2026

Single-cell profiling reveals a novel CAF subpopulation linking stromal heterogeneity to immune suppression in breast cancer subtypes.
Vigiano Benedetti, Virginia, Conte, Federica, Santoni, Daniele, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Bei, Roberto, Cifaldi, Loredana, Barillari, Giovanni, Spallotta, Francesco, Cencioni, Chiara and Melaiu, Ombretta
Journal of Translational Medicine 25 June 2026 (In Press)

circVDJ-seq for T cell clonotype detection in single-cell and spatial multi-omics.
Plumbom, Izabela ORCID: https://orcid.org/0009-0006-3720-3700, Obermayer, Benedikt ORCID: https://orcid.org/0000-0002-9116-630X, Raspe, Raphael, Pascual-Reguant, Anna, Theurillat, Ilan ORCID: https://orcid.org/0000-0002-1125-1951, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Hsieh, Yu-Hsin ORCID: https://orcid.org/0000-0003-3037-8728, Gil, Marine ORCID: https://orcid.org/0000-0002-3885-7806, Dietrich, Carola, Seeger-Zografakis, Michaela, Quedenau, Claudia ORCID: https://orcid.org/0000-0002-6846-4915, Wilde, Jeannine, Braeuning, Caroline ORCID: https://orcid.org/0009-0007-1439-9920, Fischer, Cornelius ORCID: https://orcid.org/0000-0003-0329-2435, Schuelke, Markus ORCID: https://orcid.org/0000-0003-2824-3891, Seitz, Volkhard, Ludwig, Leif S. ORCID: https://orcid.org/0000-0002-2916-2164, Eggert, Angelika, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Borodina, Tatiana ORCID: https://orcid.org/0000-0002-6978-016X, Beule, Dieter ORCID: https://orcid.org/0000-0002-3284-0632, Altmueller, Janine ORCID: https://orcid.org/0000-0003-4372-1521, Radbruch, Helena ORCID: https://orcid.org/0000-0001-6941-3397, Hauser, Anja Erika and Conrad, Thomas ORCID: https://orcid.org/0000-0001-5618-6295
Genome Medicine 18 (1): 84. 11 June 2026

Epithelial mesenchymal transition initiates precancer states in BRCA1 mutation carriers.
Bar-Hai, Neta, Ben-Yishay, Rakefet, Arbili-Yarhi, Sheli, Bernstein-Molho, Rinat, Goldinger, Gil, Balint-Lahat, Nora, Menes, Tehillah, Herman, Naama, Noy, Vered, Mansour, Aiham, Globus, Opher, Hilman, Pnina, Zehavi, Yonathan, Eizenberg-Magar, Inbal, Mahammadov, Elmir ORCID: https://orcid.org/0000-0003-0008-1413, Conrad, Thomas ORCID: https://orcid.org/0000-0001-5618-6295, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Antebi, Yaron E., Berger, Raanan and Ishay-Ronen, Dana ORCID: https://orcid.org/0000-0003-0425-1408
bioRxiv : 2026.05.06.723061. 11 May 2026

InterScale reveals multi-scale cellular interaction programs in spatial transcriptomics.
Drummer, Francesca K. ORCID: https://orcid.org/0009-0002-7156-9125, Jimenez, Sara ORCID: https://orcid.org/0000-0001-7103-7474, Marco, Federico Di ORCID: https://orcid.org/0000-0003-0376-1342, Schaar, Anna C. ORCID: https://orcid.org/0000-0003-1063-005X, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Beckmann, Julia, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332 and Theis, Fabian J. ORCID: https://orcid.org/0000-0002-2419-1943
bioRxiv : 2026.05.07.723456. 11 May 2026

pyTrance finds co-localizing RNAs in subcellular spatial transcriptomics data.
Strenger, Leon ORCID: https://orcid.org/0009-0005-0354-8631, Cerda-Jara, Cledi Alicia ORCID: https://orcid.org/0000-0003-1783-5533, Karaiskos, Nikos ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv : 2026.05.07.723470. 11 May 2026

The history and function of a circular RNA.
Cerda-Jara, Cledi A. ORCID: https://orcid.org/0000-0003-1783-5533, Scoyni, Flavia ORCID: https://orcid.org/0000-0002-2764-7336, Zolotarov, Grygoriy ORCID: https://orcid.org/0000-0002-3971-3070, Bhaskar, Poojashree ORCID: https://orcid.org/0009-0006-0027-7239, León-Periñán, Daniel ORCID: https://orcid.org/0000-0002-7970-0362, Kjems, Jørgen and Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332
Nature Communications 17 (1): 3862. 28 April 2026

Accelerating Leigh syndrome drug discovery through deep learning screening in brain organoids.
Menacho, Carmen ORCID: https://orcid.org/0000-0001-9754-6322, Okawa, Satoshi, Álvarez-Merz, Iris ORCID: https://orcid.org/0000-0002-2585-1093, Wittich, Annika, Muñoz-Oreja, Mikel, Lisowski, Pawel ORCID: https://orcid.org/0000-0002-3634-1072, Martín, Mario López, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Zakin, Shiri, Thevandavakkam, Mathuravani, Jerred, Caleb, Lickfett, Selene ORCID: https://orcid.org/0000-0002-3726-9551, Petersilie, Laura, Rybak-Wolf, Agnieszka ORCID: https://orcid.org/0000-0002-1192-5290, Seibt, Annette, Herebian, Diran, Inak, Gizem, Brodesser, Susanne ORCID: https://orcid.org/0000-0001-5631-0663, Zaliani, Andrea ORCID: https://orcid.org/0000-0002-1740-8390, Mlody, Barbara ORCID: https://orcid.org/0000-0001-5184-1772, Donnelly, Justin, Woleben, Kasey, Soriano, Francesc Xavier ORCID: https://orcid.org/0000-0003-1678-7162, Fernandez-Checa, Jose C., Ventura, Natascia ORCID: https://orcid.org/0000-0001-8718-4321, Cambridge, Sidney, Mayatepek, Ertan ORCID: https://orcid.org/0000-0001-8460-3738, Spinazzola, Antonella ORCID: https://orcid.org/0000-0003-4242-8091, Schuelke, Markus ORCID: https://orcid.org/0000-0003-2824-3891, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Rossi, Andrea ORCID: https://orcid.org/0000-0001-5863-6448, Peralvarez-Marin, Alex ORCID: https://orcid.org/0000-0002-3457-0875, Distelmaier, Felix ORCID: https://orcid.org/0000-0003-4304-7848, Perlstein, Ethan, Holt, Ian J., Puighermanal, Emma ORCID: https://orcid.org/0000-0003-4271-9104, Pless, Ole ORCID: https://orcid.org/0000-0002-1468-316X, Rose, Christine R. ORCID: https://orcid.org/0000-0002-9684-3592, Del Sol, Antonio ORCID: https://orcid.org/0000-0002-9926-617X and Prigione, Alessandro ORCID: https://orcid.org/0000-0001-9457-1952
Nature Communications 17 (1): 3570. 20 April 2026

MicroRNAs are required within a critical time window to define neural patterning during early human brain development.
Emmenegger, Lisa ORCID: https://orcid.org/0000-0003-2165-7944, Cerda Jara, Cledi Alicia ORCID: https://orcid.org/0000-0003-1783-5533, Ercolano, Matilde ORCID: https://orcid.org/0009-0009-5966-2141, Loebert, Jaden, Morando, Nicolas, Bhaskar, Poojashree ORCID: https://orcid.org/0009-0006-0027-7239, Legnini, Ivano ORCID: https://orcid.org/0000-0002-8984-5215, Rybak-Wolf, Agnieszka ORCID: https://orcid.org/0000-0002-1192-5290 and Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv : 2026.03.30.715268. 1 April 2026

miRNA regulation in brain tissue space: the 3'UTR perspective.
Aigner, Denise ORCID: https://orcid.org/0009-0001-0489-1010, Bartsch, Florian ORCID: https://orcid.org/0000-0002-8285-9964, Bhaskar, Poojashree ORCID: https://orcid.org/0009-0006-0027-7239, Emmenegger, Lisa ORCID: https://orcid.org/0000-0003-2165-7944, Karaiskos, Nikos ORCID: https://orcid.org/0000-0001-7771-3947, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332 and Rybak-Wolf, Agnieszka ORCID: https://orcid.org/0000-0002-1192-5290
RNA 32 (4): 472-488. April 2026

Pluripotent stem-cell-based screening uncovers sildenafil as a mitochondrial disease therapy.
Zink, Annika ORCID: https://orcid.org/0000-0002-8489-6339, Dai, Dao-Fu, Wittich, Annika, Henke, Marie-Thérèse ORCID: https://orcid.org/0000-0001-6572-1667, Pedrotti, Giulia, Heiduschka, Sonja, Santamaria, Guillem, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Brueser, Christian, Notopoulou, Sofia, Umar, Abdul Rahim, Zhaivoron, Aleksandra, Petersilie, Laura, Jerred, Caleb, Bergmans, Jesper, Neu, Louis Anton, Schumacher, Fabian, Keller-Findeisen, Jan, Rybak-Wolf, Agnieszka ORCID: https://orcid.org/0000-0002-1192-5290, Stach, Daniel, Reinshagen, Jeanette, Haferkamp, Undine, Krieg, Kim, Zaliani, Andrea, Euro, Liliya, Di Donfrancesco, Alessia, Santanatoglia, Chiara, Cappellozza, Enrica, Suarez Cubero, Marta, Pavez-Giani, Mario, Bakumenko, Oleh, Meierhofer, David, Foley, Alan, Morales-Gonzalez, Susanne, Tolle, Isabella, Herebian, Diran, Bonesso, Daniele, Cecchetto, Giulia, Wong, Sakurako Nagumo, Moresco, Monica, Maresca, Alessandra, Decimo, Ilaria, De Sanctis, Francesco, Adamo, Annalisa, Adjobo-Hermans, Merel J.W., Duchi, Roberto, Barandalla, Maria, Scaglia, Marco, Perota, Andrea, Galli, Cesare, Kleuser, Burkhard, Cyganek, Lukas, Mühlhausen, Chris, Schlotawa, Lars, Tiranti, Valeria, Mayatepek, Ertan, Szabo, Ildiko, La Morgia, Chiara, Klopstock, Thomas, Carelli, Valerio, Distelmaier, Felix, Rossi, Andrea, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Ullah, Ghanim, Jakobs, Stefan, Rose, Christine R., Petrakis, Spyros, Edenhofer, Frank, Koopman, Werner J.H., Lisowski, Pawel ORCID: https://orcid.org/0000-0002-3634-1072, Suomalainen, Anu, Brunetti, Dario, Del Sol, Antonio, Bottani, Emanuela, Pless, Ole ORCID: https://orcid.org/0000-0002-1468-316X, Schuelke, Markus ORCID: https://orcid.org/0000-0003-2824-3891 and Prigione, Alessandro ORCID: https://orcid.org/0000-0001-9457-1952
Cell 189 (6): 1656-1679.e42. 19 March 2026

Integrating UHPLC-MS and MALDI-MSI for spatial nucleoside profiling in FFPE breast cancer: a multimodal molecular pathology framework.
Wu, Jierong ORCID: https://orcid.org/0000-0002-2413-0411, Geisberger, Sabrina Y. ORCID: https://orcid.org/0000-0001-6477-1312, Mastrobuoni, Guido ORCID: https://orcid.org/0000-0003-4509-1295, Lisek, Kamil ORCID: https://orcid.org/0000-0002-2406-8830, Raimundo, Sandra ORCID: https://orcid.org/0009-0000-3353-5456, Nebrich, Grit, Grzeski, Marta, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Klauschen, Frederick ORCID: https://orcid.org/0000-0002-9131-2389, Klein, Oliver ORCID: https://orcid.org/0000-0001-7984-7607 and Kempa, Stefan ORCID: https://orcid.org/0000-0002-0696-9299
bioRxiv : 2026.01.28.701949. 30 January 2026

