Chair of Mathematical Modelling of Biological Systems

2025

Predicting cell morphological responses to perturbations using generative modeling

Palma, A., Theis, F. J. & Lotfollahi, M., 8 Jan 2025, In: Nature Communications. 16, 1, p. 505 1 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2024

A Dried Blood Spot protocol for high-throughput quantitative analysis of SARS-CoV-2 RBD serology based on the Roche Elecsys system

the KoCo19/ORCHESTRA Working group, Apr 2024, In: Microbiology Spectrum. 12, 4

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

A liver immune rheostat regulates CD8 T cell immunity in chronic HBV infection

Bosch, M., Kallin, N., Donakonda, S., Zhang, J. D., Wintersteller, H., Hegenbarth, S., Heim, K., Ramirez, C., Fürst, A., Lattouf, E. I., Feuerherd, M., Chattopadhyay, S., Kumpesa, N., Griesser, V., Hoflack, J. C., Siebourg-Polster, J., Mogler, C., Swadling, L., Pallett, L. J. & Meiser, P. & 36 others, Manske, K., de Almeida, G. P., Kosinska, A. D., Sandu, I., Schneider, A., Steinbacher, V., Teng, Y., Schnabel, J., Theis, F., Gehring, A. J., Boonstra, A., Janssen, H. L. A., Vandenbosch, M., Cuypers, E., Öllinger, R., Engleitner, T., Rad, R., Steiger, K., Oxenius, A., Lo, W. L., Klepsch, V., Baier, G., Holzmann, B., Maini, M. K., Heeren, R., Murray, P. J., Thimme, R., Herrmann, C., Protzer, U., Böttcher, J. P., Zehn, D., Wohlleber, D., Lauer, G. M., Hofmann, M., Luangsay, S. & Knolle, P. A., 25 Jul 2024, In: Nature. 631, 8022, p. 867-875 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

An integrated transcriptomic cell atlas of human neural organoids

Human Cell Atlas Organoid Biological Network, 21 Nov 2024, In: Nature. 635, 8039, p. 690-698 9 p.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

An open-source framework for end-to-end analysis of electronic health record data

Heumos, L., Ehmele, P., Treis, T., Upmeier zu Belzen, J., Roellin, E., May, L., Namsaraeva, A., Horlava, N., Shitov, V. A., Zhang, X., Zappia, L., Knoll, R., Lang, N. J., Hetzel, L., Virshup, I., Sikkema, L., Curion, F., Eils, R., Schiller, H. B. & Hilgendorff, A. & 1 others, Theis, F. J., Nov 2024, In: Nature Medicine. 30, 11, p. 3369-3380 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Artificial intelligence in tuberculosis: a new ally in disease control

UNITE4TB Consortium, Oct 2024, In: Breathe. 20, 3, 240056.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

CellRank 2: unified fate mapping in multiview single-cell data

Weiler, P., Lange, M., Klein, M., Pe’er, D. & Theis, F., Jul 2024, In: Nature Methods. 21, 7, p. 1196-1205 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Deep generative modeling of transcriptional dynamics for RNA velocity analysis in single cells

Gayoso, A., Weiler, P., Lotfollahi, M., Klein, D., Hong, J., Streets, A., Theis, F. J. & Yosef, N., Jan 2024, In: Nature Methods. 21, 1, p. 50-59 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Delineating the effective use of self-supervised learning in single-cell genomics

Richter, T., Bahrami, M., Xia, Y., Fischer, D. S. & Theis, F. J., 2024, (Accepted/In press) In: Nature Machine Intelligence. 6611.

Research output: Contribution to journal › Article › peer-review

Open Access

Evaluation of OCT biomarker changes in treatment-naive neovascular AMD using a deep semantic segmentation algorithm

Asani, B., Holmberg, O., Schiefelbein, J. B., Hafner, M., Herold, T., Spitzer, H., Siedlecki, J., Kern, C., Kortuem, K. U., Frishberg, A., Theis, F. J. & Priglinger, S. G., Nov 2024, In: Eye (Basingstoke). 38, 16, p. 3180-3186 7 p.

