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Computational Approaches for Improving Treatment and Prevention of Viral Infections

MPS-Authors
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Döring,  Matthias
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;
International Max Planck Research School, MPI for Informatics, Max Planck Society;

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Pfeifer,  Nico
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Lengauer,  Thomas
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Kalinina,  Olga V.
Computational Biology and Applied Algorithmics, MPI for Informatics, Max Planck Society;

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Citation

Döring, M. (2019). Computational Approaches for Improving Treatment and Prevention of Viral Infections. PhD Thesis, Universität des Saarlandes, Saarbrücken. doi:10.22028/D291-27946.


Cite as: http://hdl.handle.net/21.11116/0000-0003-AEBA-8
Abstract
The treatment of infections with HIV or HCV is challenging. Thus, novel drugs and new computational approaches that support the selection of therapies are required. This work presents methods that support therapy selection as well as methods that advance novel antiviral treatments. geno2pheno[ngs-freq] identifies drug resistance from HIV-1 or HCV samples that were subjected to next-generation sequencing by interpreting their sequences either via support vector machines or a rules-based approach. geno2pheno[coreceptor-hiv2] determines the coreceptor that is used for viral cell entry by analyzing a segment of the HIV-2 surface protein with a support vector machine. openPrimeR is capable of finding optimal combinations of primers for multiplex polymerase chain reaction by solving a set cover problem and accessing a new logistic regression model for determining amplification events arising from polymerase chain reaction. geno2pheno[ngs-freq] and geno2pheno[coreceptorhiv2] enable the personalization of antiviral treatments and support clinical decision making. The application of openPrimeR on human immunoglobulin sequences has resulted in novel primer sets that improve the isolation of broadly neutralizing antibodies against HIV-1. The methods that were developed in this work thus constitute important contributions towards improving the prevention and treatment of viral infectious diseases.