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Systematic Inference of Copy-Number Genotypes from Personal Genome Sequencing Data Reveals Extensive Olfactory Receptor Gene Content Diversity

Sebastian M. Waszak, Yehudit Hasin, Thomas Zichner, Tsviya Olender, Ifat Keydar, Miriam Khen, Adrian M. Stütz, Andreas Schlattl, Doron Lancet, Jan O. Korbel, Wyeth W. Wasserman
<span title="2010-11-11">2010</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ch57atmlprauhhbqdf7x4ytejm" style="color: black;">PLoS Computational Biology</a> </i> &nbsp;
We further demonstrated the utility of CopySeq for analyzing gene regions enriched for segmental duplications by comprehensively inferring copy-number genotypes in the CNV-enriched .800 olfactory receptor  ...  CopySeq revealed that OR loci display an extensive range of locus copy-numbers across individuals, with zero to two copies in some OR loci, and two to nine copies in others.  ...  Acknowledgments We thank the 1000 Genomes Project for data access, and Tobias Rausch, Laura Clarke, and Paul Flicek for facilitating large-scale computes with the 1000 Genomes Project data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000988">doi:10.1371/journal.pcbi.1000988</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21085617">pmid:21085617</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2978733/">pmcid:PMC2978733</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/htt2jnap2bcafbgrnrfkz4rlny">fatcat:htt2jnap2bcafbgrnrfkz4rlny</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171015132330/http://journals.plos.org/ploscompbiol/article/file?id=10.1371/journal.pcbi.1000988&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/bf/0b/bf0b6138fa5769f41b1bba38e6c42fa74844104f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pcbi.1000988"> <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/PMC2978733" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Exploring the role of copy number variants in human adaptation

Rebecca C. Iskow, Omer Gokcumen, Charles Lee
<span title="">2012</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, the ubiquity of copy number variants (CNVs, the gain or loss of genomic material) in the genomes of healthy humans has become apparent.  ...  for the creation of novel genes that may diversify the repertoire of such genes in response to rapidly changing environments.  ...  Mills for helpful discussions and comments on a previous version of this manuscript. This work was funded by R01 GM0851533-04 and F32 AG 039979.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2012.03.002">doi:10.1016/j.tig.2012.03.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22483647">pmid:22483647</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3533238/">pmcid:PMC3533238</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mz2thiojbffexlwqxspgkxnmam">fatcat:mz2thiojbffexlwqxspgkxnmam</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200210012735/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3533238&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/56/d0/56d0397dd71d5bc99dd5b3cff00367ddcde44e55.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.tig.2012.03.002"> <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/PMC3533238" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Improved Detection and Characterization of Copy Number Variations Among Diverse Pig Breeds by Array CGH

J. Wang, J. Jiang, H. Wang, H. Kang, Q. Zhang, J.-F. Liu
<span title="2015-04-22">2015</span> <i title="Genetics Society of America"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lmrbfynd2rbtzo6uhqthfvnwci" style="color: black;">G3: Genes, Genomes, Genetics</a> </i> &nbsp;
As a major component of genomic variation, copy number variations (CNVs) are considered as promising markers for some phenotypic and economically important traits in domestic animals.  ...  In total, we identified 758 CNV regions (CNVRs), covering 47.43 Mb of the pig genome sequence.  ...  expected from the variable number of gene copies.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/g3.115.018473">doi:10.1534/g3.115.018473</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25908567">pmid:25908567</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4478553/">pmcid:PMC4478553</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4wdebmfg5vhkjnkdvjjny225qq">fatcat:4wdebmfg5vhkjnkdvjjny225qq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190308073238/http://pdfs.semanticscholar.org/ef17/03ebb995ca66a91b325c7adafbe2d3d3e2ac.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/17/ef1703ebb995ca66a91b325c7adafbe2d3d3e2ac.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1534/g3.115.018473"> <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/PMC4478553" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Human genetics and genomics a decade after the release of the draft sequence of the human genome

