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CONAN: copy number variation analysis software for genome-wide association studies

Lukas Forer, Sebastian Schönherr, Hansi Weissensteiner, Florian Haider, Thomas Kluckner, Christian Gieger, Heinz-Erich Wichmann, Günther Specht, Florian Kronenberg, Anita Kloss-Brandstätter
<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;
Genome-wide association studies (GWAS) based on single nucleotide polymorphisms (SNPs) revolutionized our perception of the genetic regulation of complex traits and diseases.  ...  Copy number variations (CNVs) promise to shed additional light on the genetic basis of monogenic as well as complex diseases and phenotypes.  ...  In addition, we are grateful for the advice of Claudia Lamina and Stefan Coassin (Division of Genetic Epidemiology, Innsbruck Medical University).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-318">doi:10.1186/1471-2105-11-318</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20546565">pmid:20546565</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2894823/">pmcid:PMC2894823</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wvx6av2erzh7lmpyrtmq64uzzu">fatcat:wvx6av2erzh7lmpyrtmq64uzzu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814081541/https://www.scienceopen.com/document_file/cc150643-c2c7-469c-b7c5-8735efe67bad/PubMedCentral/cc150643-c2c7-469c-b7c5-8735efe67bad.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/17/d5/17d59062f6ff18cf602783566e5ce753304f77dd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-11-318"> <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/PMC2894823" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Mutation Discovery in Regions of Segmental Cancer Genome Amplifications with CoNAn-SNV: A Mixture Model for Next Generation Sequencing of Tumors

Anamaria Crisan, Rodrigo Goya, Gavin Ha, Jiarui Ding, Leah M. Prentice, Arusha Oloumi, Janine Senz, Thomas Zeng, Kane Tse, Allen Delaney, Marco A. Marra, David G. Huntsman (+4 others)
<span title="2012-08-16">2012</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;
Here we present CoNAn-SNV (Copy Number Annotated SNV): a novel algorithm for the inference of single nucleotide variants (SNVs) that overlap copy number alterations.  ...  This was also supported by analysis of a recently published lymphoma genome with a relatively quiescent karyotype, where CoNAn-SNV showed similar results to other callers except in regions of copy number  ...  Acknowledgments SPS is a Michael Smith Foundation for Health Research Scholar. Author Contributions  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0041551">doi:10.1371/journal.pone.0041551</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22916110">pmid:22916110</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3420914/">pmcid:PMC3420914</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/co6egfr37zcdnaehcbq7suthvy">fatcat:co6egfr37zcdnaehcbq7suthvy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171004094752/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0041551&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/54/ef/54efc0b3d8d75cdb0ff33bd8178506c57f6f9a4a.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.0041551"> <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/PMC3420914" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

CNVRuler: a copy number variation-based case–control association analysis tool

Ji-Hong Kim, Hae-Jin Hu, Seon-Hee Yim, Joon Seol Bae, Seon-Young Kim, Yeun-Jun Chung
<span title="2012-04-25">2012</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;
The method for genome-wide association study (GWAS) based on copy number variation (CNV) is not as well established as that for single nucleotide polymorphism (SNP)-GWAS.  ...  Although there are several tools for CNV association studies, most of them do not provide appropriate definitions of CNV regions (CNVRs), which are essential for CNV-association studies.  ...  For this reason, the following three steps are required to perform a CNV-based genome-wide association study (GWAS): (i) calling CNVs, (ii) merging CNVs into common CNV regions (CNVRs), and (iii) statistical  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts239">doi:10.1093/bioinformatics/bts239</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22539667">pmid:22539667</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d2wiiicc4vfi5mc62iedog4e5q">fatcat:d2wiiicc4vfi5mc62iedog4e5q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729041501/https://watermark.silverchair.com/bts239.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAcAwggG8BgkqhkiG9w0BBwagggGtMIIBqQIBADCCAaIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQM282aK5Mm9VjMlu3sAgEQgIIBczM5fTTAMWl2hDqaaVCZzM4ut1dMIMAmbpZ0qK4VJxJdCh-Pzsg_sN2Qk8zkOqIdHH28seE7o4uKuEvP-RIO5u22aLZkJFp046u_VdB1_85Pux17cfei_LKZNs3E_YGQ4zWcIUt4P9jZ_817C-k9rGVlZ0kV4cDKAqCSwFWCF8AkmmSi_BB1XfiKGyjX2IuCcz0qfJrCzi9ekLVwZ0UCmUnoL7PtFOfUKKt1OEkwlyQjMkM8PQCOc4hcIlB6bb6M1eqv-DIBt01djxItKge0jdk-k3C8W7-w4vURyABfxiU71_YArkOXMwN5t3DnO9KwxOgwfPNTJpZvKkedoOzNRvGxM7juMGMhtlBFaswSFx6ZmFu7zaXMd7HaklcUBqDNT5tmAf5PvYkSXGvdsoeqjFwO5si20MEie4HXR99CzL7vFKMwWAJiHno6Yj98yZ8RrbZ4thD6lBSpQbjA39X2ACWQxcetoBjZ1HQ295q_N9peaoJW" 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/80/19/80191aa12bdc99da32fca162ac664c5ae1691da0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bts239"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Merging structural biology with chemical biology: Structural Chemistry at Eskitis

