[Jongkees-group.beta] FW: Seminar of Gunnar Klau (professor for Algorithmic Bioinformatics at Heinrich Heine University

[Jongkees, S.A.K. (Seino)]

Could be interesting

Seino A. K. Jongkees, Ph.D.
Associate Professor
AIMMS Amsterdam Institute of Molecular and Life Sciences
[email_vu_logo_aimms_en.png]
T +31 (0)6 5722 7168<tel:+31657227168> | http://sakjongkees.wixsite.com/website | s.a.k.jongkees at vu.nl<mailto:s.a.k.jongkees at vu.nl>
Vrije Universiteit Amsterdam, Chemistry and Pharmaceutical Sciences, O|2 building
O2-03W51, De Boelelaan 1108, 1081 HZ Amsterdam, The Netherlands

From: Beta Info Aimms <info at aimms.vu.nl>
Date: Tuesday, 28 November 2023 at 13:00
To: Fonseca Guerra, C. (C) <c.fonsecaguerra at vu.nl>, Förster, A.T.L. (Arno) <a.t.l.foerster at vu.nl>, Gerber, A.J. (Alan John) <a.j.gerber at vu.nl>, Franchini, M. (M) <m.franchini at vu.nl>, Gao, M. (Meichun) <m.c.gao at vu.nl>, Gargano, A.F.G. (Andrea) <a.f.g.gargano at vu.nl>, Ge, J. (Jingjing) <j.ge at vu.nl>, Geballa-Koukoula, A. (Ariadni) <a.geballa-koukoula at vu.nl>, Geerke, D.P. (Daan) <d.p.geerke at vu.nl>, Ghavim, B. (Behrad) <b.ghavim at vu.nl>, Gritsenko, O. (Oleg) <o.gritsenko at vu.nl>, Giesbertz, K.J.H. (Klaas) <k.j.h.giesbertz at vu.nl>, Gori Giorgi, P. (P) <p.gorigiorgi at vu.nl>, Goumans, T.P.M. (TPM) <t.p.m.goumans at vu.nl>, Gran Scheuch, A.A. (Alejandro Alberto) <a.granscheuch at vu.nl>, Hariharan, S. (Seenivasan) <s.hariharan at vu.nl>, Groot, L.C. (Laurens) <l.c.groot at vu.nl>, Grossmann, T.N. (Tom) <t.n.grossmann at vu.nl>, Haim, A. (Anissa) <a.haim at vu.nl>, Hamlin, T.A. (Trevor) <t.a.hamlin at vu.nl>, Hanreich, S. (Stefanie) <s.hanreich at vu.nl>, Heukers, R.H. (Raimond) <r.heukers at vu.nl>, Hansen, T. (Thomas) <t.hansen at vu.nl>, Harteveld, J.W. (Jaap) <j.w.harteveld at vu.nl>, Hasanefendic, S. (Sandra) <s.hasanefendic at vu.nl>, Hauwert, N.J. (Niels) <n.j.hauwert at vu.nl>, Hennig, S. (Sven) <s.hennig at vu.nl>, Hes, K. (Kevin) <k.hes at vu.nl>, Hoogstraaten, M.J. (Marjolein) <m.j.hoogstraaten at vu.nl>, Hopstaken, A.J.P. (Twan) <a.j.p.hopstaken at vu.nl>, Hordijk, Y. (Yuman) <y.hordijk at vu.nl>, JIAXING, L. (Liu) <l.jiaxing at vu.nl>, Horst, B. (Brendan) <b.horst at vu.nl>, Hutchins, G.H.A. (George) <g.h.a.hutchins at vu.nl>, Iglesias Moncayo, M.E. (Maria Emilia) <m.e.iglesiasmoncayo at vu.nl>, Illies, J.H. (Jan Hendrik) <j.h.illies at vu.nl>, Isakova, E. (Elina) <e.isakova at vu.nl>, Jonker, A.M. (Anika) <a.m.jonker at vu.nl>, Janowiak, N. (Natalia) <n.janowiak at vu.nl>, Jennings, P. (Paul) <p.jennings at vu.nl>, Jongkees, S.A.K. (Seino) <s.a.k.jongkees