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Stability-Based Comparison of Class Discovery Methods for DNA Copy Number Profiles

Isabel Brito, Philippe Hupé, Pierre Neuvial, Emmanuel Barillot, Dongxiao Zhu
<span title="2013-12-05">2013</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;
An evaluation procedure is therefore required to select the best class discovery method (combination of one input data representation, one dissimilarity measure and one clustering algorithm) for array-CGH  ...  Robustness of the resulting classes is a common requirement, but no stability-based comparison of class discovery methods for array-CGH profiles has ever been reported.  ...  The x 2 -based test described was applied iteratively to detect stable class discovery methods. For all data sets, resampling was performed by establishing M~100 pairs of subsets of each data set.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0081458">doi:10.1371/journal.pone.0081458</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24339933">pmid:24339933</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3855312/">pmcid:PMC3855312</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ciwxgrspmnf7hlftdl5mifsy7e">fatcat:ciwxgrspmnf7hlftdl5mifsy7e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171009072613/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0081458&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/98/51/9851391f2bcc91b491e30091537926728f109adc.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.0081458"> <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/PMC3855312" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Minimizing acquisition-related radiomics variability by image resampling and batch effect correction to allow for large-scale data analysis

Marta Ligero, Olivia Jordi-Ollero, Kinga Bernatowicz, Alonso Garcia-Ruiz, Eric Delgado-Muñoz, David Leiva, Richard Mast, Cristina Suarez, Roser Sala-Llonch, Nahum Calvo, Manuel Escobar, Arturo Navarro-Martin (+3 others)
<span title="2020-09-09">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/y352pep6tjcphcqt3p6tv3d7se" style="color: black;">European Radiology</a> </i> &nbsp;
Resampling to isometric voxels increased the number of robust features when images were acquired with different pixel sizes (p < 0.05).  ...  SVD-based for thickness correction and ComBat correction for thickness and combined thickness–kernel increased the number of reproducible features (p < 0.05).  ...  Compliance with ethical standards Guarantor The scientific guarantor of this publication is Raquel Perez-Lopez, principal investigator of the radiomics group at Vall d'Hebron Institut of Oncology, Barcelona  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00330-020-07174-0">doi:10.1007/s00330-020-07174-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32909055">pmid:32909055</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/653vyuxkjjbynpsecw2rlas5ja">fatcat:653vyuxkjjbynpsecw2rlas5ja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210715132329/http://diposit.ub.edu/dspace/bitstream/2445/174222/1/Ligero2021_Article_MinimizingAcquisition-relatedR.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/19/25/19256ecbd808ea814314f4e15e2c98864d47d007.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00330-020-07174-0"> <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>

Merged consensus clustering to assess and improve class discovery with microarray data

T Ian Simpson, J Douglas Armstrong, Andrew P Jarman
<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;
One of the most commonly performed tasks when analysing high throughput gene expression data is to use clustering methods to classify the data into groups.  ...  There are a large number of methods available to perform clustering, but it is often unclear which method is best suited to the data and how to quantify the quality of the classifications produced.  ...  Of these methods, Monti et al. [14] is the only one to develop a generalised, model independent resampling based methodology to assess cluster stability.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-590">doi:10.1186/1471-2105-11-590</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21129181">pmid:21129181</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3002369/">pmcid:PMC3002369</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/foqn6vf4cjaohclio62j4nztoa">fatcat:foqn6vf4cjaohclio62j4nztoa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817045010/http://www.research.ed.ac.uk/portal/files/7751874/bmc_bio_simpson.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/5f/6e/5f6e79cef397504178f420204e1256d86b4129a0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-590"> <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/PMC3002369" 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 prediction-based resampling method for estimating the number of clusters in a dataset

