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Geometric Optimization Methods for Independent Component Analysis Applied on Gene Expression Data

M. Journee, A. E. Teschendorff, P.-A. Absil, R. Sepulchre
<span title="">2007</span> <i title="IEEE"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rc5jnc4ldvhs3dswicq5wk3vsq" style="color: black;">2007 IEEE International Conference on Acoustics, Speech and Signal Processing - ICASSP &#39;07</a> </i> &nbsp;
Index Terms-Independent Component Analysis (ICA), optimization on matrix manifolds, RADICAL algorithm, steepestdescent on the orthogonal group, gene expression data.  ...  Independent Component Analysis (ICA) was proposed by several authors as an interesting means.  ...  Several authors have proposed Independent Component Analysis (ICA) as an interesting means to extract information from gene expression data [2, 3, 4] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icassp.2007.367344">doi:10.1109/icassp.2007.367344</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/icassp/JourneeTAS07.html">dblp:conf/icassp/JourneeTAS07</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/33njvp5nd5crla2nxzmiu5ikhm">fatcat:33njvp5nd5crla2nxzmiu5ikhm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812155829/http://orbi.ulg.ac.be/bitstream/2268/18869/1/0401413.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/a9/f3/a9f3c5d4eaeada87f9648ebd0ed931c0efb19db2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/icassp.2007.367344"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Geometric Optimization Methods for the Analysis of Gene Expression Data [chapter]

Michel Journée, Andrew E. Teschendorff, Pierre-Antoine Absil, Simon Tavaré, Rodolphe Sepulchre
<span title="">2008</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4rhte7roibctnbr7jz7mi4vyw4" style="color: black;">Lecture Notes in Computational Science and Engineering</a> </i> &nbsp;
This work shows that Independent Component Analysis (ICA) is a promising approach for the analysis of genome-wide transcriptomic data.  ...  These algorithms are then applied on a microarray breast-cancer data set. Some issues about the application of ICA and the evaluation of biological relevance of the results are discussed.  ...  This large study also favors the use of ICA with model II for the analysis of gene expression data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-73750-6_12">doi:10.1007/978-3-540-73750-6_12</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xqinsd5fgrf4belxw7re5bbotm">fatcat:xqinsd5fgrf4belxw7re5bbotm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808145155/http://www.damtp.cam.ac.uk/user/st321/CV_&amp;_Publications_files/STpapers-pdf/JTATS07.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/57/ad/57adce454c86990568cca3276ce0e1efb82a73ac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-73750-6_12"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Robust unmixing of tumor states in array comparative genomic hybridization data

David Tolliver, Charalampos Tsourakakis, Ayshwarya Subramanian, Stanley Shackney, Russell Schwartz
<span title="2010-06-01">2010</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;
We previously proposed a method to computationally infer cell populations from measures of tumor-wide gene expression through a geometric interpretation of mixture type separation, but this approach deals  ...  The method builds on the prior geometric approach but uses a novel objective function allowing for robust fits that greatly reduces the sensitivity to noise and outliers.  ...  The recent work by Schwartz and Shackney (2010) applied the hard geometric unmixing model (see §2.1.1) to gene expression data with the goal of recovering expression signatures of tumor cell subtypes  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq213">doi:10.1093/bioinformatics/btq213</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20529894">pmid:20529894</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2881397/">pmcid:PMC2881397</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3drhfqdt6rb7fi34bqjupioev4">fatcat:3drhfqdt6rb7fi34bqjupioev4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20130423004537/http://www.math.cmu.edu:80/~ctsourak/ismb10.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/fa/9b/fa9b4f74c64de5920b1c040d629ece04db5047c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq213"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881397" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Selection of optimal reference genes for normalization in quantitative RT-PCR

Inna Chervoneva, Yanyan Li, Stephanie Schulz, Sean Croker, Chantell Wilson, Scott A Waldman, Terry Hyslop
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
To minimize this innate variability, multiple reference genes are used. Current methods of selecting reference genes make an assumption of independence in their innate variation.  ...  The results of this evaluation provide flexibility to choose from important criteria for selecting the optimal subset(s) of reference genes, unless one subset meets all the criteria.  ...  CW was enrolled in the NIH-supported institutional K30 Training Program in Human Investigation (K30 HL004522) and was supported by NIH institutional award T32 GM08562 for Postdoctoral Training in Clinical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-253">doi:10.1186/1471-2105-11-253</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20470420">pmid:20470420</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2889935/">pmcid:PMC2889935</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qvv7rci2vncp5bcawa3xt3swgy">fatcat:qvv7rci2vncp5bcawa3xt3swgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811122316/http://www.gene-quantification.de/chervoneva-et-al-opt-ref-genes-2010.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/19/e0/19e067db0ebac5c0d981bb1c610cfb3de10992ea.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-253"> <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/PMC2889935" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Blind source separation methods for deconvolution of complex signals in cancer biology

