Filters








1,362 Hits in 5.1 sec

An enhanced version of Cochran-Armitage trend test for genome-wide association studies

Mansi Ghodsi, Saeid Amiri, Hossein Hassani, Zara Ghodsi
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nfykoso3ybebrl243rvpdkxioe" style="color: black;">Meta Gene</a> </i> &nbsp;
Genome-wide association studies the evaluation of association between candidate gene and disease status is widely carried out using Cochran-Armitage trend test.  ...  In this paper, an enhanced version of Cochran-Armitage trend test based on bootstrap approach is introduced.  ...  Amiri and von Rosen (2011) use the bootstrap to carry out the test of the contingency table.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.mgene.2016.07.001">doi:10.1016/j.mgene.2016.07.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27617223">pmid:27617223</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5006094/">pmcid:PMC5006094</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pzurgh5jijhzhpmslfmj4ufxyy">fatcat:pzurgh5jijhzhpmslfmj4ufxyy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191127191429/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5006094&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/f1/1a/f11a778d8b3111ff177c4e10fc584e308ad73c4b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.mgene.2016.07.001"> <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/PMC5006094" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NOJAH: NOt Just Another Heatmap for genome-wide cluster analysis

Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski, Xia Li
<span title="2019-03-28">2019</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;
The application of such tools to the number and types of genome-wide data available from next generation sequencing (NGS) technologies requires the adaptation of statistical concepts, such as in defining  ...  Additionally, NOJAH contains five different existing R packages that are connected in the interface by their functionality as part of a defined workflow for genome-wide cluster analysis.  ...  Acknowledgments We would like to thank the Cancer Informatics Core of the Winship Cancer Institute of Emory University for hosting NOJAH on the CentOS Virtual Machine.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0204542">doi:10.1371/journal.pone.0204542</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30921318">pmid:30921318</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6438523/">pmcid:PMC6438523</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tivmirwvvncgtjbd6ijzj2vqwq">fatcat:tivmirwvvncgtjbd6ijzj2vqwq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190505074024/https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0204542&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/dd/1d/dd1da2acac0c3a80c080c71d9e6064d1363efce7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0204542"> <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/PMC6438523" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

NOJAH: Not Just Another Heatmap for Genome-Wide Cluster Analysis [article]

Manali Rupji, Bhakti Dwivedi, Jeanne Kowalski
<span title="2018-09-12">2018</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The application of such tools to the number and types of genome-wide data available from next generation sequencing (NGS) technologies requires the adaptation of statistical concepts, such as in defining  ...  Additionally, NOJAH contains five different existing R packages that are connected in the interface by their functionality as part of a defined workflow for genome-wide cluster analysis.  ...  Although used for illustration, 248 NOJAH's GWH analysis is not limited to gene expression data but may also be applied 249 to any genome-wide data type such as methylation, copy number, and variant, as  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/415398">doi:10.1101/415398</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/is7ntsp4sfeerh6ljheucbc2hi">fatcat:is7ntsp4sfeerh6ljheucbc2hi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190502051347/https://www.biorxiv.org/content/biorxiv/early/2018/09/12/415398.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/1d/0f/1d0fb8f6fa3094dbdf10889e2c77a4e606c49e07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/415398"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Novel R tools for analysis of genome-wide population genetic data with emphasis on clonality

Zhian N. Kamvar, Jonah C. Brooks, Niklaus J. Grünwald
<span title="2015-06-10">2015</span> <i title="Frontiers Media SA"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/r7trx2kj6je5jhtaoy3rztibgy" style="color: black;">Frontiers in Genetics</a> </i> &nbsp;
In this paper we provide several significant extensions to poppr with a focus on large, genome-wide SNP data.  ...  With the advent of high throughput sequencing technologies, obtaining genome-wide population genetic data has become easier than ever before.  ...  Acknowledgments We thank Ignazio Carbone for discussions on the index of association; David Cooke, Sanmohan Baby, and Jens Hansen for beta testing; and Thibaut Jombart for allowing us to incorporate the  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2015.00208">doi:10.3389/fgene.2015.00208</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26113860">pmid:26113860</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4462096/">pmcid:PMC4462096</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kqtaebpvqjgplc7hgwvdkm2zni">fatcat:kqtaebpvqjgplc7hgwvdkm2zni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171006051243/http://publisher-connector.core.ac.uk/resourcesync/data/Frontiers/pdf/0e9/aHR0cDovL2pvdXJuYWwuZnJvbnRpZXJzaW4ub3JnL2FydGljbGUvMTAuMzM4OS9mZ2VuZS4yMDE1LjAwMjA4L3BkZg%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/9a/c4/9ac47b5f8673eb6c785cad88777fb7ad78aea030.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3389/fgene.2015.00208"> <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/PMC4462096" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

