Filters








234 Hits in 3.3 sec

GenMAPP 2: new features and resources for pathway analysis

Nathan Salomonis, Kristina Hanspers, Alexander C Zambon, Karen Vranizan, Steven C Lawlor, Kam D Dahlquist, Scott W Doniger, Josh Stuart, Bruce R Conklin, Alexander R Pico
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Results: To address the growing needs of the microarray community we have released version 2 of Gene Map Annotator and Pathway Profiler (GenMAPP), a new GenMAPP database schema, and integrated resources  ...  for pathway analysis.  ...  Acknowledgements We thank the GenMAPP user community for valuable suggestions, pathway submissions, and the inspiration to keep improving GenMAPP.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-217">doi:10.1186/1471-2105-8-217</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17588266">pmid:17588266</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1924866/">pmcid:PMC1924866</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xxrpnzcivreobfrgte3lzn3kce">fatcat:xxrpnzcivreobfrgte3lzn3kce</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170830085832/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-8-217?site=http://bmcbioinformatics.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/ab/13/ab13413f0e7f405f7131fc4a0bfb9b156e1118b2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-217"> <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/PMC1924866" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Presenting and exploring biological pathways with PathVisio

Martijn P van Iersel, Thomas Kelder, Alexander R Pico, Kristina Hanspers, Susan Coort, Bruce R Conklin, Chris Evelo
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
PathVisio is a new visualization tool for biological pathways that mimics the popular GenMAPP tool with a completely new Java implementation that allows better integration with other open source projects  ...  The GenMAPP MAPP file format is replaced by GPML, a new XML file format that provides seamless exchange of graphical pathway information among multiple programs.  ...  and Hakim Achterberg for help in PathVisio development.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-399">doi:10.1186/1471-2105-9-399</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18817533">pmid:18817533</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2569944/">pmcid:PMC2569944</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ghuipbfenvfvxbkw3gg5yc3zjq">fatcat:ghuipbfenvfvxbkw3gg5yc3zjq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191117143202/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2569944&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/60/1b/601b9de735905bfbdd87196917c79f542414f8d7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-9-399"> <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/PMC2569944" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Pathway Miner: extracting gene association networks from molecular pathways for predicting the biological significance of gene expression microarray data

R. Pandey, R. K. Guru, D. W. Mount
<span title="2004-05-14">2004</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;
The genes are mapped onto pathways and gene product association networks are extracted for genes that co-occur in pathways. The networks can be filtered for analysis based on user-selected options.  ...  Pathway Miner catalogs genes based on their role in metabolic, cellular and regulatory pathways. A Fisher exact test is provided as an option to rank pathways.  ...  ACKNOWLEDGEMENTS The authors thank Nirav Merchant and Gavin Nelson of the Bio Computing Facility at the University of Arizona for systems support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth215">doi:10.1093/bioinformatics/bth215</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15145817">pmid:15145817</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3bts4ao7nbcmhemgg3xyrgnqfi">fatcat:3bts4ao7nbcmhemgg3xyrgnqfi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190228010732/http://pdfs.semanticscholar.org/8989/e2be0d4aa0fa7156050b5edcc4714db9fa33.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/89/89/8989e2be0d4aa0fa7156050b5edcc4714db9fa33.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/bth215"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a>

PathJam: a new service for integrating biological pathway information

Daniel Glez-Peña, Miguel Reboiro-Jato, Rubén Domínguez, Gonzalo Gómez-López, David G Pisano, Florentino Fdez-Riverola
<span title="2010-10-28">2010</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative  ...  PathJam's unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized  ...  Acknowledgements We thank JM Rodríguez and the National Institute of Bioinformatics (www.inab.org), a platform of Genoma España for providing useful information and advice in CARGO widget implementation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2010-147">doi:10.2390/biecoll-jib-2010-147</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20980714">pmid:20980714</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ulhsask5bzel5cwtbga2alyw2m">fatcat:ulhsask5bzel5cwtbga2alyw2m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200225041505/https://www.degruyter.com/downloadpdf/j/jib.2010.7.issue-1/biecoll-jib-2010-147/biecoll-jib-2010-147.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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.2390/biecoll-jib-2010-147"> <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>

