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Network biomarkers, interaction networks and dynamical network biomarkers in respiratory diseases

Xiaodan Wu, Luonan Chen, Xiangdong Wang
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5hmmvsw6d5aqhcgwamg652hgnu" style="color: black;">Clinical and Translational Medicine</a> </i> &nbsp;
Identification and validation of interaction networks and network biomarkers have become more critical and important in the development of disease-specific biomarkers, which are functionally changed during  ...  Clinical bioinformatics should be a key approach to the identification and validation of disease-specific biomarkers.  ...  Acknowledgements The work was supported by Shanghai Leading Academic Discipline Project  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2001-1326-3-16">doi:10.1186/2001-1326-3-16</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24995123">pmid:24995123</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4072888/">pmcid:PMC4072888</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qxjchyqltndxhdsyf3rihr5ce4">fatcat:qxjchyqltndxhdsyf3rihr5ce4</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4072888/PMC4072888-2001-1326-3-16.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> File Archive [PDF] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2001-1326-3-16"> <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/PMC4072888" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Computational Identification of Biomarkers

<span title="2020-05-22">2020</span> <i title="Blue Eyes Intelligence Engineering and Sciences Engineering and Sciences Publication - BEIESP"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cj3bm7tgcffurfop7xzswxuks4" style="color: black;">VOLUME-8 ISSUE-10, AUGUST 2019, REGULAR ISSUE</a> </i> &nbsp;
Disease detection and prediction is mostly carried out through the symptoms reported by patient and clinical test performed on the basis of it.  ...  The biomolecular data exploration is the key to identify various biomarkers. This paper presents a summary of types of biomarkers and biomarker identification techniques.  ...  Random forest classifier [8] is used to increase the classification accuracy through votes of all base classifiers. It is used to classify high dimensional data by constructing many decision trees.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35940/ijitee.g1001.0597s20">doi:10.35940/ijitee.g1001.0597s20</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6eihvip6mnb5lhyrdolkgmetsy">fatcat:6eihvip6mnb5lhyrdolkgmetsy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220228230021/https://www.ijitee.org/wp-content/uploads/papers/v9i7s/G10010597S20.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/e1/ac/e1ac3643b3a833a6d6f09f79cb1e3d8eb234aed1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.35940/ijitee.g1001.0597s20"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Pathway mapping and development of disease-specific biomarkers: protein-based network biomarkers

Hao Chen, Zhitu Zhu, Yichun Zhu, Jian Wang, Yunqing Mei, Yunfeng Cheng
<span title="2015-01-05">2015</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/o6okgawz35b2tfswpfwce3dreq" style="color: black;">Journal of Cellular and Molecular Medicine</a> </i> &nbsp;
It is known that a disease is rarely a consequence of an abnormality of a single gene, but reflects the interactions of various processes in a complex network.  ...  The network biomarkers and dynamic network biomarkers (DNBs) represent new types of biomarkers with protein-protein or gene-gene interactions that can be monitored and evaluated at different stages and  ...  Acknowledgements This work was supported by Pujiang talent research grant from the Shanghai Committee of Science and Technology (10PJ1403600), National Natural Science Foundation of China (30972737, 81170473  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/jcmm.12447">doi:10.1111/jcmm.12447</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25560835">pmid:25560835</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4407592/">pmcid:PMC4407592</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bm6le6xdffggdcbcdbxg5b4ide">fatcat:bm6le6xdffggdcbcdbxg5b4ide</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209152136/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4407592&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/75/01/750131df5291670617d8fd641170e0ad2da7312a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/jcmm.12447"> <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/PMC4407592" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biomarkers for therapeutic efficacy

Nils Brünner, Kirsten Vang Nielsen, Hanne Offenberg, Fred C.G.J. Sweep, John Martens, John Foekens, Gunnar Folprecht, Manfred P. Lutz, Eugene Mechetner
<span title="">2007</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bb52xarlwbgqtmxueq5inn5lmq" style="color: black;">EJC Supplements</a> </i> &nbsp;
As of today there is no method in routine clinical use to predict the sensitivity/resistance to chemotherapy in its broad sense in the individual patient.  ...  In that situation, an alternative, not necessarily medical, treatment would have been a better choice -and toxicity (and financial resources) could have been spared by withholding ineffective drugs.  ...  However, due to the high dimensionality of gene expression data a correction to limit false discoveries is advised [16, 17] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-6349(07)70033-2">doi:10.1016/s1359-6349(07)70033-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r3qolglpfvbwlomlvuvphnsiqy">fatcat:r3qolglpfvbwlomlvuvphnsiqy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200311103953/https://repository.ubn.ru.nl/bitstream/handle/2066/187132/187132.pdf;jsessionid=747BEA0B24F225C50A5498C918A5386F?sequence=1" 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/3e/bd/3ebdabb1fffc90aa346ddb0976108769202f7222.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s1359-6349(07)70033-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a>

Ten-gene biomarker panel: a new hope for ovarian cancer?

