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Genome Detective: An Automated System for Virus Identification from High-throughput sequencing data

Michael Vilsker, Yumna Moosa, Sam Nooij, Vagner Fonseca, Yoika Ghysens, Korneel Dumon, Raf Pauwels, Luiz Carlos Alcantara, Ewout Vanden Eynden, Anne-Mieke Vandamme, Koen Deforche, Tulio de Oliveira (+1 others)
<span title="2018-08-16">2018</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;
Genome Detective is an easy to use web-based software application that assembles the genomes of viruses quickly and accurately.  ...  The software was optimized using synthetic datasets to represent the great diversity of virus genomes. The application was then validated with next generation sequencing data of hundreds of viruses.  ...  Analysis of viral data is particularly challenging given the high variability of viruses and their deviation from reference genomes, the increasing speed of identification, the continuous emergence of  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty695">doi:10.1093/bioinformatics/bty695</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30124794">pmid:30124794</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6524403/">pmcid:PMC6524403</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gtgyp7h3vngk7cn6ltpvzdaooa">fatcat:gtgyp7h3vngk7cn6ltpvzdaooa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190225105238/http://pdfs.semanticscholar.org/6cf8/70f873d895b7800b4d55e9e870e4566f9c0c.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/6c/f8/6cf870f873d895b7800b4d55e9e870e4566f9c0c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bty695"> <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/PMC6524403" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Advanced methods in PCR product detection

J G Lazar
<span title="1994-08-01">1994</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;
Gel-based detection methods worked well for these applications when sample throughput, time, and persample costs were not important issues.  ...  For a 200-bp PCR product, this amount translates to nearly 5 x 101~ full-length product molecules and would require an amplification of 5 x 109 for detection of 10 initial target molecules in a 100-1~1  ...  ) transcribed from the plasmid DNA producing a high yield.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.4.1.s1">doi:10.1101/gr.4.1.s1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qjugkkqsnfb2jg7qlgdd26zdie">fatcat:qjugkkqsnfb2jg7qlgdd26zdie</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723081310/https://genome.cshlp.org/content/4/1/S1.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/b9/bc/b9bc4792bf2ef0ff71910d0d66a84bdae1f7665d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.4.1.s1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Biochip sensors for the rapid and sensitive detection of viral disease

Andrew D Livingston, Colin J Campbell, Edward K Wagner, Peter Ghazal
<span title="2005-05-26">2005</span> <i title="BMC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/6bzsiicmhvczjnsm7jbog7ysaa" style="color: black;">Genome Biology</a> </i> &nbsp;
The advantages of the multi-parameter microarray technologies could be combined with the speed and sensitivity of cell-based systems to give 'cell-omic' sensors.  ...  Recent advances in DNA and protein microarray methodology and the emerging technology of cell-based sensors have massively increased the speed and sensitivity with which we can detect viral infections.  ...  We thank our colleagues at the Scottish Centre for Genomic Technology and Informatics for many stimulating discussions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2005-6-6-112">doi:10.1186/gb-2005-6-6-112</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15960809">pmid:15960809</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1175961/">pmcid:PMC1175961</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/e24oq7t3ejaxfmqmfzrtmvd65q">fatcat:e24oq7t3ejaxfmqmfzrtmvd65q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723030057/https://www.pure.ed.ac.uk/ws/files/8954358/Biochip_sensors_for_the_rapid_and_sensitive_detection_of_viral_disease.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/e2/cd/e2cd1246bb811865d54dd3dec41b6a2c5c7e8135.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/gb-2005-6-6-112"> <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/PMC1175961" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Bacteriophage functional genomics and its role in bacterial pathogen detection

J. Klumpp, D. E. Fouts, S. Sozhamannan
<span title="2013-03-21">2013</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ybrdrifrfraydlephn44dplrgu" style="color: black;">Briefings in Functional Genomics</a> </i> &nbsp;
and identifying virulence and other adaptive features encoded by phages and finally, using prophage genomic information for bacterial detection/diagnostics.  ...  These include phage genome sequencing and annotation, identification of prophages in bacterial sequences and genetic characterization of phages, functional genomics of the infection process and finally  ...  Recent advances in second-and third-generation DNA sequencing technologies have led to an increasing number of phage genomic sequences, either from purified virus particles or as a result of bacterial  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/elt009">doi:10.1093/bfgp/elt009</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23520178">pmid:23520178</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ugpcw3qd6begpgy5sjxihyjcui">fatcat:ugpcw3qd6begpgy5sjxihyjcui</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190305112342/http://pdfs.semanticscholar.org/c8d6/bb6597bc718bf4ec7034376293ab4eb72d61.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/c8/d6/c8d6bb6597bc718bf4ec7034376293ab4eb72d61.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/elt009"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