Andreas Hofmann, Conan K. Wang, Asiah Osman, David Camp
<span title="2010-08-28">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rmzgutp6qvg6xmv5icryswumie" style="color: black;">Structural Chemistry</a> </i> &nbsp;
structural studies.  ...  At protein level, our thematic focus is on cytoskeletal and membrane-associated proteins.  ...  We gratefully acknowledge the Australian Synchrotron for beam time awards.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11224-010-9654-2">doi:10.1007/s11224-010-9654-2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eunc2q5tlngurhuwcl7kxrqhpe">fatcat:eunc2q5tlngurhuwcl7kxrqhpe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20120417033701/http://www98.griffith.edu.au/dspace/bitstream/handle/10072/34922/64407_1.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/57/06/570655ac920314ba249051b88a7081bec6949f4e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11224-010-9654-2"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Recurrent Horizontal Transfers of Chapaev Transposons in Diverse Invertebrate and Vertebrate Animals

Hua-Hao Zhang, Cédric Feschotte, Min-Jin Han, Ze Zhang
<span title="2014-05-27">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/c3tk2qca4vdq5htca2effydqim" style="color: black;">Genome Biology and Evolution</a> </i> &nbsp;
Horizontal transfer (HT) of a transposable element (TE) into a new genome is regarded as an important force to drive genome variation and biological innovation.  ...  Here, we provide the first documented example for the repeated HT of three families of Chapaev transposons in a wide range of animal species, including mammals, reptiles, jawed fishes, lampreys, insects  ...  Next, we used these respective consensus sequences to mask each genome in which Merrow, Garfield, and Conan were identified to estimate copy number.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gbe/evu112">doi:10.1093/gbe/evu112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24868016">pmid:24868016</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4079192/">pmcid:PMC4079192</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/56rbqhcwbjawvfdbpgrpf3or6a">fatcat:56rbqhcwbjawvfdbpgrpf3or6a</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC4079192/PMC4079192-evu112.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] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8a/7c/8a7c0a696632b974dd879c3b14296066b1022824.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/gbe/evu112"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4079192" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Synergic Effects of Temperature and Irradiance on the Physiology of the Marine Synechococcus Strain WH7803

Ulysse Guyet, Ngoc A. Nguyen, Hugo Doré, Julie Haguait, Justine Pittera, Maël Conan, Morgane Ratin, Erwan Corre, Gildas Le Corguillé, Loraine Brillet-Guéguen, Mark Hoebeke, Christophe Six (+5 others)
<span title="2020-07-24">2020</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/67anf6qgandy5adz4rakospiuq" style="color: black;">Frontiers in Microbiology</a> </i> &nbsp;
Previously published membrane lipid composition were also used for correlation analyses.  ...  Understanding how microorganisms adjust their metabolism to maintain their ability to cope with short-term environmental variations constitutes one of the major current challenges in microbial ecology.  ...  Differential expression levels and associated statistics as well as genomic features of the Synechococcus sp.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2020.01707">doi:10.3389/fmicb.2020.01707</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32793165">pmid:32793165</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC7393227/">pmcid:PMC7393227</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/d7rxl2zicrelrdql75asw5koue">fatcat:d7rxl2zicrelrdql75asw5koue</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210427225142/https://hal.sorbonne-universite.fr/hal-02929424/document" 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/74/8d/748d506aeb68e86342b7b558c334aa20960d75d1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fmicb.2020.01707"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> frontiersin.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7393227" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content

