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Alview: Portable Software for Viewing Sequence Reads in BAM Formatted Files

Richard P. Finney, Qing-Rong Chen, Cu V. Nguyen, Chih Hao Hsu, Chunhua Yan, Ying Hu, Massih Abawi, Xiaopeng Bian, Daoud M. Meerzaman
<span title="">2015</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
The name Alview is a contraction of the term Alignment Viewer. Alview is a compiled to native architecture software tool for visualizing the alignment of sequencing data. Inputs are files of short-read sequences aligned to a reference genome in the SAM/BAM format and files containing reference genome data. Outputs are visualizations of these aligned short reads. Alview is written in portable C with optional graphical user interface (GUI) code written in C, C++, and Objective-C. The application
more &raquo; ... an run in three different ways: as a web server, as a command line tool, or as a native, GUI program. Alview is compatible with Microsoft Windows, Linux, and Apple OS X. It is available as a web demo at https://cgwb.nci.nih.gov/cgi-bin/alview. The source code and Windows/Mac/Linux executables are available via https://github.com/NCIP/alview. CitAtion: finney et al. alview: Portable software for Viewing sequence reads in Bam formatted files.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s26470">doi:10.4137/cin.s26470</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26417198">pmid:26417198</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4573065/">pmcid:PMC4573065</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wffmtoymn5bgnbxhqmp6gamsqm">fatcat:wffmtoymn5bgnbxhqmp6gamsqm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170811002713/http://insights.sagepub.com/redirect_file.php?fileId=6785&amp;filename=5072-CIN-Alview:-Portable-Software-for-Viewing-Sequence-Reads-in-BAM-Formatted-.pdf&amp;fileType=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/8d/cc/8dccd0ac712ffdfd7184b95ec66615dd40ede51b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4137/cin.s26470"> <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/PMC4573065" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Multi-SNP Analysis of GWAS Data Identifies Pathways Associated with Nonalcoholic Fatty Liver Disease

Qing-Rong Chen, Rosemary Braun, Ying Hu, Chunhua Yan, Elizabeth M. Brunt, Daoud Meerzaman, Arun J. Sanyal, Kenneth Buetow, Silvia C. Sookoian
<span title="2013-07-19">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;
28 yes yes 2 B cell receptor signaling pathway KEGG 58 47 yes yes 2 BARD1 signaling events NCI-Nature 29 27 yes yes 2 Cell cycle KEGG 82 64 yes yes 2 cell cycle: g2/m  ...  inhibition of matrix metalloproteinases BioCarta 8 7 0.006 7.30 2.65E-04 Ethanol is oxidized by NAD+ to form acetaldehyde, NADH, and H+ Reactome 6 6 0.007 1.88 2.04E-03 cell cycle: g2/m  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0065982">doi:10.1371/journal.pone.0065982</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23894275">pmid:23894275</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3716806/">pmcid:PMC3716806</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m424ryag6jgkfiixairlc6gcha">fatcat:m424ryag6jgkfiixairlc6gcha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171007095610/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0065982&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/89/28/89283fa1f1ac97adf3626d125be9b90c339b219e.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.0065982"> <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/PMC3716806" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Delineating Genetic Alterations for Tumor Progression in the MCF10A Series of Breast Cancer Cell Lines

Mitsutaka Kadota, Howard H. Yang, Bianca Gomez, Misako Sato, Robert J. Clifford, Daoud Meerzaman, Barbara K. Dunn, Lalage M. Wakefield, Maxwell P. Lee, Anita Brandstaetter
<span title="2010-02-15">2010</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;
grown to 70-80% confluence in regular growth medium (for RUNX1 analysis) or in DMEM/F12 supplemented with serum replacement 1 (Sigma) (for AKT1 phosphorylation analysis) was lysed and collected using M-PER  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0009201">doi:10.1371/journal.pone.0009201</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20169162">pmid:20169162</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2821407/">pmcid:PMC2821407</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wlqc73stlfbjpaermnamlpt5sm">fatcat:wlqc73stlfbjpaermnamlpt5sm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170925020244/http://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0009201&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/69/16/691605a8b59ab765d1543004edadce057082ec1e.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.0009201"> <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/PMC2821407" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A function-blocking CD47 antibody suppresses stem cell and EGF signaling in triple-negative breast cancer