Andrei Zinovyev, Ulykbek Kairov, Tatyana Karpenyuk, Erlan Ramanculov
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ypsixbtbfrezvpluf74fdc2aeq" style="color: black;">Biochemical and Biophysical Research Communications - BBRC</a> </i> &nbsp;
We focus more specifically on the analysis of gene expression in cancer. The review is finalized by listing available software implementations for the methods described.  ...  Two blind source separation methods (Independent Component Analysis and Non-negative Matrix Factorization), developed initially for signal processing in engineering, found recently a number of applications  ...  grant INCA LABEL Cancéropole Ile-de-France, by the grant INVADE from ITMO Cancer (Call Systems Biology 2012) and by the grant "Projet Incitatif et Collaboratif Computational Systems Biology Approach for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbrc.2012.12.043">doi:10.1016/j.bbrc.2012.12.043</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23261450">pmid:23261450</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ff4hcuieovdhhjmlrxlbg76goe">fatcat:ff4hcuieovdhhjmlrxlbg76goe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200903150642/https://arxiv.org/ftp/arxiv/papers/1301/1301.2634.pdf" title="fulltext PDF download [not primary version]" 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] <span style="color: #f43e3e;">&#10033;</span> <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/73/2c/732cdd03e4e1060485179c180c81f7afadf84ab3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bbrc.2012.12.043"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Recovering key biological constituents through sparse representation of gene expression

Yosef Prat, Menachem Fromer, Nathan Linial, Michal Linial
<span title="2011-01-21">2011</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;
To demonstrate the power of our approach in extracting valuable information from the expression data, we independently applied it to large-scale experiments carried out on the yeast and malaria parasite  ...  During the last two decades, many methods were developed for extracting insights regarding the inter-relationships between genes from such data.  ...  In this study, we applied a different approach to gene expression data analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr002">doi:10.1093/bioinformatics/btr002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21258061">pmid:21258061</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gt5ghbuf5rhffgbbiqhwzfrp4m">fatcat:gt5ghbuf5rhffgbbiqhwzfrp4m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160316081758/http://www.cs.huji.ac.il/~nati/PAPERS/sparcle.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/06/17/06170f69393a9894472d244e4183a349413d1f84.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

A review of independent component analysis application to microarray gene expression data

Wei Kong, Charles R. Vanderburg, Hiromi Gunshin, Jack T. Rogers, Xudong Huang
<span title="">2008</span> <i title="Future Science, LTD"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6t7cfvh76ranblnkx6doquvcyq" style="color: black;">BioTechniques</a> </i> &nbsp;
Independent component analysis (ICA) methods have received growing attention as effective data-mining tools for microarray gene expression data.  ...  As a technique of higher-order statistical analysis, ICA is capable of extracting biologically relevant gene expression features from microarray data.  ...  Two kinds of unsupervised analysis methods for microarray data, principal component analysis (PCA) and independent component analysis (ICA), have been developed to accomplish this task.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/000112950">doi:10.2144/000112950</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19007336">pmid:19007336</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3005719/">pmcid:PMC3005719</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vcdoxu4ecjginfjj7pkrqvc7v4">fatcat:vcdoxu4ecjginfjj7pkrqvc7v4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814081641/http://www.biotechniques.com/multimedia/archive/00012/BTN_A_000112950_O_12956a.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/ac/f1/acf108561c5e28ab0750f5406f3fb742386991b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/000112950"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3005719" 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 Review of Feature Extraction Software for Microarray Gene Expression Data

Ching Siang Tan, Wai Soon Ting, Mohd Saberi Mohamad, Weng Howe Chan, Safaai Deris, Zuraini Ali Shah
<span title="">2014</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;
The software reviewed is mainly for Principal Component Analysis (PCA), Independent Component Analysis (ICA), Partial Least Squares (PLS), and Local Linear Embedding (LLE).  ...  Transforming large-scale gene expression data into a set of genes is called feature extraction.  ...  Acknowledgments The authors would like to thank Universiti Teknologi Malaysia for funding this research by Research University Grants  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/213656">doi:10.1155/2014/213656</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25250315">pmid:25250315</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4164313/">pmcid:PMC4164313</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lgv3o2o6mvhkdpzuqwezdqtc4e">fatcat:lgv3o2o6mvhkdpzuqwezdqtc4e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190303014415/http://pdfs.semanticscholar.org/a58e/818fcd408e9713a2d80160545fe069a084a7.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/a5/8e/a58e818fcd408e9713a2d80160545fe069a084a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/213656"> <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/PMC4164313" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dual Graph-Laplacian PCA: A Closed-Form Solution for Bi-clustering to Find "Checkerboard" Structures on Gene Expression Data [article]

