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An extended data mining method for identifying differentially expressed assay-specific signatures in functional genomic studies

Derrick K Rollins, AiLing Teh
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ormhpxv5gvemfj2eljfl5fxnzm" style="color: black;">BioData Mining</a> </i> &nbsp;
Thus, PM can be quite effective in producing accurate signatures from large microarray data sets for differential expression between assays groups identified in a preliminary step of the PCA procedure  ...  Data mining techniques are used to extract specific information of genes as they relate to the assays.  ...  Nettleton for his valuable advice and suggestions in conducting the simulation study. We are also grateful for his assistance in statistical software package used in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0381-3-11">doi:10.1186/1756-0381-3-11</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21162755">pmid:21162755</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3017041/">pmcid:PMC3017041</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/iirprkyca5hkjpl3pna5o4a4ze">fatcat:iirprkyca5hkjpl3pna5o4a4ze</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170920084531/https://link.springer.com/content/pdf/10.1186%2F1756-0381-3-11.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/d0/d7/d0d719d05f3e919fb1a2c1a90e14be12bad43815.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1756-0381-3-11"> <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/PMC3017041" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Toward a systems biology approach to investigate cellular networks in normal and malignant B cells

K Basso
<span title="2009-02-05">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cke3m2f5jnfjpicctij4jmwxai" style="color: black;">Leukemia</a> </i> &nbsp;
Acknowledgements I am grateful to Ulf Klein, Pavel Sumazin and Roy L Maute for critical reading of the manuscript and to Govind Bhagat for providing photographic material used in Figure 2 .  ...  I thank Riccardo Dalla-Favera and Andrea Califano for leading me into an interdisciplinary path where biological and computational sciences walk together.  ...  Studying the genome by high-throughput and high resolution assays The complete genetic information of an organism is stored in its DNA.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/leu.2009.4">doi:10.1038/leu.2009.4</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19194469">pmid:19194469</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/reeppp7cofc6rp74utuhelmeza">fatcat:reeppp7cofc6rp74utuhelmeza</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200315130544/https://www.nature.com/articles/leu20094.pdf?error=cookies_not_supported&amp;code=d4b1f6cf-d763-446f-ae86-cbea1a14a0cd" 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/53/8a/538a6ac6be60dae63387dc630828e9bcb2127214.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/leu.2009.4"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Genomic approaches to small molecule discovery

K Stegmaier
<span title="2009-03-05">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cke3m2f5jnfjpicctij4jmwxai" style="color: black;">Leukemia</a> </i> &nbsp;
This review will focus on the application of genomics to compound discovery, with an emphasis on the hematological malignancies.  ...  It will focus on the use of genomic tools to discover cancer targets and the development and application of both cell-based and in silico gene expressionbased approaches to small molecule discovery.  ...  laboratory is supported by the US National Institutes of Health, the Howard Hughes Medical Institute Physician Scientist Early Career Award, the Leukemia and Lymphoma Society, the Sidney Kimmel Foundation for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/leu.2009.29">doi:10.1038/leu.2009.29</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19262600">pmid:19262600</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5kmdxgazpfhy7huztpucmsy4mu">fatcat:5kmdxgazpfhy7huztpucmsy4mu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200316000219/https://www.nature.com/articles/leu200929.pdf?error=cookies_not_supported&amp;code=8c029215-dae5-4f91-8b5f-628683ae1a9e" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/0a/33/0a33c42f3c6fd9aed5248546c96934dc616db206.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/leu.2009.29"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Strategy for gene expression-based biomarker discovery

Joseph Monforte, Steve McPhail
<span title="">2005</span> <i title="Future Science, LTD"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6t7cfvh76ranblnkx6doquvcyq" style="color: black;">BioTechniques</a> </i> &nbsp;
In the data mining and analysis phase, specific gene expression signatures are revealed.  ...  for data mining.  ...  Steve McPhail is President and CEO of Durham-based Expression Analysis. We discuss in this article a procedure that was developed and deployed by Althea Technologies and Expression Analysis.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/05384su05">doi:10.2144/05384su05</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e75nvuxc4beczajumvim2oa7su">fatcat:e75nvuxc4beczajumvim2oa7su</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809071336/http://www.biotechniques.com/multimedia/archive/00004/BTN_A_05384SU05_O_4237a.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/fb/1ffb84de3fec0b5ec1612fd1252733bb148372c9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2144/05384su05"> <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>