Sukhbir Kaur, Abdel G. Elkahloun, Satya P. Singh, Qing-Rong Chen, Daoud M. Meerzaman, Timothy Song, Nidhi Manu, Weiwei Wu, Poonam Mannan, Susan H. Garfield, David D. Roberts
<span title="2016-01-31">2016</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Adherent MDA-MB-231 and enriched bCSCs cells were labeled with BrdU for 10 days and then chased in BrdU free medium for 3-4 days and followed by 2 µM cytochalasin.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.7100">doi:10.18632/oncotarget.7100</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26840086">pmid:26840086</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4891109/">pmcid:PMC4891109</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7upczonebnb5pasrq24m6psseu">fatcat:7upczonebnb5pasrq24m6psseu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180725020102/http://www.oncotarget.com/index.php?journal=oncotarget&amp;page=article&amp;op=download&amp;path%5B%5D=7100&amp;path%5B%5D=20207" 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/95/a2/95a2fd329333785c276876051a750015ca5f88ba.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.7100"> <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/PMC4891109" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

TCF21 hypermethylation in genetically quiescent clear cell sarcoma of the kidney

Saskia L. Gooskens, Samantha Gadd, Jaime M. Guidry Auvil, Daniela S. Gerhard, Javed Khan, Rajesh Patidar, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu (+9 others)
<span title="2015-06-29">2015</span> <i title="Impact Journals, LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/yubgl6cdcrekxpjzhshpw23l3i" style="color: black;">OncoTarget</a> </i> &nbsp;
Clear Cell Sarcoma of the Kidney (CCSK) is a rare childhood tumor whose molecular pathogenesis remains poorly understood. We analyzed a discovery set of 13 CCSKs for changes in chromosome copy number, mutations, rearrangements, global gene expression and global DNA methylation. No recurrent segmental chromosomal copy number changes or somatic variants (single nucleotide or small insertion/deletion) were identified. One tumor with t(10;17)(q22;p13) involving fusion of YHWAE with NUTM2B was
more &raquo; ... fied. Integrated analysis of expression and methylation data identified promoter hypermethylation and low expression of the tumor suppressor gene TCF21 (Pod-1/capsulin/epicardin) in all CCSKs except the case with t(10;17) (q22;p13). TARID, the long noncoding RNA responsible for demethylating TCF21, was virtually undetectable in most CCSKs. TCF21 hypermethylation and decreased TARID expression were validated in an independent set of CCSK tumor samples. The presence of significant hypermethylation of TCF21, a transcription factor known to be active early in renal development, supports the hypothesis that hypermethylation of TCF21 and/or decreased TARID expression lies within the pathogenic pathway of most CCSKs. Future studies are needed to functionally verify a tumorigenic role of TCF21 down-regulation and to tie this to the unique gene expression pattern of CCSK. Oncotarget 15829
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.4682">doi:10.18632/oncotarget.4682</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26158413">pmid:26158413</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4599240/">pmcid:PMC4599240</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fqdn4ningvb57kzigkwp5uac4e">fatcat:fqdn4ningvb57kzigkwp5uac4e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180724020939/http://www.oncotarget.com/index.php?journal=oncotarget&amp;page=article&amp;op=download&amp;path%5B%5D=4682&amp;path%5B%5D=10672" 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/ba/4dba774b62b3255959033ba513190579347f5546.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.18632/oncotarget.4682"> <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/PMC4599240" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

MLLT1 YEATS domain mutations in clinically distinctive Favourable Histology Wilms tumours

