The complete list of publications is available on Google Scholar.

We develop both computational (Karaiskos, Wahle et al., 2017, Science; Nitzan, Karaiskos et al., 2019, Nature; Sztanka-Toth et al., 2022, Gigascience; Senel et al., 2022, NAR Genomics and Bioinformatics) and experimental (Legnini, Alles et al., 2019, Nature Methods; Legnini et al., 2023, Nature Methods) methods to study tissues and answer complex biological questions.

Recently, we developed an inexpensive, do-it-yourself, high-resolution, and open-source method to quantify gene expression directly in tissues (Schott, Leon-Perinān, Splendiani et al. "Open-ST: High-resolution spatial transcriptomics in 3D" 2024, Cell; 2024, STAR Protocols; Github).

We are actively collaborating with clinicians from the Charité University and other clinics (e.g. Kidney: Hinze et al., 2022, Genome Medicine, Urine: Klocke et al., 2022, Kidney International, Lung: Pentimalli et al., 2025, Cell Systems).

We constructed the first high-resolution molecular tumor atlas in 3D (from a single patient) and learned from these ~1 million sequenced cells (in tissue space) which pathways and gene programs drive phenotypes of the primary and metastatic tumor.

We currently routinely generate spatial transcriptomics data as a highly informative readout for how cells communicate within tissues/tumors and how they react to perturbations (disease mutations, perturbations from the environment, viral infection, microplastics, etc).

In a human brain organoid model, we found that Herpes induced neural damage after Herpes activation (a debilitating clinical problem and practically impossible to study in patients) can be prevented in brain organoids by treating them not only with acyclovir (the standard drug given in the clinics) but also with inflammation blockers Rybak-Wolf et al., 2023, Nature Microbiology.

We also invented an optogenetic approach to perturb expression of specific genes at precisely located regions/cells within organoids Legnini et al., 2023, Nature Methods. This approach allows, for example, to work with "programmed organoids" to test specific questions about how gene interactions organize tissue function in health and disease.

We showed that the interaction between microRNA miR-7 and the circular RNA CDR1as (Memczak et al., 2013, Nature; Piwecka et al., 2017, Science>) is regulating glutamatergic transmission and neural connectivity (Cerda Jara et al., 2024, EMBO Reports).

We could also show that miRNA evolution in vertebrates and the octopus share common global features (Zolotarov et al., 2022, Science Advances) and, excited by these insights, are now studying the function of primate specific miRNAs in human brain development.