Intelligent Informatics in Translational Medicine 2016

Hao-Teng Chang, Tatsuya Akutsu, Oliver Ray, Sorin Draghici, Tun-Wen Pai
<span title="">2017</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;
Acknowledgments We wish to express our appreciation to all the authors for their excellent contribution. We also want to thank all reviewers and editors for their hard work on this issue.  ...  They constructed phase-specific gene coexpression network using time-series gene expression data and defined the conception of differential coexpression of genes in coexpression network.  ...  Goay et al. in their article entitled "Identification of Five Novel Salmonella Typhi-Specific Genes as Markers for Diagnosis of Typhoid Fever Using Single-Gene Target PCR Assays" identified new markers  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/1572730">doi:10.1155/2017/1572730</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28337442">pmid:28337442</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5350342/">pmcid:PMC5350342</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/yrp3n5wmujbq5ooyoq5f42bxzu">fatcat:yrp3n5wmujbq5ooyoq5f42bxzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190222054915/http://pdfs.semanticscholar.org/3467/37ced7965282a972c2681a550dd50263bce5.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/34/67/346737ced7965282a972c2681a550dd50263bce5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2017/1572730"> <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/PMC5350342" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrating ChIP-seq with other functional genomics data

Shan Jiang, Ali Mortazavi
<span title="2018-03-01">2018</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ybrdrifrfraydlephn44dplrgu" style="color: black;">Briefings in Functional Genomics</a> </i> &nbsp;
Chromatin immunoprecipitation followed by sequencing (ChIP-seq) has become the standard assay for identifying genome-wide protein-DNA interactions in vitro and in vivo.  ...  In this review, we discuss advances and challenges in integrating ChIP-seq data to identify context-specific chromatin states associated with gene activity.  ...  Acknowledgements The authors thank Dr Weihua Zeng, Rabi Murad, Camden Jansen, Dana Wyman, Katherine Williams and Sorena Rahmanian for kind suggestions on revising the manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/ely002">doi:10.1093/bfgp/ely002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29579165">pmid:29579165</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zbfaimtxrvdyvmigeepu5o4cuq">fatcat:zbfaimtxrvdyvmigeepu5o4cuq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308183243/http://pdfs.semanticscholar.org/f776/a3632479fb7f2b10539cf7f7337f41f6a3d8.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/f7/76/f776a3632479fb7f2b10539cf7f7337f41f6a3d8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/ely002"> <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>

Integrative approaches for mining transcriptional regulatory programs in Arabidopsis

A. Krishnan, A. Pereira
<span title="2008-06-25">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/db7gv4nqurbrhk7jywtr3wbcme" style="color: black;">Briefings in Functional Genomics &amp; Proteomics</a> </i> &nbsp;
Exciting inroads are being made in mining and interpretation of developmental, physiological and environmental-response 'programs' using sequence and functional information.  ...  Integrative strategies, both novel and adapted from other well-studied organisms, are being employed in the model plant Arabidopsis thaliana to interpret genomewide expression, metabolic profiling and  ...  The use of biclustering methods, which perform clustering in the two gene-condition dimensions simultaneously, has also been initiated in Arabidopsis to mine local expression signatures [39, 40] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/eln035">doi:10.1093/bfgp/eln035</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18632743">pmid:18632743</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/w4zbyxr2y5hzzl62sr4s2cptoy">fatcat:w4zbyxr2y5hzzl62sr4s2cptoy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220211851/http://pdfs.semanticscholar.org/29bf/884a0d26dbab9f63fb86de7fa4a69c7f4d6c.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/29/bf/29bf884a0d26dbab9f63fb86de7fa4a69c7f4d6c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/eln035"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Computational prognostic indicators for breast cancer

Xinan (Holly) Yang, Xindi Ai, John Cunningham
<span title="">2014</span> <i title="Dove Medical Press Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6t76u6ys3nartbykmz3tjwjufy" style="color: black;">Cancer Management and Research</a> </i> &nbsp;
Although many biomarkers have been identified through advances in data mining techniques, few have been applied broadly to make patient-specific decisions.  ...  Comprehensive genomics, proteomics, and metabolomics studies are emerging that offer an opportunity to model disease biology, prognosis, and response to specific therapies.  ...  We appreciate Zakir Gowani for his careful proofreading. Disclosure The authors report no conflicts of interest in this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2147/cmar.s46483">doi:10.2147/cmar.s46483</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25050076">pmid:25050076</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4103923/">pmcid:PMC4103923</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/suwl4fpfgza2dhxbot7gqrtnha">fatcat:suwl4fpfgza2dhxbot7gqrtnha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218123803/http://pdfs.semanticscholar.org/0bb2/c9b53da57913e43b74ca58b24260b3d3f741.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/0b/b2/0bb2c9b53da57913e43b74ca58b24260b3d3f741.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2147/cmar.s46483"> <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/PMC4103923" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrating phenotypic small-molecule profiling and human genetics: the next phase in drug discovery

