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Pathway-Based Genomics Prediction using Generalized Elastic Net

Artem Sokolov, Daniel E. Carlin, Evan O. Paull, Robert Baertsch, Joshua M. Stuart, Teresa M. Przytycka
<span title="2016-03-09">2016</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
We present a novel regularization scheme called The Generalized Elastic Net (GELnet) that incorporates gene pathway information into feature selection.  ...  The models are sorted by their % RMSE improvement over the corresponding Elastic Net models.  ...  The proposed GELnet regularization method capitalizes on this information to improve the accuracy and interpretability of linear regression-based solutions to genome-based prediction tasks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004790">doi:10.1371/journal.pcbi.1004790</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26960204">pmid:26960204</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4784899/">pmcid:PMC4784899</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ifdxumnv2rhzhciisaf4xbm3re">fatcat:ifdxumnv2rhzhciisaf4xbm3re</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015152608/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1004790&amp;type=printable" 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/63/f5/63f5b53036c05fd87dea326e9004ae9cd3df7f28.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1004790"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4784899" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Stepwise group sparse regression (SGSR): gene-set-based pharmacogenomic predictive models with stepwise selection of functional priors

In Sock Jang, Rodrigo Dienstmann, Adam A Margolin, Justin Guinney
<span title="">2015</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/d4nr2uqysjfnpiksvyxq54p5bm" style="color: black;">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</a> </i> &nbsp;
We evaluate the performance of our algorithm compared to well-known regularization methods such as LASSO, Ridge and Elastic net regression in the Cancer Cell Line Encyclopedia (CCLE) and Genomics of Drug  ...  Complex mechanisms involving genomic aberrations in numerous proteins and pathways are believed to be a key cause of many diseases such as cancer.  ...  In general, we observed an overall improvement in predictive performance using the SGSR model over Elastic Net regression, in which the latter is constrained to have the same number of features as SGSR  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25592566">pmid:25592566</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4299910/">pmcid:PMC4299910</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iqop3trv5rh2tleu4ubl6gdvbe">fatcat:iqop3trv5rh2tleu4ubl6gdvbe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191211134301/http://psb.stanford.edu/psb-online/proceedings/psb15/jang.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/e5/52/e552f8a8a7fd9dce6052cb67e400ce767f33f2f6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4299910" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Predict drug sensitivity of cancer cells with pathway activity inference

Xuewei Wang, Zhifu Sun, Michael T. Zimmermann, Andrej Bugrim, Jean-Pierre Kocher
<span title="2019-01-31">2019</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rbtzjpig4jcsfbjr5yo23sjnj4" style="color: black;">BMC Medical Genomics</a> </i> &nbsp;
As an alternative, pathway activity scores derived from gene expression could predict drug response of cancer cells.  ...  Most of current approaches predict drug sensitivity by building prediction models with individual genes, which suffer from low reproducibility due to biologic variability and difficulty to interpret biological  ...  In this study, Elastic net was used to build the predictive models of drug response.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-018-0449-4">doi:10.1186/s12920-018-0449-4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30704449">pmid:30704449</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6357358/">pmcid:PMC6357358</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7jtim6cvtzfs5o7pprcbyulxxq">fatcat:7jtim6cvtzfs5o7pprcbyulxxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209221424/https://bmcmedgenomics.biomedcentral.com/track/pdf/10.1186/s12920-018-0449-4" 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/0a/b0/0ab01f60ad458518cacdd9f5a03a8bb022a8bb12.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12920-018-0449-4"> <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/PMC6357358" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Personalized Prediction of Acquired Resistance to EGFR-Targeted Inhibitors Using a Pathway-Based Machine Learning Approach

Young Kim, Yong Kim, Suh Lee, Hye Yang, Sung Kim
<span title="2019-01-04">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
Here, we have developed a novel pipeline to build a meta-analysis-based, multivariate model for personalized pathways in AR to EGFR inhibitors, using sophisticated machine learning algorithms.  ...  Surprisingly, the model achieved excellent predictive performance, with a cross-study validation area under curve (AUC) of over 0.9, and generalization performance on independent cohorts of samples, with  ...  The regularized regression model was built using elastic net.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11010045">doi:10.3390/cancers11010045</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30621238">pmid:30621238</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6357167/">pmcid:PMC6357167</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pkmorjbst5cx7knf7vlttiyq74">fatcat:pkmorjbst5cx7knf7vlttiyq74</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211190758/https://res.mdpi.com/d_attachment/cancers/cancers-11-00045/article_deploy/cancers-11-00045.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/85/d3/85d39476ac625b914ebaf85cec2bc3951e55bd01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers11010045"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6357167" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Context-specific functional module based drug efficacy prediction