Nasheen Naidoo, Yudi Pawitan, Richie Soong, David N Cooper, Chee-Seng Ku
<span title="">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/oqcgtjrrffbixmejmuqswbwhd4" style="color: black;">Human Genomics</a> </i> &nbsp;
In parallel, the advent of high-throughput sequencing technologies has ushered in the 'personal genome sequencing' era for both normal and cancer genomes, and made possible large-scale genome sequencing  ...  Findings emanating directly from the Human Genome Project, together with those from follow-on studies, have had an enormous impact on our understanding of the architecture and function of the human genome  ...  High copy number repeat sequences The HGP revealed that repeat sequences account for at least 50 per cent of the human genome sequence.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-7364-5-6-577">doi:10.1186/1479-7364-5-6-577</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22155605">pmid:22155605</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3525251/">pmcid:PMC3525251</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/h5dzbsxxuzgpfn7egl25fez3oi">fatcat:h5dzbsxxuzgpfn7egl25fez3oi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810172737/https://humgenomics.biomedcentral.com/track/pdf/10.1186/1479-7364-5-6-577?site=humgenomics.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/fe/15/fe15bfc6c6f9fdd6cf047dca7c4a958471d9dec7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1479-7364-5-6-577"> <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/PMC3525251" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Advancing avian behavioral neuroendocrinology through genomics

David F. Clayton, Sarah E. London
<span title="">2014</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/opsuuchttfa23b4w6ft7yb2sey" style="color: black;">Frontiers in neuroendocrinology (Print)</a> </i> &nbsp;
We then consider how these are informing the study of avian behavioral neuroendocrinology, focusing in particular on lessons from the study of songbirds.  ...  We discuss the impact of having a complete "parts list" for an organism; the transformational potential of studying large sets of genes at once instead one gene at a time; the growing recognition that  ...  Examination of the chicken and zebra finch genomes, however, revealed hundreds of genes with the canonical structure of olfactory receptors (OR) Steiger et al., 2009 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.yfrne.2013.09.004">doi:10.1016/j.yfrne.2013.09.004</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24113222">pmid:24113222</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5ntu2vylrfexlgwcvjgddvwqpy">fatcat:5ntu2vylrfexlgwcvjgddvwqpy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829163532/http://rci.rutgers.edu/~advis/pdfs/09_Clayton-2014-Advancing%20avian%20behavioral%20neuroe.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/de/a6/dea620f3828b61b4f11f91223412d3600ab03003.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.yfrne.2013.09.004"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Divergence patterns of genic copy number variation in natural populations of the house mouse (Mus musculus domesticus) reveal three conserved genes with major population-specific expansions

Željka Pezer, Bettina Harr, Meike Teschke, Hiba Babiker, Diethard Tautz
<span title="2015-07-06">2015</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
We applied a read depth approach to genome resequencing data to detect copy number variants (CNVs) ≥1 kb in wild-caught mice belonging to four populations of Mus musculus domesticus.  ...  These genes encode proteins that are relevant for environmental and behavioral interactions, such as vomeronasal and olfactory receptors, as well as major urinary proteins and several proteins of unknown  ...  B.H., M.T., and H.B. collected the animals, generated sequencing data, and performed read mapping. All authors revised and approved the final manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.187187.114">doi:10.1101/gr.187187.114</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26149421">pmid:26149421</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4509996/">pmcid:PMC4509996</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xv6nokkkijeetef4amhex5qfwe">fatcat:xv6nokkkijeetef4amhex5qfwe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170816144320/http://pubman.mpdl.mpg.de/pubman/item/escidoc:2175480/component/escidoc:2175477/Pezer_et_al_2015.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/75/72/7572ae0c6ff402f79aed6dd5e599f1c07970ae02.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.187187.114"> <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/PMC4509996" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Sympatric ecological speciation meets pyrosequencing: sampling the transcriptome of the apple maggot Rhagoletis pomonella

Dietmar Schwarz, Hugh M Robertson, Jeffrey L Feder, Kranthi Varala, Matthew E Hudson, Gregory J Ragland, Daniel A Hahn, Stewart H Berlocher
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
To maximize transcript diversity we created and sequenced separate libraries from larvae, pupae, adult heads, and headless adult bodies.  ...  Preliminary comparative analysis of transcript presences and absences revealed evidence of gene loss in Drosophila and gain in the higher dipteran clade Schizophora.  ...  Acknowledgements We thank Kim Walden for technical assistance, and Shahjahan Ali for the text which we modified for the description of the 454 library construction and sequencing reactions in the Supporting  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-10-633">doi:10.1186/1471-2164-10-633</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20035631">pmid:20035631</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2807884/">pmcid:PMC2807884</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/knoobrbghvbnlnwqdtjx6kprgm">fatcat:knoobrbghvbnlnwqdtjx6kprgm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809014312/http://entnemdept.ifas.ufl.edu/Hahn/lab/pdf/Schwarzetal2009BMCGenomics.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/19/e1/19e18e4b83805903e4972b296247fe424bd7920f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-10-633"> <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/PMC2807884" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Expanding the computational toolbox for mining cancer genomes

