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Differential dependency network analysis to identify condition-specific topological changes in biological networks

Bai Zhang, Huai Li, Rebecca B. Riggins, Ming Zhan, Jianhua Xuan, Zhen Zhang, Eric P. Hoffman, Robert Clarke, Yue Wang
<span title="2008-12-26">2008</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Results: Here, we report a differential dependency network (DDN) analysis to detect statistically significant topological changes in the transcriptional networks between two biological conditions.  ...  However, gene regulatory networks are dynamic and condition-specific; under different conditions, networks exhibit different regulation patterns accompanied by different transcriptional network topologies  ...  In this article, we propose a differential dependency network (DDN) analysis to model and detect the statistically significant topological changes in transcriptional networks between two conditions.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn660">doi:10.1093/bioinformatics/btn660</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19112081">pmid:19112081</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2642641/">pmcid:PMC2642641</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/hcnphxio4bewbais73oe3ifta4">fatcat:hcnphxio4bewbais73oe3ifta4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180730145005/https://watermark.silverchair.com/btn660.pdf?token=AQECAHi208BE49Ooan9kkhW_Ercy7Dm3ZL_9Cf3qfKAc485ysgAAAb0wggG5BgkqhkiG9w0BBwagggGqMIIBpgIBADCCAZ8GCSqGSIb3DQEHATAeBglghkgBZQMEAS4wEQQMfglNe6a5EhRDekozAgEQgIIBcDY6iqLxyKxUD762TD9wIy_erwyXe2HJJKSYKUAU422R1khdeA-aC8FBLevd2_8H1w7vaCohH8ZXAGmAwLHx1KYzS-J-XC0PB0XEQhxFgFEDsWZnE4vjGGnlWZDf0qjWIyNIfSIdJ95QC7FMac7NQuNjmDH1jqura_S60slcEPRzVm75l7qQDFZoeXculMjZ-uwGSkQBZlbb8ni-CvdA7xbvbEQgOO0P_iY0O3V7aBv0HTmHFUlDe8ItN6cvEp5UCmyNQgtlEikwu9DRHP0yqsQaCygtoAFp9kR9NkcgXct5cq9EG9rixpZe7T9PjeG9HI2Cn3Wri4N40cCab7kGt-s5l6oV0D0pMp9GWUCj8qq-z4tjlXpJzTTEkMpfosvn0gZDSf74wwQ-NDw1DxQzIVisj72zCsE1cUMux8TzZwT9q6nnWNKaDwDAdGRdDGfL6HHJgePKIn4vpuuRNwmHptJZozT8DWGteiZsTfvgR4EX" 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/01/a6/01a6f46faf6fc59043b36ea0260452d141c0b830.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btn660"> <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/PMC2642641" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DDN: a caBIG® analytical tool for differential network analysis

Bai Zhang, Ye Tian, Lu Jin, Huai Li, Ie-Ming Shih, Subha Madhavan, Robert Clarke, Eric P. Hoffman, Jianhua Xuan, Leena Hilakivi-Clarke, Yue Wang
<span title="2011-02-03">2011</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
Differential dependency network (DDN) is a caBIG (cancer Biomedical Informatics Grid) analytical tool for detecting and visualizing statistically significant topological changes in transcriptional networks  ...  representing two biological conditions.  ...  DISCUSSION DDN presents a differential network analysis approach to detect significant topological changes of biological networks in response to genetic/epigenetic/environmental variants.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr052">doi:10.1093/bioinformatics/btr052</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21296752">pmid:21296752</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3065688/">pmcid:PMC3065688</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/eszfwb3imfgrzihogxakajtsma">fatcat:eszfwb3imfgrzihogxakajtsma</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209081957/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3065688&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/21/1f/211fb64128f5a5f778de42711decd6d054695835.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btr052"> <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/PMC3065688" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

