We are a team of scientists with diverse academic and cultural backgrounds, working at the intersection between 3D genome biology and cancer genomics. We have a passion for developing innovative methods to advance our understanding of the interplay between genome structure and function, in health and disease. We are based across two research institutes: Human Technopole and Karolinska Institutet.
🌐 Meet the team on our website!
A nextflow pipeline for the analysis of GPSeq sequencing data: nextflow-gpseq
A pipeline for analysis imaging data from GPSeq experiments: radiantkit
Girelli, G., Custodio, J., Kallas, T. et al. Nat Biotechnol 38, 1184–1193 (2020). https://doi.org/10.1038/s41587-020-0519-y
Code and data used for scCUTseq manuscript: scCUTseq
Zhang, N., Harbers, L., Simonetti, M. et al. Nat Commun 15, 3475 (2024). https://doi.org/10.1038/s41467-024-47664-z
Instructions for the analysis of scCircle-seq data: scCircle-seq
Chen, J.P., Diekmann, C., Wu, H. et al. Nat Commun 15, 1768 (2024). https://doi.org/10.1038/s41467-024-45972-y
This repository provides step-by-step instructions on how to process BLISS or sBLISS data: blissNP
Tutorial on Nature Protocols (s)BLISS downstream analysis: blissNPanalysis
Yan, W., Mirzazadeh, R., Garnerone, S. et al. Nat Commun 8, 15058 (2017). https://doi.org/10.1038/ncomms15058
Ballarino, R., Bouwman, B.A.M., Agostini, F. et al. Sci Data 9, 400 (2022). https://doi.org/10.1038/s41597-022-01508-x