Sandrine Dudoit, Jane Fridlyand
<span title="2002-06-25">2002</span> <i title="BMC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
Focusing on prediction accuracy in conjunction with resampling produces accurate and robust estimates of the number of clusters.  ...  Here we address the first of these problems. We have developed a new prediction-based resampling method, Clest, to estimate the number of clusters in a dataset.  ...  We also acknowledge Terry Speed for discussions on the analysis of microarray data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12184810">pmid:12184810</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC126241/">pmcid:PMC126241</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/srtgcuvrhzdrjbcij6frbk2wau">fatcat:srtgcuvrhzdrjbcij6frbk2wau</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200326122652/https://link.springer.com/content/pdf/10.1186%2Fgb-2002-3-7-research0036.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/bf/b2/bfb22cdbf8fc93050daa80839432b4661e9ab93b.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/PMC126241" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Graph-based consensus clustering for class discovery from gene expression data

Zhiwen Yu, Hau-San Wong, Hongqiang Wang
<span title="2007-09-14">2007</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;
Motivation: Consensus clustering, also known as cluster ensemble, is one of the important techniques for microarray data analysis, and is particularly useful for class discovery from microarray data.  ...  By consensus clustering, one can discover the underlying classes of the samples in gene expression data.  ...  Recently, researchers are paying more attention to class discovery based on the consensus clustering approaches.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm463">doi:10.1093/bioinformatics/btm463</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17872912">pmid:17872912</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3w7cndh4rbb4dbrtmflltxayzy">fatcat:3w7cndh4rbb4dbrtmflltxayzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20131204075702/http://bioinformatics.oxfordjournals.org:80/content/23/21/2888.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/86/20/8620020f9e854b47b5851ff873fbc4768987ba59.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btm463"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Distance-based assessment of the localization of functional annotations in 3D genome reconstructions

Daniel Capurso, Mark R Segal
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
These analyses dichotomized data point pairs belonging to a functional annotation as "close" or "far" based on some threshold and then tested for enrichment of "close" pairs.  ...  Applying affinity propagation clustering to telomere coordinates in the 3D reconstructions yielded six telomere clusters for both organisms.  ...  This research did not utilize data for human subjects or vertebrates. Acknowledgements Some computations were performed using the UCSF Biostatistics High Performance Computing System.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-992">doi:10.1186/1471-2164-15-992</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25407917">pmid:25407917</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4254257/">pmcid:PMC4254257</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/grfirxcsonfn7lnapnatrsh5rq">fatcat:grfirxcsonfn7lnapnatrsh5rq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830140334/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-992?site=http://bmcgenomics.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/48/e6/48e61650e8b1b2928b27aea3e13f61eb13314e83.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-992"> <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/PMC4254257" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Editorial

Cristián Bravo, Matt Davison, Alejandro Jofré, Sebastián Maldonado, Richard Weber
<span title="2015-10-09">2015</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lm7wouyrqzbgvenkjxkrtwootu" style="color: black;">Intelligent Data Analysis</a> </i> &nbsp;
A subsection deals with the robustness of the obtained cluster solution while the comparison with alternative cluster techniques hints at important advantages of the newly proposed method.  ...  These new formulations provide a robust and efficient framework for classification, leading to superior performance in high-dimensional data sets.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/ida-150766">doi:10.3233/ida-150766</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mxsqq5s4pvbnlle6eelbkdkzze">fatcat:mxsqq5s4pvbnlle6eelbkdkzze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721011228/https://content.iospress.com/download/intelligent-data-analysis/ida766?id=intelligent-data-analysis%2Fida766" 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/6a/41/6a413638b99c1d88ad5dcc635cc2da17395286e6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/ida-150766"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

:{unav)

Stefano Monti
<span title="2012-12-28">2012</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/h4nnd7sxwzcwhetu5qkjbcdh6u" style="color: black;">Machine Learning</a> </i> &nbsp;
In this paper we present a new methodology of class discovery and clustering validation tailored to the task of analyzing gene expression data.  ...  We call the new methodology consensus clustering, and in conjunction with resampling techniques, it provides for a method to represent the consensus across multiple runs of a clustering algorithm and to  ...  Acknowledgments We thank all the members of the Cancer Genomics group for useful discussions and assistance in the preparation and use of the data analyzed. Notes 1.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1023/a:1023949509487">doi:10.1023/a:1023949509487</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kbbzcap54zhn5fs2vpzjhvydtu">fatcat:kbbzcap54zhn5fs2vpzjhvydtu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814153232/http://www.cs.utexas.edu/users/ml/biodm/papers/MLJ-biodm2.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/1f/29/1f29553ecbaa388b6be3402bc7af28178f5e24ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1023/a:1023949509487"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Comparative Study of Recommendation Algorithms and Systems using WEKA