Hui Zhang, Zhi-Qiang Du, Jia-Qiang Dong, Hai-Xia Wang, Hong-Yan Shi, Ning Wang, Shou-Zhi Wang, Hui Li
<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;
Copy number variations (CNVs) are a form of genomic structural variation widely distributed in the genome.  ...  Conclusions: Our study provided a genome-wide CNVR map of the chicken genome, thereby contributing to our understanding of genomic structural variations and their potential roles in abdominal fat content  ...  Acknowledgments The authors would like to acknowledge members of the Poultry Breeding Group of the College of Animal Science and Technology in Northeast Agricultural University for managing the birds and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-517">doi:10.1186/1471-2164-15-517</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24962627">pmid:24962627</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4092215/">pmcid:PMC4092215</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hkzfhjszkvdf7kku5ovqqk7nia">fatcat:hkzfhjszkvdf7kku5ovqqk7nia</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830064207/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-15-517?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/8b/aa/8baa72bfcd2217be70cfee962acc091d6f59b7f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-15-517"> <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/PMC4092215" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Role of environmental factors for the vertical distribution (0–1000 m) of marine bacterial communities in the NW Mediterranean Sea

J. F. Ghiglione, C. Palacios, J. C. Marty, G. Mével, C. Labrune, P. Conan, M. Pujo-Pay, N. Garcia, M. Goutx
<span title="2008-12-16">2008</span> <i title="Copernicus GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/sqg6wlenofcqpjpw2z6rnhi7xq" style="color: black;">Biogeosciences</a> </i> &nbsp;
Bacterioplankton plays a central role in energy and matter fluxes in the sea, yet the factors that constrain its variation in marine systems are still poorly understood.  ...  Here we use the explanatory power of direct multivariate gradient analysis to evaluate the driving forces exerted by environmental parameters on bacterial community distribution in the water column.  ...  We are grateful to John Dolan and France Van Wambeke for helpful comments on the manuscript. Edited by: A. Boetius  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5194/bg-5-1751-2008">doi:10.5194/bg-5-1751-2008</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gcisiq5yyrcvxn7zlq6xvwamaq">fatcat:gcisiq5yyrcvxn7zlq6xvwamaq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720022641/https://www.biogeosciences.net/5/1751/2008/bg-5-1751-2008.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/98/96/98969b70eea6a3048aa8b5e46b1f82a22011d877.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5194/bg-5-1751-2008"> <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>

Improved Detection of CXCR4-Using HIV by V3 Genotyping: Application of Population-Based and "Deep" Sequencing to Plasma RNA and Proviral DNA

Luke C Swenson, Andrew Moores, Andrew J Low, Alexander Thielen, Winnie Dong, Conan Woods, Mark A Jensen, Brian Wynhoven, Dennison Chan, Christopher Glascock, P Richard Harrigan
<span title="">2010</span> <i title="Ovid Technologies (Wolters Kluwer Health)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yfx6m62tdbfzzhho6fghvoysfu" style="color: black;">Journal of Acquired Immune Deficiency Syndromes</a> </i> &nbsp;
Sequencing proviral DNA and "deep" V3 sequencing may also be useful tools for assessing tropism.  ...  Currently, the recombinant phenotypic Trofile assay (Monogram) is most widely utilized; however, genotypic tests may represent alternative methods.  ...  Often, there was notable variation among the 3 independent amplifications performed for each sample.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/qai.0b013e3181d0558f">doi:10.1097/qai.0b013e3181d0558f</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20512044">pmid:20512044</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zkeeiylvovhw3e747ioep4syfq">fatcat:zkeeiylvovhw3e747ioep4syfq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180729105840/https://pdfs.journals.lww.com/jaids/2010/08150/Improved_Detection_of_CXCR4_Using_HIV_by_V3.10.pdf?token=method|ExpireAbsolute;source|Journals;ttl|1532862463288;payload|mY8D3u1TCCsNvP5E421JYK6N6XICDamxByyYpaNzk7FKjTaa1Yz22MivkHZqjGP4kdS2v0J76WGAnHACH69s21Csk0OpQi3YbjEMdSoz2UhVybFqQxA7lKwSUlA502zQZr96TQRwhVlocEp/sJ586aVbcBFlltKNKo+tbuMfL73hiPqJliudqs17cHeLcLbV/CqjlP3IO0jGHlHQtJWcICDdAyGJMnpi6RlbEJaRheGeh5z5uvqz3FLHgPKVXJzdl3VU0H6g4R/Rshei0cTvYwRXqsXTPBT+D2pCrsKDoJs=;hash|q9R9AAUxFQYg/67muF2tcA==" 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/86/52/86524e8119383d1f7dae425ba60096906d606ffd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1097/qai.0b013e3181d0558f"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Genome wide analysis reveals single nucleotide polymorphisms associated with fatness and putative novel copy number variants in three pig breeds