PathJam: a new service for integrating biological pathway information

Daniel Glez-Peña, Miguel Reboiro-Jato, Rubén Domínguez, Gonzalo Gómez-López, David G. Pisano, Florentino Fdez-Riverola
<span title="2010-03-01">2010</span> <i title="Walter de Gruyter GmbH"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fvl4m6o2tre4pcvl4ljymxu4ly" style="color: black;">Journal of Integrative Bioinformatics</a> </i> &nbsp;
The tool has been designed for both (i) being intuitive for wet-lab users providing statistical enrichment analysis of pathway annotations and (ii) giving support to the development of new integrative  ...  PathJam's unique features and advantages include interactive graphs linking pathways and genes of interest, downloadable results in fully compatible formats, GSEA compatible output files and a standardized  ...  Acknowledgements We thank JM Rodríguez and the National Institute of Bioinformatics (www.inab.org), a platform of Genoma España for providing useful information and advice in CARGO widget implementation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2010-147">doi:10.1515/jib-2010-147</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/a3idtqhpgbdqbe4ohaduyycf5m">fatcat:a3idtqhpgbdqbe4ohaduyycf5m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201201144658/https://www.degruyter.com/downloadpdf/journals/jib/7/1/article-p97.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/3c/ec/3cec72e733fca2988ff8e959199537c273d6e851.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1515/jib-2010-147"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> degruyter.com </button> </a>

Public databases and software for the pathway analysis of cancer genomes

Ivy F L Tsui, Raj Chari, Timon P H Buys, Wan L Lam
<span title="2007-12-12">2007</span> <i title="Libertas Academica, Ltd"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/arhjbkogknfc5m4fvcz76b7r6m" style="color: black;">Cancer Informatics</a> </i> &nbsp;
In this review, we discuss approaches to the analysis of genomic data and describe the publicly available resources for studying biological pathways.  ...  The explosion in available data has generated opportunities for investigation of concerted changes that disrupt biological functions, this in turns created a need for computational tools for pathway analysis  ...  An important feature of Cytoscape is its extensible software framework which allows users to implement new algorithms and network computations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19455256">pmid:19455256</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2410087/">pmcid:PMC2410087</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/xb36gu4llvfzfpjyxn4bls4dsq">fatcat:xb36gu4llvfzfpjyxn4bls4dsq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209091524/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2410087&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/97/94/979459ada6ca6ce3bd5ddc71a5cc357dd94c6380.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2410087" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ArrayXPath II: mapping and visualizing microarray gene-expression data with biomedical ontologies and integrated biological pathway resources using Scalable Vector Graphics

H.-J. Chung, C. H. Park, M. R. Han, S. Lee, J. H. Ohn, J. Kim, J. Kim, J. H. Kim
<span title="2005-07-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
ACKNOWLEDGEMENTS The authors thank all SNUBI members and external testers for their efforts to input and evaluate the pathway diagrams.  ...  Funding to pay the Open Access publication charges for this article was provided by the above mentioned grant. Conflict of interest statement. None declared.  ...  ArrayXPath also provides GO-based annotation and OMIM information to complement pathway-based analysis of gene expression clusters. Figure 2 . 2 Pathway crosstalk.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki450">doi:10.1093/nar/gki450</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15980549">pmid:15980549</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1160211/">pmcid:PMC1160211</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6xnncgryifedjhr7nadys5liua">fatcat:6xnncgryifedjhr7nadys5liua</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190302175818/http://pdfs.semanticscholar.org/a73c/fbfe876726f4131dc32a00346479456a4de2.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/a7/3c/a73cfbfe876726f4131dc32a00346479456a4de2.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki450"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160211" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

WikiPathways: Pathway Editing for the People

Alexander R Pico, Thomas Kelder, Martijn P van Iersel, Kristina Hanspers, Bruce R Conklin, Chris Evelo
<span title="2008-07-22">2008</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tsaumnzpkvdmvdi3blhl5clb24" style="color: black;">PLoS Biology</a> </i> &nbsp;
with pathway visualization and analysis tools such as Cytoscape [11] , GenMAPP [9] , and PathVisio (http://www.pathvisio. org).  ...  Outside of the immediate group of developers, WikiPathways has already attracted ten new mouse pathways, nine new human pathways, six new zebrafish pathways, three new rat pathways, and one Portal for  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.0060184">doi:10.1371/journal.pbio.0060184</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18651794">pmid:18651794</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2475545/">pmcid:PMC2475545</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ohczavszz5b3dpsllugdbwxcfe">fatcat:ohczavszz5b3dpsllugdbwxcfe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190506023552/https://journals.plos.org/plosbiology/article/file?id=10.1371/journal.pbio.0060184&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] </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pbio.0060184"> <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/PMC2475545" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

