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Computational prediction and analysis of protein-protein interaction networks [article]

Somaye Hashemifar
<span title="2017-09-13">2017</span> <i > arXiv </i> &nbsp; <span class="release-stage" >pre-print</span>
The talk will consist of two parts. I will discuss several methods for protein-protein interaction network alignment and investigate their preferences to other existing methods.  ...  Further, I briefly talk about reconstruction of protein-protein interaction networks by using deep learning.  ...  Chapter 4 Module-based Global Alignment of PPI Networks 4 .1. Introduction Proteins with similar sequences are more likely to have a similar function 62 .  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1709.01923v2">arXiv:1709.01923v2</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cy63jpklarbmxbrcvfgzx2ob2q">fatcat:cy63jpklarbmxbrcvfgzx2ob2q</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200915092623/https://arxiv.org/ftp/arxiv/papers/1709/1709.01923.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/f5/67/f5674b9685151c4c63393c8cc5cd7539c63cddc5.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://arxiv.org/abs/1709.01923v2" 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>

SAlign–a structure aware method for global PPI network alignment

Umair Ayub, Imran Haider, Hammad Naveed
<span title="2020-11-04">2020</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Background High throughput experiments have generated a significantly large amount of protein interaction data, which is being used to study protein networks.  ...  Similarly, a comparative study of proteinprotein interaction (PPI) networks of different species reveals important insights which may help in disease analysis and drug design.  ...  We can represent the proteins of a particular specie as a network, where nodes in the network represent the proteins and edges show the interactions between these proteins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03827-5">doi:10.1186/s12859-020-03827-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33148180">pmid:33148180</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/gve5h23p6vhi7fivppzskot5ta">fatcat:gve5h23p6vhi7fivppzskot5ta</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20201106101607/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/s12859-020-03827-5" 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/11/dc/11dca40f12945f212a4281a3c457bc8f353d3200.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s12859-020-03827-5"> <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>

Unified Alignment of Protein-Protein Interaction Networks

Noël Malod-Dognin, Kristina Ban, Nataša Pržulj
<span title="2017-04-19">2017</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/tnqhc2x2aneavcd3gx5h7mswhm" style="color: black;">Scientific Reports</a> </i> &nbsp;
Paralleling the increasing availability of protein-protein interaction (PPI) network data, several network alignment methods have been proposed.  ...  Globally aligning the PPI networks of two species means finding a one-to-one correspondence between the proteins of the two networks (also called an alignment) that highlights functionally and evolutionary  ...  MODULEALIGN 32 , which is the most recent aligner, uses a hierarchical clustering of functionally related proteins to define its module-based homology scores between proteins.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-01085-9">doi:10.1038/s41598-017-01085-9</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/28424527">pmid:28424527</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC5430463/">pmcid:PMC5430463</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/dc3tokdnqjcpnlkynbe3s2zm3e">fatcat:dc3tokdnqjcpnlkynbe3s2zm3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180721234800/http://discovery.ucl.ac.uk/1557414/1/Malod-Dognin_s41598-017-01085-9.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/67/54/67546ce1f18791d2538611e5f4a2afd93b1f99ae.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/s41598-017-01085-9"> <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/PMC5430463" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Discovery of two-level modular organization from matched genomic data via joint matrix tri-factorization

Jinyu Chen, Shihua Zhang
<span title="2018-06-06">2018</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;
We respectively identified a twolevel miRNA-gene module network and a two-level gene-drug module network.  ...  NetNMF could reveal the modules of each dimension and the connections within and between both types of modules.  ...  ModuleAlign (22) is a module-based global alignment of protein-protein interaction networks from two species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky440">doi:10.1093/nar/gky440</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29878151">pmid:29878151</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cqajazfxezbplpf3pvvoiqc23a">fatcat:cqajazfxezbplpf3pvvoiqc23a</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190218171705/http://pdfs.semanticscholar.org/0e93/0ae9c1af8ac458d14de5007925b2a00eb147.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/0e/93/0e930ae9c1af8ac458d14de5007925b2a00eb147.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/nar/gky440"> <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>

Pairwise Biological Network Alignment Based on Discrete Bat Algorithm

Jing Chen, Ying Zhang, Jin-Fang Xia
<span title="2021-11-03">2021</span>
Network alignment is used to analyze these data to identify conserved functional network modules and understand evolutionary relationships across species.  ...  Based on the bat algorithm, the global pairwise alignment algorithm BatAlign is proposed. In BatAlign, the individual velocity and the position are represented by a discrete code.  ...  Acknowledgments This research was funded by the 2015 Jiangsu Province Science Foundation for Youths of China (Grant No. BK20150159).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/5548993">doi:10.1155/2021/5548993</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/34777564">pmid:34777564</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC8580637/">pmcid:PMC8580637</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3zimeaq4uvfojnxtaq3ryyq7ba">fatcat:3zimeaq4uvfojnxtaq3ryyq7ba</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20211130212137/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC8580637&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/44/54/44545a989ac848d2af34765c5f9cd7b133e4a059.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1155/2021/5548993"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> hindawi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8580637" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>