Katie E Fowler, Ricardo Pong-Wong, Julien Bauer, Emily J Clemente, Christopher P Reitter, Nabeel A Affara, Stephen Waite, Grant A Walling, Darren K Griffin
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
in terms of single nucleotide polymorphisms (SNPs) and copy number variants (CNVs).  ...  The pig is an excellent model organism for the study of various human disorders, including obesity, as well as being the foremost agricultural species.  ...  That is, post-genomic technologies such as SNP microarrays have permitted genome wide association studies (GWAS) for thousands of traits in humans.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-784">doi:10.1186/1471-2164-14-784</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24225222">pmid:24225222</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3879217/">pmcid:PMC3879217</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r452c2chbvbfvfu4rwiyt7222i">fatcat:r452c2chbvbfvfu4rwiyt7222i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171014013101/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/6b8/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvMTQ3MS0yMTY0LTE0LTc4NC5wZGY%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/ef/69/ef69f0d99f9d72a6ba73fff04518c83e25d835e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-14-784"> <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/PMC3879217" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Testing the Utility of an Integrated Analysis of Copy Number and Transcriptomics Datasets for Inferring Gene Regulatory Relationships

Xin Yi Goh, Richard Newton, Lorenz Wernisch, Rebecca Fitzgerald, Janet Shipley
<span title="2013-05-30">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;
Correlation patterns between matched copy number variation and gene expression data in cancer samples enable the inference of causal gene regulatory relationships by exploiting the natural randomization  ...  The aim of this study was to test and verify experimentally the accuracy of a causal inference approach based on genomic randomization using esophageal cancer samples.  ...  The last step is required since copy number variation not only affects the coding sequence for one gene but possibly many genes in the neighborhood on a genome level.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0063780">doi:10.1371/journal.pone.0063780</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23737949">pmid:23737949</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3667814/">pmcid:PMC3667814</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/76peg276dvfnpiyf4qdsebxsei">fatcat:76peg276dvfnpiyf4qdsebxsei</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007032438/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0063780&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/9a/11/9a11c947a3a51a4f978e3c4a76346080f5a5a2dd.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.0063780"> <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/PMC3667814" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Impact of Clinical, Demographic and Risk Factors on Rates of HIV Transmission: A Population-based Phylogenetic Analysis in British Columbia, Canada

Art F. Y. Poon, Jeffrey B. Joy, Conan K. Woods, Susan Shurgold, Guillaume Colley, Chanson J. Brumme, Robert S. Hogg, Julio S. G. Montaner, P. Richard Harrigan
<span title="2014-10-13">2014</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6eizmyf7jjbndicuzr52yx465q" style="color: black;">Journal of Infectious Diseases</a> </i> &nbsp;
Infections were grouped into clusters based on phylogenetic distances, as a proxy for variation in transmission rates.  ...  Hotspots of ongoing HIV transmission can be characterized in near real time by the secondary analysis of HIV resistance genotypes, providing an important potential resource for targeting public health  ...  All authors have submitted the ICMJE Form for Disclosure of Potential Conflicts of Interest. Conflicts that the editors consider relevant to the content of the manuscript have been disclosed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/infdis/jiu560">doi:10.1093/infdis/jiu560</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25312037">pmid:25312037</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4351365/">pmcid:PMC4351365</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n7psyoa4rnhsnfgy6woxagq2au">fatcat:n7psyoa4rnhsnfgy6woxagq2au</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190307063443/http://pdfs.semanticscholar.org/dc52/c74c1c444d00269b203becd71e1bd916c229.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/dc/52/dc52c74c1c444d00269b203becd71e1bd916c229.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/infdis/jiu560"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4351365" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Pancreatic cancer genomes reveal aberrations in axon guidance pathway genes

