New Approaches to in silico Design of Epitope-Based Vaccines
New Approaches to in silico Design of Epitope-Based Vaccines
New Approaches to in silico Design of Epitope-Based Vaccines
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110 APPENDIX D. CONTRIBUTIONS<br />
Chapter 5 — Epi<strong>to</strong>pe Selection<br />
This work is part <strong>of</strong> a manuscript that has previously been published <strong>in</strong> PLoS Computational<br />
Biology [102]. It is jo<strong>in</strong>t work with Pierre Dönnes (PD) and Oliver Kohlbacher<br />
(OK). NCT, PD and OK conceived and designed the experiments. NCT performed the<br />
experiments. NCT and OK analyzed the data.<br />
Chapter 6 — Epi<strong>to</strong>pe Assembly<br />
This work is part <strong>of</strong> a manuscript that has previously been published <strong>in</strong> Vacc<strong>in</strong>e [162].<br />
It is jo<strong>in</strong>t work with Yaakov Maman (YM), Oliver Kohlbacher (OK) and Yoram Louzoun<br />
(YL). The contributions <strong>of</strong> YM have not been <strong>in</strong>corporated <strong>in</strong> this chapter. NCT and YL<br />
conceived and designed the experiments. NCT conceived the algorithm and performed the<br />
experiments. OK contributed <strong>to</strong> the discussion.<br />
Chapter 7 — Applications<br />
Section 7.1 — OptiTope – A Web Server for Epi<strong>to</strong>pe Selection<br />
This work has previously been published <strong>in</strong> the web server issue <strong>of</strong> Nucleic Acids Research<br />
[103]. It is jo<strong>in</strong>t work with Oliver Kohlbacher (OK). NCT and OK designed the<br />
structure <strong>of</strong> the web server. NCT implemented the web server.<br />
Section 7.2 — <strong>Design</strong> <strong>of</strong> a Peptide Cocktail Vacc<strong>in</strong>e<br />
This work is part <strong>of</strong> a manuscript that has previously been published <strong>in</strong> PLoS Computational<br />
Biology [102]. It is jo<strong>in</strong>t work with Pierre Dönnes (PD) and Oliver Kohlbacher<br />
(OK). NCT, PD and OK conceived and designed the experiments. NCT performed the<br />
experiments. NCT and OK analyzed the data.<br />
Section 7.3 — <strong>Design</strong> <strong>of</strong> Str<strong>in</strong>g-<strong>of</strong>-Beads Vacc<strong>in</strong>es<br />
This work is part <strong>of</strong> a manuscript that has previously been published <strong>in</strong> Vacc<strong>in</strong>e [162]. It is<br />
jo<strong>in</strong>t work with Yaakov Maman (YM), Oliver Kohlbacher (OK) and Yoram Louzoun (YL).<br />
NCT and YL conceived and designed the experiments. NCT performed the experiments.<br />
OK contributed <strong>to</strong> the discussion. YM retrieved the <strong>in</strong>fluenza sequences. YL and YM<br />
performed the biological analysis.