KNOWLEDGE-ASSISTED APPROACH TO IDENTIFY PATHWAYS WITH DIFFERENTIAL DEPENDENCIES

Gil Speyer, Jeff Kiefer, Harshil Dhruv, Michael Berens, Seungchan Kim
<span title="">2016</span> <i > <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/d4nr2uqysjfnpiksvyxq54p5bm" style="color: black;">Pacific Symposium on Biocomputing. Pacific Symposium on Biocomputing</a> </i> &nbsp;
Further analysis of topological characteristics of gene differential dependency networks provides a new approach to identify genes that could play important roles in biological signaling in a specific  ...  We have previously developed a statistical method to identify gene sets enriched with condition-specific genetic dependencies.  ...  Further analysis of topological characteristics of gene differential dependency networks provides a new approach to identify genes that could play important roles in biological signaling in a specific  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26776171">pmid:26776171</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4721243/">pmcid:PMC4721243</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ap5x54la65bkhfskcrwmp4gqb4">fatcat:ap5x54la65bkhfskcrwmp4gqb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170317081022/http://psb.stanford.edu/psb-online/proceedings/psb16/speyer.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/7d/d5/7dd52e273fd59f91505e7a5c29be0b3bebc8ea23.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4721243" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Dynamic network topology changes in functional modules predict responses to oxidative stress in yeast

Peddinti V. Gopalacharyulu, Vidya R. Velagapudi, Erno Lindfors, Eran Halperin, Matej Orešič
<span title="">2009</span> <i title="Royal Society of Chemistry (RSC)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/zcnlz4nminfhjcp5esifetrr4u" style="color: black;">Molecular Biosystems</a> </i> &nbsp;
Here we hypothesize that dynamic changes in the topology of functional modules of integrated biological networks reflect their activity under specific environmental challenges.  ...  In response to environmental challenges, biological systems respond with dynamic adaptive changes in order to maintain the functionality of the system.  ...  Functional modules in the network are identified using the Gene Ontology 20 and condition specific networks corresponding to all time points are constructed.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b815347g">doi:10.1039/b815347g</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/19225619">pmid:19225619</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/s6m43mnsijdy7gn7lm5rqjknti">fatcat:s6m43mnsijdy7gn7lm5rqjknti</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170810225241/http://lib.tkk.fi/Diss/2011/isbn9789513877590/article6.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/8a/ce/8acec95ad5ea65c3992863ad64cf561381b000e6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1039/b815347g"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

Analysis of Alzheimer's disease severity across brain regions by topological analysis of gene co-expression networks

Monika Ray, Weixiong Zhang
<span title="">2010</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/xua5vbjwszdirewaoqnikiu5zm" style="color: black;">BMC Systems Biology</a> </i> &nbsp;
Genes with zero topological overlap between two region-specific networks were used to characterise the differences between the two regions.  ...  We developed a novel method involving the differential topology of gene coexpression networks to understand the association among affected regions and disease severity.  ...  Acknowledgements The authors would like to thank Winnie Liang from the Translational Genomics Institute (TGen) for her assistance with the data.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-136">doi:10.1186/1752-0509-4-136</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20925940">pmid:20925940</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2976747/">pmcid:PMC2976747</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/2sspzv7qhnfsjpepfufd2zkeai">fatcat:2sspzv7qhnfsjpepfufd2zkeai</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190428214356/https://digitalcommons.wustl.edu/cgi/viewcontent.cgi?article=1116&amp;context=open_access_pubs" 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/9b/25/9b25756096fed43e7f9148ca47f13ba03b80eedc.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1752-0509-4-136"> <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/PMC2976747" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Differential Co-Expression Analyses Allow the Identification of Critical Signalling Pathways Altered during Tumour Transformation and Progression

