SNEEP

17 May 2024·
Nina Baumgarten
Nina Baumgarten
Laura Rumpf
Laura Rumpf
Marcel H. Schulz, PhD
Marcel H. Schulz, PhD
tools

SNEEP is a statistical approach to predict the effect of non-coding genetic variants on transcription factor (TF) binding sites. It scales to large genomic datasets and can integrate cell type specific genetic and epigenetic information such as open chromatin or expression data to prioritize functional non-coding variants. Further, by linking variants to target genes via enhancer-gene interactions, SNEEP enables mechanistic interpretation of genetic associations.

Nina Baumgarten
Authors
Postdoc
I am a bioinformatician with a diverse background in analyzing genetic and epigenetic data. I have had the chance to work on a variety of projects since I joined the lab, like decoding the effect of non-coding variations, analysing GWAS data, and studying TF binding. Recently, my focus has been shifted toward spatial transcriptomics, which allows me to map genetic findings directly onto tissue architecture. I am motivated by the possibility that these data-driven insights might lead to a better understanding of complex diseases. In my free time, I love spending time in nature for hiking—it’s where the best ideas come to me!
Laura Rumpf
Authors
Laura Rumpf (she/her)
PhD student
I’m a computer scientist by training who found my way into bioinformatics during my master’s. My work focuses on understanding enhancer–gene regulation using machine learning and single-cell transcriptomic and epigenomic data. I’m particularly interested in how computational models can help uncover regulatory mechanisms and translate these insights into disease-related questions in computational medicine. Outside the lab, I’m usually fueled by coffee and a slightly too serious interest in latte art.
Marcel H. Schulz, PhD
Authors
Professor for Computational Biology
I am a Computational Biologist by education. I develop computational systems biology models and machine learning algorithms that further the understanding of gene regulation. We work on groundbreaking computational methods that enable novel approaches for personalized medicine applications in the context of different human diseases. We live and breathe open-source development.