RaBoT: a rarefaction-by-bootstrap method to compare genome-wide levels of genetic diversity

Ivan Scotti, William Montaigne, Klára Cseke, Stéphane Traissac
<span title="2013-06-07">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wuinenwsbbdshheyn7pwuiwzbe" style="color: black;">Annals of Forest Science</a> </i> &nbsp;
The advent of genome scan approaches makes the development of such tests absolutely necessary. & Aims We developed a method to compare genome-wide diversity estimates while taking into account-and factoring  ...  When applied to empirical data, RaBoT detected higher genetic diversity in a post-disturbance than in an undisturbed population and lower genetic diversity in a seedling than in the corresponding adult  ...  Acknowledgments The authors wish to thank Saint-Omer Cazal for plant material collection and DNA extractions. We wish to thank Eric Marcon, Caroline Scotti-Saintagne, Rosane G.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13595-013-0302-z">doi:10.1007/s13595-013-0302-z</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/bshdlxo4hrag7ki4kfm2okvyda">fatcat:bshdlxo4hrag7ki4kfm2okvyda</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170922072926/http://prodinra.inra.fr/ft?id=BB02DD89-9288-48A9-9D54-0D815CC22EED" 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/71/33/7133126660aeb7e50faf839db59ff6000e654c17.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s13595-013-0302-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

A Bayesian approach to efficient differential allocation for resampling-based significance testing

Shane T Jensen, Sameer Soi, Li-San Wang
<span title="">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Large-scale statistical analyses have become hallmarks of post-genomic era biological research due to advances in high-throughput assays and the integration of large biological databases.  ...  randomized data.  ...  The original genotyping was performed in the laboratories of Drs. Singleton and Hardy, (NIA, LNG), Bethesda, MD USA.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-198">doi:10.1186/1471-2105-10-198</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19558706">pmid:19558706</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2718927/">pmcid:PMC2718927</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/blfzvq7zhra5ff32ziejukgzcq">fatcat:blfzvq7zhra5ff32ziejukgzcq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20090709161700/http://stat.wharton.upenn.edu/~stjensen/papers/shanejensen.diffalloc09.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/d1/55/d15558ceb92e3e65a270d1361f1473a92f6d59b5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-10-198"> <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/PMC2718927" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Associative Clustering for Exploring Dependencies between Functional Genomics Data Sets

S. Kaski, J. Nikkila, J. Sinkkonen, L. Lahti, J.E.A. Knuuttila, C. Roos
<span title="">2005</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q75ftrlivrhrnno5ijjuyufx5a" style="color: black;">IEEE/ACM Transactions on Computational Biology &amp; Bioinformatics</a> </i> &nbsp;
ACKNOWLEDGMENTS The authors would like to thank Jaakko Peltonen for the code for IB. This work has been supported by the Academy of Finland, decisions #79017 and #207467. During part of the work, S.  ...  Nikkilä were with Helsinki University of Technology.  ...  The resulting grid of so-called cross clusters then corresponds to the contingency table; the number of dots within each grid cell gives the amount of data in a contingency table cell.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2005.32">doi:10.1109/tcbb.2005.32</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17044184">pmid:17044184</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qfsbhrcdqbgzraiirzj5tarxju">fatcat:qfsbhrcdqbgzraiirzj5tarxju</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808025927/http://lib.tkk.fi/Diss/2005/isbn9512279096/article8.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/76/4c/764c61b13b58bb80190d976fff00b22d516556da.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2005.32"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a>

Appraising the relevance of DNA copy number loss and gain in prostate cancer using whole genome DNA sequence data

