Motivation. Predominant pathway analysis approaches treat pathways as collections of
individual genes and consider all pathway members as equally informative. As a result, at …

We are concerned with a situation in which we would like to test multiple hypotheses with
tests whose p‐values cannot be computed explicitly but can be approximated using Monte …

Ontology is the backbone of the Semantic Web, helping users search for relevant resources
from the Web of linked data. The existing context-free mapping approach between tags and …

In biological networks of molecular interactions in a cell, network motifs that are biologically
relevant are also functionally coherent, or form functional modules. These functionally …

This thesis explores a combination of genomics analysis and semantic knowledge
representation useful for computational toxicology. I first discuss a novel approach to infer …

Statistical hypothesis testing is a key technique to perform statistical inference. The main
focus of this work is to investigate multiple testing under the assumption that the analytical p …

The innate immune response is a critical branch of immunity, providing a first line of defense
against pathogens and shaping subsequent adaptive immune responses. The complexity of …

Most procedures which correct for multiple tests assume ideal p-values, for instance the
Bonferroni correction or the procedures of Bonferroni-Holm, Sidak, Hochberg or Benjamini …