Woochang Hwang, Jaejoon Choi, Mijin Kwon, Doheon Lee
<span title="">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;
Our method was compared with elastic net model, which is a popular model for drug efficacy prediction.  ...  Current computational drug sensitivity prediction approaches use general biological network modules as their prediction features.  ...  In this paper, we generated the model which predicts efficacy of drugs, using 60 cell lines from NCI 60.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1078-6">doi:10.1186/s12859-016-1078-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27490093">pmid:27490093</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4965733/">pmcid:PMC4965733</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5eypjek4wncgbh7hhgr43p6qrm">fatcat:5eypjek4wncgbh7hhgr43p6qrm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190416092031/https://core.ac.uk/download/pdf/81570332.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/dc/c7/dcc7a2cc254f1d9eaf1f8ab33b2c7e56346c5c01.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-016-1078-6"> <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/PMC4965733" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Feature selection strategies for drug sensitivity prediction [article]

Krzysztof Koras, Dilafruz Juraeva, Julian Kreis, Johanna Mazur, Eike Staub, Ewa Szczurek
<span title="2019-11-29">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Based on GDSC drug data, we find that feature selection driven by prior knowledge tends to yield better results for drugs targeting specific genes and pathways, while models with the genome-wide features  ...  The best correlation of observed and predicted response using the test set is achieved for Linifanib (r=0.75).  ...  (a) 1 -RMSE vs correlation per drug, obtained by elastic net using genome-wide gene expression data as predictors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/856013">doi:10.1101/856013</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dsbj43fmyfczhd3d4cgpibigzy">fatcat:dsbj43fmyfczhd3d4cgpibigzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201214032514/https://www.biorxiv.org/content/biorxiv/early/2019/11/29/856013.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/ee/9e/ee9e3964dceee6ba38359beae8875c8c6c238d22.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/856013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Prediction with random forest involving sampling and feature selection strategies

Min Cao, Xiaolong Zhang, Bo Li, Jiafu Zhao
<span title="">2018</span> <i title="IEEE"> 2018 13th IEEE Conference on Industrial Electronics and Applications (ICIEA) </i> &nbsp;
Based on GDSC drug data, we find that feature selection driven by prior knowledge tends to yield better results for drugs targeting specific genes and pathways, while models with the genome-wide features  ...  The best correlation of observed and predicted response using the test set is achieved for Linifanib (r=0.75).  ...  (a) 1 -RMSE vs correlation per drug, obtained by elastic net using genome-wide gene expression data as predictors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/iciea.2018.8397786">doi:10.1109/iciea.2018.8397786</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xlkztejlffhsld4s5dedvkmdqu">fatcat:xlkztejlffhsld4s5dedvkmdqu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200325040749/https://www.biorxiv.org/content/biorxiv/early/2019/11/29/856013.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/8a/d7/8ad7ad2646cb8ec3829f50a5ec3e8ee6409d8fe2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/iciea.2018.8397786"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Molecular pathway identification using biological network-regularized logistic models

Wen Zhang, Ying-wooi Wan, Genevera I Allen, Kaifang Pang, Matthew L Anderson, Zhandong Liu
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
A number of tools, such as L 1 -norm based regularization and its extensions elastic net and fused lasso, have been introduced to deal with this challenge.  ...  Utility of this algorithm is also validated by its ability to reliably differentiate breast cancer subtypes using a large breast cancer dataset recently generated by the Cancer Genome Atlas (TCGA) consortium  ...  This article has been published as part of BMC Genomics  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-s8-s7">doi:10.1186/1471-2164-14-s8-s7</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24564637">pmid:24564637</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4046566/">pmcid:PMC4046566</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/flpewauoxjhpzoi6oqvmsc5vvq">fatcat:flpewauoxjhpzoi6oqvmsc5vvq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190430023139/https://scholarship.rice.edu/bitstream/handle/1911/88640/10.1186_1471-2164-14-S8-S7.pdf;jsessionid=76E5F4B1F661B521B7B3116A074548CF?sequence=4" 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/ec/95/ec95e20806f40229f80d76d01fb86093406483b5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-s8-s7"> <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/PMC4046566" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An image based system biology approach for Alzheimer's disease pathway analysis