OpenDVP: an experimental and computational framework for community-empowered deep visual proteomics.
Nimo, Jose ORCID: https://orcid.org/0000-0002-1565-7799, Fritzsche, Sonja ORCID: https://orcid.org/0000-0003-3335-3534, Valdes, Daniela S. ORCID: https://orcid.org/0000-0002-1309-5147, Trinh, Minh Tien ORCID: https://orcid.org/0009-0000-2727-8449, Pentimalli, Tancredi ORCID: https://orcid.org/0000-0002-8461-7918, Klingeberg, Melissa ORCID: https://orcid.org/0009-0002-4778-2874, Schallenberg, Simon ORCID: https://orcid.org/0000-0002-7897-7116, Klauschen, Frederick ORCID: https://orcid.org/0000-0002-9131-2389, Herse, Florian ORCID: https://orcid.org/0000-0002-9305-8134, Florian, Stefan ORCID: https://orcid.org/0000-0002-0193-1320, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332 and Coscia, Fabian ORCID: https://orcid.org/0000-0002-2244-5081
bioRxiv : 2025.07.13.662099v2. 15 January 2026

2025

Microglia from patients with multiple sclerosis display a cell-autonomous immune activation state.
Hyvärinen, Tanja, Tilvis, Johanna, Giudice, Luca, Tujula, Iisa, Nylund, Marjo, Ohtonen, Sohvi, Scoyni, Flavia ORCID: https://orcid.org/0000-0002-2764-7336, Jäntti, Henna, Virtanen, Lassi, Pihlava, Sara, Kattelus, Roosa, Skottman, Heli, Narkilahti, Susanna, Airas, Laura, Malm, Tarja and Hagman, Sanna
Journal of Neuroinflammation 22 (1): 255. 31 October 2025

Lineage origin and microenvironment shape neuroblastoma transcriptional state and plasticity.
Fresmann, Nora ORCID: https://orcid.org/0000-0002-9233-5101, Koeppke, Julia, Gauert, Anton ORCID: https://orcid.org/0000-0002-3013-5374, Senoussi, Anis ORCID: https://orcid.org/0000-0002-7066-8917, Olivares-Chauvet, Pedro ORCID: https://orcid.org/0009-0008-4684-255X, Schott, Marie ORCID: https://orcid.org/0009-0000-7393-2421, Hoefer, Lennart, Henssen, Anton G. ORCID: https://orcid.org/0000-0003-1534-778X, Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Spanjaard, Bastiaan ORCID: https://orcid.org/0000-0003-1309-8839, Hagemann, Anja I.H. ORCID: https://orcid.org/0000-0001-5491-4607 and Junker, Jan Philipp ORCID: https://orcid.org/0000-0002-2826-8290
bioRxiv : 2025.10.13.682025. 14 October 2025

The Biodiversity Cell Atlas: mapping the tree of life at cellular resolution.
Sebé-Pedrós, Arnau, Tanay, Amos, Lawniczak, Mara K.N., Arendt, Detlev, Aerts, Stein, Archibald, John, Arnone, Maria Ina, Blaxter, Mark, Cleves, Phillip, Coelho, Susana M., Dias, Mafalda, Dunn, Casey, Elek, Anamaria, Frazer, Jonathan, Gabaldón, Toni, Gillis, Jesse, Grau-Bové, Xavier, Guigó, Roderic, Hobert, Oliver, Huerta-Cepas, Jaime, Irimia, Manuel, Klein, Allon, Lewin, Harris, Lowe, Christopher J., Marlow, Heather, Musser, Jacob M, Nagy, László G., Najle, Sebastián R., Pachter, Lior, Paez, Sadye, Papatheodorou, Irene, Passalacqua, Michael J., Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332, Rhee, Seung Y., Richards, Thomas A., Sauka-Spengler, Tatjana, Saunders, Lauren M., Seuntjens, Eve, Solana, Jordi ORCID: https://orcid.org/0000-0002-6770-3929, Song, Yuyao, Technau, Ulrich and Wang, Bo
Nature 645 (8082): 877-885. 25 September 2025

Code and pre-processed data for figure reproducibility of the manuscript 'Spatiotemporal dynamics of tumour microenvironment remodelling' Lisek, Theurillat, Pentimalli et al., bioRxiv 2025.
Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918
[Dataset] 15 September 2025

Spatiotemporal dynamics of tumor microenvironment remodeling.
Lisek, Kamil ORCID: https://orcid.org/0000-0002-2406-8830, Theurillat, Ilan ORCID: https://orcid.org/0000-0002-1125-1951, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Beier, Svea ORCID: https://orcid.org/0009-0006-6473-8487, León-Periñán, Daniel ORCID: https://orcid.org/0000-0002-7970-0362, Antonatou, Anna, Dubnov, Serafima, Müller, Marion, Hubl, Florian, Xhuri, Artemis, Romanowicz, Hanna, Smolarz, Beata, Montaudon, Elodie, Raimundo, Sandra ORCID: https://orcid.org/0009-0000-3353-5456, Margineanu, Anca ORCID: https://orcid.org/0000-0002-6634-9729, Schott, Marie ORCID: https://orcid.org/0009-0000-7393-2421, Kunz, Séverine ORCID: https://orcid.org/0000-0002-0131-3506, Marangoni, Elisabetta, Karaiskos, Nikos ORCID: https://orcid.org/0000-0001-7771-3947, Nitzan, Mor, Birchmeier, Walter ORCID: https://orcid.org/0000-0003-1173-0829 and Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv : 2025.07.15.662972. 18 July 2025

Spatiotemporal dynamics of tumor microenvironment remodeling.
Lisek, Kamil ORCID: https://orcid.org/0000-0002-2406-8830, Theurillat, Ilan ORCID: https://orcid.org/0000-0002-1125-1951, Pentimalli, Tancredi Massimo ORCID: https://orcid.org/0000-0002-8461-7918, Beier, Svea ORCID: https://orcid.org/0009-0006-6473-8487, León-Periñán, Daniel ORCID: https://orcid.org/0000-0002-7970-0362, Antonatou, Anna, Dubnov, Serafima, Müller, Marion, Hubl, Florian, Xhuri, Artemis, Romanowicz, Hanna, Smolarz, Beata, Montaudon, Elodie, Raimundo, Sandra ORCID: https://orcid.org/0009-0000-3353-5456, Margineanu, Anca ORCID: https://orcid.org/0000-0002-6634-9729, Schott, Marie ORCID: https://orcid.org/0009-0000-7393-2421, Kunz, Séverine ORCID: https://orcid.org/0000-0002-0131-3506, Marangoni, Elisabetta, Karaiskos, Nikos ORCID: https://orcid.org/0000-0001-7771-3947, Nitzan, Mor, Birchmeier, Walter ORCID: https://orcid.org/0000-0003-1173-0829 and Rajewsky, Nikolaus ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv : 2025.07.15.662972. 18 July 2025

Cytoplasmic DIS3 is an exosome-independent endoribonuclease with catalytic activity toward circular RNAs.
Latini, C., Eichlinger, J., Fuchs, A.L., Zhai, S.N., Ho-Xuan, H., Lehmann, G., Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Bruckmann, A., Yang, L., Sprangers, R. and Meister, G.
Cell Reports 44 (6): 115769. 24 June 2025

Combining spatial transcriptomics and ECM imaging in 3D for mapping cellular interactions in the tumor microenvironment.
Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Schallenberg, S., León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Theurillat, I. ORCID: https://orcid.org/0000-0002-1125-1951, Thomas, G., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Fritzsche, S. ORCID: https://orcid.org/0000-0003-3335-3534, Nimo, J. ORCID: https://orcid.org/0000-0002-1565-7799, Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M.T., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Klauschen, F. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Systems 16 (5): 101261. 21 May 2025

Scalable image-based visualization and alignment of spatial transcriptomics datasets.
Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Innerberger, M., León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Systems 16 (5): 101264. 21 May 2025

UBE3C links ubiquitin signaling to epitranscriptomic control of cortical neurogenesis.
Borisova, Ekaterina, Cuthill, Katherine J. ORCID: https://orcid.org/0000-0003-3328-3249, Dannenberg, Rike, Koch, Janina, Nowaczyk, Julius ORCID: https://orcid.org/0009-0009-7068-4958, Schaub, Theres, Schwark, Manuela ORCID: https://orcid.org/0009-0008-1711-457X, Kastelic, N., Kupryianchyk-Schultz, I. ORCID: https://orcid.org/0009-0007-6442-4469, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Fokkens, T.J. ORCID: https://orcid.org/0009-0005-4689-4024, Stein, F., Dietrich, C., Quedenau, C. ORCID: https://orcid.org/0000-0002-6846-4915, Borodina, T. ORCID: https://orcid.org/0000-0002-6978-016X, Schwefel, D. ORCID: https://orcid.org/0000-0002-2945-0908, Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Haberkant, P. ORCID: https://orcid.org/0000-0002-5608-9062, Lorenz, S. ORCID: https://orcid.org/0000-0002-9639-2381, Brose, N. ORCID: https://orcid.org/0000-0003-0938-8534, Kawabe, H. ORCID: https://orcid.org/0000-0001-5650-8696, Tarabykin, V. ORCID: https://orcid.org/0000-0001-8931-7263 and Ambrozkiewicz, M.C. ORCID: https://orcid.org/0000-0001-5225-5230
bioRxiv : 2025.04.09.646620v2. 29 April 2025

Interleukin-12 signaling drives Alzheimer’s disease pathology through disrupting neuronal and oligodendrocyte homeostasis.
Schneeberger, S., Kim, S.J. ORCID: https://orcid.org/0000-0001-8357-0073, Geesdorf, M.N., Friebel, E. ORCID: https://orcid.org/0000-0003-1419-2376, Eede, P., Jendrach, M. ORCID: https://orcid.org/0000-0002-8601-2277, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Braeuning, C. ORCID: https://orcid.org/0009-0007-1439-9920, Ruhwedel, T. ORCID: https://orcid.org/0000-0002-9535-9395, Hülsmeier, A.J. ORCID: https://orcid.org/0000-0001-6987-8979, Gimber, N. ORCID: https://orcid.org/0000-0001-9456-3063, Foerster, M., Obst, J., Andreadou, M. ORCID: https://orcid.org/0000-0001-6757-4664, Mundt, S. ORCID: https://orcid.org/0000-0003-2169-2109, Schmoranzer, J., Prokop, S., Kessler, W., Kuhlmann, T., Möbius, W. ORCID: https://orcid.org/0000-0002-2902-7165, Nave, K.A. ORCID: https://orcid.org/0000-0001-8724-9666, Hornemann, T. ORCID: https://orcid.org/0000-0002-4218-1087, Becher, B. ORCID: https://orcid.org/0000-0002-1541-7867, Edgar, J.M. ORCID: https://orcid.org/0000-0002-3869-0962, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Heppner, F.L. ORCID: https://orcid.org/0000-0001-9816-8917
Nature Aging 5 (4): 622-641. April 2025

Protocol for high-resolution 3D spatial transcriptomics using Open-ST.
Schott, M. ORCID: https://orcid.org/0009-0000-7393-2421, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Splendiani, E. ORCID: https://orcid.org/0000-0003-4259-9093, Ferretti, E., Macino, G., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
STAR Protocols 6 (1): 103521. 21 March 2025

Centromere positioning orchestrates telomere bouquet formation and the initiation of meiotic differentiation.
Jiménez-Martín, A. ORCID: https://orcid.org/0000-0001-7628-1273, Pineda-Santaella, A. ORCID: https://orcid.org/0000-0003-1156-8104, Martín-García, R. ORCID: https://orcid.org/0000-0001-8318-2898, Esteban-Villafañe, R., Matarrese, A., Pinto-Cruz, J., Camacho-Cabañas, S., León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Terrizzano, A. ORCID: https://orcid.org/0009-0003-1601-997X, Daga, R.R., Braun, S. ORCID: https://orcid.org/0000-0001-6399-8574 and Fernández-Álvarez, A. ORCID: https://orcid.org/0000-0002-7455-1425
Nature Communications 16 (1): 837. 20 January 2025

