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Computational modeling of biological nanopores KU Leuven
Throughout our history, we, humans, have sought to better control and understand our environment. To this end, we have extended our natural senses with a host of sensors—tools that enable us to detect both the very large, such as the merging of two black holes at a distance of 1.3 billion light years from earth, and the very small, such as the identification of individual viral particles from a complex mixture. This dissertation is devoted to ...
Computational optimization of an optical sensor design KU Leuven
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Integrating computational biology and forward genetics in drosophila KU Leuven
Genetic screens are powerful methods for the discovery of gene-phenotype associations. However, a systems biology approach to genetics must leverage the massive amount of "omics" data to enhance the power and speed of functional gene discovery in vivo. Thus far, few computational methods for gene function prediction have been rigorously tested for their performance on a genome-wide scale in vivo. In this work, we demonstrate that integrating ...
Effective use of latent semantic indexing and computational linguistics in biological and biomedical applications University of Antwerp
Text mining is rapidly becoming an essential technique for the annotation and analysis of large biological data sets. Biomedical literature currently increases at a rate of several thousand papers per week, making automated information retrieval methods the only feasible method of managing this expanding corpus. With the increasing prevalence of open-access journals and constant growth of publicly-available repositories of biomedical literature, ...
Conceptual and Computational DFT-based In Silico Fragmentation Method for the Identification of MetaboliteMass Spectra Vrije Universiteit Brussel
Metabolomics is recognized as a crucial scientific domain, promising to advance our understanding of cell biology, physiology and medicine. Tandem mass spectrometry (MS/MS) has strong potential to elucidate the metabolites in complex biological samples and to become a standard tool complementing established techniques. However, despite its potential for answering many key questions, a major challenge in the use of tandem mass spectrometry for ...
Computational design targeting the androgen receptor, CCR8 receptor, and NSP15 enzyme KU Leuven
We successfully employed computational methods to discover a new AR-targeted therapy for the treatment of prostate cancer. Prostate cancer is the second most common cancer and affects millions of men each year worldwide. Targeting AR LBD dimerization could discover novel inhibitors that might overcome resistance mechanisms that occur in the current therapy. Here, we successfully developed the first-generation AR LBD dimerization inhibitors using ...
Fragment Based Drug Design: From Experimental to Computational Approaches KU Leuven
Fragment based drug design has emerged as an effective alternative to high throughput screening for the identification of lead compounds in drug discovery in the past fifteen years. Fragment based screening and optimization methods have achieved credible success in many drug discovery projects with one approved drug and many more compounds in clinical trials. The fragment based drug design starts with the identification of fragments or low ...
Computational strategies and challenges for using native ion mobility mass spectrometry in biophysics and structural biology University of Antwerp
Native mass spectrometry (MS) allows the interrogation of structural aspects of macromolecules in the gas phase, under the premise of having initially maintained their solution-phase noncovalent interactions intact. In the more than 25 years since the first reports, the utility of native MS has become well established in the structural biology community. The experimental and technological advances during this time have been rapid, resulting in ...
COMMBINI: an experimentally-informed COmputational Model of Macrophage dynamics in the Bone INjury Immunoresponse KU Leuven
Bone fracture healing is a well-orchestrated but complex process that involves numerous regulations at different scales. This complexity becomes particularly evident during the inflammatory stage, as immune cells invade the healing region and trigger a cascade of signals to promote a favorable regenerative environment. Thus, the emergence of criticalities during this stage might hinder the rest of the process. Therefore, the investigation of the ...