Elizabeth J. Perlman, Samantha Gadd, Stefan T. Arold, Anand Radhakrishnan, Daniela S. Gerhard, Lawrence Jennings, Vicki Huff, Jaime M. Guidry Auvil, Tanja M. Davidsen, Jeffrey S. Dome, Daoud Meerzaman, Chih Hao Hsu (+13 others)
<span title="">2015</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/a4wan6l5o5dfzn767kyz7jqevi" style="color: black;">Nature Communications</a> </i> &nbsp;
Wilms tumour is an embryonal tumour of childhood that closely resembles the developing kidney. Genomic changes responsible for the development of the majority of Wilms tumours remain largely unknown. Here we identify recurrent mutations within Wilms tumours that involve the highly conserved YEATS domain of MLLT1 (ENL), a gene known to be involved in transcriptional elongation during early development. The mutant MLLT1 protein shows altered binding to acetylated histone tails. Moreover,
more &raquo; ... ant tumours show an increase in MYC gene expression and HOX dysregulation. Patients with MLLT1-mutant tumours present at a younger age and have a high prevalence of precursor intralobar nephrogenic rests. These data support a model whereby activating MLLT1 mutations early in renal development result in the development of Wilms tumour. | www.nature.com/naturecommunications ILNR, Intralobar nephrogenic rest; LOH, loss of heterozygosity; LOI, Loss of imprinting; ROI, retention of normal imprinting.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms10013">doi:10.1038/ncomms10013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26635203">pmid:26635203</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4686660/">pmcid:PMC4686660</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jqdatub2uvbylaq3f4pj5dxk2m">fatcat:jqdatub2uvbylaq3f4pj5dxk2m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200318151829/https://hsrc.himmelfarb.gwu.edu/cgi/viewcontent.cgi?referer=&amp;httpsredir=1&amp;article=2600&amp;context=smhs_peds_facpubs" 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/5f/1e/5f1ef7f3bd6cc97386faeb5cd0c081407da999b7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ncomms10013"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> nature.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4686660" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Rare Germline Copy Number Variations and Disease Susceptibility in Familial Melanoma

Jianxin Shi, Weiyin Zhou, Bin Zhu, Paula L. Hyland, Hunter Bennett, Yanzi Xiao, Xijun Zhang, Laura S. Burke, Lei Song, Chih Hao Hsu, Chunhua Yan, Qingrong Chen (+10 others)
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hxva2c3v7rgxffw6x5wzadfdrm" style="color: black;">Journal of Investigative Dermatology</a> </i> &nbsp;
Mounting evidence suggests that copy number variations (CNVs) can contribute to cancer susceptibility. The main goal of this study was to evaluate the role of germline CNVs in melanoma predisposition in high-risk melanoma families. We used genome-wide tiling comparative genomic hybridization and SNP arrays to characterize CNVs in 335 individuals (240 melanoma cases) from American melanoma-prone families (22 with germline CDKN2A or CDK4 mutations). We found that the global burden of overall CNVs
more &raquo; ... (or deletions or duplications separately) was not significantly associated with case-control or CDKN2A/CDK4 mutation status after accounting for the familial dependence. However, we identified several rare CNVs that either involved known melanoma genes (e.g. PARP1, CDKN2A) or co-segregated with melanoma (duplication on 10q23.23, 3p12.2 and deletions on 8q424.3, 2q22.1) in families without mutations in known melanoma high-risk genes. Some of these CNVs were correlated with expression changes in disrupted genes based on RNASeq data from a subset of melanoma cases included in the CNV study. These results suggest that rare co-segregating CNVs may influence melanoma susceptibility in some melanoma-prone families and genes found in our study warrant further evaluation in future genetic analyses of melanoma.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jid.2016.07.023">doi:10.1016/j.jid.2016.07.023</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27476724">pmid:27476724</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5123914/">pmcid:PMC5123914</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5fq3tb5bcbflnovo3wvccou6j4">fatcat:5fq3tb5bcbflnovo3wvccou6j4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200205225231/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5123914&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/f0/6f/f06f92ae625fd350d9b42676f4dccc84946c168e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jid.2016.07.023"> <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/PMC5123914" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Addition of MR imaging features and genetic biomarkers strengthens glioblastoma survival prediction in TCGA patients

Manal Nicolasjilwan, Ying Hu, Chunhua Yan, Daoud Meerzaman, Chad A. Holder, David Gutman, Rajan Jain, Rivka Colen, Daniel L. Rubin, Pascal O. Zinn, Scott N. Hwang, Prashant Raghavan (+10 others)
<span title="">2015</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wqfo7i73yzahrdelxdt7eqkwa4" style="color: black;">Journal of neuroradiology</a> </i> &nbsp;
PURPOSE-The purpose of our study was to assess whether a model combining clinical factors, MR imaging features, and genomics would better predict overall survival of patients with glioblastoma (GBM) than either individual data type.
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neurad.2014.02.006">doi:10.1016/j.neurad.2014.02.006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24997477">pmid:24997477</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5511631/">pmcid:PMC5511631</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xzv6rs3vufgarlxjjpu5rkfrje">fatcat:xzv6rs3vufgarlxjjpu5rkfrje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209005430/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5511631&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/13/ba/13ba74aecd2eb2e67f5445ffd2bd2de7568b275b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neurad.2014.02.006"> <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/PMC5511631" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