Challenges and opportunities in the clinical translation of high-resolution spatial transcriptomics.
Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Annual Review of Pathology : Mechanisms of Disease 20 : 405-432. January 2025

2024

Sex-specific molecular signature of mouse podocytes in homeostasis and in response to pharmacological challenge with rapamycin.
Al-Diab, O., Sünkel, C. ORCID: https://orcid.org/0000-0002-5326-6043, Blanc, E. ORCID: https://orcid.org/0000-0002-4369-0254, Catar, R.A., Ashraf, M.I., Zhao, H., Wang, P., Rinschen, M.M., Fritsche-Guenther, R. ORCID: https://orcid.org/0000-0002-6965-0226, Grahammer, F., Bachmann, S., Beule, D. ORCID: https://orcid.org/0000-0002-3284-0632, Kirwan, J.A. ORCID: https://orcid.org/0000-0002-5423-1651, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Huber, T.B., Gürgen, D. ORCID: https://orcid.org/0000-0001-9241-6537 and Kusch, A. ORCID: https://orcid.org/0000-0002-6666-7081
Biology of Sex Differences 15 (1): 72. 15 September 2024

Mutant huntingtin impairs neurodevelopment in human brain organoids through CHCHD2-mediated neurometabolic failure.
Lisowski, P. ORCID: https://orcid.org/0000-0002-3634-1072, Lickfett, S. ORCID: https://orcid.org/0000-0002-3726-9551, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Menacho, C. ORCID: https://orcid.org/0000-0001-9754-6322, Le, S. ORCID: https://orcid.org/0000-0002-7500-1759, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Notopoulou, S., Dykstra, W. ORCID: https://orcid.org/0000-0002-7663-4689, Oehler, D. ORCID: https://orcid.org/0000-0002-0435-4119, López-Calcerrada, S., Mlody, B. ORCID: https://orcid.org/0000-0001-5184-1772, Otto, M. ORCID: https://orcid.org/0009-0003-1919-5880, Wu, H., Richter, Y., Roth, P. ORCID: https://orcid.org/0009-0006-8642-2993, Anand, R. ORCID: https://orcid.org/0000-0001-7337-6007, Kulka, L.A.M. ORCID: https://orcid.org/0009-0001-3640-3886, Meierhofer, D. ORCID: https://orcid.org/0000-0002-0170-868X, Glazar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Telugu, N.S. ORCID: https://orcid.org/0000-0003-4509-7056, Hahn, T., Neuendorf, N., Miller, D.C. ORCID: https://orcid.org/0000-0001-9852-677X, Böddrich, A. ORCID: https://orcid.org/0000-0001-9118-050X, Polzin, A., Mayatepek, E. ORCID: https://orcid.org/0000-0001-8460-3738, Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Olzscha, H. ORCID: https://orcid.org/0000-0002-1929-1384, Kirstein, J. ORCID: https://orcid.org/0000-0003-4990-2497, Ugalde, C. ORCID: https://orcid.org/0000-0002-9742-1877, Petrakis, S. ORCID: https://orcid.org/0000-0001-9094-3480, Cambridge, S., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630, Priller, J. ORCID: https://orcid.org/0000-0001-7596-0979, Metzger, J.J. ORCID: https://orcid.org/0000-0001-6813-4425 and Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952
Nature Communications 15 (1): 7027. 22 August 2024

Identifying chromosome movement patterns during meiosis using ChroMo.
Pinto-Cruz, J. ORCID: https://orcid.org/0000-0002-2497-6783, Correas, M., Mendoza-Madrigal, R., León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362 and Fernández-Álvarez, A. ORCID: https://orcid.org/0000-0002-7455-1425
Methods in Molecular Biology 2818 : 271-288. 11 August 2024

Open-ST: high-resolution spatial transcriptomics in 3D.
Schott, M. ORCID: https://orcid.org/0009-0000-7393-2421, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Splendiani, E. ORCID: https://orcid.org/0000-0003-4259-9093, Strenger, L. ORCID: https://orcid.org/0009-0005-0354-8631, Licha, J.R., Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Schallenberg, S., Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Tagliaferro, S.S. ORCID: https://orcid.org/0000-0001-9183-5887, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Ehrig, S. ORCID: https://orcid.org/0000-0002-5118-7405, Abbiati, S., Dommerich, S., Pagani, M., Ferretti, E., Macino, G., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell 187 (15): 3953-3972.e26. 25 July 2024

Deep learning-driven neuromorphogenesis screenings identify repurposable drugs for mitochondrial disease.
Menacho, C., Okawa, S., Alvarez-Merz, I., Wittich, A., Muñoz-Oreja, M., Lisowski, P. ORCID: https://orcid.org/0000-0002-3634-1072, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Inak, G., Zakin, S., Thevandavakkam, M., Petersilie, L., Zaliani, A., Mlody, B. ORCID: https://orcid.org/0000-0001-5184-1772, Seibt, A., Donnelly, J., Woleben, K., Fernandez-Checa, J., Herebian, D., Mayatepek, E., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Spinazzola, A., Schuelke, M. ORCID: https://orcid.org/0000-0003-2824-3891, Perlstein, E. ORCID: https://orcid.org/0000-0002-4734-4391, Rossi, A., Distelmaier, F., Holt, I.J., Pless, O. ORCID: https://orcid.org/0000-0002-1468-316X, Rose, C., Del Sol, A. and Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952
bioRxiv : 2024.07.08.602501. 12 July 2024

miR-7 controls glutamatergic transmission and neuronal connectivity in a Cdr1as-dependent manner.
Cerda Jara, C.A. ORCID: https://orcid.org/0000-0003-1783-5533, Kim, S.J. ORCID: https://orcid.org/0000-0001-8357-0073, Thomas, G., Farsi, Z. ORCID: https://orcid.org/0000-0001-7274-981X, Zolotarov, G. ORCID: https://orcid.org/0000-0002-3971-3070, Dube, G., Deter, A., Bahry, E. ORCID: https://orcid.org/0000-0002-6358-2576, Georgii, E., Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
EMBO Reports 25 (7): 3039. July 2024

Oropharyngeal microbial ecosystem perturbations influence the risk for acute respiratory infections in common variable immunodeficiency.
Pulvirenti, F., Giufrè, M., Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Camilli, R., Milito, C., Villa, A., Sculco, E., Cerquetti, M., Pantosti, A. and Quinti, I.
Frontiers in Immunology 15 : 1371118. 30 May 2024

Twisted-plywood-like tissue formation in vitro. Does curvature do the twist?
Schamberger, B. ORCID: https://orcid.org/0000-0001-5491-3620, Ehrig, S. ORCID: https://orcid.org/0000-0002-5118-7405, Dechat, T. ORCID: https://orcid.org/0000-0003-3236-7889, Spitzer, S. ORCID: https://orcid.org/0000-0002-1728-5896, Bidan, C.M. ORCID: https://orcid.org/0000-0002-6243-562X, Fratzl, P. ORCID: https://orcid.org/0000-0003-4437-7830, Dunlop, J.W.C. ORCID: https://orcid.org/0000-0003-2741-6383 and Roschger, A. ORCID: https://orcid.org/0000-0003-0353-8239
PNAS Nexus 3 (4): pgae121. April 2024

Generation and downstream analysis of single-cell and single-nuclei transcriptomes in brain organoids.
Wandres, M., Aigner, D. ORCID: https://orcid.org/0009-0001-0489-1010, Kastelic, N., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Journal of Visualized Experiments (205): e66225. 29 March 2024

ciRS-7 and miR-7 regulate ischemia-induced neuronal death via glutamatergic signaling.
Scoyni, F. ORCID: https://orcid.org/0000-0002-2764-7336, Sitnikova, V., Giudice, L., Korhonen, P., Trevisan, D.M., Hernandez de Sande, A., Gomez-Budia, M., Giniatullina, R., Ugidos, I.F., Dhungana, H., Pistono, C., Korvenlaita, N., Välimäki, N.N., Kangas, S.M., Hiltunen, A.E., Gribchenko, E., Kaikkonen-Määttä, M.U., Koistinaho, J., Ylä-Herttuala, S., Hinttala, R., Venø, M.T., Su, J., Stoffel, M., Schaefer, A., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kjems, J., LaPierre, M.P., Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577, Jolkkonen, J., Giniatullin, R., Hansen, T.B. and Malm, T.
Cell Reports 43 (3): 113862. 26 March 2024

SetQuence & SetOmic: deep set transformers for whole genome and exome tumour analysis.
Jurenaite, N. ORCID: https://orcid.org/0000-0002-3959-7452, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Donath, V., Torge, S. ORCID: https://orcid.org/0000-0001-9756-6390 and Jäkel, R. ORCID: https://orcid.org/0000-0001-6260-5222
Biosystems 235 : 105095. January 2024

2023

SLAM-Drop-seq reveals mRNA kinetic rates throughout the cell cycle.
Liu, H. ORCID: https://orcid.org/0009-0007-4871-452X, Arsiè, R. ORCID: https://orcid.org/0000-0002-7869-7624, Schwabe, D. ORCID: https://orcid.org/0000-0003-2825-3352, Schilling, M. ORCID: https://orcid.org/0000-0002-3453-7792, Minia, I. ORCID: https://orcid.org/0000-0003-1012-3373, Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114, Friedman, N. ORCID: https://orcid.org/0000-0002-9678-3550, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Molecular Systems Biology 19 (10): e11427. 12 October 2023

Spatiotemporal, optogenetic control of gene expression in organoids.
Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Emmenegger, L. ORCID: https://orcid.org/0000-0003-2165-7944, Zappulo, A., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Oliveras Martinez, A. ORCID: https://orcid.org/0000-0002-5880-5245, Cerda Jara, C. ORCID: https://orcid.org/0000-0003-1783-5533, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hessler, T., Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Methods 20 (10): 1544-1552. October 2023

Prox2 and Runx3 vagal sensory neurons regulate esophageal motility.
Lowenstein, E.D. ORCID: https://orcid.org/0000-0003-3755-0818, Ruffault, P.L. ORCID: https://orcid.org/0000-0002-3378-3828, Misios, A., Osman, K.L., Li, H., Greenberg, R.S., Thompson, R., Song, K. ORCID: https://orcid.org/0000-0001-6216-8157, Dietrich, S. ORCID: https://orcid.org/0000-0002-0753-9266, Li, X. ORCID: https://orcid.org/0000-0002-1173-1066, Vladimirov, N. ORCID: https://orcid.org/0000-0002-1159-0689, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Brunet, J.F., Zampieri, N. ORCID: https://orcid.org/0000-0002-2228-9453, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Liberles, S.D., Jia, S., Lewin, G.R. ORCID: https://orcid.org/0000-0002-2890-6352, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Lever, T.E. and Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872
Neuron 111 (14): 2184-2200.e7. 19 July 2023