at vu.nl>, Jongsma, M.V. (Mirella) <mirella.jongsma at vu.nl>, Jooß, K. (Kevin) <k.jooss at vu.nl>, Josimovic, I. (Ivana) <i.josimovic at vu.nl>, Kerkhoven, A.H. (Anne) <a.h.kerkhoven at vu.nl>, Kets, J. (J) <j.kets at vu.nl>, Khandaviili, S.S. (Srinivasa Sarathchandra) <s.s.khandaviili at vu.nl>, Klatt, O.C. (Olivia) <o.c.klatt at vu.nl>, Kraakman- - van der Zwet, M. (Ria) <m.van.der.zwet at vu.nl>, Kohler, I. (Isabelle) <i.kohler at vu.nl>, Kontochristou, A. (Amalia) <a.kontochristou at student.vu.nl>, Kooi, D.P. (Derk) <d.p.kooi at vu.nl>, Kool, J. (J) <j.kool at vu.nl>, Koridon, E.F. (Emiel) <e.f.koridon at vu.nl>, Kruijswijk, J.D. (Jordy) <j.d.kruijswijk at vu.nl>, Kyllesbech, V. (Victor) <v.kyllesbech at vu.nl>, Liu, M.Z. (Meizhe) <m.z.liu at vu.nl>, Lamme, T.D. (Thomas) <t.d.lamme at student.vu.nl>, Lekanne gezegd Deprez, S.J. (Siebe) <s.j.lekanne.deprez at vu.nl>, Leurs, R. (Rob) <r.leurs at vu.nl>, Li, L.Y. (Yun) <l.y.li at vu.nl>, Lizandra Pérez, J. (Juan) <j.lizandraperez at vu.nl>, Lopez-Lopez, S. (S) <s.lopez-lopez at vu.nl>, Ma, Z.X. (Zhongxuan) <z.x.ma at vu.nl>, Majeed, H.A. (Hany) <h.a.majeed at vu.nl>, Martin, N.S. (Nicolas) <n.s.martin at vu.nl>, Meijer, T. (Tamara) <t.meijer at vu.nl>, Mobach, S. (Simon) <s.mobach at vu.nl>, Moco, S. (Sofia) <s.moco at vu.nl>, Molenaar, S.R.A. (Stef) <s.r.a.molenaar at vu.nl>, Neubacher, S.A. (Saskia) <s.a.neubacher at vu.nl>, Moloto, B.P. (Bryan Phuti) <b.p.moloto at vu.nl>, Mousavi, S. (Seyedesmaeil) <s.mousavi at vu.nl>, Murphy, C. (Cormac) <c.murphy at vu.nl>, Nagasundaram, S. (Sathyanarayanan) <s.nagasundaram at vu.nl>, Nesheva, D. (Desislava) <d.nesheva at vu.nl>, Nieuwland, C. (Celine) <c.nieuwland at vu.nl>, Nygren, J.K.O. (Jonatan) <j.k.o.nygren at vu.nl>, Paulus, J. (Jannik) <j.paulus at vu.nl>, Paulußen, F.M. (Felix) <f.m.paulussen at vu.nl>, Perez Almeria, C.V. (Claudia Victoria) <c.v.perezalmeria at vu.nl>, Pfeil, E.M. (Cy) <c.pfeil at vu.nl>, Philipsen, P.H.T. (PHT) <p.h.t.philipsen at vu.nl>, Poole, D.A. (David) <d.a.poole at vu.nl>, Pozo García, M.V. (Maria Victoria) <m.v.pozo.garcia at vu.nl>, Randoe, R.E. (Rosa) <r.e.randoe at vu.nl>, Ren, J. (Jiyu) <j.ren at vu.nl>, Rijs, A.M. (Anouk) <a.m.rijs at vu.nl>, Rodrigues Silva, D. (Daniela) <d.rodriguessilva at vu.nl>, Roose, T. (Thomas) <t.r.roose at vu.nl>, Ruger, R. (R) <r.ruger at vu.nl>, Ruijter, E. (Eelco) <e.ruijter at vu.nl>, Ruiter, J.C. (Jesper) <j.c.ruiter at vu.nl>, Saha, S. (Sneha) <s.s.saha at vu.nl>, Santos Capinha, L.M. (Liliana Monica) <l.santoscapinha at vu.nl>, Sen, S.S. (Souloke) <s.sen