Lokesh S.Katore, J.S.Umale J.S.Umale
<span title="2015-01-16">2015</span> <i title="Foundation of Computer Science"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/b637noqf3vhmhjevdfk3h5pdsu" style="color: black;">International Journal of Computer Applications</a> </i> &nbsp;
This paper presents the performance of the specific algorithms of the data mining class in view to observe their suitability for recommender systems.  ...  The accurate prediction of business decision accurately depends on heuristic algorithms used for analytics.  ...  An explicit probability for hypothesis is calculated by the Naïve Bayes and it is robust to noise in input data. The main drawback of this approach is it is feature based.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/19295-0731">doi:10.5120/19295-0731</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/espdb6o3hnbkdlocnuonziupfu">fatcat:espdb6o3hnbkdlocnuonziupfu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719163529/https://research.ijcaonline.org/volume110/number3/pxc3900731.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/ec/96/ec9645ea7b67e85ed10cb973df5d6ff5fee3e605.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/19295-0731"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Tumor classification using phylogenetic methods on expression data

Richard Desper, Javed Khan, Alejandro A. Schäffer
<span title="">2004</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fydada535zbx7el5lxtbdrx6ga" style="color: black;">Journal of Theoretical Biology</a> </i> &nbsp;
We tested our method for class discovery on two data sets: a data set of 87 tissues, comprised mostly of small, round, blue-cell tumors (SRBCTs), and a data set of 22 breast tumors.  ...  We also demonstrate the flexibility of the class discovery method with regard to standard resampling methodology such as jackknifing and noise perturbation.  ...  Acknowledgements Our thanks go to John Powell for his assistance installing CLUSTER.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jtbi.2004.02.021">doi:10.1016/j.jtbi.2004.02.021</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15178197">pmid:15178197</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7urg6jw34bfopkopuu2bwgybtq">fatcat:7urg6jw34bfopkopuu2bwgybtq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808093053/https://home.ccr.cancer.gov/oncology/oncogenomics/papers/tumorclassphylo_desperkhanshaffer.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/7b/3d/7b3d4d76796dad5ae87a27baeab4eaf11168ee66.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jtbi.2004.02.021"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Quantitative proteomics signature profiling based on network contextualization

Wilson Wen Bin Goh, Tiannan Guo, Ruedi Aebersold, Limsoon Wong
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/m5tyg6kdofe7db2hdtm2zxndi4" style="color: black;">Biology Direct</a> </i> &nbsp;
We present a network-based method, namely quantitative proteomic signature profiling (qPSP) that improves the biological content of proteomic data by converting protein expressions into hit-rates in protein  ...  Conclusions: Given qPSP's ability to discriminate phenotype classes even at small sample sizes, high robustness to noise, and better summary statistics, it can be deployed towards analysis of highly heterogeneous  ...  In qPSP, the clustering is done based on the vector of hit-rates against the complexes, and never based on the protein expression levels themselves.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-015-0098-x">doi:10.1186/s13062-015-0098-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26666224">pmid:26666224</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4678536/">pmcid:PMC4678536</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ovmd7rdfhzcy3l3lhlvn5td2ri">fatcat:ovmd7rdfhzcy3l3lhlvn5td2ri</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812031248/https://biologydirect.biomedcentral.com/track/pdf/10.1186/s13062-015-0098-x?site=biologydirect.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/34/0b/340bf737c823b0263944e662d47cc73b9fcc9c52.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13062-015-0098-x"> <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/PMC4678536" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Gene expression meta-analysis supports existence of molecular apocrine breast cancer with a role for androgen receptor and implies interactions with ErbB family