Cory M. Johannessen, Paul A. Clemons, Bridget K. Wagner
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/alw4ab5u3vdqlgfh3smvbfnjqu" style="color: black;">Trends in Genetics</a> </i> &nbsp;
Over the past decade, tremendous progress in high-throughput small-molecule screening methods has facilitated the rapid expansion of phenotype-based data.  ...  We additionally provide a perspective for future developments in phenotypic profiling efforts guided by genomic science.  ...  such as gene-expression in response to compound treatmentQuantitative trait locus a genetic determinant of a quantitative trait of an organism, such as size Signature specific set of multiple features  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2014.11.002">doi:10.1016/j.tig.2014.11.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25498789">pmid:25498789</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4281276/">pmcid:PMC4281276</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6j4mfhnhuvel3aukob6oz4wxii">fatcat:6j4mfhnhuvel3aukob6oz4wxii</a> </span>
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Defining new criteria for selection of cell-based intestinal models using publicly available databases

Jon Christensen, Sara El-Gebali, Manuela Natoli, Thierry Sengstag, Mauro Delorenzi, Susanne Bentz, Hanifa Bouzourene, Martin Rumbo, Armando Felsani, Sanna Siissalo, Jouni Hirvonen, Maya R Vila (+3 others)
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Regarding drug absorption, we confirmed that differentiated Caco-2 cells are the model of choice for active uptake studies in the small intestine.  ...  Results: We made use of publicly available expression signatures and cell based functional assays to delineate differences between various intestinal colon carcinoma cell lines and normal intestinal epithelium  ...  Acknowledgments The ileum samples used for LDM were kindly provided by Jose Castell (University Hospital 'La Fe', Valencia, Spain) and Biopredic International (Rennes, France).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-274">doi:10.1186/1471-2164-13-274</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22726358">pmid:22726358</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3412164/">pmcid:PMC3412164</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wyvooz2n6zh55jl2r67qjh4eja">fatcat:wyvooz2n6zh55jl2r67qjh4eja</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171120074816/https://core.ac.uk/download/pdf/33043479.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/b0/10/b0109fce255e7541c471607b5760adec77f5c9ee.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-274"> <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/PMC3412164" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

From Single Level Analysis to Multi-Omics Integrative Approaches: A Powerful Strategy towards the Precision Oncology

Maria Gallo Cantafio, Katia Grillone, Daniele Caracciolo, Francesca Scionti, Mariamena Arbitrio, Vito Barbieri, Licia Pensabene, Pietro Guzzi, Maria Di Martino
<span title="2018-10-26">2018</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lqiqj4bisndfnkjl2sk5l3qqie" style="color: black;">High-Throughput</a> </i> &nbsp;
Comprehensive analysis of multi-omics data in an integrated framework, which includes cumulative effects in the context of biological pathways, is therefore eagerly awaited.  ...  We will discuss the available technical approach and more recent developments in the specific field.  ...  A nine-microRNA signature was identified and specifically, let-7d, miR-210, and miR-221 were downregulated in the in situ and upregulated in the invasive transition, thus featuring an expression reversal  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ht7040033">doi:10.3390/ht7040033</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30373182">pmid:30373182</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6306876/">pmcid:PMC6306876</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/usqtuskklng55fptttdvntwfcm">fatcat:usqtuskklng55fptttdvntwfcm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302030530/http://pdfs.semanticscholar.org/9cd1/a1fb4c324e4649ed96bf6044039725daaadf.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/9c/d1/9cd1a1fb4c324e4649ed96bf6044039725daaadf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ht7040033"> <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/PMC6306876" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Interpreting noncoding genetic variation in complex traits and human disease

Lucas D Ward, Manolis Kellis
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/t2bqrmk7orfmxpqzqwiiyjwide" style="color: black;">Nature Biotechnology</a> </i> &nbsp;
Ultimately, advances in regulatory and systems genomics can help unleash the value of whole-genome sequencing for personalized genomic risk assessment, diagnosis, and treatment.  ...  This picture has changed with advances in the systematic annotation of functional non-coding elements.  ...  Epigenome-phenotype association Microarray-based assays for methylation are now allowing for the first time "epigenomewide association studies" (EWAS) 118 , which identify differentially-methylated sites  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.2422">doi:10.1038/nbt.2422</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23138309">pmid:23138309</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3703467/">pmcid:PMC3703467</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aieipb57pjbe5cm3nvsc4smivy">fatcat:aieipb57pjbe5cm3nvsc4smivy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817045925/http://dspace.mit.edu/bitstream/handle/1721.1/87003/Kellis_Interpreting%20noncoding.pdf?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/23/44/23446a6bed460fdf4edc588c3ee61f65c32aaac3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nbt.2422"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3703467" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Strategies to discover regulatory circuits of the mammalian immune system