Niedzica Camacho, Peter Van Loo, Sandra Edwards, Jonathan D. Kay, Lucy Matthews, Kerstin Haase, Jeremy Clark, Nening Dennis, Sarah Thomas, Barbara Kremeyer, Jorge Zamora, Adam P. Butler (+45 others)
<span title="2017-09-25">2017</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/j6fzfstrmzcj3aeps7bx6tpoy4" style="color: black;">PLoS Genetics</a> </i> &nbsp;
Our study employs Whole Genome DNA Sequence (WGS) data from tumor samples (n = 103) to comprehensively assess the role of the Knudson two hit genetic model in SCNA generation in prostate cancer. 64 recurrent  ...  A variety of models have been proposed to explain regions of recurrent somatic copy number alteration (SCNA) in human cancer.  ...  Results Genome wide copy number profiles ASCAT 2.2 [14, 15] was used to identify somatic copy number alterations (SCNAs; S2 Table; types of alteration defined in S1 Table) in WGS data for malignant  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1007001">doi:10.1371/journal.pgen.1007001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28945760">pmid:28945760</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5628936/">pmcid:PMC5628936</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kcqfnqkchfdhxcczrhncpmizqe">fatcat:kcqfnqkchfdhxcczrhncpmizqe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719183613/https://research-repository.st-andrews.ac.uk/bitstream/handle/10023/11812/Lynch_2017_PLoSGenetics_CopyNumber_CC.pdf;jsessionid=7E355F984337D0AB1FBFB5B2C41D5F6F?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/4a/bb/4abbb53a5fdcd9b03d9e62e179ff186a6d1694ef.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pgen.1007001"> <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/PMC5628936" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Probabilistic analysis of the human transcriptome with side information [article]

Leo Lahti
<span title="2011-02-27">2011</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The key contributions of the thesis are general exploratory tools for high-throughput data analysis that have provided new insights to cell-biological networks, cancer mechanisms and other aspects of genome  ...  By combining statistical evidence across multiple measurement sources and the wealth of background information in genomic data repositories it has been possible to solve some the uncertainties associated  ...  Contingency table analysis Contingency table analysis is a classical approach used to study associations between co-occurring categorical observations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1102.5509v1">arXiv:1102.5509v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/zlwxrob7c5hapgje2v2tstx6uy">fatcat:zlwxrob7c5hapgje2v2tstx6uy</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/arxiv-1102.5509/1102.5509.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/08/f6/08f69806d3d02d3bba34320807ddff97bcf5e919.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1102.5509v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Comparative Genomics of Mycoplasma: Analysis of Conserved Essential Genes and Diversity of the Pan-Genome

Wei Liu, Liurong Fang, Mao Li, Sha Li, Shaohua Guo, Rui Luo, Zhixin Feng, Bin Li, Zhemin Zhou, Guoqing Shao, Huanchun Chen, Shaobo Xiao (+1 others)
<span title="2012-04-20">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;
Mycoplasma, the smallest self-replicating organism with a minimal metabolism and little genomic redundancy, is expected to be a close approximation to the minimal set of genes needed to sustain bacterial  ...  This study employs comparative evolutionary analysis of twenty Mycoplasma genomes to gain an improved understanding of essential genes.  ...  Maojun Liu (Jiangsu Academy of Agricultural Sciences, Nanjing, China), Dr. Lei Wang (Nankai University, Tianjin, China), Mr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0035698">doi:10.1371/journal.pone.0035698</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22536428">pmid:22536428</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3335003/">pmcid:PMC3335003</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3qvbzmy3djdblpdsmff7nyptfu">fatcat:3qvbzmy3djdblpdsmff7nyptfu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170809021729/http://www.siga.fiocruz.br/arquivos/ss/documentos/editais/64_Comparative%20Genomics%20of%20Mycoplasma.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/18/4a18a8f783ec0858309e65fc1f7af262ad840bbd.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.0035698"> <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/PMC3335003" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genomic variant identification methods alter Mycobacterium tuberculosis transmission inference [article]

Katharine S. Walter, Caroline Colijn, Ted Cohen, Barun Mathema, Qingyun Liu, Jolene R. Bowers, David M. Engelthaler, Apurva Narechania, Julio Croda, Jason R. Andrews
<span title="2019-08-24">2019</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
Pathogen genomic data are increasingly used to characterize global and local transmission patterns of important human pathogens and to inform public health interventions.  ...  Yet there is no current consensus on how to measure genomic variation.  ...  identify different sets of M. tuberculosis genomic variants when applied to the 256 same sequence data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/733642">doi:10.1101/733642</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fgq7oyhkrvgmhhu55tkb5h262e">fatcat:fgq7oyhkrvgmhhu55tkb5h262e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200323095727/https://www.biorxiv.org/content/biorxiv/early/2019/08/24/733642.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/c1/ce/c1ced13262b4fa9fb02e1f7bf6c578d99bba155c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/733642"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Determination of Quantitative Trait Loci (QTL) for Early Maturation in Rainbow Trout (Oncorhynchus mykiss)

