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publications.html
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<!DOCTYPE html>
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<meta name="Keywords" content="KnetMiner, tool, Gene, Genome, QTL, Ondex, Plant, Animal, Data Mining, Candidate Gene, Ranking, Prioritization, Bioinformatics, knowledge graph, network" />
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<p style="color:white; display:inline-block;">Try our new website <a target="_blank" href="https://knetminer.com/wordpress/" style="color:darkorange;">here</a>. Note: under active development, may be unavailable at times.</p>
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<h3 id="writing">Lab Publications <i class="glyphicon glyphicon-pencil" alt="pencil"></i></h3>
<ul class="publi">
<li>Hassani-Pak K, Singh A, Brandizi M, Hearnshaw J, Phillips AL, Doonan JH and Rawlings C. (2020). <a class="link-publications" href="https://www.biorxiv.org/content/10.1101/2020.04.02.017004v1">KnetMiner - Intelligent search and visualisation of connected data to explain complex traits and diseases</a>. bioRxiv</li>
<li>Brandizi M, Singh A, Rawlings C and Hassani-Pak K. (2018). <a class="link-publications" href="https://doi.org/10.6084/m9.figshare.7314323.v1">Getting the best of Linked Data and Property Graphs: rdf2neo and the KnetMiner Use Case</a>. SWAT4LS Paper Proceedings.</li>
<li>Singh A, Rawlings C and Hassani-Pak K. (2018). <a class="link-publications" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6347035/">KnetMaps: a BioJS component to visualize biological knowledge networks</a>. F1000 Research.</li>
<li>Brandizi M, Singh A, Rawlings C and Hassani-Pak K. (2018). <a class="link-publications" href="https://www.degruyter.com/view/j/jib.ahead-of-print/jib-2018-0023/jib-2018-0023.xml">Towards FAIRer Biological Knowledge Networks Using a Hybrid Linked Data and Graph Database Approach</a>. Journal of Integrative Bioinformatics.</li>
<li>Hassani-Pak K (2017). <a class="link-publications" href="https://pub.uni-bielefeld.de/publication/2915227">KnetMiner - An integrated data platform for gene mining and biological knowledge discovery</a>. Dissertation. Bielefeld University.</li>
<li>Hassani-Pak K and Rawlings C. (2017). <a class="link-publications" href="https://www.degruyter.com/view/j/jib.2017.14.issue-1/jib-2016-0002/jib-2016-0002.xml"> Knowledge Discovery in Biological Databases for Revealing Candidate Genes Linked to Complex Phenotypes</a>. Journal of Integrative Bioinformatics.</li>
<li>Hassani-Pak K, Castellote M, Esch M, Hindle M, Lysenko A, Taubert J and Rawlings C. (2016). <a class="link-publications" href="http://www.sciencedirect.com/science/article/pii/S2212066116300308">Developing integrated crop knowledge networks to advance candidate gene discovery</a>. Applied & Translational Genomics.</li>
<li>Taubert J, Hassani-Pak K, Castells-Brooke N and Rawlings C. (2014). <a class="link-publications" href="http://bioinformatics.oxfordjournals.org/content/early/2014/01/11/bioinformatics.btt740.full">Ondex Web: web-based visualization and exploration of heterogeneous biological networks</a>. Bioinformatics.</li>
<li>Lysenko A, Defoin-Platel M, Hassani-Pak K, Taubert J, Hodgman C, Rawlings C and Saqi M. (2011).<a class="link-publications" href="http://dx.doi.org/10.1186/1471-2105-12-203"> Assessing the functional coherence of modules found in multiple-evidence networks from Arabidopsis</a>. BMC Bioinformatics.</li>
<li>Defoin-Platel M, Hassani-Pak K, Rawlings C. (2011)<a class="link-publications" href="http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3272443/"> Gaining confidence in cross-species annotation transfer: from simple molecular function to complex phenotypic traits</a>. Aspects of Applied Biology.</li>
<li>Hassani-Pak K, Legaie R, Canevet C, van den Berg H, Moore J and Rawlings C. (2010). <a class="link-publications" href="http://dx.doi.org/10.2390/biecoll-jib-2010-121">Enhancing Data Integration with Text Analysis to Find Proteins Implicated in Plant Stress Response.</a> Journal of Integrative Bioinformatics.</li>
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<h3 id="writing">Selected Citations <i class="glyphicon glyphicon-pencil" alt="pencil"></i></h3>
<ul class="publi">
<li>Adamsky N et al. (2019). <a class="link-publications" href="https://peerj.com/preprints/26877/"/>A roadmap for gene functional characterisation in wheat</a>. PeerJ.</li>
<li>Harrington SA et al. (2019). <a class="link-publications" href="https://www.biorxiv.org/content/10.1101/684183v1.abstract"/>Validation and Characterisation of a Wheat GENIE3 Network Using an Independent RNA-Seq Dataset</a>. bioRxiv.</li>
<li>Alabdullah AK et al. (2019). <a class="link-publications" href="https://www.frontiersin.org/articles/10.3389/fpls.2019.01325/full"/>A Co-Expression Network in Hexaploid Wheat Reveals Mostly Balanced Expression and Lack of Significant Gene Loss of Homeologous Meiotic Genes Upon Polyploidization</a>. Frontiers in Plant Science.</li>
<li>Hanley SJ and Karp A. (2014). <a class="link-publications" href="https://academic.oup.com/treephys/article/34/11/1167/1677451"/>Genetic strategies for dissecting complex traits in biomass willows (Salix spp.)</a>. Tree Physiology.</li>
</ul>
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<h3 id="writing">Press Releases <i class="glyphicon glyphicon-pencil" alt="pencil"></i></h3>
<ul class="publi">
<li>Open Access Government(January 2020). <a class="link-publications" href="https://edition.pagesuite-professional.co.uk/html5/reader/production/default.aspx?pnum=370&edid=e7e65f16-14bb-415e-a4a7-84c443d8db40&isshared=true">Fighting infectious crop diseases with big data analyses</a>.</li>
<li>Rothamsted Research (September 2017). <a class="link-publications" href="https://www.rothamsted.ac.uk/news/visualising-data-connections-promises-faster-discoveries">Visualising data connections promises faster discoveries</a>.</li>
<li>Genestack (September 2017). <a class="link-publications" href="https://genestack.com/news/pressreleases/visualising-gene-trait-networks-for-faster-discovery/">Visualising gene-trait networks for faster discoveries</a>.</li>
<li>BBSRC (September 2017). <a class="link-publications" href="http://www.bbsrc.ac.uk/news/research-technologies/2017/170907-pr-visualising-data-connections-promises-faster-discoveries/">Visualising data connections promises faster discoveries</a>.</li>
</ul>
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<h3 id="writing">Presentations <i class="glyphicon glyphicon-pencil" alt="pencil"></i></h3>
<iframe src="//www.slideshare.net/slideshow/embed_code/key/HSqM1BwZUAdafP" width="595" height="485" frameborder="0" marginwidth="0" marginheight="0" scrolling="no" style="border:1px solid #CCC; border-width:1px; margin-left:0px; margin-bottom:5px; max-width: 100%;" allowfullscreen> </iframe> <div style="margin-bottom:5px"> <strong> <a href="//www.slideshare.net/KeywanHassaniPak/knetminer-overview-oct-2017" title="KnetMiner Overview Oct 2017" target="_blank">KnetMiner Overview Oct 2017</a> </strong> from <strong><a href="https://www.slideshare.net/KeywanHassaniPak" target="_blank">Keywan Hassani-Pak</a></strong> </div>
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