Jin-Xing Liu, Chun-Mei Feng, Xiang-Zhen Kong, Yong Xu
<span title="2019-01-21">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
We apply this new method to simultaneously cluster genes and conditions (e.g., different samples) with the aim of finding internal "checkerboard" structures on gene expression data, if they exist.  ...  Promising results on gene expression data have been verified by extensive experiments  ...  principal component analysis (DGPCA).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1901.06794v1">arXiv:1901.06794v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3vnj4ud65bgtpj2riqhu6lpsvu">fatcat:3vnj4ud65bgtpj2riqhu6lpsvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191016000557/https://arxiv.org/pdf/1901.06794v1.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/61/6f61f8fc70350fed4219ac7bfda9331347ff14f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1901.06794v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Prediction of Missing Values in Microarray and Use of Mixed Models to Evaluate the Predictors

Guri Feten, Trygve Almøy, Are H. Aastveit
<span title="2005-01-05">2005</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ovi3nz5yt5gl5g22j72wpmtl2m" style="color: black;">Statistical Applications in Genetics and Molecular Biology</a> </i> &nbsp;
Gene expression microarray experiments generate data sets with multiple missing expression values. In some cases, analysis of gene expression requires a complete matrix as input.  ...  The study showed that different methods' capability to predict is dependent on the data, hence the ideal choice of method and number of components are different for each data set.  ...  This model was also used to decide if the optimal method and the optimal number of components were different for each gene. analysis based on absolute error was carried out.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2202/1544-6115.1120">doi:10.2202/1544-6115.1120</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16646827">pmid:16646827</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ztwl7jnjyjd3xmnsaqlpxzwflu">fatcat:ztwl7jnjyjd3xmnsaqlpxzwflu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811102213/http://www.umb.no/statisk/ikbm_english/genomics/publications/feten_1.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/15/68/15688e1cfd4401f3a63409b3c6585937b82ed0a7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2202/1544-6115.1120"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Independent Component Analysis for Unraveling the Complexity of Cancer Omics Datasets

Nicolas Sompairac, Petr V. Nazarov, Urszula Czerwinska, Laura Cantini, Anne Biton, Askhat Molkenov, Zhaxybay Zhumadilov, Emmanuel Barillot, Francois Radvanyi, Alexander Gorban, Ulykbek Kairov, Andrei Zinovyev
<span title="2019-09-07">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Independent component analysis (ICA) is a matrix factorization approach where the signals captured by each individual matrix factors are optimized to become as mutually independent as possible.  ...  We particularly focus on the technical aspects of ICA application in omics studies such as using different protocols, determining the optimal number of components, assessing and improving reproducibility  ...  In the case of ICA, which geometrically only rotates the PCA axes, choosing the number of independent components can rely either on the methods for determining the number of relevant principal components  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20184414">doi:10.3390/ijms20184414</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31500324">pmid:31500324</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6771121/">pmcid:PMC6771121</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4njbii3nqvhvvaykspvbw7cp24">fatcat:4njbii3nqvhvvaykspvbw7cp24</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200212172036/https://res.mdpi.com/d_attachment/ijms/ijms-20-04414/article_deploy/ijms-20-04414.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/dd/7e/dd7e9e40626d99249c252218262dfc28b0446213.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms20184414"> <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/PMC6771121" 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 Multiobjective Evolutionary Conceptual Clustering Methodology for Gene Annotation Within Structural Databases: A Case of Study on the Gene Ontology Database

