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<p class="MsoNormal"><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">Seino A. K. Jongkees, Ph.D.</span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:black">Associate Professor</span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#0089CF">AIMMS Amsterdam Institute of Molecular and Life Sciences</span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-GB" style="font-size:12.0pt;font-family:"Times New Roman",serif;color:black"><img width="312" height="63" style="width:3.25in;height:.6562in" id="Picture_x0020_1" src="cid:image001.png@01DA1F06.E6834B80" alt="email_vu_logo_aimms_en.png"></span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B">T <a href="tel:+31657227168"><span style="color:#0078D7">+31 (0)6 5722 7168</span></a> | </span><span lang="EN-US" style="font-size:8.5pt;font-family:Helvetica;color:#4472C4"><a href="http://sakjongkees.wixsite.com/website"><span style="color:#0078D7">http://sakjongkees.wixsite.com/website</span></a></span><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B"> | </span><span lang="EN-US" style="font-size:8.5pt;font-family:Helvetica;color:#4472C4"><a href="mailto:s.a.k.jongkees@vu.nl"><span style="color:#0078D7">s.a.k.jongkees@vu.nl</span></a></span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="EN-US" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B">Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, O|2 building</span><span style="font-size:11.0pt;color:#212121"><o:p></o:p></span></p>
<p class="MsoNormal"><span lang="NL" style="font-size:7.5pt;font-family:"Arial",sans-serif;color:#5B5B5B">O2-03W51, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands</span><span style="font-size:11.0pt;mso-fareast-language:EN-US"><o:p></o:p></span></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt"><b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">From:
</span></b><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Geerke, D.P. (Daan) <d.p.geerke@vu.nl><br>
<b>Date: </b>Friday, 24 November 2023 at 15:43<br>
<b>To: </b>Mouhib, H. (Halima) <h.mouhib@vu.nl><br>
<b>Subject: </b>Seminar Gunnar Klau (HHU Düsseldorf): Tue. 12 Dec., 14.00-15.00 h, O|2 Auditorium<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Dear colleagues,</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">You are cordially invited to join the seminar of Gunnar Klau (professor for Algorithmic Bioinformatics at Heinrich Heine University, Düsseldorf,
Germany) on Tue. 12 December at 14.00-15.00 h in the O|2 auditorium. He will talk about his combinatorial approach to SARS-CoV-2 peptide vaccine design. See below for the full details of his talk, including an abstract.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">We hope to see you all, and please feel free to share this invitation with other potentially interested colleagues.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Kind regards, Halima Mouhib and Daan Geerke</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">---</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Speaker: prof. dr. Gunnar Klau (Algorithmic Bioinformatics, Dept. Computer Science, HHU Düsseldorf, Germany)</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Date: Tue. 12 December, 14.00-15.00 h</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Location: Auditorium O|2 building</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Title: A combinatorial approach to SARS-CoV-2 peptide vaccine design</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:11.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Abstract:</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">Peptide vaccines present a safe and cost-efficient alternative to traditional vaccines. Their efficacy depends on the peptides included in
the vaccine and the ability of major histocompatibility complex (MHC) molecules to bind and present these peptides. However, choosing a set of peptides that effectively achieve immunization across a large proportion of the population is challenging.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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<p class="MsoNormal" style="background:white"><span style="font-size:12.0pt;font-family:"Aptos",sans-serif;color:black">We present HOGVAX, a population-coverage-optimizing combinatorial approach to peptide vaccine design. Uniquely, HOGVAX exploits overlaps
between peptides to increase the number of peptides encoded in limited space, thereby enabling consideration of rare MHC alleles. We formalize the vaccine design task as a theoretical problem, which we call the Maximum Scoring k-Superstring Problem (MSKS).
We show that MSKS is NP-hard, and reformulate it into a graph problem using the hierarchical overlap graph (HOG). We give an integer linear programming formulation for the graph problem and provide an open source implementation.</span><span style="font-size:11.0pt"><o:p></o:p></span></p>
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