at vu.nl>, Sapova, M. (Mariia) <m.sapova at vu.nl>, Schafer, C.T. (Chris) <c.t.schafer at vu.nl>, Scharapow, N. (Nelli) <n.scharapow at vu.nl>, Scholten, D.J. (DJ) <danny.scholten at vu.nl>, Scuric, E.W.J. (Emma) <e.w.j.scuric at vu.nl>, Seidl, M.W.J. (Michael) <m.w.j.seidl at vu.nl>, Setiawan, I.M. (Irfan) <i.m.setiawan at vu.nl>, Shi, S. (Shuang) <s.shi at vu.nl>, Siderius, M.H. (MH) <m.siderius at vu.nl>, Smit, M.J. (MJ) <mj.smit at vu.nl>, Soini, T. (Thomas) <t.soini at vu.nl>, Somsen, G.W. (Govert) <g.w.somsen at vu.nl>, Spadetto, E. (Edoardo) <e.spadetto at vu.nl>, Tibaldi, M. (Marco) <m.tibaldi at vu.nl>, Steen, E.J.L. (Johanna) <e.j.l.steen at vu.nl>, Sterk, J.O. (John) <j.o.sterk at vu.nl>, Still, K.B.M. (Kristina) <k.b.m.still at vu.nl>, Stroganova, I. (Iuliia) <i.stroganova at vu.nl>, Veizaj, D. (Dejvid) <d.veizaj at vu.nl>, Sutter, S.M. (Sarina Mirjam) <s.m.sutter at vu.nl>, Tiekink, E.H. (Eveline) <e.h.tiekink2 at vu.nl>, Tran, T.D. (Thuy Duong) <t.d.tran at vu.nl>, Turina, V. (Valeria) <v.turina at vu.nl>, Tutiš, L. (Luca) <l.tutis at vu.nl>, Uzoamaka Godwin, I.U.G. (Ikenga) <i.u.g.uzoamakagodwin at vu.nl>, Bor, J. van den (Jelle) <j.vanden.bor at vu.nl>, Vreede, J. (Jocelyne) <j.vreede at vu.nl>, Brekel, V.B.M. van den (Vincent) <v.b.m.van.den.brekel at student.vu.nl>, Heijningen, J.V. van (Joris) <j.v.van.heijningen at vu.nl>, Lenthe, E. van (E) <e.van.lenthe at vu.nl>, Linden, O.P.J. van (Oscar) <oscar.van.linden at vu.nl>, Windhorst, A.D. (Bert (Albert D.)) <a.d.windhorst at vu.nl>, Muijlwijk - Koezen, J.E. van (Jacqueline) <j.e.van.muijlwijk-koezen at vu.nl>, Scheijen, S. van (Sonja) <s.van.scheijen at vu.nl>, Tonder, C. van (Chanté) <c.vantonder at vu.nl>, Yamazaki, K.B.Y. (Ken Barrett) <k.b.y.yamazaki at vu.nl>, Verduin, J. (Joshka) <j.verduin at vu.nl>, Vermeeren, P. (Pascal) <p.vermeeren at vu.nl>, Vischer, H.F. (HF) <h.f.vischer at vu.nl>, Visscher, L. (Luuk) <l.visscher at vu.nl>, Visser, O. (O) <o.visser at vu.nl>, Voeten, R.L.C. (Robert) <r.l.c.voeten at vu.nl>, Vos, J.C. (JC) <j.c.vos at vu.nl>, Wang, S. (Siyu) <s.wang2 at vu.nl>, Wang, R. (Rong) <r4.wang at vu.nl>, Wang, H. (Huan) <h.wang at vu.nl>, Weber, P. (Peter) <p.weber at vu.nl>, Weng, X. (Xiangmin) <x.weng at vu.nl>, Hoorn, P. van (Peter) <p.van.hoorn at vu.nl>, Wijffelaars, L.H.A. (Laura) <l.h.a.wijffelaars at vu.nl>, Wijtmans, M. (Maikel) <m.wijtmans at vu.nl>, Wilmes, A. (Anja) <a.wilmes at vu.nl>, Wu, X. (Xia) <x.wu at vu.nl>, Schoot, J.F. van (JF) <j.f.van.schoot at vu.nl>, Xu, H. (Haifeng) <h.xu at vu.nl>, Vreumingen, D. van (Dyon) <d.van.vreumingen