A Children's Oncology Group and TARGET initiative exploring the genetic landscape of Wilms tumor

Samantha Gadd, Vicki Huff, Amy L Walz, Ariadne H A G Ooms, Amy E Armstrong, Daniela S Gerhard, Malcolm A Smith, Jaime M Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan (+19 others)
<span title="2017-08-21">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ndd3azjmwfh45iqb6bvdfttaf4" style="color: black;">Nature Genetics</a> </i> &nbsp;
In cluster 1, genes encoding targets of E2F transcription factors, mitotic spindle assembly proteins, G2/M checkpoint proteins, and 1q genes were significantly enriched.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ng.3940">doi:10.1038/ng.3940</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28825729">pmid:28825729</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5712232/">pmcid:PMC5712232</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/otpa4xvizjgpdauzombs52yywa">fatcat:otpa4xvizjgpdauzombs52yywa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200211042201/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC5712232&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/f4/77/f477bf3fc14d1bef425ec7fbb2195db25d9fc2e1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/ng.3940"> <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/PMC5712232" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Internal checkpoint regulates T cell neoantigen reactivity and susceptibility to PD1 blockade [article]

Douglas C Palmer, Beau R. Webber, Yogin Patel, Matthew J. Johnson, Christine M. Kariya, Walker S. Lahr, Maria R. Parkhurst, Jared J Gartner, Todd D Prickett, Frank J. Lowery, Rigel J. Kishton, Devikala Gurusamy (+26 others)
<span title="2020-09-25">2020</span> <i title="Cold Spring Harbor Laboratory"> bioRxiv </i> &nbsp; <span class="release-stage" >pre-print</span>
C a n c e r i m m u n o l o g y .  ...  T u m o r m u t a t i o n a l l o a d p r e d i c t s s u r v i v a l a f t e r i m m u n o t h e r a p y a c r o s s m u l t i p l e  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.09.24.306571">doi:10.1101/2020.09.24.306571</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hxx4b34uhfcd7gvwqagayc2bxq">fatcat:hxx4b34uhfcd7gvwqagayc2bxq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201212120101/https://www.biorxiv.org/content/biorxiv/early/2020/09/25/2020.09.24.306571.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/2e/42/2e421cedf33017b5e34405b98f655ab08d5a2614.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/2020.09.24.306571"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> biorxiv.org </button> </a>

Significance of TP53 Mutation in Wilms Tumors with Diffuse Anaplasia: A Report from the Children's Oncology Group

Ariadne H.A.G. Ooms, Samantha Gadd, Daniela S. Gerhard, Malcolm A. Smith, Jaime M. Guidry Auvil, Daoud Meerzaman, Qing-Rong Chen, Chih Hao Hsu, Chunhua Yan, Cu Nguyen, Ying Hu, Yussanne Ma (+19 others)
<span title="2016-10-04">2016</span> <i title="American Association for Cancer Research (AACR)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zm56axre7rgihh5sznxp65np5i" style="color: black;">Clinical Cancer Research</a> </i> &nbsp;
Meerzaman, Q.-R. Chen, C.H. Hsu, C. Yan, C. Nguyen, Y. Hu, Y. Ma, Z. Zong, J.S. Dome, Y.-Y. Chi, J. Tian, J.I. Geller, C.G. Mullighan, J. Ma, D.A. Wheeler, O.A. Hampton, A.L.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/1078-0432.ccr-16-0985">doi:10.1158/1078-0432.ccr-16-0985</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27702824">pmid:27702824</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5290091/">pmcid:PMC5290091</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fnmh6635ejelxckplyq7egngcy">fatcat:fnmh6635ejelxckplyq7egngcy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190426071906/http://clincancerres.aacrjournals.org/content/clincanres/22/22/5582.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/cc/07/cc073d03046eb96d27d033c4fcd28ebd7be64f1e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1158/1078-0432.ccr-16-0985"> <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/PMC5290091" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Page 19 of American Journal of Physiology Vol. 7, Issue 4 [page]