Aurora Savino, Paolo Provero, Valeria Poli
<span title="2020-12-12">2020</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/3loumxx7kzamnlu4h6x3xoz6ay" style="color: black;">International Journal of Molecular Sciences</a> </i> &nbsp;
Differential co-expression networks are useful tools to identify changes in response to an external perturbation, such as mutations predisposing to cancer development, and leading to changes in the activity  ...  Biological systems respond to perturbations through the rewiring of molecular interactions, organised in gene regulatory networks (GRNs).  ...  These motivations led to the definition of several methods for differential co-expression analysis, aimed at identifying changes in networks' structure across conditions [36] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21249461">doi:10.3390/ijms21249461</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33322692">pmid:33322692</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/qlhz3uathrcnpfzt7y2uqyz57u">fatcat:qlhz3uathrcnpfzt7y2uqyz57u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201218060638/https://res.mdpi.com/d_attachment/ijms/ijms-21-09461/article_deploy/ijms-21-09461.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/73/82/7382a0f9e947e0fa2a518ea70ce8d8e7d5ccaad7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/ijms21249461"> <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>

Integration of Network Biology and Imaging to Study Cancer Phenotypes and Responses

Ye Tian, Sean S. Wang, Zhen Zhang, Olga C. Rodriguez, Emanuel Petricoin III, Ie-Ming Shih, Daniel Chan, Maria Avantaggiati, Guoqiang Yu, Shaozhen Ye, Robert Clarke, Chao Wang (+3 others)
<span title="2014-11-01">2014</span> <i title="Institute of Electrical and Electronics Engineers (IEEE)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/q75ftrlivrhrnno5ijjuyufx5a" style="color: black;">IEEE/ACM Transactions on Computational Biology &amp; Bioinformatics</a> </i> &nbsp;
Specifically, Differential Dependence Network (DDN) analysis was used to detect statistically significant topological rewiring in molecular networks between two phenotypic conditions, and in vivo Magnetic  ...  Resonance Imaging (MRI) was used to more accurately define phenotypic sample groups for such differential analysis.  ...  This work was supported in part by the National Institutes of Health under Grants CA129003, CA149147, HL111362, CA164384, NS029525, and CA160036 from Clinical Proteomic Tumor Analysis Consortium (CPTAC  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2014.2338304">doi:10.1109/tcbb.2014.2338304</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/25750594">pmid:25750594</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4348060/">pmcid:PMC4348060</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/g7q7q7wnyrhpfdagnyno6j5zdm">fatcat:g7q7q7wnyrhpfdagnyno6j5zdm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200206073046/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4348060&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/c9/21/c921a9bd5291ba220f551c8fbcdbf88ec724e0db.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1109/tcbb.2014.2338304"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> ieee.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4348060" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Ranking differential genes in co-expression networks

Omar Odibat, Chandan K. Reddy
<span title="">2011</span> <i title="ACM Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7y7p3qrae5bnlok65yvbqtexc4" style="color: black;">Proceedings of the 2nd ACM Conference on Bioinformatics, Computational Biology and Biomedicine - BCB &#39;11</a> </i> &nbsp;
Therefore, these methods cannot capture all the topological changes in the network structure.  ...  Identifying the genes that change between two conditions, such as normal versus cancer, is a crucial task in understanding the causes of diseases.  ...  Differential dependency network (DDN) [20] performs a permutation test to detect local topological changes in gene subnetworks, and Ryan et al.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2147805.2147849">doi:10.1145/2147805.2147849</a> <a target="_blank" rel="external noopener" href="https://dblp.org/rec/conf/bcb/OdibatR11.html">dblp:conf/bcb/OdibatR11</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cc66a7ds35g2hbrdvh7yqsxrni">fatcat:cc66a7ds35g2hbrdvh7yqsxrni</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829030026/http://www.cs.wayne.edu/~reddy/Papers/BCB11a.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/52/e9/52e95b397c190ef76e6fab4c63a79960af506676.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1145/2147805.2147849"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> acm.org </button> </a>

Comparison of low and high dose ionising radiation using topological analysis of gene coexpression networks

