Nora C. Toussaint

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BACKGROUND The lack of sufficient training data is the limiting factor for many Machine Learning applications in Computational Biology. If data is available for several different but related problem domains, Multitask Learning algorithms can be used to learn a model based on all available information. In Bioinformatics, many problems can be cast into the(More)
The intestinal microbiota is a microbial ecosystem of crucial importance to human health. Understanding how the microbiota confers resistance against enteric pathogens and how antibiotics disrupt that resistance is key to the prevention and cure of intestinal infections. We present a novel method to infer microbial community ecology directly from(More)
BACKGROUND The Biochemical Algorithms Library (BALL) is a comprehensive rapid application development framework for structural bioinformatics. It provides an extensive C++ class library of data structures and algorithms for molecular modeling and structural bioinformatics. Using BALL as a programming toolbox does not only allow to greatly reduce application(More)
Epitope-based vaccines (EVs) have a wide range of applications: from therapeutic to prophylactic approaches, from infectious diseases to cancer. The development of an EV is based on the knowledge of target-specific antigens from which immunogenic peptides, so-called epitopes, are derived. Such epitopes form the key components of the EV. Due to regulatory,(More)
BACKGROUND String kernels are commonly used for the classification of biological sequences, nucleotide as well as amino acid sequences. Although string kernels are already very powerful, when it comes to amino acids they have a major short coming. They ignore an important piece of information when comparing amino acids: the physico-chemical properties such(More)
Epitope-based vaccines (EVs) have recently been attracting significant interest. They trigger an immune response by confronting the immune system with immunogenic peptides derived from, e.g. viral- or cancer-related proteins. Binding of these peptides to proteins from the major histocompatibility complex (MHC) is crucial for immune system activation.(More)
The gastrointestinal tracts of mammals are colonized by hundreds of microbial species that contribute to health, including colonization resistance against intestinal pathogens 1. Many antibiotics destroy intestinal microbial communities and increase susceptibility to intestinal pathogens 2. Among these, Clostridium difficile, a major cause of(More)
MHC class I molecules are key players in the human immune system. They bind small peptides derived from intracellular proteins and present them on the cell surface for surveillance by the immune system. Prediction of such MHC class I binding peptides is a vital step in the design of peptide-based vaccines and therefore one of the major problems in(More)
T-cell epitopes, i.e., peptides capable of inducing a T-cell mediated immune response, represent suitable components for vaccines against infectious diseases and cancer. The development of accurate T-cell epitope prediction methods is thus of great interest to immunologists and the pharmaceutical industry. Whether a particular peptide is a T-cell epitope(More)
Computational protein design aims at constructing novel or improved functions on the structure of a given protein backbone and has important applications in the pharmaceutical and biotechnical industry. The underlying combi-natorial side-chain placement problem consists of choosing a side-chain placement for each residue position such that the resulting(More)