Organisation
Laboratory of Computational Biology (VIB-KU Leuven)
Division
Research in the Laboratory of Computational Biology is focusing on gene and genome regulation, with applications in Drosophila and cancer, and on integrative genomics, developing computational methods for genomic data integration and analysis of next-generation sequence data.
Current researchers
1 - 10 of 21 results
- Stein Aerts (Responsible)
- Darina Abaffyová (Member)
- Stein Aerts (Member)
- Sara Aibar Santos (Member)
- Cas Blaauw (Member)
- Carmen Bravo González-Blas (Member)
- Florian De Rop (Member)
- Seppe De Winter (Member)
- Hannah Dickmänken (Member)
- Sam Dieltiens (Member)
Projects
1 - 10 of 64
- Understanding gene regulation in a whole animal: From building a regulatory atlas to decoding gene regulation with deep learningFrom10 Jan 2024 → TodayFunding: Own budget, for example: patrimony, inscription fees, gifts
- SpaceTimeOmics: combining high-throughput spatial omics with AI to model gene regulation in space and timeFrom1 Jan 2024 → TodayFunding: FWO research project (including WEAVE projects)
- Interpretation of genomic regulatory variation in the human brain and Parkinson’s Disease by integrating deep learning with single-cell multi-omicsFrom1 Oct 2023 → TodayFunding: FWO junior postdoctoral fellowship
- Deep learning based synthetic design and massively parallel reporter assays to characterize and exploit cell type specific enhancersFrom1 Oct 2023 → TodayFunding: Own budget, for example: patrimony, inscription fees, gifts
- Enhancer-AI: AI-driven modelling and design of cell type specific enhancers for gene therapyFrom1 Oct 2023 → TodayFunding: FWO Strategic Basic Research (SBO)
- Deep learning solutions for deciphering gene regulation in the human brainFrom7 Mar 2023 → TodayFunding: FWO Strategic Basic Research Grant
- The role of smORF encoded polypeptides in lager beer fermentationFrom1 Jan 2023 → TodayFunding: FWO research project (including WEAVE projects)
- Applications of deep learning for cancer genomicsFrom1 Jan 2023 → TodayFunding: Own budget, for example: patrimony, inscription fees, gifts
- Evolution of the genomic regulatory code underlying neuronal diversityFrom1 Oct 2022 → TodayFunding: Own budget, for example: patrimony, inscription fees, gifts
- SymBioSys: Computationally mapping genomic heterogeneity from long read sequencing dataFrom1 Oct 2022 → TodayFunding: BOF - projects
Publications
21 - 30 of 177
- Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks(2017)
Authors: Zeynep Kalender Atak, Hana Imrichova, Valerie Christiaens, Stein Aerts
Pages: 80 - p53 shapes genome-wide and cell type-specific changes in microRNA expression during the human DNA damage response(2014)
Authors: Stein Aerts
Pages: 2572 - 2586 - Cross-species analysis of enhancer logic using deep learning(2020)
Authors: Liesbeth Minnoye, Ibrahim Ihsan Taskiran, David Mauduit, Linde Van Aerschot, Panagiotis Karras, Chris Marine, Jasper Wouters, Stein Aerts
- Dissecting the interplay of chromatin accessibility and enhancer activity(2018)
Authors: Jelle Jacobs, Stein Aerts, Georg Halder
- iRegulon and i-cisTarget: Reconstructing Regulatory Networks Using Motif and Track Enrichment(2015)
Authors: Annelien Verfaillie, Hana Imrichova, Stein Aerts
Pages: 2 - Fly Cell Atlas: A single-nucleus transcriptomic atlas of the adult fruit fly(2022)
Authors: Jasper Janssens, Kristofer Davie, Stein Aerts
Pages: 991 - + - Text-mining assisted regulatory annotation(2008)
Authors: Stein Aerts, Steven Van Vooren
- Analysis of long and short enhancers in melanoma cell states(2021)
Authors: David Mauduit, Ibrahim Ihsan Taskiran, Jonas Demeulemeester, Jasper Wouters, Stein Aerts
- A scalable SCENIC workflow for single-cell gene regulatory network analysis(2020)
Authors: Kristofer Davie, Sara Aibar Santos, Stein Aerts
Pages: 2247 - 2276 - Yin Yang 1 Orchestrates a Metabolic Program Required for Both Neural Crest Development and Melanoma Formation(2019)
Authors: Jasper Wouters, Stein Aerts
Pages: 637 - +