Monika Ray, Reem Yunis, Xiucui Chen, David M Rocke
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4srzxifvfrdlhjhg3dimznkp7m" style="color: black;">BMC Genomics</a> </i> &nbsp;
Conclusions: Our method of applying network topological differences can aid in identifying the differences among similar (eg: radiation effect) yet very different biological conditions (eg: different dose  ...  This is the first study where a network level analysis was performed across two different radiation doses at various time points, thereby illustrating changes in the cellular response over time.  ...  Acknowledgments The research reported in this paper was supported by grants from the National Institutes of Health (NHGRI R01-HG003352, NIAID R21-AI080604, NCRR UL1-RR024146), the Department of Energy  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-190">doi:10.1186/1471-2164-13-190</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22594378">pmid:22594378</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3443446/">pmcid:PMC3443446</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ra4dgqcy6bghhmy6utwkqsihxu">fatcat:ra4dgqcy6bghhmy6utwkqsihxu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722000807/https://cloudfront.escholarship.org/dist/prd/content/qt4tt7q5sx/qt4tt7q5sx.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/dd/ed/dded61a9654f58d8b0319f8b148651902e212c43.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2164-13-190"> <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/PMC3443446" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

DNF: A differential network flow method to identify rewiring drivers for gene regulatory networks

Jiang Xie, Fuzhang Yang, Jiao Wang, Mathew Karikomi, Yiting Yin, Jiamin Sun, Tieqiao Wen, Qing Nie
<span title="2020-05-26">2020</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/bby322qx6ndsje4ypr56c7nnly" style="color: black;">Neurocomputing</a> </i> &nbsp;
Differential network analysis has become an important approach in identifying driver genes in development and disease.  ...  We propose the differential network flow (DNF) method to identify key regulators of progression in development or disease.  ...  Differential network analysis aims to identify the differences between networks under different conditions [6] .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neucom.2020.05.028">doi:10.1016/j.neucom.2020.05.028</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34025035">pmid:34025035</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8139126/">pmcid:PMC8139126</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dmgzowdfa5gmnmjdhxhuku3ohq">fatcat:dmgzowdfa5gmnmjdhxhuku3ohq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210428200959/https://escholarship.org/content/qt7hp5k78t/qt7hp5k78t.pdf?t=ql2ey0" 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/ba/f0babfd80d597dbba8fafb68b0b06f0d06ec428a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.neucom.2020.05.028"> <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/PMC8139126" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Survey of Network-Based Approaches to Research of Cardiovascular Diseases

Anida Sarajlić, Nataša Pržulj
<span title="">2014</span> <i title="Hindawi Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/icbhosh775h7bgzgot6avm3cua" style="color: black;">BioMed Research International</a> </i> &nbsp;
Consequently, topology of biological networks has successfully been used for identifying genes, pathways, and modules that govern molecular actions underlying various complex diseases.  ...  Here, we review approaches that explore and use relationships between topological properties of biological networks and mechanisms underlying CVDs.  ...  However, topological analysis was usually limited to the disease specific subnetwork, without observing it in the context of a larger, more complete network.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/527029">doi:10.1155/2014/527029</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24772427">pmid:24772427</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3977459/">pmcid:PMC3977459</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/pu2qrjtgg5hm7j6htwcm3koi2u">fatcat:pu2qrjtgg5hm7j6htwcm3koi2u</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190304123239/http://pdfs.semanticscholar.org/c685/743bc5c3b1c578e648eef394290c32a40f07.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/c6/85/c685743bc5c3b1c578e648eef394290c32a40f07.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2014/527029"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3977459" 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 conserved drought stress responsive gene-network across tissues and developmental stages in rice

