Article

Systemic effects of cystic fibrosis transmembrane conductance regulator modulators on the plasma and serum proteome.
Fentker, Kerstin ORCID: https://orcid.org/0009-0005-0437-1049, Kirchner, Marieluise ORCID: https://orcid.org/0000-0002-7049-534X, Ziehm, Matthias ORCID: https://orcid.org/0000-0001-7074-4054, Niquet, Sylvia, Popp, Oliver ORCID: https://orcid.org/0000-0001-6240-4666, Duerr, Julia, Schaupp, Laura, Roehmel, Jobst, Thee, Stephanie, Hämmerling, Susanne, Sommerburg, Olaf, Stahl, Mirjam, Graeber, Simon Y., Mall, Marcus A. and Mertins, Philipp ORCID: https://orcid.org/0000-0002-2245-528X
Cell Systems 17 : 101569. 20 May 2026

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

Inference of differentiation trajectories by transfer learning across biological processes.
Jumde, G., Spanjaard, B. ORCID: https://orcid.org/0000-0003-1309-8839 and Junker, J.P. ORCID: https://orcid.org/0000-0002-2826-8290
Cell Systems 15 (1): 75-82.e5. 17 January 2024

A framework for ultra-low-input spatial tissue proteomics.
Makhmut, A. ORCID: https://orcid.org/0009-0009-6913-4289, Qin, D. ORCID: https://orcid.org/0000-0002-9730-4072, Fritzsche, S. ORCID: https://orcid.org/0000-0003-3335-3534, Nimo, J. ORCID: https://orcid.org/0000-0002-1565-7799, König, J. and Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081
Cell Systems 14 (11): 1002-1014. 15 November 2023

Dynamics of huntingtin protein interactions in the striatum identifies candidate modifiers of Huntington disease.
Greco, T.M., Secker, C. ORCID: https://orcid.org/0000-0002-7222-536X, Silva Ramos, E. ORCID: https://orcid.org/0000-0002-8520-9107, Federspiel, J.D., Liu, J.P., Perez, A.M., Al-Ramahi, I., Cantle, J.P., Carroll, J.B., Botas, J., Zeitlin, S.O., Wanker, E.E. ORCID: https://orcid.org/0000-0001-8072-1630 and Cristea, I.M.
Cell Systems 13 (4): 304-320.e5. 22 April 2022

Pairwise stimulations of pathogen-sensing pathways predict immune responses to multi-adjuvant combinations.
Pandey, S., Gruenbaum, A., Kanashova, T., Mertins, P. ORCID: https://orcid.org/0000-0002-2245-528X, Cluzel, P. and Chevrier, N.
Cell Systems 11 (5): 495-508. 18 November 2020

Genomic rewiring of SOX2 chromatin interaction network during differentiation of ESCs to postmitotic neurons.
Bunina, D. ORCID: https://orcid.org/0000-0002-5885-7440, Abazova, N., Diaz, N., Noh, K.M., Krijgsveld, J. and Zaugg, J.B.
Cell Systems 10 (6): 480-494. 24 June 2020

Of gene expression and cell division time: a mathematical framework for advanced differential gene expression and data analysis.
Baum, K. ORCID: https://orcid.org/0000-0001-7256-0566, Schuchhardt, J., Wolf, J. ORCID: https://orcid.org/0000-0003-3254-5868 and Busse, D.
Cell Systems 9 (6): 569-579. 18 December 2019

Integrated transcriptome and proteome analyses reveal organ-specific proteome deterioration in old rats.
Ori, A., Toyama, B.H., Harris, M.S., Bock, T., Iskar, M., Bork, P. ORCID: https://orcid.org/0000-0002-2627-833X, Ingolia, N.T., Hetzer, M.W. and Beck, M.
Cell Systems 1 (3): 224-237. 23 September 2015

Review

Keeping the proportions of protein complex components in check.
Taggart, J.C., Zauber, H. ORCID: https://orcid.org/0000-0003-2595-1147, Selbach, M. ORCID: https://orcid.org/0000-0003-2454-8751, Li, G.W. and McShane, E. ORCID: https://orcid.org/0000-0002-7806-2063
Cell Systems 10 (2): 125-132. 26 February 2020

Editorial

What do you most hope spatial molecular profiling will help us understand? Part 2.
Yanai, I., Fertig, E.J., Li, M., Coscia, F. ORCID: https://orcid.org/0000-0002-2244-5081, Klughammer, J., Nie, Q., Chen, J. and Coskun, A.F.
Cell Systems 14 (7): 543-546. 19 July 2023