Dong-Joo Cheon, Sandra Orsulic
<span title="">2014</span> <i title="Future Medicine Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4qnglatiwfdvznlhdbzx52atda" style="color: black;">Biomarkers in Medicine</a> </i> &nbsp;
The recent publication of a 10-gene biomarker panel generates new hope for the prognostication and personalization of therapy in ovarian cancer.  ...  Importantly, the utility of the 10-gene panel extends beyond biomarkers since most of these genes play key roles in tumor progression and some have already been shown to be effective therapeutic targets  ...  data to develop biomarker panels that predict clinical outcomes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2217/bmm.14.16">doi:10.2217/bmm.14.16</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24796616">pmid:24796616</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4330556/">pmcid:PMC4330556</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h5dw6phhgrhs7jjcpdoauqqsh4">fatcat:h5dw6phhgrhs7jjcpdoauqqsh4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208024931/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4330556&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/3d/bd/3dbd94d0d793d190731a0859e4f396ed412b6367.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2217/bmm.14.16"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4330556" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Prognostic Genomic Predictive Biomarkers for Early-Stage Lung Cancer Patients

Hojin Moon, Alex Nguyen, Evan Lee
<span title="2021-09-17">2021</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/dc5r5bkgonbsfj4kcexh6hzjgm" style="color: black;">The Open Biomarkers Journal</a> </i> &nbsp;
Conclusion: Based on validation data, patients who follow our predicted recommendation by genomic biomarkers selected from the proposed model will likely benefit from ACT.  ...  Thus, the purpose of this research is to utilize gene expression and clinical data from lung cancer patients to find treatment-associated genomic biomarkers.  ...  ACKNOWLEDGEMENTS We thank CSULB for their help in the research.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1875318302111010069">doi:10.2174/1875318302111010069</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d5zvxeduivfnjmmhm2pjufqjiq">fatcat:d5zvxeduivfnjmmhm2pjufqjiq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220119110435/https://openbiomarkerjournal.com/contents/volumes/V11/TOBIOMJ-11-69/TOBIOMJ-11-69.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/f4/2f/f42ff45dc16842a8cc7e6b8ddb6aab1bcecfcc9b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/1875318302111010069"> <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>

Network-Guided Biomarker Discovery [chapter]

Chloé-Agathe Azencott
<span title="">2016</span> <i title="Springer International Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
In machine learning terms, biomarker discovery can be framed as a feature selection problem on whole-genome data sets.  ...  This can be addressed by making the assumption that genetic features that are linked on a biological network are more likely to work jointly towards explaining the phenotype of interest.  ...  Most of the work in that domain has tried to yield lower-dimensional representations by grouping features together in meta-features, based either on the data or on prior knowledge [82, 83] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-50478-0_16">doi:10.1007/978-3-319-50478-0_16</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/na4p4yse4bfi7abmpbcifijf2y">fatcat:na4p4yse4bfi7abmpbcifijf2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226100354/http://pdfs.semanticscholar.org/6fe2/c91922f34e48ad13f102f533fe3d50787498.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/e2/6fe2c91922f34e48ad13f102f533fe3d50787498.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-319-50478-0_16"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Biomarkers