Defining the landscape of circular RNAs in neuroblastoma unveils a global suppressive function of MYCN.
Fuchs, S. ORCID: https://orcid.org/0000-0001-9619-4329, Danßmann, C., Klironomos, F., Winkler, A., Fallmann, J. ORCID: https://orcid.org/0000-0002-4573-9939, Kruetzfeldt, L.M. ORCID: https://orcid.org/0000-0003-3630-3727, Szymansky, A. ORCID: https://orcid.org/0000-0003-4797-4526, Naderi, J., Bernhart, S.H. ORCID: https://orcid.org/0000-0002-5928-9449, Grunewald, L., Helmsauer, K. ORCID: https://orcid.org/0000-0003-0773-4114, Rodriguez-Fos, E. ORCID: https://orcid.org/0000-0002-2555-0178, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Astrahantseff, K. ORCID: https://orcid.org/0000-0002-7872-1997, Suenkel, C. ORCID: https://orcid.org/0000-0002-5326-6043, Toedling, J. ORCID: https://orcid.org/0000-0003-1471-1295, Meggetto, F. ORCID: https://orcid.org/0000-0002-2610-0144, Remke, M. ORCID: https://orcid.org/0000-0002-9404-9993, Stadler, P.F., Hundsdoerfer, P., Deubzer, H.E. ORCID: https://orcid.org/0000-0002-6115-4893, Künkele, A. ORCID: https://orcid.org/0000-0002-8406-5412, Lang, P. ORCID: https://orcid.org/0000-0001-7737-2142, Fuchs, J., Henssen, A.G. ORCID: https://orcid.org/0000-0003-1534-778X, Eggert, A. ORCID: https://orcid.org/0000-0003-3476-8184, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Hertwig, F. ORCID: https://orcid.org/0000-0003-4784-6516 and Schulte, J.H. ORCID: https://orcid.org/0000-0003-0671-1201
Nature Communications 14 (1): 3936. 4 July 2023

Modelling viral encephalitis caused by herpes simplex virus 1 infection in cerebral organoids.
Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Oliveras Martinez, A. ORCID: https://orcid.org/0000-0002-5880-5245, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Loewa, A. ORCID: https://orcid.org/0000-0002-5551-731X, Kim, S.J. ORCID: https://orcid.org/0000-0001-8357-0073, Kaufer, B.B. ORCID: https://orcid.org/0000-0003-1328-2695, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Microbiology 8 (7): 1252-1266. July 2023

A circular RNA expressed from the FAT3 locus regulates neural development.
Seeler, S., Andersen, M.S., Sztanka-Toth, T. ORCID: https://orcid.org/0000-0003-0185-5978, Rybiczka-Tešulov, M., van den Munkhof, M.H., Chang, C.C., Maimaitili, M., Venø, M.T., Hansen, T.B., Pasterkamp, R.J., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Denham, M., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kristensen, L.S. and Kjems, J. ORCID: https://orcid.org/0000-0003-4128-9317
Molecular Neurobiology 60 (6): 3239–3260. June 2023

Single-cell and spatial transcriptomics: deciphering brain complexity in health and disease.
Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290
Nature Reviews Neurology 19 (6): 346-362. June 2023

Establishment of gastrointestinal assembloids to study the interplay between epithelial crypts and their mesenchymal niche.
Lin, M. ORCID: https://orcid.org/0000-0003-4093-9277, Hartl, K. ORCID: https://orcid.org/0000-0002-2965-0512, Heuberger, J. ORCID: https://orcid.org/0000-0001-7205-732X, Beccaceci, G. ORCID: https://orcid.org/0000-0002-6453-3725, Berger, H. ORCID: https://orcid.org/0000-0002-6304-4946, Li, H. ORCID: https://orcid.org/0000-0001-5677-3377, Liu, L. ORCID: https://orcid.org/0000-0002-9553-5475, Müllerke, S., Conrad, T. ORCID: https://orcid.org/0000-0001-5618-6295, Heymann, F., Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Tacke, F. ORCID: https://orcid.org/0000-0001-6206-0226, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Sigal, M. ORCID: https://orcid.org/0000-0003-4772-0761
Nature Communications 14 (1): 3025. 25 May 2023

Sites of transcription initiation drive mRNA isoform selection.
Alfonso-Gonzalez, C., Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Holec, S., Arrigoni, L., Ozbulut, H.C., Mateos, F., Koppstein, D., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Bönisch, U., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Hilgers, V.
Cell 186 (11): 2438-2455. 25 May 2023

High-resolution molecular atlas of a lung tumor in 3D.
Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Schallenberg, Simon, León-Periñán, D. ORCID: https://orcid.org/0000-0002-7970-0362, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Theurillat, I. ORCID: https://orcid.org/0000-0002-1125-1951, Thomas, G., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Fritzsche, S. ORCID: https://orcid.org/0000-0003-3335-3534, Nimo, J. ORCID: https://orcid.org/0000-0002-1565-7799, Ruff, L., Dernbach, G., Jurmeister, P., Murphy, S., Gregory, M., Liang, Y., Cordenonsi, M., Piccolo, S., Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Klauschen, F. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
bioRxiv : 2023.05.10.539644. 10 May 2023

Curvature in biological systems: its quantification, emergence and implications across the scales.
Schamberger, B., Roschger, A., Ziege, R., Anselme, K., Amar, M.B., Bykowski, M., Castro, A.P.G., Cipitria, A., Coles, R., Dimova, R., Eder, M., Ehrig, S. ORCID: https://orcid.org/0000-0002-5118-7405, Escudero, L.M., Evans, M.E., Fernandes, P.R., Fratzl, P., Geris, L., Gierlinger, N., Hannezo, E., Iglič, A., Kirkensgaard, J.J.K., Kollmannsberger, P., Kowalewska, Ł., Kurniawan, N.A., Papantoniou, I., Pieuchot, L., Pires, T.H.V., Renner, L., Sageman-Furnas, A., Schröder-Turk, G.E., Sengupta, A., Sharma, V.R., Tagua, A., Tomba, C., Trepat, X., Waters, S.L., Yeo, E., Bidan, C.M. and Dunlop, J.W.C.
Advanced Materials 35 (13): e2206110. 15 March 2023

C. elegans gene regulatory alleles and reporter bashing studies.
Froehlich, J.J. ORCID: https://orcid.org/0000-0002-9176-4633 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
microPublication Biology 2023 20 January 2023

Rapid nuclear deadenylation of mammalian messenger RNA.
Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Pacelli, M. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
iScience 26 (1): 105878. 20 January 2023

A guide to naming eukaryotic circular RNAs.
Chen, L.L. ORCID: https://orcid.org/0000-0001-9501-0305, Bindereif, A. ORCID: https://orcid.org/0000-0002-7730-7380, Bozzoni, I. ORCID: https://orcid.org/0000-0002-3485-8537, Chang, H.Y. ORCID: https://orcid.org/0000-0002-9459-4393, Matera, A.G. ORCID: https://orcid.org/0000-0002-6406-0630, Gorospe, M. ORCID: https://orcid.org/0000-0001-5439-3434, Hansen, T.B. ORCID: https://orcid.org/0000-0002-7573-9657, Kjems, J. ORCID: https://orcid.org/0000-0003-4128-9317, Ma, X.K., Pek, J.W. ORCID: https://orcid.org/0000-0001-6089-6900, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Salzman, J., Wilusz, J.E. ORCID: https://orcid.org/0000-0001-6929-8755, Yang, L. ORCID: https://orcid.org/0000-0001-8833-7473 and Zhao, F. ORCID: https://orcid.org/0000-0002-6216-1235
Nature Cell Biology 25 (1): 1-5. January 2023

2022

SARS-CoV-2 infection dynamics revealed by wastewater sequencing analysis and deconvolution.
Schumann, V.F. ORCID: https://orcid.org/0000-0003-0227-7428, de Castro Cuadrat, R.R. ORCID: https://orcid.org/0000-0001-8289-2599, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Deter, A., Quedenau, C. ORCID: https://orcid.org/0000-0002-6846-4915, Dohmen, J. ORCID: https://orcid.org/0000-0002-7826-3025, Faxel, M. ORCID: https://orcid.org/0009-0007-4891-1734, Borodina, T. ORCID: https://orcid.org/0000-0002-6978-016X, Blume, A. ORCID: https://orcid.org/0000-0003-3045-8234, Freimuth, J. ORCID: https://orcid.org/0000-0002-9259-3696, Meixner, M., Grau, J.H., Liere, K., Hackenbeck, T., Zietzschmann, F., Gnirss, R., Böckelmann, U., Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Barke, N. ORCID: https://orcid.org/0009-0004-5862-6628, Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Science of the Total Environment 853 : 158931. 20 December 2022

Long-term imaging reveals behavioral plasticity during C. elegans dauer exit.
Preusser, F. ORCID: https://orcid.org/0000-0001-8231-2195, Neuschulz, A. ORCID: https://orcid.org/0000-0001-6163-3344, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X
BMC Biology 20 (1): 277. 13 December 2022

Mechanisms of IRF2BPL-related disorders and identification of a potential therapeutic strategy.
Sinha Ray, S., Dutta, D., Dennys, C., Powers, S., Roussel, F., Lisowski, P. ORCID: https://orcid.org/0000-0002-3634-1072, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Zhang, X., Biswas, P., Caporale, J.R., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Bickle, M., Wein, N., Bellen, H.J., Likhite, S., Marcogliese, P.C. and Meyer, K.C. ORCID: https://orcid.org/0000-0002-5052-2101
Cell Reports 41 (10): 111751. 6 December 2022

Urinary single-cell sequencing captures kidney injury and repair processes in human acute kidney injury.
Klocke, J., Kim, S.J., Skopnik, C.M., Hinze, C. ORCID: https://orcid.org/0000-0003-2526-1621, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Metzke, D., Grothgar, E., Prskalo, L., Wagner, L., Freund, P., Görlich, N., Muench, F., Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142, Mashreghi, M.F., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Eckardt, K.U., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Enghard, P.
Kidney International 102 (6): 1359-1370. December 2022

Cell type diversity in a developing octopus brain.
Styfhals, R. ORCID: https://orcid.org/0000-0002-5287-8830, Zolotarov, G. ORCID: https://orcid.org/0000-0002-3971-3070, Hulselmans, G., Spanier, K.I. ORCID: https://orcid.org/0000-0002-1375-4157, Poovathingal, S., Elagoz, A.M. ORCID: https://orcid.org/0000-0002-1639-0619, De Winter, S. ORCID: https://orcid.org/0000-0001-7907-1247, Deryckere, A. ORCID: https://orcid.org/0000-0001-6227-7759, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ponte, G. ORCID: https://orcid.org/0000-0002-1779-958X, Fiorito, G. ORCID: https://orcid.org/0000-0003-2926-9479, Aerts, S. ORCID: https://orcid.org/0000-0002-8006-0315 and Seuntjens, E. ORCID: https://orcid.org/0000-0002-0126-461X
Nature Communications 13 (1): 7392. 30 November 2022

MicroRNAs are deeply linked to the emergence of the complex octopus brain.
Zolotarov, G. ORCID: https://orcid.org/0000-0002-3971-3070, Fromm, B. ORCID: https://orcid.org/0000-0003-0352-3037, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Polese, G. ORCID: https://orcid.org/0000-0002-6322-7769, Maselli, V. ORCID: https://orcid.org/0000-0002-1452-8063, Chabot, P.J. ORCID: https://orcid.org/0000-0001-6001-3346, Vinther, J. ORCID: https://orcid.org/0000-0002-3584-9616, Styfhals, R. ORCID: https://orcid.org/0000-0002-5287-8830, Seuntjens, E., Di Cosmo, A. ORCID: https://orcid.org/0000-0002-1018-9957, Peterson, K.J. ORCID: https://orcid.org/0000-0002-6780-0964 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Science Advances 8 (47): eadd9938. 25 November 2022

Epigenetic targeting of transposon relics: beating the dead horses of the genome?
Sammarco, I. ORCID: https://orcid.org/0000-0002-4101-6223, Pieters, J. ORCID: https://orcid.org/0000-0001-7887-7863, Salony, S., Toman, I., Zolotarov, G. ORCID: https://orcid.org/0000-0002-3971-3070 and Lafon Placette, C. ORCID: https://orcid.org/0000-0001-6634-8104
Epigenetics 17 (11): 1331-1344. November 2022