<span title="">1992</span> <i title="American Physiological Society"> <a target="_blank" rel="noopener" href="https://archive.org/details/pub_american-journal-of-physiology" style="color: black;">American Journal of Physiology </a> </i> &nbsp;
Joel Schmidt, Daoud Meerzaman, and Kathryn Peters) for appraisal and criticism of this paper at various stages of its preparation. Address for reprint requests: M. C.  ...  Porchet, M. Crepin, M. Duterque-Co- quillaud, G. Vergnes, M. Mazzuca, B. Debuire, D. Pettprez, and P. Degand.  ... 
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Construction and characterization of a chimeric receptor containing the cytoplasmic domain of MUC1 mucin

Daoud Meerzaman, P. X. Xing, K. Chul Kim
<span title="">2000</span> <i title="American Physiological Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ok5lktf725bsfiv2ygtooufz74" style="color: black;">American Journal of Physiology - Lung cellular and Molecular Physiology</a> </i> &nbsp;
Meerzaman, Daoud, P. X. Xing, and K. Chul Kim. Construction and characterization of a chimeric receptor containing the cytoplasmic domain of MUC1 mucin. Am. J. Physiol. Lung Cell. Mol.  ...  were lysed on ice for 20 min in a lysis buffer [1% Nonidet P-40 (NP-40), 50 mM Tris · HCl, pH 7.4, 150 mM NaCl, 10 mM benzamidine, 6.25 mM phenylmethylsulfonyl fluoride, 10 µg/ml of leupeptin, and 200 µM  ...  treatment, the cells were lysed immediately on ice for 20 min in a lysis buffer (50 mM Tris · HCl, pH 7.4, 150 mM NaCl, 10 mM benzamidine, 6.25 mM phenylmethylsulfonyl fluoride, 10 µg/ml of leupeptin, 200 µM  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/ajplung.2000.278.3.l625">doi:10.1152/ajplung.2000.278.3.l625</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/10710536">pmid:10710536</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2lmiuakwlzcdbpgvvbnp5xf6fq">fatcat:2lmiuakwlzcdbpgvvbnp5xf6fq</a> </span>
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Inferring causal molecular networks: empirical assessment through a community-based effort

Steven M Hill, Laura M Heiser, Thomas Cokelaer, Michael Unger, Nicole K Nesser, Daniel E Carlin, Yang Zhang, Artem Sokolov, Evan O Paull, Chris K Wong, Kiley Graim, Adrian Bivol (+161 others)
<span title="2016-02-22">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/l6cw2tyvgrhytbvantrj2os37y" style="color: black;">Nature Methods</a> </i> &nbsp;
Specifically, we let m i c (normalized to be between zero and one; AUROC). For each team, AUROC scores were calculated for each of the 32 contexts.  ...  A paired t-test was used to assess whether m i c , D was significantly different from m i c , I , resulting in a P value p ic for each phosphoprotein and context.  ...  . , D and m i c , I denote the mean abundance levels of phosphoprotein i for (cell line, stimulus) context c under DMSO control conditions and mTOR inhibition, respectively (mean values were calculated  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nmeth.3773">doi:10.1038/nmeth.3773</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26901648">pmid:26901648</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4854847/">pmcid:PMC4854847</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s4kohpsugrdexedxtp7ujvht4q">fatcat:s4kohpsugrdexedxtp7ujvht4q</a> </span>
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Involvement of the MAP kinase ERK2 in MUC1 mucin signaling

Daoud Meerzaman, Paul S. Shapiro, K. Chul Kim
<span title="">2001</span> <i title="American Physiological Society"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ok5lktf725bsfiv2ygtooufz74" style="color: black;">American Journal of Physiology - Lung cellular and Molecular Physiology</a> </i> &nbsp;
Meerzaman) and a Designated Research Incentive Fund from the University of Maryland School of Pharmacy.  ...  Each histogram represents the relative kinase activity of total ERK2 when compared with that of "untreated (0 M)" and "unactivated (AbϪ)" samples.  ...  Immunoblots were washed with TBS (50 mM Tris, pH 7.6, and 0.15 M NaCl) containing 0.1% (vol/vol) Tween 20 for 45 min, incubated with the secondary antibody conjugated with horseradish peroxidase (diluted  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1152/ajplung.2001.281.1.l86">doi:10.1152/ajplung.2001.281.1.l86</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11404250">pmid:11404250</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/33awtdot4vgyteeccgycxol5sq">fatcat:33awtdot4vgyteeccgycxol5sq</a> </span>
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