Publications

Preprints

Genome-scale mapping of variant, enhancer and gene function in primary human CD4+ T cells
Moonen, D.P.I., Claringbould, A., Gschwind, A.R., Schrod, S., Braunger, J.M., Feng, C., Rauscher, B., Yi, J., Bi, S.Z., Matthess, Y., Kaulich, M., Acob, R.A., Ayer, A., Engreitz, J.M., Velten, B., Stegle, O., Trynka, G., Zaugg, J.B., Schraivogel, D., Steinmetz, L.M.
bioRxiv, 2026

Journal Articles

A genome-scale single-cell CRISPRi map of trans gene regulation across human pluripotent stem cell lines
Feng, C., Peets, E.M., Zhou, Y., Crepaldi, L., Usluer, S., Dunham, A., Braunger, J.M., Su, J., Strauss, M.E., Muraro, D., Cheam, K.A.X., Bonder, M.J., Garriga Nogales, E., Cooper, S., Bassett, A., Leonard, S., Gu, Y., Fussing, B., Burke, D., Parts, L., Stegle, O., Velten, B.
Cell Genomics, 2026

Remodeling of cytoskeleton, chromatin, and gene expression during mechanical rejuvenation of aged human dermal fibroblasts
Sornapudi, T.R., Yuan, L., Braunger, J.M., Uhler, C., Shivashankar, G.V.
Molecular Biology of the Cell, 2025

Guide assignment in single-cell CRISPR screens using crispat
Braunger, J.M., Velten, B.
Bioinformatics, 2024

Transcriptional changes are tightly coupled to chromatin reorganization during cellular aging
Braunger, J.M., Cammarata, L.V., Sornapudi, T.R., Uhler, C., Shivashankar, G.V.
Aging Cell, 2023

Metabolomic profiles predict individual multidisease outcomes
Buergel, T., Steinfeldt, J., Ruyoga, G., Pietzner, M., Bizzarri, D., Vojinovic, D., Upmeier zu Belzen, J., Loock, L., Kittner, P., Christmann, L., Hollmann, N., Strangalies, H., Braunger, J.M., Wild, B., Chiesa, S.T., Spranger, J., Klostermann, F., van den Akker, E.B., Trompet, S., Mooijaart, S.P., Sattar, N., Jukema, J.W., Lavrijssen, B., Kavousi, M., Ghanbari, M., Ikram, M.A., Slagboom, E., Kivimaki, M., Langenberg, C., Deanfield, J., Eils, R., Landmesser, U.
Nature Medicine, 2022

decoupleR: ensemble of computational methods to infer biological activities from omics data
Badia-i-Mompel, P., Vélez Santiago, J., Braunger, J.M., Geiss, C., Dimitrov, D., Müller-Dott, S., Taus, P., Dugourd, A., Holland, C.H., Ramirez Flores, R.O., Saez-Rodriguez, J.
Bioinformatics Advances, 2022

Identifying temporal and spatial patterns of variation from multimodal data using MEFISTO
Velten, B., Braunger, J.M., Argelaguet, R., Arnol, D., Wirbel, J., Bredikhin, D., Zeller, G., Stegle, O.
Nature Methods, 2022