Integrated genomic surveillance enables tracing of person-to-person SARS-CoV-2 transmission chains during community transmission and reveals extensive onward transmission of travel-imported infections, Germany, June to July 2021.
Houwaart, Torsten, Belhaj, S., Tawalbeh, E., Nagels, D., Fröhlich, Y., Finzer, P., Ciruela, P., Sabrià, A., Herrero, M., Andrés, C., Antón, A., Benmoumene, A., Asskali, D., Haidar, H., von Dahlen, J., Nicolai, J., Stiller, M., Blum, J., Lange, C., Adelmann, C., Schroer, B., Osmers, U., Grice, C., Kirfel, P.P., Jomaa, H., Strelow, D., Hülse, L., Pigulla, M., Kreuzer, P., Tyshaieva, A., Weber, J., Wienemann, T., Kohns Vasconcelos, M., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Scholz, C.J., Jazmati, N., Göbels, K., Zotz, R., Pfeffer, K., Timm, J., Ehlkes, L., Walker, A. and Dilthey, A.T.
Eurosurveillance 27 (43): 2101089. 27 October 2022

Best practice standards for circular RNA research.
Nielsen, A.F. ORCID: https://orcid.org/0000-0003-2653-4863, Bindereif, A., Bozzoni, I. ORCID: https://orcid.org/0000-0002-3485-8537, Hanan, M., Hansen, T.B., Irimia, M., Kadener, S., Kristensen, L.S. ORCID: https://orcid.org/0000-0002-5980-7939, Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Morlando, M., Jarlstad Olesen, M.T., Pasterkamp, R.J. ORCID: https://orcid.org/0000-0003-1631-6440, Preibisch, S. ORCID: https://orcid.org/0000-0002-0276-494X, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Suenkel, C. ORCID: https://orcid.org/0000-0002-5326-6043 and Kjems, J. ORCID: https://orcid.org/0000-0003-4128-9317
Nature Methods 19 (10): 1208-1220. October 2022

Single-cell transcriptomics reveals common epithelial response patterns in human acute kidney injury.
Hinze, C. ORCID: https://orcid.org/0000-0003-2526-1621, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Leiz, J. ORCID: https://orcid.org/0000-0002-6531-7047, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Cao, S. ORCID: https://orcid.org/0000-0001-7195-8193, Skopnik, C.M. ORCID: https://orcid.org/0000-0002-6089-4769, Klocke, J. ORCID: https://orcid.org/0000-0002-7723-9234, Hardenberg, J.H. ORCID: https://orcid.org/0000-0001-9548-2118, Stockmann, H. ORCID: https://orcid.org/0000-0002-0934-7620, Gotthardt, I. ORCID: https://orcid.org/0000-0001-6033-0093, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Haghverdi, L. ORCID: https://orcid.org/0000-0001-9280-9170, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Bachmann, S., Hocke, A.C. ORCID: https://orcid.org/0000-0002-6935-8612, Corman, V., Busch, J., Schneider, W., Himmerkus, N. ORCID: https://orcid.org/0000-0002-2910-6728, Bleich, M. ORCID: https://orcid.org/0000-0002-1745-2295, Eckardt, K.U. ORCID: https://orcid.org/0000-0003-3823-0920, Enghard, P. ORCID: https://orcid.org/0000-0002-7254-3931, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142
Genome Medicine 14 (1): 103. 9 September 2022

Spacemake: processing and analysis of large-scale spatial transcriptomics data.
Sztanka-Toth, T.R. ORCID: https://orcid.org/0000-0003-0185-5978, Jens, M. ORCID: https://orcid.org/0000-0002-6660-8743, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
GigaScience 11 : giac064. 19 July 2022

Optocoder: computational decoding of spatially indexed bead arrays.
Senel, E. ORCID: https://orcid.org/0000-0003-1966-1186, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947
NAR Genomics and Bioinformatics 4 (2): lqac042. June 2022

Characterization of Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) infection clusters based on integrated genomic surveillance, outbreak analysis and contact tracing in an urban setting.
Walker, A., Houwaart, T., Finzer, P., Ehlkes, L., Tyshaieva, A., Damagnez, M., Strelow, D., Duplessis, A., Nicolai, J., Wienemann, T., Tamayo, T., Kohns Vasconcelos, M., Hülse, L., Hoffmann, K., Lübke, N., Hauka, S., Andree, M., Däumer, M.P., Thielen, A., Kolbe-Busch, S., Göbels, K., Zotz, R., Pfeffer, K., Timm, J. and Dilthey, A.T.
Clinical Infectious Diseases 74 (6): 1039-1046. 15 March 2022

Expression of circ_Satb1 is decreased in mesial temporal lobe epilepsy and regulates dendritic spine morphology.
Gomes-Duarte, A., Venø, M.T., de Wit, M., Senthilkumar, K., Broekhoven, M.H., van den Herik, J., Heeres, F.R., van Rossum, D., Rybiczka-Tesulov, M., Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, van Rijen, P.C., van Eijsden, P., Gosselaar, P.H., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kjems, J., Vangoor, V.R. and Pasterkamp, R.J.
Frontiers in Molecular Neuroscience 15 : 832133. 3 March 2022

2021

Early IFN-α signatures and persistent dysfunction are distinguishing features of NK cells in severe COVID-19.
Krämer, B., Knoll, R. ORCID: https://orcid.org/0000-0001-8320-5885, Bonaguro, L., ToVinh, M. ORCID: https://orcid.org/0000-0002-1625-9741, Raabe, J. ORCID: https://orcid.org/0000-0002-6894-1451, Astaburuaga-García, R., Schulte-Schrepping, J., Kaiser, K.M., Rieke, G.J., Bischoff, J., Monin, M.B., Hoffmeister, C. ORCID: https://orcid.org/0000-0001-6473-4087, Schlabe, S., De Domenico, E., Reusch, N. ORCID: https://orcid.org/0000-0001-5625-0701, Händler, K., Reynolds, G., Blüthgen, N. ORCID: https://orcid.org/0000-0002-0171-7447, Hack, G., Finnemann, C., Nischalke, H.D., Strassburg, C.P., Stephenson, E., Su, Y., Gardner, L., Yuan, D., Chen, D., Goldman, J., Rosenstiel, P., Schmidt, S.V., Latz, E., Hrusovsky, K., Ball, A.J., Johnson, J.M., Koenig, P.A., Schmidt, F.I., Haniffa, M., Heath, J.R., Kümmerer, B.M., Keitel, V., Jensen, B., Stubbemann, P., Kurth, F., Sander, L.E., Sawitzki, B., Aschenbrenner, A.C., Schultze, J.L. and Nattermann, J.
Immunity 54 (11): 2650-2669. 9 November 2021

NovoSpaRc: flexible spatial reconstruction of single-cell gene expression with optimal transport.
Moriel, N., Senel, E. ORCID: https://orcid.org/0000-0003-1966-1186, Friedman, N. ORCID: https://orcid.org/0000-0002-9678-3550, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947 and Nitzan, M. ORCID: https://orcid.org/0000-0003-0074-9196
Nature Protocols 16 (9): 4177-4200. September 2021

Nuclei isolation from adult mouse kidney for single-nucleus RNA-sequencing.
Leiz, J. ORCID: https://orcid.org/0000-0002-6531-7047, Hinze, C. ORCID: https://orcid.org/0000-0003-2526-1621, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Braeuning, C. ORCID: https://orcid.org/0009-0007-1439-9920, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142
Journal of Visualized Experiments (175): e62901. September 2021

Generation of human brain organoids for mitochondrial disease modeling.
Le, S., Petersilie, L., Inak, G., Menacho-Pando, C., Kafitz, K.W., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Rose, C.R. and Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952
Journal of Visualized Experiments (172): e62756. 21 June 2021

Swarm Learning for decentralized and confidential clinical machine learning.
Warnat-Herresthal, S., Schultze, H., Shastry, K.L., Manamohan, S., Mukherjee, S., Garg, V., Sarveswara, R., Händler, K., Pickkers, P., Aziz, N.A., Ktena, S., Tran, F., Bitzer, M., Ossowski, S., Casadei, N., Herr, C., Petersheim, D., Behrends, U., Kern, F., Fehlmann, T., Schommers, P., Lehmann, C., Augustin, M., Rybniker, J., Altmüller, J. ORCID: https://orcid.org/0000-0003-4372-1521, Mishra, N., Bernardes, J.P., Krämer, B., Bonaguro, L., Schulte-Schrepping, J., De Domenico, E., Siever, C., Kraut, M., Desai, M., Monnet, B., Saridaki, M., Siegel, C.M., Drews, A., Nuesch-Germano, M., Theis, H., Heyckendorf, J., Schreiber, S., Kim-Hellmuth, S., Nattermann, J., Skowasch, D., Kurth, I., Keller, A., Bals, R., Nürnberg, P., Rieß, O., Rosenstiel, P., Netea, M.G., Theis, F., Mukherjee, S., Backes, M., Aschenbrenner, A.C., Ulas, T., Breteler, M.M.B., Giamarellos-Bourboulis, E.J., Kox, M., Becker, M., Cheran, S., Woodacre, M.S., Goh, E.L. and Schultze, J.L.
Nature 594 (7862): 265-270. 10 June 2021

SARS-CoV-2 infection paralyzes cytotoxic and metabolic functions of the immune cells.
Singh, Y. ORCID: https://orcid.org/0000-0001-6919-6273, Trautwein, C., Fendel, R. ORCID: https://orcid.org/0000-0003-4716-0311, Krickeberg, N., Berezhnoy, G., Bissinger, R., Ossowski, S., Salker, M.S., Casadei, N. ORCID: https://orcid.org/0000-0003-2209-0580 and Riess, O.
Heliyon 7 (6): e07147. June 2021

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
Glazar, Peter ORCID: https://orcid.org/0000-0003-0842-0088
[Dataset] 20 April 2021

iPSC-derived 2D and 3D models of mitochondrial disease reveal early defects in neuronal morphogenesis and identify intervention strategies.
Inak, G., Rybak, A. ORCID: https://orcid.org/0000-0002-1192-5290, Lisowski, P. ORCID: https://orcid.org/0000-0002-3634-1072, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Schuelke, M. ORCID: https://orcid.org/0000-0003-2824-3891 and Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952
[Dataset] 20 April 2021

Parallel genetics of regulatory sequences using scalable genome editing in vivo.
Froehlich, J.J. ORCID: https://orcid.org/0000-0002-9176-4633, Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Herzog, M., Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Reports 35 (2): 108988. 13 April 2021

Defective metabolic programming impairs early neuronal morphogenesis in neural cultures and an organoid model of Leigh syndrome.
Inak, G., Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Lisowski, P. ORCID: https://orcid.org/0000-0002-3634-1072, Pentimalli, T.M. ORCID: https://orcid.org/0000-0002-8461-7918, Jüttner, R. ORCID: https://orcid.org/0000-0003-3565-0698, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Uppal, K., Bottani, E. ORCID: https://orcid.org/0000-0003-1217-8722, Brunetti, D. ORCID: https://orcid.org/0000-0002-2740-9370, Secker, C. ORCID: https://orcid.org/0000-0002-7222-536X, Zink, A. ORCID: https://orcid.org/0000-0002-8489-6339, Meierhofer, D. ORCID: https://orcid.org/0000-0002-0170-868X, Henke, M.T. ORCID: https://orcid.org/0000-0001-6572-1667, Dey, M. ORCID: https://orcid.org/0000-0002-9987-575X, Ciptasari, U. ORCID: https://orcid.org/0000-0003-4577-3069, Mlody, B. ORCID: https://orcid.org/0000-0001-5184-1772, Hahn, T., Berruezo-Llacuna, M., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Di Virgilio, M. ORCID: https://orcid.org/0000-0001-5189-0793, Mayr, J.A. ORCID: https://orcid.org/0000-0001-6970-336X, Wortmann, S.B., Priller, J. ORCID: https://orcid.org/0000-0001-7596-0979, Gotthardt, M. ORCID: https://orcid.org/0000-0003-1788-3172, Jones, D.P., Mayatepek, E., Stenzel, W., Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Schuelke, M. ORCID: https://orcid.org/0000-0003-2824-3891 and Prigione, A. ORCID: https://orcid.org/0000-0001-9457-1952
Nature Communications 12 (1): 1929. 26 March 2021