PathwayExplorer: web service for visualizing high-throughput expression data on biological pathways

B. Mlecnik, M. Scheideler, H. Hackl, J. Hartler, F. Sanchez-Cabo, Z. Trajanoski
<span title="2005-07-01">2005</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
KEGG, BioCarta and GenMAPP.  ...  Mapped pathways are ranked for the easy selection of the pathway of interest, displaying all available genes of this pathway with their expression profiles in a selectable and intuitive color code.  ...  ACKNOWLEDGEMENTS The authors thank all members of the Institute for Genomics and Bioinformatics and external scientists who contributed to this work and James McNally for critically reviewing the manuscript  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki391">doi:10.1093/nar/gki391</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15980551">pmid:15980551</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1160152/">pmcid:PMC1160152</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pb34fnphzfckppcqxcgeok3zmu">fatcat:pb34fnphzfckppcqxcgeok3zmu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218101329/http://pdfs.semanticscholar.org/0b06/047063760f55db45d9f01432e1c4177ce4a6.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/0b/06/0b06047063760f55db45d9f01432e1c4177ce4a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gki391"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1160152" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Linking microarray reporters with protein functions

Stan Gaj, Arie van Erk, Rachel IM van Haaften, Chris TA Evelo
<span title="">2007</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
to a local GenMAPP pathway from 9.6% to 16.7%.  ...  For Agilent, 35.3% of the total reporters are now linked towards GO nodes and 7.1% on local pathways.  ...  Korbeeck and W.P.A. Ligtenberg from the Technological University of Eindhoven for their contribution on the cEMBL approach.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-360">doi:10.1186/1471-2105-8-360</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17897448">pmid:17897448</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2140066/">pmcid:PMC2140066</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/n5ejn6b4ybe3hiikqq2jry4oae">fatcat:n5ejn6b4ybe3hiikqq2jry4oae</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170914123232/https://link.springer.com/content/pdf/10.1186%2F1471-2105-8-360.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/8e/a1/8ea11f2577e4f001e65db1c42c6d4667148dc9be.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-8-360"> <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/PMC2140066" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Visualizing Biological Pathways: Requirements Analysis, Systems Evaluation and Research Agenda

Purvi Saraiya, Chris North, Karen Duca
<span title="2005-06-23">2005</span> <i title="SAGE Publications"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/fbfm5bozvfey7fdx64xnpusfgi" style="color: black;">Information Visualization</a> </i> &nbsp;
The recent shift towards data-intensive bioinformatics and systems-level science has created a strong need for advanced pathway visualizations that support exploratory analysis.  ...  This paper presents a comprehensive list of requirements for pathway visualization systems, based on interviews conducted to understand life scientists' needs for pathway analysis.  ...  Table 1 1 Summary of requirements for pathway visualization systems Categories Requirements Tasks Pathway assembly 1. Construct and Update Collect and link pathways from multiple resources 2.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1057/palgrave.ivs.9500102">doi:10.1057/palgrave.ivs.9500102</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dhiv6vhyuva5jczsaq6nyo4w7i">fatcat:dhiv6vhyuva5jczsaq6nyo4w7i</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20061208102156/http://infovis.cs.vt.edu:80/papers/IVS-pathways.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/20/cd/20cd469eb445217aa19246dc1a00016d74d391f5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1057/palgrave.ivs.9500102"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

