Ralf Eggeling
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View article: HIV multidrug class resistance prediction with a time sliding anchor approach
HIV multidrug class resistance prediction with a time sliding anchor approach Open
Motivation The emergence of multidrug class resistance (MDR) in Human Immunodeficiency Virus (HIV) is a rare but significant challenge in antiretroviral therapy (ART). MDR, which may arise from prolonged drug exposure, treatment failures, …
View article: Transfer Learning for T-Cell Response Prediction
Transfer Learning for T-Cell Response Prediction Open
We study the prediction of T-cell response for specific given peptides, which could, among other applications, be a crucial step towards the development of personalized cancer vaccines. It is a challenging task due to limited, heterogeneou…
View article: Dynamics and durability of HIV-1 neutralization are determined by viral replication
Dynamics and durability of HIV-1 neutralization are determined by viral replication Open
Human immunodeficiency virus type 1 (HIV-1)-neutralizing antibodies (nAbs) that prevent infection are the main goal of HIV vaccine discovery. But as no nAb-eliciting vaccines are yet available, only data from HIV-1 neutralizers—persons wit…
View article: Durability of Omicron-neutralizing serum activity following mRNA booster immunization in elderly individuals
Durability of Omicron-neutralizing serum activity following mRNA booster immunization in elderly individuals Open
Elderly individuals are at high risk for severe COVID-19. Due to modest vaccine responses compared to younger individuals and the time elapsed since prioritized vaccinations, the emerging immune-evasive Omicron variant of SARS-CoV-2 is a p…
View article: Respiratory Viruses Dynamics and Interactions: Ten Years of Surveillance in Central Europe
Respiratory Viruses Dynamics and Interactions: Ten Years of Surveillance in Central Europe Open
Background: Lower respiratory tract infections are among the main causes of death. Although there are many respiratory viruses, diagnostic efforts are focused mainly on influenza. The Respiratory Viruses Network (RespVir) collects infectio…
View article: Evaluation of a Rapid Antigen Test To Detect SARS-CoV-2 Infection and Identify Potentially Infectious Individuals
Evaluation of a Rapid Antigen Test To Detect SARS-CoV-2 Infection and Identify Potentially Infectious Individuals Open
The identification and isolation of highly infectious SARS-CoV-2-infected individuals is an important public health strategy. Rapid antigen detection tests (RADT) are promising candidates for large-scale screenings due to timely results an…
View article: Assessment of SARS-CoV-2 infectivity by a Rapid Antigen Detection Test
Assessment of SARS-CoV-2 infectivity by a Rapid Antigen Detection Test Open
The identification and isolation of highly infectious SARS-CoV-2-infected individuals is an important public health strategy. Rapid antigen detection tests (RADT) are promising candidates for large-scale screenings due to timely results an…
View article: Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2
Kinetics and correlates of the neutralizing antibody response to SARS-CoV-2 Open
A detailed understanding of antibody-based SARS-CoV-2 immunity has critical implications for overcoming the COVID-19 pandemic and for informing on vaccination strategies. In this study, we evaluated the dynamics of the SARS-CoV-2 antibody …
View article: DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq
DNA-binding properties of the MADS-domain transcription factor SEPALLATA3 and mutant variants characterized by SELEX-seq Open
Key message We studied the DNA-binding profile of the MADS-domain transcription factor SEPALLATA3 and mutant variants by SELEX-seq. DNA-binding characteristics of SEPALLATA3 mutant proteins lead us to propose a novel DNA-binding mode. Abst…
View article: Learning Bayesian networks with local structure, mixed variables, and exact algorithms
Learning Bayesian networks with local structure, mixed variables, and exact algorithms Open
Modern exact algorithms for structure learning in Bayesian networks first compute an exact local score of every candidate parent set, and then find a network structure by combinatorial optimization so as to maximize the global score. This …
View article: Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data
Weighted elastic net for unsupervised domain adaptation with application to age prediction from DNA methylation data Open
Motivation Predictive models are a powerful tool for solving complex problems in computational biology. They are typically designed to predict or classify data coming from the same unknown distribution as the training data. In many real-wo…
View article: On Structure Priors for Learning Bayesian Networks
On Structure Priors for Learning Bayesian Networks Open
To learn a Bayesian network structure from data, one popular approach is to maximize a decomposable likelihood-based score. While various scores have been proposed, they usually assume a uniform prior, or ``penalty,'' over the possible dir…
View article: Algorithms for learning parsimonious context trees
Algorithms for learning parsimonious context trees Open
Parsimonious context trees, PCTs, provide a sparse parameterization of conditional probability distributions. They are particularly powerful for modeling context-specific independencies in sequential discrete data. Learning PCTs from data …
View article: Disentangling transcription factor binding site complexity
Disentangling transcription factor binding site complexity Open
The binding motifs of many transcription factors (TFs) comprise a higher degree of complexity than a single position weight matrix model permits. Additional complexity is typically taken into account either as intra-motif dependencies via …
View article: Intersection-Validation: A Method for Evaluating Structure Learning without Ground Truth
Intersection-Validation: A Method for Evaluating Structure Learning without Ground Truth Open
To compare learning algorithms that differ by the adopted statistical paradigm, model class, or search heuristic, it is common to evaluate the performance on training data of varying size. Measuring the performance is straightforward if th…
View article: InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites
InMoDe: tools for learning and visualizing intra-motif dependencies of DNA binding sites Open
Summary Recent studies have shown that the traditional position weight matrix model is often insufficient for modeling transcription factor binding sites, as intra-motif dependencies play a significant role for an accurate description of b…
View article: Pruning rules for learning parsimonious context trees
Pruning rules for learning parsimonious context trees Open
We give a novel algorithm for finding a parsimonious context tree (PCT) that best fits a given data set. PCTs extend traditional context trees by allowing context-specific grouping of the states of a context variable, also enabling skippin…
View article: PCT and conditional sequence logo at position 19.
PCT and conditional sequence logo at position 19. Open
The structure of this figure is identical to that of Figure 7. Here, we observe more contexts representing a considerable amount of realizations, since only three context (III, VI, VII) represent so few sequences that they can be neglected…