Transcriptomic profiling of SARS-CoV-2 infected human cell lines identifies HSP90 as target for COVID-19 therapy.
Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Mösbauer, K., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Diag, A., Gottula, L.T., Arsiè, R. ORCID: https://orcid.org/0000-0002-7869-7624, Klironomos, F., Koppstein, D. ORCID: https://orcid.org/0000-0002-8618-7237, Hönzke, K., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Buccitelli, C. ORCID: https://orcid.org/0000-0002-2637-2131, Hoffmann, K., Richter, A., Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Ivanov, A. ORCID: https://orcid.org/0000-0002-4824-1925, Mari, T. ORCID: https://orcid.org/0000-0001-6011-9386, Del Giudice, S. ORCID: https://orcid.org/0000-0003-0194-3767, Papies, J., Praktiknjo, S. ORCID: https://orcid.org/0000-0002-0186-5271, Meyer, T.F., Müller, M.A., Niemeyer, D. ORCID: https://orcid.org/0000-0002-1897-6365, Hocke, A., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Drosten, C. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
iScience 24 (3): 102151. 19 March 2021

Kidney single-cell transcriptomes predict spatial corticomedullary gene expression and tissue osmolality gradients.
Hinze, C. ORCID: https://orcid.org/0000-0003-2526-1621, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Walentin, K., Redo, K., Himmerkus, N., Bleich, M., Potter, S.S., Potter, A.S., Eckardt, K.U., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Schmidt-Ott, K.M. ORCID: https://orcid.org/0000-0002-7700-7142
Journal of the American Society of Nephrology 32 (2): 291-306. February 2021

Disease severity-specific neutrophil signatures in blood transcriptomes stratify COVID-19 patients.
Aschenbrenner, A.C., Mouktaroudi, M., Krämer, B., Oestreich, M., Antonakos, N., Nuesch-Germano, M., Gkizeli, K., Bonaguro, L., Reusch, N., Baßler, K., Saridaki, M., Knoll, R., Pecht, T., Kapellos, T.S., Doulou, S., Kröger, C., Herbert, M., Holsten, L., Horne, A. ORCID: https://orcid.org/0000-0002-4209-4573, Gemünd, I.D., Rovina, N., Agrawal, S., Dahm, K., van Uelft, M., Drews, A., Lenkeit, L., Bruse, N., Gerretsen, J., Gierlich, J., Becker, M., Händler, K., Kraut, M., Theis, H., Mengiste, S., Domenico, E., Schulte-Schrepping, J., Seep, L., Raabe, J., Hoffmeister, C., ToVinh, M., Keitel, V., Rieke, G., Talevi, V., Skowasch, D., Aziz, N.A., Pickkers, P., van de Veerdonk, F.L., Netea, M.G., Schultze, J.L., Kox, M., Breteler, M.M.B., Nattermann, J., Koutsoukou, A., Giamarellos-Bourboulis, E.J. and Ulas, T. ORCID: https://orcid.org/0000-0002-9785-4197
Genome Medicine 13 (1): 7. 13 January 2021

Estimation of C. elegans cell- and tissue volumes.
Froehlich, J.J. ORCID: https://orcid.org/0000-0002-9176-4633, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Ewald, C.Y.
microPublication Biology : 000345. 4 January 2021

Gene expression signatures of a preclinical mouse model during colorectal cancer progression under low-dose metronomic chemotherapy.
Ho-Xuan, H. ORCID: https://orcid.org/0000-0003-2911-1559, Lehmann, G., Glazar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Gypas, F., Eichner, N., Heizler, K., Schlitt, H.J. ORCID: https://orcid.org/0000-0002-3874-0296, Zavolan, M., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Meister, G. ORCID: https://orcid.org/0000-0002-2098-9923 and Hackl, C.
Cancers 13 (1): 49. 2021

2020

Longitudinal multi-omics analyses identify responses of megakaryocytes, erythroid cells, and plasmablasts as hallmarks of severe COVID-19.
Bernardes, J.P., Mishra, N., Tran, F., Bahmer, T., Best, L., Blase, J.I., Bordoni, D., Franzenburg, J., Geisen, U., Josephs-Spaulding, J., Köhler, P., Künstner, A., Rosati, E., Aschenbrenner, A.C., Bacher, P., Baran, N., Boysen, T., Brandt, B., Bruse, N., Dörr, J., Dräger, A., Elke, G., Ellinghaus, D., Fischer, J., Forster, M., Franke, A., Franzenburg, S., Frey, N., Friedrichs, A., Fuß, J., Glück, A., Hamm, J., Hinrichsen, F., Hoeppner, M.P., Imm, S., Junker, R., Kaiser, S., Kan, Y.H., Knoll, R., Lange, C., Laue, G., Lier, C., Lindner, M., Marinos, G., Markewitz, R., Nattermann, J., Noth, R., Pickkers, P., Rabe, K.F., Renz, A., Röcken, C., Rupp, J., Schaffarzyk, A., Scheffold, A., Schulte-Schrepping, J., Schunk, D., Skowasch, D., Ulas, T., Wandinger, K.P., Wittig, M., Zimmermann, J., Busch, H., Hoyer, B.F., Kaleta, C., Heyckendorf, J., Kox, M., Rybniker, J., Schreiber, S., Schultze, J.L. and Rosenstiel, P.
Immunity 53 (6): 1296-1314. 15 December 2020

LifeTime and improving European healthcare through cell-based interceptive medicine.
Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Almouzni, G. ORCID: https://orcid.org/0000-0001-5570-0723, Gorski, S.A. ORCID: https://orcid.org/0000-0003-0539-3395, Aerts, S. ORCID: https://orcid.org/0000-0002-8006-0315, Amit, I. ORCID: https://orcid.org/0000-0003-2968-877X, Bertero, M.G., Bock, C. ORCID: https://orcid.org/0000-0001-6091-3088, Bredenoord, A.L. ORCID: https://orcid.org/0000-0002-7542-8963, Cavalli, G. ORCID: https://orcid.org/0000-0003-3709-3469, Chiocca, S. ORCID: https://orcid.org/0000-0002-9721-0850, Clevers, H. ORCID: https://orcid.org/0000-0002-3077-5582, De Strooper, B., Eggert, A., Ellenberg, J. ORCID: https://orcid.org/0000-0001-5909-701X, Fernández, X.M. ORCID: https://orcid.org/0000-0001-7139-6215, Figlerowicz, M., Gasser, S.M. ORCID: https://orcid.org/0000-0003-3610-9123, Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223, Kjems, J., Knoblich, J.A. ORCID: https://orcid.org/0000-0002-6751-3404, Krabbe, G., Lichter, P. ORCID: https://orcid.org/0000-0002-2960-5279, Linnarsson, S. ORCID: https://orcid.org/0000-0002-3491-3444, Marine, J.C., Marioni, J. ORCID: https://orcid.org/0000-0001-9092-0852, Marti-Renom, M.A. ORCID: https://orcid.org/0000-0002-0151-4279, Netea, M.G. ORCID: https://orcid.org/0000-0003-2421-6052, Nickel, D., Nollmann, M. ORCID: https://orcid.org/0000-0003-3339-2349, Novak, H.R., Parkinson, H., Piccolo, S. ORCID: https://orcid.org/0000-0002-1600-3092, Pinheiro, I., Pombo, A. ORCID: https://orcid.org/0000-0002-7493-6288, Popp, C., Reik, W. ORCID: https://orcid.org/0000-0003-0216-9881, Roman-Roman, S., Rosenstiel, P., Schultze, J.L. ORCID: https://orcid.org/0000-0003-2812-9853, Stegle, O., Tanay, A. ORCID: https://orcid.org/0000-0001-9419-3824, Testa, G., Thanos, D., Theis, F.J. ORCID: https://orcid.org/0000-0002-2419-1943, Torres-Padilla, M.E. ORCID: https://orcid.org/0000-0002-1020-2074, Valencia, A., Vallot, C. ORCID: https://orcid.org/0000-0003-1601-2359, van Oudenaarden, A. ORCID: https://orcid.org/0000-0002-9442-3551, Vidal, M. ORCID: https://orcid.org/0000-0003-1186-9994 and Voet, T.
Nature 587 (7834): 377-386. 19 November 2020

The transcriptome dynamics of single cells during the cell cycle.
Schwabe, D. ORCID: https://orcid.org/0000-0003-2825-3352, Formichetti, S. ORCID: https://orcid.org/0000-0002-7907-2239, Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290, Falcke, M. ORCID: https://orcid.org/0000-0001-7137-1114 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Molecular Systems Biology 16 (11): e9946. 1 November 2020

Gene selection for optimal prediction of cell position in tissues from single-cell transcriptomics data.
Tanevski, J. ORCID: https://orcid.org/0000-0001-7177-1003, Nguyen, T., Truong, B., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Ahsen, M.E., Zhang, X., Shu, C. ORCID: https://orcid.org/0000-0002-3730-5102, Xu, K. ORCID: https://orcid.org/0000-0002-6472-7052, Liang, X., Hu, Y. ORCID: https://orcid.org/0000-0002-0794-742X, Pham, H.V.V. ORCID: https://orcid.org/0000-0002-8884-3584, Xiaomei, L., Le, T.D. ORCID: https://orcid.org/0000-0002-9732-4313, Tarca, A.L. ORCID: https://orcid.org/0000-0003-1712-7588, Bhatti, G., Romero, R., Karathanasis, N. ORCID: https://orcid.org/0000-0003-4119-0851, Loher, P., Chen, Y. ORCID: https://orcid.org/0000-0003-0147-3443, Ouyang, Z. ORCID: https://orcid.org/0000-0003-2842-8503, Mao, D., Zhang, Y. ORCID: https://orcid.org/0000-0001-8986-0354, Zand, M., Ruan, J., Hafemeister, C., Qiu, P., Tran, D. ORCID: https://orcid.org/0000-0003-2918-8601, Nguyen, T. ORCID: https://orcid.org/0000-0001-8001-9470, Gabor, A. ORCID: https://orcid.org/0000-0002-0776-1182, Yu, T., Guinney, J., Glaab, E. ORCID: https://orcid.org/0000-0003-3977-7469, Krause, R. ORCID: https://orcid.org/0000-0001-9938-7126, Banda, P. ORCID: https://orcid.org/0000-0001-6678-490X, Stolovitzky, G. ORCID: https://orcid.org/0000-0002-9618-2819, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Saez-Rodriguez, J. and Meyer, P. ORCID: https://orcid.org/0000-0001-5281-4661
Life Science Alliance 3 (11): e202000867. November 2020

Comprehensive analysis of translation from overexpressed circular RNAs reveals pervasive translation from linear transcripts.
Ho-Xuan, H. ORCID: https://orcid.org/0000-0003-2911-1559, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Latini, C., Heizler, K., Haase, J., Hett, R., Anders, M., Weichmann, F., Bruckmann, A., Van den Berg, D., Hüttelmaier, S. ORCID: https://orcid.org/0000-0001-9335-4227, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Hackl, C. and Meister, G. ORCID: https://orcid.org/0000-0002-2098-9923
Nucleic Acids Research 48 (18): 10368-10382. 9 October 2020

Tracing tumorigenesis in a solid tumor model at single-cell resolution.
Praktiknjo, S.D. ORCID: https://orcid.org/0000-0002-0186-5271, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Zhu, Q., Fang, L., Liu, H. ORCID: https://orcid.org/0009-0007-4871-452X, Quinn, H. ORCID: https://orcid.org/0000-0002-1336-5709, Stoeckius, M. ORCID: https://orcid.org/0000-0002-5658-029X, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Birchmeier, W. ORCID: https://orcid.org/0000-0003-1173-0829 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Communications 11 (1): 991. 20 February 2020

A highly conserved circular RNA is required to keep neural cells in a progenitor state in the mammalian brain.
Suenkel, C. ORCID: https://orcid.org/0000-0002-5326-6043, Cavalli, D., Massalini, S., Calegari, F. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Reports 30 (7): 2170-2179. 18 February 2020