Li Ding, Michael C. Wendl, Joshua F. McMichael, Benjamin J. Raphael
<span title="2014-07-08">2014</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wg7vnqrxzveutlxxgtyxqydvjy" style="color: black;">Nature reviews genetics</a> </i> &nbsp;
Collectively, these tools have advanced the study of genomic, transcriptomic, epigenomic  ...  High-throughput DNA sequencing has revolutionized cancer genomics with numerous discoveries relevant to cancer diagnosis and treatment.  ...  Accurate inference of copy number from sequence data requires normalization procedures that consider certain biases inherent to short read sequencing methods (such as GC content and library biases).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg3767">doi:10.1038/nrg3767</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25001846">pmid:25001846</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4168012/">pmcid:PMC4168012</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wgpspotu3jfp3ahhilcxzz7z5i">fatcat:wgpspotu3jfp3ahhilcxzz7z5i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191208021126/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4168012&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/5c/27/5c279f05181615ae81ff4fdcfb83a9a6e1ad8ef9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg3767"> <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/PMC4168012" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome Evolution in Reptilia, the Sister Group of Mammals

Daniel E. Janes, Christopher L. Organ, Matthew K. Fujita, Andrew M. Shedlock, Scott V. Edwards
<span title="">2010</span> <i title="Annual Reviews"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/76paa6gbdzdsdhhe62uk3giv3m" style="color: black;">Annual review of genomics and human genetics (Print)</a> </i> &nbsp;
Despite decades of study at the chromosomal and single-gene levels, and the evidence for great diversity in genome size, karyotype, and sex chromosome diversity, reptile genomes are virtually unknown in  ...  The recent sequencing of the chicken and zebra finch genomes, in conjunction with genome scans and the online publication of the Anolis lizard genome, has begun to clarify the events leading from an ancestral  ...  Graves, and Stephen Sarre for their constructive reviews of this manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-genom-082509-141646">doi:10.1146/annurev-genom-082509-141646</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20590429">pmid:20590429</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rioxicutcfgcpehfnktaddlke4">fatcat:rioxicutcfgcpehfnktaddlke4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190309035824/http://pdfs.semanticscholar.org/fe2f/1c5839408fe28d9ebd6a698d129696eebc98.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/fe/2f/fe2f1c5839408fe28d9ebd6a698d129696eebc98.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1146/annurev-genom-082509-141646"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

CNVIntegrate: the first multi-ethnic database for identifying copy number variations associated with cancer

