Publications

Bridging the gap in precision medicine: TranSYS training programme for next-generation scientists

Andreoli Lara , Berca Catalina , Katz Sonja , Korshevniuk Maryna , Head Ritchie M. , Van Steen Kristel , TranSYS Consortium , Steen Kristel Van , Dierickx Kris , Andreoli Lara , Melograna Federico , Li Zuqi , Lalli Giada , Kros Johan M. , Najjary Shiva , Rozman Damjana , Walakira Andrew , Skupin Alexander , Wilson Elle , Real Francisco X. , Berca Catalina , Schwikowski Benno , Yousefi Behnam , Pržulj Nataša , Mihajlovic Katarina , Binder Elisabeth B. , Taheri Nahid , Hryhorzhevska Anastasiia , Franke Lude , Korshevniuk Maryna , Patrinos George P. , Karamperis Kariofyllis , Lao Oscar , dos Santos Vitor A. P. Martins , Katz Sonja , Olsen Christina , Head Ritchie DOI=10.3389/fmed.2024.1348148

Multi-omics analysis of the molecular response to glucocorticoids – insights into shared genetic risk from psychiatric to medical disorders

Janine Knauer-Arloth, Anastasiia Hryhorzhevska, Elisabeth B. Binder doi: https://doi.org/10.1101/2023.12.05.23299430

Individual-specific networks for prediction modelling – A scoping review of methods

Gregorich, M., Melograna, F., Sunqvist, M. et al. Individual-specific networks for prediction modelling – A scoping review of methods. BMC Med Res Methodol 22, 62 (2022). https://doi.org/10.1186/s12874-022-01544-6

Edge and modular significance assessment in individual-specific networks

Federico Melograna, Zuqi Li, Gianluca Galazzo, Niels van Best, Monique Mommers, John Penders, Fabio Stella & Kristel Van Steen.  Edge and modular significance assessment in individual-specific networks. Sci Rep 13, 7868 (2023). https://doi.org/10.1038/s41598-023-34759-8

Capturing the dynamics of microbial interactions through individual-specific networks

Yousefi B, Melograna F, Galazzo G, van Best N, Mommers M, Penders J, Schwikowski B and Van Steen K (2023) Capturing the dynamics of microbial interactions through individual-specific networks.
Front. Microbiol. 14:1170391. doi: 10.3389/fmicb.2023.1170391

Detecting Genetic Interactions with Visible Neural Networks

netMUG: a novel network-guided multi-view clustering workflow for dissecting genetic and facial heterogeneity

Novel multi-omics deconfounding variational autoencoders can obtain meaningful disease subtyping

Non-Small Cell Lung Cancer Brain Metastasis: The Link between Molecular Mechanisms and Novel Therapeutic Approaches

Association of blood-cell-based inflammatory markers with gut microbiota and cancer incidence in the Rotterdam Study

Guided extraction of genome-scale metabolic models for the integration and analysis of omics data

Detecting gene-gene interactions from GWAS using diffusion kernel principal components

Integrative computational modeling to unravel novel potential biomarkers in hepatocellular carcinoma

Taking the risk. A systematic review of ethical reasons and moral arguments in the clinical use of polygenic risk scores

An overview of machine learning methods for monotherapy drug response prediction

PLEX.I: a tool to discover features in multiplex networks that reflect clinical variation

Consensus Clustering for Robust Bioinformatics Analysis

MONFIT: Multi-omics factorization-based integration of time-series data sheds light on Parkinson’s disease

Multi-omics integration of scRNA-seq time series data predicts new intervention points for Parkinson’s disease

A multi-omics integrative approach unravels novel genes and pathways associated with senescence escape after targeted therapy in NRAS mutant melanoma

A global omics data sharing and analytics marketplace: Case study of a rapid data COVID-19 pandemic response platform

ISN-tractor: a python library for the fast and scalable computation of biologically meaningful Individual-Specific Networks

Identification of genetic variants that impact gene co-expression relationships using large-scale single-cell data

Economic evaluation in psychiatric pharmacogenomics: a systematic review

Genome-based therapeutic interventions for β-type hemoglobinopathies

Adoption of Pharmacogenomic Testing: A Marketing Perspective

mEthAE: an Explainable AutoEncoder for methylation data

Decision support system and outcome prediction in a cohort of patients with necrotizing soft-tissue infections