2019

Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7.
Marg, A. ORCID: https://orcid.org/0000-0003-3673-4244, Escobar Fernandez, H. ORCID: https://orcid.org/0000-0002-8128-7845, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Grunwald, S.A. ORCID: https://orcid.org/0000-0002-3899-5424, Metzler, E. ORCID: https://orcid.org/0000-0003-1735-6364, Kieshauer, J. ORCID: https://orcid.org/0000-0002-6924-8616, Sauer, S. ORCID: https://orcid.org/0000-0002-4794-3693, Pasemann, D., Malfatti, E., Mompoint, D., Quijano-Roy, S., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Schneider, J. ORCID: https://orcid.org/0000-0001-8810-0492, Schülke, M. ORCID: https://orcid.org/0000-0003-2824-3891, Kunz, S. ORCID: https://orcid.org/0000-0002-0131-3506, Carlier, R. ORCID: https://orcid.org/0000-0002-9417-0726, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Amthor, H., Spuler, A., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Spuler, S. ORCID: https://orcid.org/0000-0002-0155-1117
Nature Communications 10 (1): 5776. 18 December 2019

Gene expression cartography.
Nitzan, M., Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Friedman, N. ORCID: https://orcid.org/0000-0002-9678-3550 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature 576 (7785): 132-137. 5 December 2019

Context-specific regulation of cell survival by a miRNA-controlled BIM rheostat.
Labi, V. ORCID: https://orcid.org/0000-0001-7538-1520, Peng, S., Klironomos, F., Munschauer, M. ORCID: https://orcid.org/0000-0001-6143-4548, Kastelic, N., Chakraborty, T., Schoeler, K., Derudder, E. ORCID: https://orcid.org/0000-0003-1421-4045, Martella, M., Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Hernandez-Miranda, L.R. ORCID: https://orcid.org/0000-0002-0498-708X, Lahmann, I. ORCID: https://orcid.org/0000-0003-0640-4519, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Quintanilla-Martinez de Fend, L., Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Rajewsky, K. ORCID: https://orcid.org/0000-0002-6633-6370
Genes & Development 33 : 23-24. 7 November 2019

Single-cell RNA-sequencing of herpes simplex virus 1-infected cells connects NRF2 activation to an antiviral program.
Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Menegatti, J., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Praktiknjo, S. ORCID: https://orcid.org/0000-0002-0186-5271, Walch-Rückheim, B., Bosse, J. ORCID: https://orcid.org/0000-0001-7252-5541, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Grässer, F., Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
Nature Communications 10 (1): 4878. 25 October 2019

Identification of proteins and miRNAs that specifically bind an mRNA in vivo.
Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Imami, K. ORCID: https://orcid.org/0000-0002-7451-4982 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Communications 10 (1): 4205. 16 September 2019

FLAM-seq: full-length mRNA sequencing reveals principles of poly(A) tail length control.
Legnini, I. ORCID: https://orcid.org/0000-0002-8984-5215, Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Nature Methods 16 (9): 879-886. September 2019

The translational landscape of the human heart.
van Heesch, S. ORCID: https://orcid.org/0000-0001-9593-1980, Witte, F., Schneider-Lunitz, V. ORCID: https://orcid.org/0000-0002-3980-3789, Schulz, J.F. ORCID: https://orcid.org/0000-0002-8157-2224, Adami, E. ORCID: https://orcid.org/0000-0002-1813-6681, Faber, A. ORCID: https://orcid.org/0000-0003-0178-7653, Kirchner, M. ORCID: https://orcid.org/0000-0002-7049-534X, Maatz, H. ORCID: https://orcid.org/0000-0002-9232-6272, Blachut, S. ORCID: https://orcid.org/0009-0007-0102-9867, Sandmann, C.L. ORCID: https://orcid.org/0000-0002-3847-0708, Kanda, M. ORCID: https://orcid.org/0000-0003-3468-3586, Worth, C.L. ORCID: https://orcid.org/0000-0002-1796-9606, Schafer, S., Calviello, L. ORCID: https://orcid.org/0000-0002-5600-0988, Merriott, R., Patone, G. ORCID: https://orcid.org/0000-0002-7242-0341, Hummel, O. ORCID: https://orcid.org/0009-0000-9986-8333, Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Mücke, M. ORCID: https://orcid.org/0000-0002-4957-3307, Lindberg, E.L. ORCID: https://orcid.org/0000-0002-2979-433X, Trnka, F., Memczak, S. ORCID: https://orcid.org/0000-0001-9518-7135, Schilling, M. ORCID: https://orcid.org/0000-0002-3453-7792, Felkin, L.E., Barton, P.J.R., Quaife, N.M., Vanezis, K., Diecke, S. ORCID: https://orcid.org/0000-0002-5219-5992, Mukai, M., Mah, N. ORCID: https://orcid.org/0000-0002-1240-8076, Oh, S.J., Kurtz, A., Schramm, C., Schwinge, D., Sebode, M., Harakalova, M., Asselbergs, F.W., Vink, A., de Weger, R.A., Viswanathan, S., Widjaja, A.A., Gärtner-Rommel, A., Milting, H., Dos Remedios, C., Knosalla, C., Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Vingron, M., Linke, W.A., Seidman, J.G., Seidman, C.E., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Cook, S.A. and Hubner, N. ORCID: https://orcid.org/0000-0002-1218-6223
Cell 178 (1): 242-260. 27 June 2019

Roles of long noncoding RNAs and circular RNAs in translation.
Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cold Spring Harbor Perspectives in Biology 11 (6): a032680. 3 June 2019

PAGA: graph abstraction reconciles clustering with trajectory inference through a topology preserving map of single cells.
Wolf, F.A. ORCID: https://orcid.org/0000-0002-8760-7838, Hamey, F.K., Plass, M. ORCID: https://orcid.org/0000-0002-9891-2723, Solana, J. ORCID: https://orcid.org/0000-0002-6770-3929, Dahlin, J.S., Göttgens, B., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Simon, L. and Theis, F.J.
Genome Biology 20 (1): 59. 19 March 2019

BCR-dependent lineage plasticity in mature B cells.
Graf, R. ORCID: https://orcid.org/0000-0002-5400-9938, Seagal, J., Otipoby, K.L., Lam, K.P., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Zhang, B., Sander, S. ORCID: https://orcid.org/0000-0003-4645-3366, Chu, V.T. ORCID: https://orcid.org/0000-0003-1327-8696 and Rajewsky, K. ORCID: https://orcid.org/0000-0002-6633-6370
Science 363 (6428): 748-753. 15 February 2019

2018

Spatiotemporal m(i)RNA architecture and 3' UTR regulation in the C. elegans germline.
Diag, A., Schilling, M. ORCID: https://orcid.org/0000-0002-3453-7792, Klironomos, F., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Developmental Cell 47 (6): 785-800. 17 December 2018

The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea.
Schmidt, D. ORCID: https://orcid.org/0000-0003-2005-4244, Reuter, H., Hüttner, K., Ruhe, L., Rabert, F., Seebeck, F., Irimia, M., Solana, J. ORCID: https://orcid.org/0000-0002-6770-3929 and Bartscherer, K. ORCID: https://orcid.org/0000-0002-3070-4389
PLoS Genetics 14 (12): e1007828. 17 December 2018

Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis.
Zywitza, V. ORCID: https://orcid.org/0000-0003-3055-8569, Misios, A., Bunatyan, L., Willnow, T.E. ORCID: https://orcid.org/0000-0001-9515-7921 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Reports 25 (9): 2457-2469. 27 November 2018

A single-cell transcriptome atlas of the mouse glomerulus.
Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Rahmatollahi, M., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Liu, H. ORCID: https://orcid.org/0009-0007-4871-452X, Hoehne, M., Rinschen, M., Schermer, B., Benzing, T., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Kann, M. and Müller, R.U.
Journal of the American Society of Nephrology 29 (8): 2060-2068. August 2018

Cell type atlas and lineage tree of a whole complex animal by single-cell transcriptomics.
Plass, M. ORCID: https://orcid.org/0000-0002-9891-2723, Solana, J. ORCID: https://orcid.org/0000-0002-6770-3929, Wolf, F.A., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Misios, A., Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Theis, F.J., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Science 360 (6391): eaaq1723. 25 May 2018

Selective targeting of pro-inflammatory Th1 cells by microRNA-148a-specific antagomirs in vivo.
Maschmeyer, P. ORCID: https://orcid.org/0000-0002-1705-5302, Petkau, G., Siracusa, F., Zimmermann, J., Zügel, F., Kühl, A.A., Lehmann, K., Schimmelpfennig, S., Weber, M., Haftmann, C., Riedel, R., Bardua, M., Heinz, G.A., Tran, C.L., Hoyer, B.F., Hiepe, F., Herzog, S., Wittmann, J., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Melchers, F.G., Chang, H.D., Radbruch, A. and Mashreghi, M.F.
Journal of Autoimmunity 89 : 41-52. May 2018

Characterization of transcription termination-associated RNAs: new insights into their biogenesis, tailing, and expression in primary tumors.
Laudadio, I. ORCID: https://orcid.org/0000-0002-0990-3201, Formichetti, S., Gioiosa, S., Klironomos, F., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Macino, G., Carissimi, C. ORCID: https://orcid.org/0000-0002-9885-2855 and Fulci, V.
International Journal of Genomics 2018 : 1243858. 26 April 2018

Post-transcriptional regulation by 3' UTRs can be masked by regulatory elements in 5' UTRs.
Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Herzog, M. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Cell Reports 22 (12): 3217-3226. 20 March 2018

Single-molecule fluorescence in situ hybridization (FISH) of circular RNA CDR1as.
Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Methods in Molecular Biology 1724 : 77-96. 2018

Toward living nanomachines.
Mast, C., Möller, F., Kreysing, M., Schink, S., Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, Gerland, U. and Braun, D.
In: Living machines: a handbook of research in biomimetics and biohybrid systems. Oxford University Press, Oxford, 380-389. ISBN 9780199674923 2018

2017

The oncogenic role of circPVT1 in head and neck squamous cell carcinoma is mediated through the mutant p53/YAP/TEAD transcription-competent complex.
Verduci, L., Ferraiuolo, M., Sacconi, A., Ganci, F., Vitale, J., Colombo, T. ORCID: https://orcid.org/0000-0003-2415-7507, Paci, P., Strano, S., Macino, G., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Blandino, G.
Genome Biology 18 (1): 237. 20 December 2017

RNA-bioinformatics: tools, services and databases for the analysis of RNA-based regulation.
Backofen, R., Engelhardt, J., Erxleben, A., Fallmann, J., Grüning, B., Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Stadler, P.F.
Journal of Biotechnology 261 : 76-84. 10 November 2017

A map of human circular RNAs in clinically relevant tissues.
Maass, P.G. ORCID: https://orcid.org/0000-0002-2742-8301, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Memczak, S. ORCID: https://orcid.org/0000-0001-9518-7135, Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, Hollfinger, I. ORCID: https://orcid.org/0000-0002-6233-8395, Schreyer, L., Sauer, A.V., Toka, O., Aiuti, A., Luft, F.C. ORCID: https://orcid.org/0000-0002-8635-1199 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Journal of Molecular Medicine 95 (11): 1179-1189. November 2017

Widespread activation of antisense transcription of the host genome during herpes simplex virus 1 infection.
Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Menegatti, J., Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Hennig, T., Theil, K. ORCID: https://orcid.org/0000-0002-7205-6308, Rutkowski, A., Ferrai, C. ORCID: https://orcid.org/0000-0002-8088-2757, Baer, L., Kermas, L., Friedel, C. ORCID: https://orcid.org/0000-0003-3569-4877, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117, Dölken, L., Grässer, F. and Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734
Genome Biology 18 (1): 209. 31 October 2017

The Drosophila embryo at single-cell transcriptome resolution.
Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Kipar, C., Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Zinzen, R.P. ORCID: https://orcid.org/0000-0002-8638-5102
Science 358 (6360): 194-199. 13 October 2017