Andrew V. Biankin, Nicola Waddell, Karin S. Kassahn, Marie-Claude Gingras, Lakshmi B. Muthuswamy, Amber L. Johns, David K. Miller, Peter J. Wilson, Ann-Marie Patch, Jianmin Wu, David K. Chang, Mark J. Cowley (+114 others)
<span title="2012-10-24">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Detailed analysis of 99 informative tumours identified substantial heterogeneity with 2,016 nonsilent mutations and 1,628 copy-number variations.  ...  We performed exome sequencing and copy number analysis to define genomic aberrations in a prospectively accrued clinical cohort (n = 142) of early (stage I and II) sporadic pancreatic ductal adenocarcinoma  ...  number variation in axon guidance genesAxon guidance pathway genes with recurrent mutations and/or copy-number changes defined by GISTIC2.0 analysis (Q < 0.2), and manually reviewed for focal alterations  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11547">doi:10.1038/nature11547</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23103869">pmid:23103869</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3530898/">pmcid:PMC3530898</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vsr3tr4a65ah5pnhy4iiaeskru">fatcat:vsr3tr4a65ah5pnhy4iiaeskru</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170817150859/https://espace.library.uq.edu.au/data/UQ_284064/UQ284064_OA.pdf?Expires=1503068928&amp;Signature=LE2fP5F~N8JywyhPfHhiUJtmkLYqpSa9SLmbUkvHVHDQW7aZgUM~IxrwWzB~OLAmLXRSkwuGJo0D5PsEw9zZ2o5~koaB-3G~RuqnWWAZvfErzJSISCrwLRNDzhLLrVmB1a1gtvjXmjbTWhsO-nGUV1bBi3N7y6UhkK708mp1zIFenu1fbo6OGdX295uxYrxd-e-kAw67OEoHFrhWjEm1PglxguKU-bJkR5w0DzXvM7b-0KDhHP0YeESsDpBu0c8MwLMbUug~MUKdJjoL-RCMnr6an0lzQcHj-2BkJi-LAhocrzytTlWbrNaPdYdHbKlsA3Ws-w5GqJ7kyEvRnf3vGA__&amp;Key-Pair-Id=APKAJKNBJ4MJBJNC6NLQ" 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/aa/d9/aad93663bd676c2ba28f72ff6830320333bd521f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature11547"> <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/PMC3530898" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of genomic regions associated with tiller number in Iranian bread wheat under different water regimes using genome-wide association study

Sayedeh Saba Bilgrami, Hadi Darzi Ramandi, Vahid Shariati, Khadijeh Razavi, Elahe Tavakol, Barat Ali Fakheri, Nafiseh Mahdi Nezhad, Mostafa Ghaderian
<span title="2020-08-20">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
A total of 6,349 single nucleotide polymorphism (SNP) markers from the 15 K wheat Infinium array were employed for genome-wide association study (GWAS) of tillering number traits, generating a physical  ...  GWAS analysis using Fixed and random model Circulating Probability Unification (FarmCPU) identified a total of 47 significant marker-trait associations (MTAs) for total tiller number (TTN) and fertile  ...  Acknowledgments This study was funded and supported by the National Institute of Genetic Engineering and Biotechnology of Iran (Grant Number 451M).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-69442-9">doi:10.1038/s41598-020-69442-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/32820220">pmid:32820220</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rxxmmomprfc6tenaw4llzvos6u">fatcat:rxxmmomprfc6tenaw4llzvos6u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201107222844/https://www.nature.com/articles/s41598-020-69442-9.pdf?error=cookies_not_supported&amp;code=dc247f93-9b23-4ca4-934a-45c1b4c9ea8a" 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/14/26/14266504f0a85b502d50fe3ed676055053f010bd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-020-69442-9"> <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>

SMYD5 Controls Heterochromatin and Chromosome Integrity during Embryonic Stem Cell Differentiation

Benjamin L. Kidder, Runsheng He, Darawalee Wangsa, Hesed M. Padilla-Nash, M. Margarida Bernardo, Shijie Sheng, Thomas Ried, Keji Zhao
<span title="2017-09-26">2017</span> <i title="American Association for Cancer Research (AACR)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/czhppgb4znaghaxcyto6oc7jhe" style="color: black;">Cancer Research</a> </i> &nbsp;
Here, we show that depletion of SET and MYND domain-containing protein 5 (SMYD5), which mediates H4K20me3, leads to genome-wide decreases in H4K20me3 and H3K9me3 levels and derepression of endogenous LTR-and  ...  Moreover, dysregulated gene expression in SMYD5 cancer cells was associated with LTR and endogenous retrovirus elements and decreased H4K20me3.  ...  Zhiyong Ding, Wenfei Jin, Gangqing Hu, Ana Robles, and Curt Harris for helpful discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/0008-5472.can-17-0828">doi:10.1158/0008-5472.can-17-0828</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28951459">pmid:28951459</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5804482/">pmcid:PMC5804482</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/t3o6oufk3fehfdfippki7m44z4">fatcat:t3o6oufk3fehfdfippki7m44z4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501015638/http://cancerres.aacrjournals.org/content/canres/77/23/6729.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/81/cd/81cdca275261168cb366514037759c9042b70f27.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/0008-5472.can-17-0828"> <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/PMC5804482" 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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