability', supplementary and complementary efforts have been undertaken.  ...  in a populationbased genome-wide screening [160] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbr012">doi:10.1093/bib/bbr012</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21441561">pmid:21441561</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3kojyhlvfrgjrjbjtrovmg2aaa">fatcat:3kojyhlvfrgjrjbjtrovmg2aaa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170706083853/http://www.montefiore.ulg.ac.be/%7Ekvansteen/GeneticEpi-PublicHealth/ac1112/VanSteen2011.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b1/73/b1739466efe72413ac55dc1cc10cd0424383524d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbr012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Genotypic Context and Epistasis in Individuals and Populations

Timothy B. Sackton, Daniel L. Hartl
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iwommhyo5bdk7c3u37mhjzexfe" style="color: black;">Cell</a> </i> &nbsp;
Epistasis is important in predicting phenotype from genotype for an individual.  ...  We argue that predicting genotype from phenotype for individuals based on population studies is difficult and, especially in human genetics, likely to result in underestimating the effects of genotypic  ...  Hartl, and three anonymous reviewers for their comments and suggestions for improving the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2016.06.047">doi:10.1016/j.cell.2016.06.047</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27419868">pmid:27419868</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4948997/">pmcid:PMC4948997</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d2zawsakvffd7bmyz3445e6sue">fatcat:d2zawsakvffd7bmyz3445e6sue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209134903/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4948997&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/39/52/3952df27915404b48055c31dc4655597e55e08ca.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.cell.2016.06.047"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4948997" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

SNPInterForest: A new method for detecting epistatic interactions

Makiko Yoshida, Asako Koike
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Detecting such genetic interactive effects, i.e., epistatic interactions, however, remains a significant challenge in large-scale association studies.  ...  Random forest is a predictive method that has been proposed for use in discovering single-nucleotide polymorphisms (SNPs), which are most predictive of the disease status in association studies.  ...  Acknowledgements This study was supported by the integrated database project of Ministry of Education, Culture, Sports, Science and Technology Japan.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-469">doi:10.1186/1471-2105-12-469</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22151604">pmid:22151604</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3260223/">pmcid:PMC3260223</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/liveerjiifhbvgyoexwkoul33u">fatcat:liveerjiifhbvgyoexwkoul33u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830062452/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-12-469?site=http://bmcbioinformatics.biomedcentral.com" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/5d/60/5d6015bc1449005c66fefc0571754b04f4493c4b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-12-469"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3260223" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The landscape of microbial phenotypic traits and associated genes

Maria Brbić, Matija Piškorec, Vedrana Vidulin, Anita Kriško, Tomislav Šmuc, Fran Supek
<span title="2016-10-24">2016</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Notably, we find that gene synteny is highly predictive of many phenotypes, and highlight examples of gene neighborhoods associated with spore-forming ability.  ...  Moreover, the Pro-Traits pipeline assigns phenotypes by drawing extensively on comparative genomics, capturing patterns in gene repertoires, codon usage biases, proteome composition and co-occurrence in  ...  Epistatic interactions associate genes with diverse phenotypes Of the detected genetic interactions, 56% are instances of antagonistic epistasis, where the phenotype is associated with gene mutual exclusivity  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw964">doi:10.1093/nar/gkw964</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27915291">pmid:27915291</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5137458/">pmcid:PMC5137458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xnrilp536japlcojdc3xysfl3m">fatcat:xnrilp536japlcojdc3xysfl3m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720150059/http://fulir.irb.hr/3207/1/Nucl.%20Acids%20Res.-2016-Brbi--nar-gkw964.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/ef/fc/effc716429da49fba20072571327e4a312cd4fb6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkw964"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5137458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome-wide Marginal Epistatic Association Mapping in Case-Control Studies [article]

Lorin Crawford, Xiang Zhou
<span title="2018-07-23">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Most existing epistatic mapping methods in genome-wide association studies explicitly search over all pairwise or higher-order interactions.  ...  By searching for marginal epistatic effects, one can identify genetic variants that are involved in epistasis without the need to identify the exact partners with which the variants interact --- thus,  ...  This study also makes use of data generated by the Wellcome Trust Case Control Consortium (WTCCC). A full list of the investigators who contributed to  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/374983">doi:10.1101/374983</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dcm324fmrva6db3zt65htf75ka">fatcat:dcm324fmrva6db3zt65htf75ka</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501155344/https://www.biorxiv.org/content/biorxiv/early/2018/07/23/374983.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/3b/7c/3b7c22e26d9f850134d13c6a985d99af0ebfed98.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/374983"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Epistasis within the MHC contributes to the genetic architecture of celiac disease [article]

Ben Goudey, Gad Abraham, Eder Kikianty, Qiao Wang, Dave Rawlinson, Fan Shi, Izhak Haviv, Linda Stern, Adam Kowalczyk, Michael Inouye
<span title="2014-02-07">2014</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We have conducted exhaustive genome-wide scans for pairwise epistasis in five independent celiac disease (CD) case-control studies, using a rapid model-free approach to examine over 500 billion SNP pairs  ...  Epistasis has long been thought to contribute to the genetic aetiology of complex diseases, yet few robust epistatic interactions in humans have been detected.  ...  These findings support powerful and routine epistasis scans for the next generation of genome-wide association studies and indicate that the genetic architecture of celiac disease, and potentially other  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/002485">doi:10.1101/002485</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ny4m4yjcxjg6dltt3nmqocullm">fatcat:ny4m4yjcxjg6dltt3nmqocullm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809064630/http://www.biorxiv.org/content/biorxiv/early/2014/02/07/002485.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/fd/20/fd207cf6fd4ef7b625ddc7c77bc76ae90739298f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/002485"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Estimating the genetic architecture of quantitative traits

ZHAO-BANG ZENG, CHEN-HUNG KAO, CHRISTOPHER J. BASTEN
<span title="">1999</span> <i title="Cambridge University Press (CUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kwycjho53jhehm5smyok47gujy" style="color: black;">Genetics Research</a> </i> &nbsp;
One application of the analysis is to improve genome-wide marker-assisted selection, particularly when the information about epistasis is used for selection with mating.  ...  parameters, including the number, genomic positions, effects and interactions of significant QTL and their contribution to the genetic variance.  ...  This study was partially supported by grants GM 45344 from the National Institutes of Health and no. 9801300 from USDA Plant Genome Program, USA. C. H.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0016672399004255">doi:10.1017/s0016672399004255</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10689805">pmid:10689805</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g2l35aj4wzc4bblicbwvjsdxgq">fatcat:g2l35aj4wzc4bblicbwvjsdxgq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20070329215212/http://journals.cambridge.org:80/download.php?file=%2FGRH%2FGRH74_03%2FS001667239900425Xa.pdf&amp;code=57833e983db92210b1a15cd526574854" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/12/db1242c125af8de014de9f33c532078fb39e3710.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1017/s0016672399004255"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> cambridge.org </button> </a>
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