R.C. Romero-Zaliz, C. Rubio-Escudero, J.P. Cobb, F. Herrera, O. Cordon, I. Zwir
<span title="">2008</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dqtjwgdgmjazlimlppwouyrzcq" style="color: black;">IEEE Transactions on Evolutionary Computation</a> </i> &nbsp;
We apply this methodology to identify conceptual models in structural databases generated from gene ontologies.  ...  The combination of evolutionary algorithms with multiobjective and multimodal optimization techniques constitutes a suitable tool for solving this problem.  ...  Polpitiya for useful suggestions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tevc.2008.915995">doi:10.1109/tevc.2008.915995</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dbgsmopsgfbknprjhcpf43u47a">fatcat:dbgsmopsgfbknprjhcpf43u47a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810230548/http://sci2s.ugr.es/sites/default/files/ficherosPublicaciones/0768_2008-Romero-IEEETEC.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/33/15/331543c9830508a24d7d367a24f4660277f3c5d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tevc.2008.915995"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

ascend: R package for analysis of single-cell RNA-seq data

Anne Senabouth, Samuel W Lukowski, Jose Alquicira Hernandez, Stacey B Andersen, Xin Mei, Quan H Nguyen, Joseph E Powell
<span title="2019-08-01">2019</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/apde6vbe7vfoxkfibp7n4mzonm" style="color: black;">GigaScience</a> </i> &nbsp;
The package incorporates both novel and established methods to provide a framework to perform cell and gene filtering, quality control, normalization, dimension reduction, clustering, differential expression  ...  Analysis of scRNA-seq data is multidisciplinary in nature, requiring careful consideration of the application of statistical methods with respect to the underlying biology.  ...  r ascend optimizes parallelization and algorithms for improving speed of each analysis step (e.g., differential expression analysis). r ascend implements Clustering by Optimal REsolution (CORE) for unsupervised  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gigascience/giz087">doi:10.1093/gigascience/giz087</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31505654">pmid:31505654</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6735844/">pmcid:PMC6735844</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r6f6d5orgffdnfugzku5qb7o4u">fatcat:r6f6d5orgffdnfugzku5qb7o4u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200503085840/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6735844&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/00/25/00255b8a57cfb0812a4e88139802b6993144364d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gigascience/giz087"> <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/PMC6735844" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Spatial mapping of single cells in the Drosophila embryo from transcriptomic data based on topological consistency

Maryam Zand, Jianhua Ruan
<span title="2020-08-20">2020</span> <i title="F1000 Research Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lz7xw3k77zcg5f66jhfurufu64" style="color: black;">F1000Research</a> </i> &nbsp;
Evaluation results based on DREAM scores show that our method accurately predicts the location of single cells, and the predictions lead to successful recovery of the spatial expression patterns for most  ...  The first step involves identifying a set of most informative genes based on the consistency between gene expression similarity and cell proximity.  ...  On the other hand, although our analysis indicated that using raw data instead of the binarized data can potentially increase the consistency between gene expression pattern similarity and cell proximity  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.24163.1">doi:10.12688/f1000research.24163.1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33824719">pmid:33824719</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7993407/">pmcid:PMC7993407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4apfjf57wfgllliqfrkklmupye">fatcat:4apfjf57wfgllliqfrkklmupye</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200821084019/https://f1000researchdata.s3.amazonaws.com/manuscripts/26653/4c282a19-08b6-4ce3-8a02-b1fd809f578f_24163_-_maryam_zand.pdf?doi=10.12688/f1000research.24163.1&amp;numberOfBrowsableCollections=24&amp;numberOfBrowsableInstitutionalCollections=5&amp;numberOfBrowsableGateways=25" 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/ce/22/ce2267b93fbac64dc4b1a7a12985e34a9952b080.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.12688/f1000research.24163.1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7993407" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Discovery and replication of microRNAs for breast cancer risk using genome-wide profiling

Cenny Taslim, Daniel Y. Weng, Theodore M. Brasky, Ramona G. Dumitrescu, Kun Huang, Bhaskar VS. Kallakury, Shiva Krishnan, Adana A. Llanos, Catalin Marian, Joseph McElroy, Sallie S. Schneider, Scott L. Spear (+4 others)
<span title="2016-11-09">2016</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
profiling data is to apply optimal normalization method.  ...  At present, there is little consensus on normalization methods for pre-processing of miRNA expression [1] .  ...  Supplementary Loadings shown was calculated in the discovery study for the first component in standardized unit.) See Supplementary File S1. Supplementary  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.13241">doi:10.18632/oncotarget.13241</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27833082">pmid:27833082</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5349926/">pmcid:PMC5349926</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/55mnekxjzbez7c7wwdkttqguk4">fatcat:55mnekxjzbez7c7wwdkttqguk4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220205156/http://pdfs.semanticscholar.org/27fc/964184054aaf93f730152451ead5cf4d16d4.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/27/fc/27fc964184054aaf93f730152451ead5cf4d16d4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.13241"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5349926" 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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