Microarrays for Pathogen Detection and Analysis

K. S. McLoughlin
<span title="2011-09-19">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ybrdrifrfraydlephn44dplrgu" style="color: black;">Briefings in Functional Genomics</a> </i> &nbsp;
These microbial detection arrays occupy a middle ground between low cost, narrowly focused assays such as multiplex PCR and more expensive, broad-spectrum technologies like high-throughput sequencing.  ...  Statistical algorithms that can analyze data from microbial detection arrays and provide easily interpretable results are absolutely required in order for these efforts to succeed.  ...  Coefficients for the model predictors are fitted to data from hybridizations to targets with known genome sequences.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/elr027">doi:10.1093/bfgp/elr027</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21930658">pmid:21930658</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245552/">pmcid:PMC3245552</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/um7x35qvjvandhmbu5ohfsvwci">fatcat:um7x35qvjvandhmbu5ohfsvwci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190226161155/http://pdfs.semanticscholar.org/6fa6/49c67f566b9bcd0450e3a9614cbd6fddf74c.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/6f/a6/6fa649c67f566b9bcd0450e3a9614cbd6fddf74c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bfgp/elr027"> <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/PMC3245552" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection and whole genome sequence analysis of an enterovirus 68 cluster

Angela K Todd, Richard J Hall, Jing Wang, Mathew Peacey, Sharla McTavish, Christy J Rand, Jo-Ann Stanton, Susan Taylor, Q Sue Huang
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iufy3qwbujc45bx7atkztxh2oi" style="color: black;">Virology Journal</a> </i> &nbsp;
All fifteen specimens showed high similarity with enterovirus 68 by VP1 sequencing.  ...  Results: Based on sequence analysis of the VP1 region and the full genome of one representative isolate, the New Zealand enterovirus 68 isolates clustered with contemporary enterovirus 68 viruses and do  ...  Funding The national poliovirus/enterovirus surveillance is funded by the Ministry of Health who kindly permitted the use of relevant data for publication.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1743-422x-10-103">doi:10.1186/1743-422x-10-103</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23548106">pmid:23548106</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3621541/">pmcid:PMC3621541</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3wwbroyfmvelvg2n7ekwal6kwi">fatcat:3wwbroyfmvelvg2n7ekwal6kwi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170814041222/https://virologyj.biomedcentral.com/track/pdf/10.1186/1743-422X-10-103?site=virologyj.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/9d/52/9d52685e542cddb293168f69cd128152748e0fc1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1743-422x-10-103"> <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/PMC3621541" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Genomics in Infectious Diseases

Mitesh Shetty
<span title="">2021</span> <i title="Jaypee Brothers Medical Publishing"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/qybrow4jnrhrhnvz2slqte35cm" style="color: black;">Pediatric Infectious Disease</a> </i> &nbsp;
Currently, the principal possible applications of WGS in the diagnostic microbiology laboratory for characterizing bacterial pathogen are identification, typing, detection of resistance, and virulence  ...  Genomics and whole-genome sequencing (WGS) can greatly enhance human knowledge and understanding of infectious diseases.  ...  • Requires separate emulsion PCR library amplification before sequencing (slow and complicated), though automation can be performed using the separate Ion Chef systemHigh er er ro r r ates ,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5005/jp-journals-10081-1296">doi:10.5005/jp-journals-10081-1296</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/kfvcug7c5fe5pjmfv6ahxnjhfa">fatcat:kfvcug7c5fe5pjmfv6ahxnjhfa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210701224203/https://www.pidjournal.com/doi/pdf/10.5005/jp-journals-10081-1296" 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/78/e6/78e6444bb6fcd1f17c8640b87e5b34f24e149629.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5005/jp-journals-10081-1296"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Next-generation sequencing of HIV-1 single genome amplicons

