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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.