<span title="2010-10-01">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/e5h4j5uhcja4bkjtqzyebndxcq" style="color: black;">Annals of Oncology</a> </i> &nbsp;
PIK3CA mutation in 7 of 144 (4.8 %), EGFR mutation was detected in 42 of 166 patients (25.3%), and KRAS mutation in 11 of 160 (6.8%).  ...  Because the prognostic and predictive roles of this mutation remain unclear due to the small sample size of most studies, we undertook this pooled analysis of KRAS mutation status in 1751 patients who  ...  After combining the data from the 13 studies, it was found that mutations in KRAS consist a negative predictive biomarker for the response to cetuximab with very high specificity 0,96 (0,84-0,99) and low  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/annonc/mdq514">doi:10.1093/annonc/mdq514</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5gh53zgs4ba4tkpxar2w7ngw2y">fatcat:5gh53zgs4ba4tkpxar2w7ngw2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180727162612/https://watermark.silverchair.com/mdq514.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAbMwggGvBgkqhkiG9w0BBwagggGgMIIBnAIBADCCAZUGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMsYKfZ_lyTimeXGRtAgEQgIIBZjCCYAm5APmNPcJvmRbGJGOIAYn2eLp7VAGAR23U8JFBBhjOVtK11Q7B23xF7cK93DzJamOQkTewR6vIBFdlQIy55tgNkqD2MyziCaP4g-WznSpUF35EqFLcCDABlVcu98zYTnU5tvvPtg722Dbp1bi_do2-wCr0ot6lilaTXJa20br22TUX13NoIjUgK4Lg0aB56JBosokhzVEdBsnuJ8dNyOAnp3QtIOFRsNPzEfQtiLoVleBqCp3o5c5d6tIwc3Ulht0VuH-eyZAA2ANm3Oz84EsJyWoRQ_mDJnlUA5lvFXwuAqVo_3Ia_rMLY74ogM4wwXvioi_KIeY3GCzVMbY2QL0c4ltHX8gYcMKMfPNzfMZO0dKWWbLhdbhiA0EKRVRUzRo8w3Uv60PNodsqfMdAoGKoqsS_XNN0wslnHoHtM6gVGVdMq2KebyX9lofZ_RkZF42ce6wyhRo1X5Q0sO-Mg6moN6A" 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/72/6e/726ea071453ab7c8d87f9a69b203d6335f452a53.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/annonc/mdq514"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

From biomarker development towards implementation of multidimensional biomarker panels in a clinical setting

Léon C. van Kempen, Alan Spatz
<span title="2014-05-14">2014</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wilcjb4re5hs5egpxpnhcm4lj4" style="color: black;">Molecular Oncology</a> </i> &nbsp;
However, these analyses depend on the quality of the starting material, the quality of the molecular profiling data, and correct clinical annotation of the samples in the study: Garbage in, garbage out  ...  This is now standard of care for all tumors, however not yet for prediction of treatment response where, with some notable exceptions like in gliomas (Erdem-Eraslan et al., 2013) , predictive variables  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molonc.2014.05.002">doi:10.1016/j.molonc.2014.05.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24863246">pmid:24863246</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5528538/">pmcid:PMC5528538</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d5fms2ripfb4jegls74kdnypjq">fatcat:d5fms2ripfb4jegls74kdnypjq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201104105346/https://www.rug.nl/research/portal/files/122707330/From_biomarker_development_towards_implementation_of_multidimensional_biomarker_panels_in_a_clinical_setting.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/f4/9e/f49ec122e1da0841c3b9de474ca75870e8c383cd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.molonc.2014.05.002"> <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/PMC5528538" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Cardiovascular Genomics: A Biomarker Identification Pipeline

J. H. Phan, C. F. Quo, M. D. Wang
<span title="">2012</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/opxxmwcvy5fnnhqoc4wtvb4etm" style="color: black;">IEEE Transactions on Information Technology in Biomedicine</a> </i> &nbsp;
Alternative approaches to biomarker identification use knowledge in the form of protein or gene interaction networks.  ...  Generally, they are able to represent high-dimensional data in a low-dimensional space, while spatially preserving the similarity of data points [68] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2012.2199570">doi:10.1109/titb.2012.2199570</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22614726">pmid:22614726</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5003026/">pmcid:PMC5003026</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zkre2bctmjhj5mxecz2l4i7azm">fatcat:zkre2bctmjhj5mxecz2l4i7azm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210125352/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5003026&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/6e/40/6e4029d90a6f25c983dcb0e35c6654bb659661e2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/titb.2012.2199570"> <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/PMC5003026" 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 Flexible Approach for Predictive Biomarker Discovery [article]

Philippe Boileau, Nina Ting Qi, Mark J. van der Laan, Sandrine Dudoit, Ning Leng
<span title="2022-06-01">2022</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Using treatment rule estimation methods to identify predictive biomarkers in clinical trials where the number of covariates exceeds the number of participants often results in high false discovery rates  ...  Our procedure is then used to discover predictive biomarkers from among the tumor gene expression data of metastatic renal cell carcinoma patients enrolled in recently completed clinical trials.  ...  Acknowledgement PB gratefully acknowledges the support of the Fonds de recherche du Québec -Nature et technologies and the Natural Sciences and Engineering Research Council of Canada.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2205.01285v2">arXiv:2205.01285v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tfwgk4c6t5e6bks7nnqljanxyy">fatcat:tfwgk4c6t5e6bks7nnqljanxyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220618062825/https://arxiv.org/pdf/2205.01285v2.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/ca/ab/caabc63be534392ab8153334f1137da65b3f5a7b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/2205.01285v2" 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>