Loss of a mammalian circular RNA locus causes miRNA deregulation and affects brain function.
Piwecka, M. ORCID: https://orcid.org/0000-0003-4104-6577, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Hernandez-Miranda, L.R. ORCID: https://orcid.org/0000-0002-0498-708X, Memczak, S. ORCID: https://orcid.org/0000-0001-9518-7135, Wolf, S.A. ORCID: https://orcid.org/0000-0003-0922-8418, Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Filipchyk, A. ORCID: https://orcid.org/0000-0002-2029-8460, Klironomos, F., Cerda Jara, C.A. ORCID: https://orcid.org/0000-0003-1783-5533, Fenske, P., Trimbuch, T. ORCID: https://orcid.org/0000-0001-7512-8955, Zywitza, V. ORCID: https://orcid.org/0000-0003-3055-8569, Plass, M. ORCID: https://orcid.org/0000-0002-9891-2723, Schreyer, L., Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334, Kühn, R. ORCID: https://orcid.org/0000-0003-1694-9803, Rosenmund, C. ORCID: https://orcid.org/0000-0002-3905-2444, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Science 357 (6357): eaam8526. 22 September 2017

RNA localization is a key determinant of neurite-enriched proteome.
Zappulo, A., van den Bruck, D., Ciolli Mattioli, C. ORCID: https://orcid.org/0000-0002-8499-1387, Franke, V. ORCID: https://orcid.org/0000-0003-3606-6792, Imami, K. ORCID: https://orcid.org/0000-0002-7451-4982, McShane, E. ORCID: https://orcid.org/0000-0002-7806-2063, Moreno-Estelles, M., Calviello, L. ORCID: https://orcid.org/0000-0002-5600-0988, Filipchyk, A. ORCID: https://orcid.org/0000-0002-2029-8460, Peguero-Sanchez, E. ORCID: https://orcid.org/0000-0002-8317-5572, Müller, T. ORCID: https://orcid.org/0000-0001-8096-1853, Woehler, A. ORCID: https://orcid.org/0000-0001-5157-9313, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Merino, E., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116, Mazzoni, E.O., Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117 and Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887
Nature Communications 8 (1): 583. 19 September 2017

Viral infection identifies micropeptides differentially regulated in smORF-containing lncRNAs.
Razooky, B.S. ORCID: https://orcid.org/0000-0002-5263-1512, Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X, O'May, J.B. and Tarakhovsky, A.
Genes 8 (8): 206. 21 August 2017

RCAS: an RNA centric annotation system for transcriptome-wide regions of interest.
Uyar, B. ORCID: https://orcid.org/0000-0002-3170-4890, Yusuf, D. ORCID: https://orcid.org/0000-0001-8683-7845, Wurmus, R. ORCID: https://orcid.org/0009-0003-0140-4189, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Ohler, U. ORCID: https://orcid.org/0000-0002-0881-3116 and Akalin, A. ORCID: https://orcid.org/0000-0002-0468-0117
Nucleic Acids Research 45 (10): e91. 2 June 2017

Cell fixation and preservation for droplet-based single-cell transcriptomics.
Alles, J. ORCID: https://orcid.org/0000-0003-0681-0410, Karaiskos, N. ORCID: https://orcid.org/0000-0001-7771-3947, Praktiknjo, S.D. ORCID: https://orcid.org/0000-0002-0186-5271, Grosswendt, S. ORCID: https://orcid.org/0000-0001-7722-2937, Wahle, P. ORCID: https://orcid.org/0000-0002-4728-806X, Ruffault, P.L. ORCID: https://orcid.org/0000-0002-3378-3828, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Schreyer, L., Boltengagen, A. ORCID: https://orcid.org/0000-0002-8356-9766, Birchmeier, C. ORCID: https://orcid.org/0000-0002-2041-8872, Zinzen, R. ORCID: https://orcid.org/0000-0002-8638-5102, Kocks, C. ORCID: https://orcid.org/0000-0003-1749-3334 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
BMC Biology 15 (1): 44. 19 May 2017

Circ-ZNF609 is a circular RNA that can be translated and functions in myogenesis.
Legnini, I., Di Timoteo, G., Rossi, F., Morlando, M., Briganti, F., Sthandier, O., Fatica, A., Santini, T., Andronache, A., Wade, M., Laneve, P., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Bozzoni, I.
Molecular Cell 66 (1): 22-37.e9. 6 April 2017

Translation of circRNAs.
Pamudurti, N.R. ORCID: https://orcid.org/0000-0001-9527-1118, Bartok, O., Jens, M. ORCID: https://orcid.org/0000-0002-6660-8743, Ashwal-Fluss, R., Stottmeister, C. ORCID: https://orcid.org/0000-0002-5326-6043, Ruhe, L. ORCID: https://orcid.org/0009-0003-1401-8009, Hanan, M., Wyler, E. ORCID: https://orcid.org/0000-0002-9884-1806, Perez-Hernandez, D. ORCID: https://orcid.org/0000-0003-0266-9050, Ramberger, E. ORCID: https://orcid.org/0000-0003-2760-2696, Shenzis, S., Samson, M., Dittmar, G. ORCID: https://orcid.org/0000-0003-3647-8623, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734, Chekulaeva, M. ORCID: https://orcid.org/0000-0002-6868-7887, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332 and Kadener, S.
Molecular Cell 66 (1): 9-21. 6 April 2017

Essentials of miRNA-dependent control of mRNA translation and decay, miRNA targeting principles, and methods for target identification.
Grosswendt, S. ORCID: https://orcid.org/0000-0001-7722-2937 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
In: Essentials of noncoding RNA in neuroscience: ontogenetics, plasticity of the vertebrate brain. Academic Press, London, 19-38. ISBN 978-012804402-5 2017

Plant epigenetics.
Rajewsky, N., Jurga, S. and Barciszewski, J., eds.
RNA Technologies . Springer, Cham. ISBN 978-3-319-55519-5 2017

2016

The International Human Epigenome Consortium: a blueprint for scientific collaboration and discovery.
Stunnenberg, H.G. and Hirst, M.
Cell 167 (7): 1145-1149. 17 November 2016

Epigenomic profiling of human CD4(+) T cells supports a linear differentiation model and highlights molecular regulators of memory development.
Durek, P., Nordström, K., Gasparoni, G., Salhab, A., Kressler, C., de Almeida, M., Bassler, K., Ulas, T., Schmidt, F., Xiong, J. ORCID: https://orcid.org/0000-0002-4302-3515, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Klironomos, F., Sinha, A., Kinkley, S., Yang, X., Arrigoni, L., Amirabad, A.., Ardakani, F.B., Feuerbach, L., Gorka, O., Ebert, P., Müller, F., Li, N., Frischbutter, S., Schlickeiser, S., Cendon, C., Fröhler, S. ORCID: https://orcid.org/0000-0001-8000-2927, Felder, B., Gasparoni, N., Imbusch, C.D., Hutter, B., Zipprich, G., Tauchmann, Y., Reinke, S., Wassilew, G., Hoffmann, U., Richter, A.S., Sieverling, L., Chang, H.D., Syrbe, U., Kalus, U., Eils, J., Brors, B., Manke, T., Ruland, J., Lengauer, T., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Dong, J., Sawitzki, B., Chung, H.R., Rosenstiel, P., Schulz, M.H., Schultze, J.L., Radbruch, A., Walter, J., Hamann, A. and Polansky, J.K.
Immunity 45 (5): 1148-1161. 15 November 2016

Conserved functional antagonism of CELF 1 and MBNL proteins controls stem cell-specific alternative splicing in planarians.
Solana, J. ORCID: https://orcid.org/0000-0002-6770-3929, Irimia, M. ORCID: https://orcid.org/0000-0002-2179-2567, Ayoub, S. ORCID: https://orcid.org/0000-0001-5043-8922, Orejuela, M.R. ORCID: https://orcid.org/0000-0002-8900-1442, Zywitza, V. ORCID: https://orcid.org/0000-0003-3055-8569, Jens, M. ORCID: https://orcid.org/0000-0002-6660-8743, Tapial, J., Ray, D., Morris, Q.D., Hughes, T.R., Blencowe, B.J. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
eLife 5 : e16797. 9 August 2016

Epigenetic dynamics of monocyte-to-macrophage differentiation.
Wallner, S., Schroeder, C., Leitão, E., Berulava, T., Haak, C., Beißer, D., Rahmann, S., Richter, A.S., Manke, T., Bönisch, U., Arrigoni, L., Fröhler, S. ORCID: https://orcid.org/0000-0001-8000-2927, Klironomos, F., Chen, W. ORCID: https://orcid.org/0000-0003-3263-1627, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Müller, F., Ebert, P., Lengauer, T., Barann, M., Rosenstiel, P., Gasparoni, G., Nordström, K., Walter, J., Brors, B., Zipprich, G., Felder, B., Klein-Hitpass, L., Attenberger, C., Schmitz, G. and Horsthemke, B.
Epigenetics & Chromatin 9 : 33. 29 July 2016

The Lupus autoantigen La prevents Mis-channeling of tRNA fragments into the human microRNA pathway.
Hasler, D., Lehmann, G., Murakawa, Y., Klironomos, F., Jakob, L., Grässer, F.A., Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Landthaler, M. ORCID: https://orcid.org/0000-0002-1075-8734 and Meister, G.
Molecular Cell 63 (1): 110-124. 7 July 2016

A pipeline for PAR-CLIP data analysis.
Jens, M. ORCID: https://orcid.org/0000-0002-6660-8743
Methods in Molecular Biology 1358 : 197-207. 2016

2015

Identification and characterization of circular RNAs as a new class of putative biomarkers in human blood.
Memczak, S. ORCID: https://orcid.org/0000-0001-9518-7135, Papavasileiou, P. ORCID: https://orcid.org/0000-0002-9655-9612, Peters, O. ORCID: https://orcid.org/0000-0003-0568-2998 and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
PLoS ONE 10 (10): e0141214. 20 October 2015

4-fragment gateway cloning format for MosSCI-compatible vectors integrating promoterome and 3'UTRome libraries of Caenorhabditis elegans.
Kogame, T.
Journal of Medical Investigation 62 (3.4): 161-166. 18 September 2015

Extensive identification and analysis of conserved small ORFs in animals.
Mackowiak, S.D. ORCID: https://orcid.org/0000-0003-1673-5389, Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Bielow, C. ORCID: https://orcid.org/0000-0001-5756-3988, Thiel, D. ORCID: https://orcid.org/0000-0001-8677-2420, Kutz, K., Calviello, L. ORCID: https://orcid.org/0000-0002-5600-0988, Mastrobuoni, G. ORCID: https://orcid.org/0000-0003-4509-1295, Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332, Kempa, S. ORCID: https://orcid.org/0000-0002-0696-9299, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751 and Obermayer, B. ORCID: https://orcid.org/0000-0002-9116-630X
Genome Biology 16 : 179. 14 September 2015

Circular RNAs in the mammalian brain are highly abundant, conserved, and dynamically expressed.
Rybak-Wolf, A. ORCID: https://orcid.org/0000-0002-1192-5290, Stottmeister, C. ORCID: https://orcid.org/0000-0002-5326-6043, Glažar, P. ORCID: https://orcid.org/0000-0003-0842-0088, Jens, M. ORCID: https://orcid.org/0000-0002-6660-8743, Pino, N., Giusti, S., Hanan, M., Behm, M., Bartok, O., Ashwal-Fluss, R., Herzog, M., Schreyer, L., Papavasileiou, P. ORCID: https://orcid.org/0000-0002-9655-9612, Ivanov, A. ORCID: https://orcid.org/0000-0002-4824-1925, Öhman, M., Refojo, D., Kadener, S. and Rajewsky, N. ORCID: https://orcid.org/0000-0002-4785-4332
Molecular Cell 58 (5): 870-885. 4 June 2015