Amrita Chattopadhyay, Zi Han Teoh, Chi-Yun Wu, Jyh-Ming Jimmy Juang, Liang-Chuan Lai, Mong-Hsun Tsai, Chia-Hsin Wu, Tzu-Pin Lu, Eric Y Chuang
<span title="2021-01-01">2021</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ejkvir3kzbdojf5kygupkidsca" style="color: black;">Database: The Journal of Biological Databases and Curation</a> </i> &nbsp;
CNVs further cause genetic diversity in healthy populations and are predominant drivers of gene/genome evolution.  ...  Human copy number variations (CNVs) and copy number alterations (CNAs) are DNA segments (&gt;1000 base pairs) of duplications or deletions with respect to the reference genome, potentially causing genomic  ...  Funding The Center of Genomic and Precision Medicine, National Taiwan University, the Ministry of Science and Technology, Taiwan (MOST-110-2634-F-002-044) and the Center for Biotechnology, National Taiwan  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baab044">doi:10.1093/database/baab044</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34259866">pmid:34259866</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8278790/">pmcid:PMC8278790</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kjnrxxikq5dmzic3hbgxchpmkm">fatcat:kjnrxxikq5dmzic3hbgxchpmkm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210716210151/https://watermark.silverchair.com/baab044.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAuAwggLcBgkqhkiG9w0BBwagggLNMIICyQIBADCCAsIGCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMK2b1ONvKVG_cIK20AgEQgIICk_xzwE7ArPmBuYmUa7tHh_KWKzGeJkQyWk2KZgtOVGROMAnOm6fSUj5T4HzsSVV_t9viw59lJpkP9J1BoW_JRbnKbUXoeK7xFVoAZwDf4x2sbakkyCG9OwMGPBrs3TT5tzxQx9byeSW1B71eLigI48K9vk4hicSHDM6yCJDSV6ambhkgN8otcyumZHITfK0g_vmvEmj9z8uGH-stn0IC6dDBxJLcrFhfb6tlHiARXtpLP7LXswOA6egaE2_sNQ8hF6Yh081EiJAmQWDIT2QIoho-jyh1GG2cpa4w9Tcr2CXKwBy1g9untgCPbx9nhpJjtEAfRdTDELquwtANus04LoAfkIztsihCIZB6y_B7bUA4rbKL1vkwWq_7ESJfpxbYvXuS0LFiUpGBP062M-m5_MtTmVFCQtDhhy7zt4HP17i8HfKFqzZktNunuNx5YXEcNdTKYHOO7urj9cAwtUwVJH0kFMYV8_G-rgOY9kh5GZH3tybQtu5x4x4w81FigW1xaGW_xdrFf6evZ7u1Tb4JqupSD5JCNpZiN2XU8k80EGAEU3sfV95RvyA9Pr0zJ8-OVMQq2mOMNX3UUr7Ny5vyvTjrN-8h-Qf5NDPZQ3TnckH-sGfnDtyvhUYA4lW5dS3j7y6k7dmJma3wyNinBEtKPZlqPP21G0C37MUVkjqJwXGRhvCNI3WUHgWdW2xu_e1Pxzu0HadMkE1A19NsvP0GKZFxYYcz7Tdo9yYWM9EyEbqmSPQ6wJHd62dpShK-OeUR3bkFbBqSztHwaeaFcM-kqDUya9dRaGScdnowu90f3LwjWXnoS5zIqDlMwTfrZ-4M-XpWzcKfaiI9jcW9ddpGUAokUFheuBvWCB_W-pMzyfHPhjeT" 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/f3/83/f383dfab434fef56690a3afbc3ef50eba2696712.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/database/baab044"> <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/PMC8278790" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Structural variation in the human genome

Yong-Shu HE, Wen ZHANG, Zhao-Qing YANG
<span title="2009-12-01">2009</span> <i title="China Science Publishing &amp; Media Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rfwmxvqsfjgk3ob74u4axovnni" style="color: black;">Hereditas (Beijing)</a> </i> &nbsp;
Larger structural variation including duplications, insertions, deletions, termed as copy number variation (CNV), inversions and translocations are more challenging to discover.  ...  Ohsuke Migita for co-leading the inversion genotyping project, for sharing many of his interesting stories, and for his kindness. I'd like to thank Dr.  ...  Since the publication of the first personal genome, the HuRef genome, in 2007, several personal genomes have been sequenced, capturing different extents of their genetic variation content (Table I . 2  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3724/sp.j.1005.2009.00771">doi:10.3724/sp.j.1005.2009.00771</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19689936">pmid:19689936</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3wlkvpj7yjaixmwky6gy6qt4qu">fatcat:3wlkvpj7yjaixmwky6gy6qt4qu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200318055051/https://tspace.library.utoronto.ca/bitstream/1807/35919/1/Pang_AndyWingChun_201306_PhD_thesis.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/0c/6d/0c6d97a5dfbd5c89df521da732a68da8c6bb4d2c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3724/sp.j.1005.2009.00771"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Article Watch: April 2016

Clive A. Slaughter
<span title="">2016</span> <i title="Association of Biomolecular Resource Facilities"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zlb4hq4hkfgptl2zq3dbo5nqpa" style="color: black;">Journal of Biomolecular Techniques</a> </i> &nbsp;
The copy number of DNA sequences from actively dividing cells is expected to vary with proximity to the origin of replication.  ...  families, notably GPCRs and olfactory receptors.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7171/jbt.16-2701-006">doi:10.7171/jbt.16-2701-006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/clplu56kn5bj5aencccz5y434a">fatcat:clplu56kn5bj5aencccz5y434a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191112233925/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4765765&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/24/d3/24d3b0553e7aada20448b77be3b3378b5595fe34.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.7171/jbt.16-2701-006"> <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>