Yue Huang, Xiaobo Zhou, Benchun Miao, Marta Lipinski, Zheng Xia, Guangshu Hu, Alexei Degterev, Junying Yuan, Stephen T.C. Wong
<span title="">2009</span> <i title="IEEE"> 2009 IEEE/NIH Life Science Systems and Applications Workshop </i> &nbsp;
Gene network and biological pathways analysis for those genes were further analyzed and led to several novel pathways that may contribute to amyloid plaque triggered neurite loss. II.  ...  Comparison between prediction results based on 'elastic net' and randomly selection.  ...  From Fig.4 it is obvious that prediction based on 'elastic net' was more accurate than random selection. Gene network resulting from "elastic net" analysis is shown in Fig. 5 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/lissa.2009.4906726">doi:10.1109/lissa.2009.4906726</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20585413">pmid:20585413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2888520/">pmcid:PMC2888520</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/nzkogwttrzapvnjo2kzimgcngy">fatcat:nzkogwttrzapvnjo2kzimgcngy</a> </span>
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Context Sensitive Modeling of Cancer Drug Sensitivity

Bo-Juen Chen, Oren Litvin, Lyle Ungar, Dana Pe'er, Julio Vera
<span title="2015-08-14">2015</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
CHER provides significantly more accurate models of drug sensitivity than comparable elastic-net-based models.  ...  To balance this trade-off, we present CHER (Contextual Heterogeneity Enabled Regression), an algorithm that builds predictive models for drug sensitivity by selecting predictive genomic features and deciding  ...  Elastic net regression enables selection of predictive genomics features based on L1-and L2-norms; the latter is suitable for highly correlated gene expression features [32] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0133850">doi:10.1371/journal.pone.0133850</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26274927">pmid:26274927</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4537214/">pmcid:PMC4537214</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/37rqbtzmlvbmlf2r5l3j4heb6e">fatcat:37rqbtzmlvbmlf2r5l3j4heb6e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171011015556/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0133850&amp;type=printable" 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/a1/ba/a1baed15a6b2fcbdc9fd25c4cf6fb3f1f6d36fc5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0133850"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> plos.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4537214" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genetic determinants of the molecular portraits of epithelial cancers

Youli Xia, Cheng Fan, Katherine A. Hoadley, Joel S. Parker, Charles M. Perou
<span title="2019-12-11">2019</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
In this study, we present an integrative computational approach using a genome-wide association analysis and an Elastic Net prediction method to analyze the relationship between DNA copy number alterations  ...  These Elastic Net DNA predictors could also be called from DNA-based gene panels, thus facilitating their use as biomarkers to guide therapeutic decision making.  ...  All computational analyses are done using public R packages. published here are in whole or part based upon data from the Cancer Genome Atlas managed by the NCI and NHGRI (dbGaP accession phs000178).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-13588-2">doi:10.1038/s41467-019-13588-2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31827079">pmid:31827079</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6906458/">pmcid:PMC6906458</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wrrgubp545gv3jaymgwvkbka3e">fatcat:wrrgubp545gv3jaymgwvkbka3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191212042534/https://www.nature.com/articles/s41467-019-13588-2.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/bc/c4/bcc49e6adf968f26c428bfb2fc662fa75d69fd95.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41467-019-13588-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6906458" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Systematic assessment of analytical methods for drug sensitivity prediction from cancer cell line data

In Sock Jang, Elias Chaibub Neto, Juistin Guinney, Stephen H Friend, Adam A Margolin
<span title="">2014</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/d4nr2uqysjfnpiksvyxq54p5bm" style="color: black;">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</a> </i> &nbsp;
Our results also provide a statistically principled set of recommended modeling guidelines, including: using elastic net or ridge regression with input features from all genomic profiling platforms, most  ...  importantly, gene expression features, to predict continuous-valued sensitivity scores summarized using the area under the dose response curve, with pathway targeted compounds most likely to yield the  ...  While the sparse feature selection encouraged by lasso indeed leads to inferior predictive performance, elastic net performs as well as ridge regression based on predictive accuracy, suggesting that elastic  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24297534">pmid:24297534</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3995541/">pmcid:PMC3995541</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dq6ikba54vfe3c3mqthewcpuoy">fatcat:dq6ikba54vfe3c3mqthewcpuoy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191117153730/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3995541&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/71/80/7180776b107e8ae05aa1f910d3bd49f930ead812.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3995541" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cancer Progression Prediction Using Gene Interaction Regularized Elastic Net