at vu.nl>, Yakovlev, A.L. (AL) <a.l.yakovlev at vu.nl>, Yang, F. (Fan) <f.yang at vu.nl>, Yeste Vazquez, A. (Alejandro) <a.yestevazquez at vu.nl>, Yoshisada, R. (Ryoji) <r.yoshisada at vu.nl>, Zarzycka, B.A. (Barbara) <b.a.zarzycka at vu.nl>, Zhang, X. (Xiaoyi) <x.zhang3 at vu.nl>, Vies, S.M. van der (Saskia) <s.m.vander.vies at vu.nl>, Abeln, S. (Sanne) <s.abeln at vu.nl>, Bosdriesz, E. (Evert) <e.bosdriesz at vu.nl>, Branco dos Santos, F. (Filipe) <f.brancodossantos at vu.nl>, Feenstra, K.A. (Anton) <k.a.feenstra at vu.nl>, Gogishvili, D. (Dea) <d.gogishvili at vu.nl>, Hamoen, L.W. (Leendert) <l.w.hamoen at vu.nl>, Haydarlou, A.R. (Reza) <r.haydarlou at vu.nl>, Hoekstra, L. (Laura) <l.hoekstra at vu.nl>, Lakbir, S. (Soufyan) <s.lakbir at vu.nl>, Liu, T. (Ting) <t.liu at vu.nl>, Machado de Faria, L. (Laura) <l.machado.de.faria at vu.nl>, Mouhib, H. (Halima) <h.mouhib at vu.nl>, Pissis, S. (Solon) <s.pissis at vu.nl>, Postma, M. (Marten) <m2.postma at vu.nl>, Stohn, T. (Tim) <t.stohn at vu.nl>, Waury, K. (Katharina) <k.waury at vu.nl>, Westerhuis, J.A. (Johan) <j.a.westerhuis at vu.nl>, Wortel, M.T.M. (Meike) <m.t.wortel at vu.nl>, Wit, H.C. de (Renske) <h.c.de.wit at student.vu.nl>
Subject: FW: Seminar of Gunnar Klau (professor for Algorithmic Bioinformatics at Heinrich Heine University

Dear colleagues,

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 abstract.
We hope to see you all, and please feel free to share this invitation with other potentially interested colleagues.

---
Speaker:  prof. dr. Gunnar Klau (Algorithmic Bioinformatics, Dept. Computer Science, HHU Düsseldorf, Germany)
Date:         Tue. 12 December, 14.00-15.00 h
Location: Auditorium O|2 building
Title:           A combinatorial approach to SARS-CoV-2 peptide vaccine design

Abstract:

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.

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.

[signature_1667789437]



-------------- next part --------------
An HTML attachment was scrubbed...
URL: <https://listserver.vu.nl/pipermail/jongkees-group.beta/attachments/20231128/22f3f17a/attachment-0001.html>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image001.png
Type: image/png
Size: 49843 bytes
Desc: image001.png
URL: <https://listserver.vu.nl/pipermail/jongkees-group.beta/attachments/20231128/22f3f17a/attachment-0002.png>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: image002.png
Type: image/png
Size: 11996 bytes
Desc: image002.png
URL: <https://listserver.vu.nl/pipermail/jongkees-group.beta/attachments/20231128/22f3f17a/attachment-0003.png>