Shuchi Smita, Amit Katiyar, Dev Mani Pandey, Viswanathan Chinnusamy, Sunil Archak, Kailash Chander Bansal
<span title="2013-01-18">2013</span> <i title="Biomedical Informatics"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iztfdaqh6bclfpgb2mitxtn5sm" style="color: black;">Bioinformation</a> </i> &nbsp;
study, while down regulation appears to be regulated by tissue specific pathways in rice.  ...  Genes with correlated expression patterns can be best identified by using coexpression network analysis of transcriptome data.  ...  Results & Discussion: Signed WGCNA modules in temporal-spatial data set Differential expression analysis identified 8244 DEGs (2 fold up or down) in at least one of the tissues under drought condition.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630009072">doi:10.6026/97320630009072</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23390349">pmid:23390349</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3563401/">pmcid:PMC3563401</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tw4q456rwfbvtbm42dts2wxokq">fatcat:tw4q456rwfbvtbm42dts2wxokq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20150922091148/http://bioinformation.net/009/97320630009072.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/20/12/201213161e50f9f068c9dd92a4ce3082e0657189.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6026/97320630009072"> <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/PMC3563401" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Integrative approaches for finding modular structure in biological networks

Koyel Mitra, Anne-Ruxandra Carvunis, Sanath Kumar Ramesh, Trey Ideker
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/wg7vnqrxzveutlxxgtyxqydvjy" style="color: black;">Nature reviews genetics</a> </i> &nbsp;
A recent focus of bioinformatics research has been to integrate these networks with each other and with diverse molecular profiles to identify sets of molecules and interactions that participate in a common  ...  biological function -that is, 'modules'.  ...  Acknowledgements We gratefully acknowledge US National Institutes of Health (NIH) grants P41 GM103504 and P50 GM085764 in support of this work.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg3552">doi:10.1038/nrg3552</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24045689">pmid:24045689</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3940161/">pmcid:PMC3940161</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4b5rihmvyzefrm3om7vzanvqc4">fatcat:4b5rihmvyzefrm3om7vzanvqc4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808064914/http://med.ucsd.edu/som/medicine/research/labs/ideker/publications/Documents/mitra2013.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/ea/99ea2db35ea00745b148a2ad21888da9f4029863.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/nrg3552"> <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/PMC3940161" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Network Medicine in the age of biomedical big data [article]

Abhijeet R. Sonawane, Scott T. Weiss, Kimberly Glass, Amitabh Sharma
<span title="2019-03-13">2019</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
More importantly, we delve into ways in which the network medicine approach, aided by phenotype-specific biomedical data, can be gainfully applied.  ...  Taken together, the understanding gained from combining biomedical data with networks can be useful for characterizing disease etiologies and identifying therapeutic targets, which, in turn, will lead  ...  Changes in network topology, driven by underlying condition-specific data, can yield valuable insights and help to identify driver nodes and network biomarkers, such as a set of strengthened or weakened  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1903.05449v1">arXiv:1903.05449v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/7v4pvoxezjd55ex5ei2jbteswm">fatcat:7v4pvoxezjd55ex5ei2jbteswm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200826012910/https://arxiv.org/ftp/arxiv/papers/1903/1903.05449.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/ce/46/ce46b883756c987f1ae3c62ce10b70dd5fab8d9f.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1903.05449v1" title="arxiv.org access"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> arxiv.org </button> </a>

Graphite Web: web tool for gene set analysis exploiting pathway topology

Gabriele Sales, Enrica Calura, Paolo Martini, Chiara Romualdi
<span title="2013-05-10">2013</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;
Biological pathways are, in fact, not only gene lists but can be represented through a network where genes and connections are, respectively, nodes and edges.  ...  These methods can be further divided into 'topological' and 'non-topological' methods according to their ability to gain power from pathway topology.  ...  ACKNOWLEDGEMENTS The authors acknowledge the CARIPARO Foundation (Project for Excellence 2012: 'Role of coding and noncoding RNA in chronic myeloproliferative neoplasms: from bioinformatics to translational  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt386">doi:10.1093/nar/gkt386</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23666626">pmid:23666626</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3977659/">pmcid:PMC3977659</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/acv5nfnqincd5k7kibg6psiuny">fatcat:acv5nfnqincd5k7kibg6psiuny</a> </span>
<a target="_blank" rel="noopener" href="https://archive.org/download/pubmed-PMC3977659/PMC3977659-gkt386.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> File Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/f4/d7/f4d73c942a1496f770f9fc704d889aee09d58efd.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gkt386"> <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/PMC3977659" 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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