WikiPathways: building research communities on biological pathways

T. Kelder, M. P. van Iersel, K. Hanspers, M. Kutmon, B. R. Conklin, C. T. Evelo, A. R. Pico
<span title="2011-11-16">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
New features include a zoomable pathway viewer, support for pathway ontology annotations, the ability to mark pathways as private for a limited time and the availability of stable hyperlinks to pathways  ...  New features are discussed, as well as developments in the community of contributors.  ...  Figure 1 . 1 The new interactive pathway viewer. Figure 2 . 2 Size and growth of the human pathway archive before and after launching WikiPathways.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1074">doi:10.1093/nar/gkr1074</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22096230">pmid:22096230</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3245032/">pmcid:PMC3245032</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wmolsaazdnhpbd27cydgovi2hu">fatcat:wmolsaazdnhpbd27cydgovi2hu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304113523/http://pdfs.semanticscholar.org/db42/af6329ba1c164b8e4fad27b9b8a7626aea67.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/db/42/db42af6329ba1c164b8e4fad27b9b8a7626aea67.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkr1074"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3245032" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The role of bioinformatics in pathway curation

A. S. Waagmeester, T. Kelder, C. T. A. Evelo
<span title="2008-11-26">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/cm37q7fk2zhc7nbgwhszqpwzd4" style="color: black;">Genes &amp; Nutrition</a> </i> &nbsp;
Diagrams and models of biological pathways are useful tools in biology. Pathway diagrams are mainly used for illustrative purposes for instance in textbooks and in presentations.  ...  Pathway models are used in the analysis of genomic data.  ...  the original author(s) and source are credited.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12263-008-0098-x">doi:10.1007/s12263-008-0098-x</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19034548">pmid:19034548</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2593017/">pmcid:PMC2593017</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/rzbowrplindixfl3sdtbjrh5ca">fatcat:rzbowrplindixfl3sdtbjrh5ca</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171114180233/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/ecb/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjEwMDcvczEyMjYzLTAwOC0wMDk4LXgucGRm.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/28/c9/28c94b66d50e9a4bc911b90b78eae2edba41e746.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12263-008-0098-x"> <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/PMC2593017" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Disease proteomics

<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/omnhw57bqbd55ogboeeeyr7kqy" style="color: black;">Genomic Medicine</a> </i> &nbsp;
Pathway analysis of these proteins was carried out using KEGG, IPA, GenMAPP and their gene ontology classification revealed transcription regulators, signal transducers, cell cycle and differentiation  ...  Stem cells have great potential for developing new approaches for the treatment of degenerative diseases including neurons, skeletal and cardiac muscles, beta cells of pancreas, and cancer cells.  ...  Pathway analysis of these proteins was carried out using KEGG, IPA, GenMAPP and their gene ontology classification revealed transcription regulators, signal transducers, cell cycle and differentiation  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-009-9091-8">doi:10.1007/s11568-009-9091-8</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19444648">pmid:19444648</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2694876/">pmcid:PMC2694876</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/fqidbx6kjzcvtmbhqhy5n7mozq">fatcat:fqidbx6kjzcvtmbhqhy5n7mozq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191102055033/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC2694876&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/b3/d5/b3d57a355c83f716dc04325bae5a0d2c88853320.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s11568-009-9091-8"> <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/PMC2694876" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

miRGator: an integrated system for functional annotation of microRNAs

S. Nam, B. Kim, S. Shin, S. Lee
<span title="2007-12-23">2007</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/hfp6p6inqbdexbsu4r7usndpte" style="color: black;">Nucleic Acids Research</a> </i> &nbsp;
Implemented functional categories include the GO, KEGG/GenMAPP/ BioCarta pathways (18, 19) and disease ontology of Ingenuity Pathway Analysis.  ...  Our pathway analysis includes the KEGG, GenMAPP and BioCarta pathway databases. Disease classification of the Ingenuity systems Inc. was used to test disease implications.  ...  normal tissues supports seven tissues including bladder, breast, colon, eye, kidney, lung and uterus. Conflict of interest statement. None declared.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkm829">doi:10.1093/nar/gkm829</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/17942429">pmid:17942429</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2238850/">pmcid:PMC2238850</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/heth457hgfbxla4pmp4hjesaxe">fatcat:heth457hgfbxla4pmp4hjesaxe</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160824044516/http://www.gene-quantification.com:80/nam-et-al-mirgator1.0-2008.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/d5/d6/d5d6b9748642d9a9ef54e10f18d9975c73e51e32.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkm829"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2238850" 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 234 results