Validation of pharmacogenomic biomarker classifiers for treatment selection

Richard Simon, Ziding Feng
<span title="2006-09-14">2006</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/kms4diiogbahlokdlkdjaplhym" style="color: black;">Cancer Biomarkers</a> </i> &nbsp;
In spite of the large literature on developing predictive biomarkers and on statistical methodology for analysis of high dimensional data, there is considerable uncertainty about the validation of biomarker  ...  In this paper we attempt to clarify these issues and to provide guidance on the design of clinical trials for evaluating the clinical utility and robustness of pharmacogenomic classifiers.  ...  Wenu Jiang for the computing of Tables 1 and 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/cbm-2006-23-402">doi:10.3233/cbm-2006-23-402</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/avszc674ljaupelatdbq5ndg2i">fatcat:avszc674ljaupelatdbq5ndg2i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811084409/https://linus.nci.nih.gov/techreport/DiseaseMarkers.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/09/6b/096b2f7fc787edb8d178231893d9e3c754618ed2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3233/cbm-2006-23-402"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Biological Networks for Cancer Candidate Biomarkers Discovery

Wenying Yan, Wenjin Xue, Jiajia Chen, Guang Hu
<span title="">2016</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
A variety of genomic alterations, such as point mutations, copy number variations, and gene rearrangements, contribute  ...  prognostic biomarkers of cancers based on expression data of microR-NAs and their predicted target genes by regression models.  ...  A series of GCNs were constructed for genes identified by a guilt-by-association algorithm, and the conserved gene interactions that impact cancer outcomes were detected. 17 Malusa et al. 18 built coexpression  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s39458">doi:10.4137/cin.s39458</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27625573">pmid:27625573</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5012434/">pmcid:PMC5012434</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zuqt2qdd7bejvfsex5dipfmbgy">fatcat:zuqt2qdd7bejvfsex5dipfmbgy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720061625/http://insights.sagepub.com/redirect_file.php?fileId=7815&amp;filename=5879-CIN-Biological-Networks-for-Cancer-Candidate-Biomarkers-Discovery.pdf&amp;fileType=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/03/d2/03d2907bb578784c7035c0e0ab38aa1f72558440.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s39458"> <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/PMC5012434" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Biomarker Gene Signature Discovery Integrating Network Knowledge

Yupeng Cun, Holger Fröhlich
<span title="2012-02-27">2012</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j5h4zct24vcofi5scx6ttoapnq" style="color: black;">Biology</a> </i> &nbsp;
However, one important obstacle for making gene signatures a standard tool in clinical diagnosis is the typical low reproducibility of these signatures combined with the difficulty to achieve a clear biological  ...  Here we review the current state of research in this field by giving an overview about so-far proposed approaches.  ...  Acknowledgements This work was partially supported by the state of NRW via the B-IT research school.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology1010005">doi:10.3390/biology1010005</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24832044">pmid:24832044</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4011032/">pmcid:PMC4011032</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/uxm4rhr5nze3nkf76yszg7tnai">fatcat:uxm4rhr5nze3nkf76yszg7tnai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150926041234/http://www.mdpi.com/2079-7737/1/1/5/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/8e/72/8e7222e163be85aaa025d35f0ad1b0c9cefdc7d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/biology1010005"> <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/PMC4011032" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Transcriptional biomarkers – High throughput screening, quantitative verification, and bioinformatical validation methods

Irmgard Riedmaier, Michael W. Pfaffl
<span title="">2013</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3jmevtg2ajcdnpgyntimblv7iu" style="color: black;">Methods</a> </i> &nbsp;
Hereby physiological changes, caused by treatment with anabolic agents are detected on the level of the transcriptome and those differentially expressed genes should act as first biomarker candidates  ...  The technological progress in all those ''omic'' fields allows the identification of molecular biomarkers in a high number of research areas.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymeth.2012.08.012">doi:10.1016/j.ymeth.2012.08.012</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22967906">pmid:22967906</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eo7y4aujdrf4dinsspwv6bp4r4">fatcat:eo7y4aujdrf4dinsspwv6bp4r4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809135532/http://gene-quantification.de/riedmaier-methods-59-transcriptional-biomarkers-2013.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/4b/5c/4b5cd12db6a255ce12cb92581776008394663386.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.ymeth.2012.08.012"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>
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