Gustavo H. Kijak, Eric Sanders-Buell, Phuc Pham, Elizabeth A. Harbolick, Celina Oropeza, Anne Marie O'Sullivan, Meera Bose, Charmagne G. Beckett, Mark Milazzo, Merlin L. Robb, Sheila A. Peel, Paul T. Scott (+5 others)
<span title="2019-03-11">2019</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/73ub45gc3vdgjfznghcxzbesym" style="color: black;">Biomolecular Detection and Quantification</a> </i> &nbsp;
With lower sample requirements and higher throughput, this approach is suitable to support the increasing demand for high-quality and cost-effective HIV-1 sequences in fields such as molecular epidemiology  ...  Sequencing of SGA amplicons is performed by capillary Sanger sequencing, which presents low throughput, requires a high amount of template, and is highly sensitive to template/primer mismatching.  ...  An author is an employee of the U.S. Government and as such under the provisions of 17 U.S.C. 105, copyright protection is not available for this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bdq.2019.01.002">doi:10.1016/j.bdq.2019.01.002</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/30923677">pmid:30923677</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6423504/">pmcid:PMC6423504</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/c2ubeq4bz5bixii7qiuyguprlq">fatcat:c2ubeq4bz5bixii7qiuyguprlq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210526111939/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC6423504&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/04/2a/042aea17fe8c0723b6b3252a5f7509f070fe9496.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.bdq.2019.01.002"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6423504" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Real-Time PCR: Revolutionizing Detection and Expression Analysis of Genes

S.A. Deepak, K.R. Kottapalli, R. Rakwal, G. Oros, K.S. Rangappa, H. Iwahashi, Y. Masuo, G.K. Agrawal
<span title="2007-06-01">2007</span> <i title="Bentham Science Publishers Ltd."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/mqegkl27nzckpogkyj47kjwblu" style="color: black;">Current Genomics</a> </i> &nbsp;
Real-time PCR, hereafter abbreviated RT PCR, is becoming a common tool for detecting and quantifying expression profiles of selected genes.  ...  The overwhelming majority of the current publications in the field of the genomics have been dealing with the various aspects of the application of methods in medicine, with the search for new techniques  ...  A high throughput identification of Fusarium at genus level or distinguishing species [96] [97] has been published.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920207781386960">doi:10.2174/138920207781386960</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18645596">pmid:18645596</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2430684/">pmcid:PMC2430684</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/mt3spansyzdlvfzhhygtu73fzy">fatcat:mt3spansyzdlvfzhhygtu73fzy</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200328225215/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2430684&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/31/d0/31d03f8b92eedea2da1f28caa3b409006e784f5c.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2174/138920207781386960"> <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/PMC2430684" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Applying Rapid Genome Sequencing Technologies To Characterize Pathogen Genomes

Karyn Meltz Steinberg, David T. Okou, and Michael E. Zwick
<span title="2008-02-01">2008</span> <i title="American Chemical Society (ACS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/nx5fizmox5he5k23oobehznqna" style="color: black;">Analytical Chemistry</a> </i> &nbsp;
Automated data-quality assessment and sequence-assembly algorithms are then used to reconstruct the original genome sequence.  ...  Lin et al. developed an R A called RPM v.1 that contains 57 genomic sequences from diagnostic regions of 26 different respiratory pathogens, including human adenovirus and influenza A virus (38) .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ac086027z">doi:10.1021/ac086027z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18320606">pmid:18320606</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5628356/">pmcid:PMC5628356</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/j6mudkkqnfgm3map7oggy3c5vi">fatcat:j6mudkkqnfgm3map7oggy3c5vi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20100727160548/http://a-s.clayton.edu/burnett/old_courses/2008-01/BIOL4500/readings/05-ZwickME_2008_AnalyticalChem.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/99/bc/99bc91376c5c13a231eae20a6c11695fda5711fc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1021/ac086027z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acs.org </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5628356" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of Adventitious Viruses from Biologicals Using a Broad-Spectrum Microbial Detection Array

C. Jaing, S. Gardner, K. McLoughlin, J. B. Thissen, T. Slezak
<span title="2011-11-01">2011</span> <i title="Parenteral Drug Association, Inc."> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/huo5wnn4qzcphjidblnxa6nqnu" style="color: black;">PDA journal of pharmaceutical science and technology</a> </i> &nbsp;
We recently used this array to identify an adventitious virus from a vaccine product. We have also used this array to detect viral and bacterial infections from various human clinical samples.  ...  We designed the Lawrence Livermore Microbial Detection Array (LLMDA), which contains 388,000 DNA probes. This array can detect any sequenced viruses or bacteria within 24 hours.  ...  LLMDA probe design for broad spectrum detection of viruses and bacteria The original LLMDA design covers all bacteria and viruses with sequenced genomes available in spring of 2007, including 38,000 virus  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5731/pdajpst.2011.00838">doi:10.5731/pdajpst.2011.00838</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22294595">pmid:22294595</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pqr5p4ol6rdqnbomutkrf5djci">fatcat:pqr5p4ol6rdqnbomutkrf5djci</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723224222/https://digital.library.unt.edu/ark:/67531/metadc868592/m2/1/high_res_d/1122212.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/30/86/3086d966879576e20b444fc339f0934ba4907983.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5731/pdajpst.2011.00838"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Antibacterial vaccine design using genomics and proteomics