Lin Zhang, Hui Liu, Yufei Huang, Xuesong Wang, Yidong Chen, Jia Meng
<span title="2017-01-01">2017</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q75ftrlivrhrnno5ijjuyufx5a" style="color: black;">IEEE/ACM Transactions on Computational Biology &amp; Bioinformatics</a> </i> &nbsp;
For this purpose, we propose a Gene Interaction Regularized Elastic Net (GIREN) model that predicts clinical outcome by integrating multiple data types.  ...  Result shows that, the proposed GIREN algorithm obtained more accurate and robust performance over competing algorithms (LASSO, Elastic Net and superPC, with or without average pathway expression features  ...  Zhang Breast cancer progression prediction based on the gene list selected by GIREN, LASSO, Elastic Net and SuperPC with original gene measurement or average pathway expression.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2015.2511758">doi:10.1109/tcbb.2015.2511758</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28055897">pmid:28055897</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5374042/">pmcid:PMC5374042</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/guwxcd77kbchzmq3grwunxq4oe">fatcat:guwxcd77kbchzmq3grwunxq4oe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209172606/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5374042&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/ba/8a/ba8a47b756e7351d6e2b535b6b8c84af65e7a6a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2015.2511758"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5374042" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Network-Based Logistic Classification with an EnhancedL1/2Solver Reveals Biomarker and Subnetwork Signatures for Diagnosing Lung Cancer

Hai-Hui Huang, Yong Liang, Xiao-Ying Liu
<span title="">2015</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
Identifying biomarker and signaling pathway is a critical step in genomic studies, in which the regularization method is a widely used feature extraction approach.  ...  Furthermore, we applied our method for lung cancer data analysis and found that our method achieves higher predictive accuracy thanL1regularization, the oldL1/2penalized solver, and the Elastic net approaches  ...  Both simulation and real genomic data studies showed that the enhanced 1/2 net is a ranking procedure compared with 1/2 net (using the old thresholding operator), 1 net, and the Elastic net in the selection  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/713953">doi:10.1155/2015/713953</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26185761">pmid:26185761</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4488258/">pmcid:PMC4488258</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/msk37n2lqbbjnkqbsw55lyl6ue">fatcat:msk37n2lqbbjnkqbsw55lyl6ue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309074918/http://pdfs.semanticscholar.org/f5cc/57364958b437f241ac560459e811ff9b4844.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/f5/cc/f5cc57364958b437f241ac560459e811ff9b4844.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2015/713953"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4488258" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Elastic Net Models Based on DNA Copy Number Variations Predicts Clinical Features, Expression Signatures, and Mutations in Lung Adenocarcinoma

Yi Xiang, Xiaohuan Zou, Huaqiu Shi, Xueming Xu, Caixia Wu, Wenjuan Zhong, Jinfeng Wang, Wenting Zhou, Xiaoli Zeng, Miao He, Ying Wang, Li Huang (+1 others)
<span title="2021-05-31">2021</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;
These Elastic Net prediction methods can also be applied to other gene sets, thereby facilitating their use as biomarkers in monitoring therapy.  ...  In this study, we propose a comprehensive analysis combining genome-wide association analysis and an Elastic Net Regression predictive model, focus on predicting the levels of many gene expression signatures  ...  Elastic Net-Mediated CNV-Based Predictions of Clinical Features Furthermore, we explored whether CNV-based Elastic Net predictive regression models can be used to forecast clinical features.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2021.668040">doi:10.3389/fgene.2021.668040</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34135942">pmid:34135942</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8202527/">pmcid:PMC8202527</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/q2cw7xkqmfaejgwfrvnxpwrbky">fatcat:q2cw7xkqmfaejgwfrvnxpwrbky</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210602135259/https://fjfsdata01prod.blob.core.windows.net/articles/files/668040/pubmed-zip/.versions/2/.package-entries/fgene-12-668040-r1/fgene-12-668040.pdf?sv=2018-03-28&amp;sr=b&amp;sig=qJZUrz51jnelk6%2FM01nyHPPEgE6TKfjNy5LuBaTqBJA%3D&amp;se=2021-06-02T13%3A53%3A28Z&amp;sp=r&amp;rscd=attachment%3B%20filename%2A%3DUTF-8%27%27fgene-12-668040.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/2a/2d/2a2d558b017fc8d7b304042b857faeb5cbc0c834.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2021.668040"> <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/PMC8202527" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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