Ido Amit, Aviv Regev, Nir Hacohen
<span title="2011-11-18">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/eelfs4w3x5gbrp2exm7msxfbhe" style="color: black;">Nature reviews. Immunology</a> </i> &nbsp;
Although these datasets have provided important starting points for specific studies of the individual components in these processes, there have been few, if any, attempts to both generate and functionally  ...  This approach has been used to study T-cell activation signatures 1 , blood cell states in patients with autoimmunity 2 , the responses of host cells to infection 3, 4 and expression patterns that predict  ...  Acknowledgments The authors would like to thank the NIH, HHMI, HFSP and the Broad Institute for funding the work presented here.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nri3109">doi:10.1038/nri3109</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22094988">pmid:22094988</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3747038/">pmcid:PMC3747038</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ye7fokg7l5bo3e4xyxdlqdgazq">fatcat:ye7fokg7l5bo3e4xyxdlqdgazq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170819234043/http://dspace.mit.edu/bitstream/handle/1721.1/84993/Regev_Strategies%20to%20discover.pdf?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/dd/79/dd7902beba968eaa45ef63df4953ddd2dc7b06c2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nri3109"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3747038" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Chronic cocaine-regulated epigenomic changes in mouse nucleus accumbens

Jian Feng, Matthew Wilkinson, Xiaochuan Liu, Immanuel Purushothaman, Deveroux Ferguson, Vincent Vialou, Ian Maze, Ningyi Shao, Pamela Kennedy, JaWook Koo, Caroline Dias, Benjamin Laitman (+5 others)
<span title="">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rnpxl3dy6jexfas5kegb73tnbi" style="color: black;">Genome Biology</a> </i> &nbsp;
In addition, we identify combinations of chromatin changes, or signatures, that correlate with cocaine-dependent regulation of gene expression, including those involving pre-mRNA alternative splicing.  ...  Results: We use next generation sequencing methods, RNA-seq and ChIP-seq for RNA polymerase II and several histone methylation marks, to obtain a more complete view of cocaine-induced changes in gene expression  ...  identified 29 chromatin signatures that differentially predict alterations in gene expression and, more specifically, regulation of alternative splicing.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2014-15-4-r65">doi:10.1186/gb-2014-15-4-r65</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24758366">pmid:24758366</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4073058/">pmcid:PMC4073058</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gpoy42wv4zd5jgwuo7zw2x7irm">fatcat:gpoy42wv4zd5jgwuo7zw2x7irm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719142758/https://genomebiology.biomedcentral.com/track/pdf/10.1186/gb-2014-15-4-r65?site=genomebiology.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/a3/c0/a3c0adc638e832200e3927f11575e844a73a45c1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2014-15-4-r65"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4073058" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Interactive Big Data Resource to Elucidate Human Immune Pathways and Diseases

Dmitriy Gorenshteyn, Elena Zaslavsky, Miguel Fribourg, Christopher Y. Park, Aaron K. Wong, Alicja Tadych, Boris M. Hartmann, Randy A. Albrecht, Adolfo García-Sastre, Steven H. Kleinstein, Olga G. Troyanskaya, Stuart C. Sealfon
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tvhuecy4ejhg3bjanzbp6hjbmm" style="color: black;">Immunity</a> </i> &nbsp;
The exponential growth in public high-throughput data offers an opportunity to expand this knowledge.  ...  Graphical Abstract Highlights d Interactive web-accessible immunology resource leverages 38,088 experiments d Powerful computational methods generate big-data-driven hypotheses for immunology d Predicts  ...  Judy Cho and Gareth John for helpful discussions or manuscript comments, Nada Marjanovic for technical support, and the Icahn School of Medicine qPCR Core Facility.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.immuni.2015.08.014">doi:10.1016/j.immuni.2015.08.014</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26362267">pmid:26362267</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4753773/">pmcid:PMC4753773</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/adwa3kb5pnbw3mw65gppschhly">fatcat:adwa3kb5pnbw3mw65gppschhly</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170926225145/http://publisher-connector.core.ac.uk/resourcesync/data/elsevier/pdf/46b/aHR0cDovL2FwaS5lbHNldmllci5jb20vY29udGVudC9hcnRpY2xlL3BpaS9zMTA3NDc2MTMxNTAwMzQ2NQ%3D%3D.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/4a/06/4a060337a44e93d4ef3eee61a6ef13e5df091fcf.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.immuni.2015.08.014"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4753773" 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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