Lisa Haidle, Jennifer E. Janssen, Karim Gharbi, Hooman K. Moghadam, Moira M. Ferguson, Roy G. Danzmann
<span title="2008-05-20">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yim6oxk3f5ecpidaxovc55pxce" style="color: black;">Marine Biotechnology</a> </i> &nbsp;
Alleles derived from both parental sources were observed to contribute to the expression of EM in the progeny of the brothers. Four genome-wide significant QTL regions (i.e., were observed.  ...  Significant genome-wide and several strong chromosome-wide QTL for EM localized to different regions in males and females, suggesting some sex-specific control.  ...  We also wish to acknowledge the contributions of Michael Burke and the support staff of the Alma Aquaculture Research Station in Ontario for rearing and maintaining the experimental rainbow trout families  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10126-008-9098-5">doi:10.1007/s10126-008-9098-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18491191">pmid:18491191</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2516301/">pmcid:PMC2516301</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/livmldqoingc7chstmym37wrtm">fatcat:livmldqoingc7chstmym37wrtm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208191209/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2516301&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/4d/26/4d261e4d42f352bec3273c0317a4567ecc9c17dc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10126-008-9098-5"> <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/PMC2516301" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Stabilizing selection maintains exuberant colour polymorphism in the spider Theridion californicum (Araneae, Theridiidae)

PETER J. P. CROUCHER, GEOFFREY S. OXFORD, ATHENA LAM, ROSEMARY G. GILLESPIE
<span title="2010-12-02">2010</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nbyiz76nd5hj5pb4uyhtgl3cxe" style="color: black;">Molecular Ecology</a> </i> &nbsp;
We also examine the patterns of selection in the genome-wide sample of AFLP loci and compare approaches to detecting signatures of selection in this context.  ...  We compare population differentiation estimated from colour phenotypic data to differentiation at neutral amplified fragment length polymorphisms (AFLP) loci and demonstrate that the colour polymorphism  ...  DiDonato of the East Bay Regional Parks District for permission to collect in Tilden Regional Park, and the California State Parks.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-294x.2010.04941.x">doi:10.1111/j.1365-294x.2010.04941.x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21121989">pmid:21121989</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5qww53bhkffbxkxl4wg66fiuf4">fatcat:5qww53bhkffbxkxl4wg66fiuf4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811105640/http://nature.berkeley.edu/~gillespie/Publications_files/CroucherMolEcol.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/0a/a2/0aa2ee5fe6b1d77359840014720d7e6a5c1265e9.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1111/j.1365-294x.2010.04941.x"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

On safari to Random Jungle: a fast implementation of Random Forests for high-dimensional data

D. F. Schwarz, I. R. Konig, A. Ziegler
<span title="2011-01-31">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wmo54ba2jnemdingjj4fl3736a" style="color: black;">Bioinformatics</a> </i> &nbsp;
Motivation: Genome-wide association (GWA) studies have proven to be a successful approach for helping unravel the genetic basis of complex genetic diseases.  ...  Results: Here, we present the new freely available software package Random Jungle (RJ), which facilitates the rapid analysis of GWA data.  ...  Conflict of Interest: none declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr004">doi:10.1093/bioinformatics/btr004</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3105450/">pmcid:PMC3105450</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jk5b7aqw3zcwzbzqdaq5owytli">fatcat:jk5b7aqw3zcwzbzqdaq5owytli</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190220153249/http://pdfs.semanticscholar.org/25c4/e18205962c4f0acf73fc066a3fcc22fddbc3.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/25/c4/25c4e18205962c4f0acf73fc066a3fcc22fddbc3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr004"> <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/PMC3105450" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

How to evaluate performance of prediction methods? Measures and their interpretation in variation effect analysis

Mauno Vihinen
<span title="2012-06-18">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;
A checklist of items to look at is provided.  ...  Together with receiver operating characteristics (ROC) analysis they provide a good picture about the performance of methods and allow their objective and quantitative comparison.  ...  Acknowledgements This work was supported by the Sigrid Jusélius Foundation, Biocenter Finland and the Competitive Research Funding of Tampere University Hospital.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-s4-s2">doi:10.1186/1471-2164-13-s4-s2</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22759650">pmid:22759650</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3303716/">pmcid:PMC3303716</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6atzh6niufhoritsc7jxd6kv34">fatcat:6atzh6niufhoritsc7jxd6kv34</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180719184422/https://bmcgenomics.biomedcentral.com/track/pdf/10.1186/1471-2164-13-S4-S2?site=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/12/56/1256bd78d3d62e74f4ade27af96cdac385973247.180px.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-s4-s2"> <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/PMC3303716" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
&laquo; Previous Showing results 1 &mdash; 15 out of 1,362 results