Sandeep Sanga, Bradley M Broom, Vittorio Cristini, Mary E Edgerton
<span title="2009-09-11">2009</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;
Methods: We combine data from two studies that propose the existence of the Molecular Apocrine phenotype. We use quantile normalization and XPN to minimize institutional bias in the data.  ...  Data mining strategies used here provide an alternative method to comparison with cell lines for discovering seminal pathways and interactions between signaling networks.  ...  We would like to dedicate this work to the memory of Vivian Cooper, a close friend and colleague of Dr. Fisher, who died of breast cancer on April 10 of this year.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1755-8794-2-59">doi:10.1186/1755-8794-2-59</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19747394">pmid:19747394</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2753593/">pmcid:PMC2753593</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pntyzjjsunbvrizmszdeu6ouoe">fatcat:pntyzjjsunbvrizmszdeu6ouoe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120425003733/http://www.biomedcentral.com:80/content/pdf/1755-8794-2-59.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/a8/ae/a8ae47c0f11f006e101200dfc25221f14d2caefc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1755-8794-2-59"> <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/PMC2753593" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Study on Preprocessing and Classifying Mass Spectral Raw Data Concerning Human Normal and Disease Cases [chapter]

Xenofon E. Floros, George M. Spyrou, Konstantinos N. Vougas, George T. Tsangaris, Konstantina S. Nikita
<span title="">2006</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
The classification performance was assessed for distinct values of the parameters involved in the feature extraction pipeline.  ...  Here we address a feature exraction method for mass spectra which consists of two main steps : In the first step an algorithm for low level preprocessing of mass spectra is applied, including denoising  ...  The maximization was carried out using a simple exhaustive search algorithm based on a 10-fold cross validation scheme which provides a robust estimation of the performance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11946465_35">doi:10.1007/11946465_35</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/alwpu6icivalpedv3evqx3mf6q">fatcat:alwpu6icivalpedv3evqx3mf6q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190219044838/http://pdfs.semanticscholar.org/15e1/d9c9855c80f992daebc33592af09bc7dd3b6.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/e1/15e1d9c9855c80f992daebc33592af09bc7dd3b6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/11946465_35"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Distinguishing Kawasaki Disease from Febrile Infectious Disease Using Gene Pair Signatures

Jiayong Zhong, Qingsheng Huang, Yanfei Wang, Huan Gao, Hongling Jia, Jun Fan, Huiying Liang
<span title="2020-04-27">2020</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;
In this study, we aimed to use a relative-expression-based method k-TSP and resampling framework to identify robust gene pair signatures to distinguish KD from bacterial and virus febrile infectious diseases  ...  Kawasaki disease (KD) is an acute systemic vasculitis of childhood with prolonged fever, and the diagnosis of KD is mainly based on clinical criteria, which is prone to misdiagnosis with other febrile  ...  In this study, based on the k-TSP method, we applied a resampling framework to identify robust gene pair features and distinguish Kawasaki disease from febrile control disease.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2020/6539398">doi:10.1155/2020/6539398</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32420360">pmid:32420360</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7201505/">pmcid:PMC7201505</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/liqbykocojhxrpsbbycjox7seu">fatcat:liqbykocojhxrpsbbycjox7seu</a> </span>
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Functional Transcription Factor Target Networks Illuminate Control of Epithelial Remodelling

Ian M. Overton, Andrew H. Sims, Jeremy A. Owen, Bret S. E. Heale, Matthew J. Ford, Alexander L. R. Lubbock, Erola Pairo-Castineira, Abdelkader Essafi
<span title="2020-09-30">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2zwku6u6nfdcri773tpisi6ldi" style="color: black;">Cancers</a> </i> &nbsp;
We developed the NetNC software to predict functionally active regulation of TF targets; demonstrated on nine datasets for the TFs Snail, Twist, and modENCODE Highly Occupied Target (HOT) regions.  ...  Expression of orthologous functional TF targets discriminated breast cancer molecular subtypes and predicted novel tumour biology, with implications for precision medicine.  ...  Conflicts of Interest: The authors declare no conflict of interest.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12102823">doi:10.3390/cancers12102823</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33007944">pmid:33007944</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zhi56rxfbjgddojsnn4lpr6tqa">fatcat:zhi56rxfbjgddojsnn4lpr6tqa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201001170512/https://res.mdpi.com/d_attachment/cancers/cancers-12-02823/article_deploy/cancers-12-02823.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/25/c5/25c5cc0a5c787538bfe935ffeea67fdadd61ba24.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/cancers12102823"> <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>
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