Copy number variation of individual cattle genomes using next-generation sequencing

D. M. Bickhart, Y. Hou, S. G. Schroeder, C. Alkan, M. F. Cardone, L. K. Matukumalli, J. Song, R. D. Schnabel, M. Ventura, J. F. Taylor, J. F. Garcia, C. P. Van Tassell (+3 others)
<span title="2012-02-02">2012</span> <i title="Cold Spring Harbor Laboratory"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nwro4atxwbec5pfkpfslaxbdae" style="color: black;">Genome Research</a> </i> &nbsp;
Surveys of the top 25 most variable genes revealed that the Nelore individual had the lowest copy numbers in 13 cases (~52%, x 2 test; P-value <0.05).  ...  We further estimated absolute copy numbers for genomic segments and annotated genes in each individual.  ...  E.E.E. is supported by NIH grants GM058815, HG002385 and is an investigator of the Howard Hughes Medical Institute.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.133967.111">doi:10.1101/gr.133967.111</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22300768">pmid:22300768</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3317159/">pmcid:PMC3317159</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/l24rs5k3yvh3bj5lbvpbaanmde">fatcat:l24rs5k3yvh3bj5lbvpbaanmde</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428032144/http://repository.bilkent.edu.tr/bitstream/handle/11693/21516/Copy%20number%20variation%20of%20individual%20cattle%20genomes%20using%20next-generation%20sequencing.pdf;jsessionid=03492B68AD0B1E20E2C383F89DC94C53?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/b5/e6/b5e609f075f1006cdfd25b542473a7977b6d6a05.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.133967.111"> <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/PMC3317159" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genome sequence, comparative analysis and haplotype structure of the domestic dog

Kerstin Lindblad-Toh, Claire M Wade, Tarjei S. Mikkelsen, Elinor K. Karlsson, David B. Jaffe, Michael Kamal, Michele Clamp, Jean L. Chang, Edward J. Kulbokas, Michael C. Zody, Evan Mauceli, Xiaohui Xie (+34 others)
<span title="">2005</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/drfdii35rzaibj3aml5uhvr5xm" style="color: black;">Nature</a> </i> &nbsp;
Analysis of SNPs reveals long-range haplotypes across the entire dog genome, and defines the nature of genetic diversity within and across breeds.  ...  We use sequence comparison with the primate and rodent lineages to shed light on the structure and evolution of genomes and genes.  ...  Lark, whose vision and research convinced the NIH of the importance of generating a canine genome sequence.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature04338">doi:10.1038/nature04338</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16341006">pmid:16341006</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wed5sgoqqza77h5hbivkxvnb7i">fatcat:wed5sgoqqza77h5hbivkxvnb7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20060902160935/http://www.lsu.edu:80/deafness/NatureDogGenome2005.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/b0/1f/b01f00857b9abec4f245c665c5042824f5430711.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nature04338"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> nature.com </button> </a>

HGM 2010 Programme / Abstract

<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/rn2dm7ildza6bbitx34suzwoay" style="color: black;">The HUGO Journal</a> </i> &nbsp;
We are currently RT-PCR-amplifying RNA from the lymphocytes of patients to identify aberrant transcripts.  ...  ACKNOWLEDGEMENTS HGM 2010 has received financial support from the following organisations. We would like to extend our utmost appreciation to them for all of their support.  ...  The copy number results were subsequently compared with the expected genotypes of mouse samples.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-010-9143-0">doi:10.1007/s11568-010-9143-0</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/oykxd6u7snfi5o7m6tst7wi6yq">fatcat:oykxd6u7snfi5o7m6tst7wi6yq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200509010014/https://iris.unimore.it/retrieve/handle/11380/1114304/96179/HGM%25202010%2520-%2520Programs%26abstracts.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/c9/2a/c92aaccb8b9781ee0dbfd1d66cfa4a97395e3787.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-010-9143-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>
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