Guido Grandi
<span title="">2001</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/va62z7g5ofgoday6mzmc4uzqgm" style="color: black;">Trends in Biotechnology</a> </i> &nbsp;
As for other fields of medical sciences, it is expected that vaccinology will greatly benefit from the emerging genomics technologies such as bioinformatics, proteomics and DNA microarrays.  ...  Secondly, regulatory authorities now require vaccines to meet extremely high standards of safety and chemical-physical characterization.  ...  Valiante for his critical review of the manuscript, Monica Guerrieri for up-dated information on currently available vaccines and Antionetta Maiorino for her expert secretarial assistance.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01600-6">doi:10.1016/s0167-7799(01)01600-6</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/11301131">pmid:11301131</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7ddyppndqjczjm6h2deav3j22a">fatcat:7ddyppndqjczjm6h2deav3j22a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808215241/http://biotecnologie.unipr.it/didattica/att/416f.file.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/ae/b0/aeb06bce064633540388b4e5b76ea829cf7cf7f8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/s0167-7799(01)01600-6"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Single-Cell Genomics: Enabling the Functional Elucidation of Infectious Diseases in Multi-Cell Genomes

Shweta Sahni, Partha Chattopadhyay, Kriti Khare, Rajesh Pandey
<span title="2021-11-12">2021</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zxssj3u7b5f7zbfrb4egitf67q" style="color: black;">Pathogens</a> </i> &nbsp;
Since the time when detection of gene expression in single cells by microarrays to the Next Generation Sequencing (NGS) enabled Single Cell Genomics (SCG), it has played a pivotal role to understand and  ...  The increasing role of AI in SCG data analysis has further enhanced its applicability in building models for clinical intervention.  ...  Acknowledgments: P.C. and K.K. acknowledge the CSIR for their Research Fellowship. The authors acknowledge Aradhita Baral for valuable help with research management for the projects funding the work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pathogens10111467">doi:10.3390/pathogens10111467</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34832622">pmid:34832622</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8624509/">pmcid:PMC8624509</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rmvykiywpzatzkb464dhvu62ni">fatcat:rmvykiywpzatzkb464dhvu62ni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211123193857/https://mdpi-res.com/d_attachment/pathogens/pathogens-10-01467/article_deploy/pathogens-10-01467.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/04/d2/04d263a4ea54d5e5a8cf79706f72e70017cb509e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/pathogens10111467"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8624509" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Detection of Peptides, Proteins, and Drugs That Selectively Interact With Protein Targets

I. G. Serebriiskii
<span title="2002-11-01">2002</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;
Genome sequencing has been completed for multiple organisms, and pilot proteomic analyses reported for yeast and higher eukaryotes.  ...  We summarize the use of this system to detect proteins and peptides that target well-defined specific motifs in larger protein structures, to facilitate rapid identification of specific interactors from  ...  We thank Antje Taliana, Marijane Russell, and Michelle Berman for contributing work in the area of Dual Bait reagent construction.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.450702">doi:10.1101/gr.450702</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/12421766">pmid:12421766</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC187545/">pmcid:PMC187545</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ulqmbgf3ijfdhobv4o5tapojvu">fatcat:ulqmbgf3ijfdhobv4o5tapojvu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180720025720/https://genome.cshlp.org/content/12/11/1785.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/fe/30/fe30f4a7b0f16ed47e9fd464a5a80697839184f5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.450702"> <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/PMC187545" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Identification of novel mammalian growth regulatory factors by genome-scale quantitative image analysis

J. N. Harada
<span title="2005-08-01">2005</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;
However, the current repertoire of high-throughput detection methodologies has limited the scope of cellular phenotypes that can be studied.  ...  In this report, we describe the systematic identification of mammalian growth-regulatory factors achieved through the integration of automated microscopy, pattern recognition analysis, and cell-based functional  ...  Moran for helpful comments on the manuscript and advice.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.3889305">doi:10.1101/gr.3889305</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16024821">pmid:16024821</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1182226/">pmcid:PMC1182226</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/737glezjvzdsjazuehovglzgem">fatcat:737glezjvzdsjazuehovglzgem</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722214536/https://genome.cshlp.org/content/15/8/1136.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/e5/b8/e5b8728843702564c46fcfdac108a8346789f04d.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1101/gr.3889305"> <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/PMC1182226" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>
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