EDCB Published theses

It is our pleasure to present the theses undertaken in the frame of the EPFL PhD Program in Computational and Quantitative Biology.

2024

Structures of the Foamy virus fusion protein reveal an unexpected link with the F protein of paramyxo- and pneumoviruses

I. Fernández; F. Bontems; D. Brun; Y. Coquin; C. Goverde et al. 

Science Advances. 2024. Vol. 10, num. 41, p. eado7035. DOI : 10.1126/sciadv.ado7035.

Meeting our Makers: Uncovering the cis-regulatory activity of transposable elements using statistical learning

C. D. S-T. Pulver / D. Trono (Dir.)  

Lausanne, EPFL, 2024. 

Deciphering the nature of cell state transitions in single cells using quantitative modeling of temporal dynamics

A. R. Lederer / G. La Manno (Dir.)  

Lausanne, EPFL, 2024. 

Development of Machine Learning methods for the kinetic modelling of metabolic networks for biotechnological and biomedical applications

S. Choudhury / V. Hatzimanikatis; L. Miskovic (Dir.)  

Lausanne, EPFL, 2024. 

Quantifying Interaction of Single Molecules with Surfaces using Label-Free Microscopy

J. Sülzle / S. Manley (Dir.)  

Lausanne, EPFL, 2024. 

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Z. Zhang / M. Dal Peraro; H. Lashuel (Dir.)  

Lausanne, EPFL, 2024. 

Characterisation of EIF5A perturbations on ribosome dynamics with single-molecule imaging

I. Lamberti / F. Naef (Dir.)  

Lausanne, EPFL, 2024. 

Coarse grain modelling of DNA self-assembly over multiple scales

V. Caroprese / M. Bastings (Dir.)  

Lausanne, EPFL, 2024. 

Predicting protein interactions using geometric deep learning on protein surfaces

F. Sverrisson / B. E. Ferreira De Sousa Correia; M. Bronstein (Dir.)  

Lausanne, EPFL, 2024. 

Study of disease-associated proteins using integrative structural biology: the case of GOLPH3 and PREPL

A. Theodoropoulou / M. Dal Peraro (Dir.)  

Lausanne, EPFL, 2024. 

2023

A single-cell-based characterization of mammalian adipose stem and progenitor cell heterogeneity and function

P. Y. Rainer / B. Deplancke (Dir.)  

Lausanne, EPFL, 2023. 

Host-Pathogen Interactions Through the Genomic Lens

Z. M. Xu / J. Fellay (Dir.)  

Lausanne, EPFL, 2023. 

Deconvolution of ex-vivo drug screening data and bulk tissue expression predicts the abundance and viability of cancer cell subpopulations

A. Coudray / D. Trono; G. La Manno (Dir.)  

Lausanne, EPFL, 2023. 

2022

Integrative transcriptome analyses of Transposable Elements (TEs) and genes contribute to a better understanding of colorectal cancer

E. Shin / D. Trono; G. Ciriello (Dir.)  

Lausanne, EPFL, 2022. 

The interplay between human genetic variation, chronic inflammation and persistent infection: relevance for cardiovascular morbidity

F. A. S. Hodel / J. Fellay (Dir.)  

Lausanne, EPFL, 2022. 

2021

On the use of applied machine learning and digital infrastructure to leverage social media data in health and epidemiology

M. M. Müller / M. Salathé (Dir.)  

Lausanne, EPFL, 2021. 

New Methods for the Integrative Dynamic Modeling of Biomolecular Structures

S. Träger / M. Dal Peraro (Dir.)  

Lausanne, EPFL, 2021. 

2020

Computational study of transcription factor binding sites

R. F. P. Groux / B. Deplancke; P. Bucher (Dir.)  

Lausanne, EPFL, 2020. 

Multi-omics reveals abundant mitochondrial genomic and circadian expression variation in the Drosophila Genetic Reference Panel

M. Litovchenko / B. Deplancke (Dir.)  

Lausanne, EPFL, 2020. 

Contact networks across ages: computational analysis of epidemiological dynamics

G. Lazzari / M. Salathé (Dir.)  

Lausanne, EPFL, 2020.