Research output: Contribution to journal › Article › peer-review

Open Access

GraphCompass: spatial metrics for differential analyses of cell organization across conditions

Ali, M., Kuijs, M., Hediyeh-Zadeh, S., Treis, T., Hrovatin, K., Palla, G., Schaar, A. C. & Theis, F. J., 1 Jul 2024, In: Bioinformatics. 40, Supplement_1, p. i548-i557

Research output: Contribution to journal › Article › peer-review

Open Access

hadge: a comprehensive pipeline for donor deconvolution in single-cell studies

Curion, F., Wu, X., Heumos, L., André, M. M. G., Halle, L., Ozols, M., Grant-Peters, M., Rich-Griffin, C., Yeung, H. Y., Dendrou, C. A., Schiller, H. B. & Theis, F. J., Dec 2024, In: Genome Biology. 25, 1, 109.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Heterogeneity-driven phenotypic plasticity and treatment response in branched-organoid models of pancreatic ductal adenocarcinoma

Papargyriou, A., Najajreh, M., Cook, D. P., Maurer, C. H., Bärthel, S., Messal, H. A., Ravichandran, S. K., Richter, T., Knolle, M., Metzler, T., Shastri, A. R., Öllinger, R., Jasper, J., Schmidleitner, L., Wang, S., Schneeweis, C., Ishikawa-Ankerhold, H., Engleitner, T., Mataite, L. & Semina, M. & 24 others, Trabulssi, H., Lange, S., Ravichandra, A., Schuster, M., Mueller, S., Peschke, K., Schäfer, A., Dobiasch, S., Combs, S. E., Schmid, R. M., Bausch, A. R., Braren, R., Heid, I., Scheel, C. H., Schneider, G., Zeigerer, A., Luecken, M. D., Steiger, K., Kaissis, G., van Rheenen, J., Theis, F. J., Saur, D., Rad, R. & Reichert, M., 2024, (Accepted/In press) In: Nature Biomedical Engineering. 102858.

Research output: Contribution to journal › Article › peer-review

Open Access

Leveraging Integrated RNA Sequencing to Decipher Adrenomedullin’s Protective Mechanisms in Experimental Bronchopulmonary Dysplasia

Palit, S., Shrestha, A. K., Thapa, S., L Grimm, S., Coarfa, C., Theis, F., Simon, L. M. & Shivanna, B., Jun 2024, In: Genes. 15, 6, 806.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

longmixr: a tool for robust clustering of high-dimensional cross-sectional and longitudinal variables of mixed data types

Hagenberg, J., Budde, M., Pandeva, T., Kondofersky, I., Schaupp, S. K., Theis, F. J., Schulze, T. G., Muller, N. S., Heilbronner, U., Batra, R. & Knauer-Arloth, J., 1 Apr 2024, In: Bioinformatics. 40, 4, btae137.

Research output: Contribution to journal › Article › peer-review

Open Access

Mapping lineage-traced cells across time points with moslin

Lange, M., Piran, Z., Klein, M., Spanjaard, B., Klein, D., Junker, J. P., Theis, F. J. & Nitzan, M., Dec 2024, In: Genome Biology. 25, 1, 277.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

MISATO: machine learning dataset of protein–ligand complexes for structure-based drug discovery

Siebenmorgen, T., Menezes, F., Benassou, S., Merdivan, E., Didi, K., Mourão, A. S. D., Kitel, R., Liò, P., Kesselheim, S., Piraud, M., Theis, F. J., Sattler, M. & Popowicz, G. M., May 2024, In: Nature Computational Science. 4, 5, p. 367-378 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

9 Scopus citations

Modeling fragment counts improves single-cell ATAC-seq analysis

Martens, L. D., Fischer, D. S., Yépez, V. A., Theis, F. J. & Gagneur, J., Jan 2024, In: Nature Methods. 21, 1, p. 28-31 4 p.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Modulation of TCR stimulation and pifithrin-α improves the genomic safety profile of CRISPR-engineered human T cells

Ursch, L. T., Müschen, J. S., Ritter, J., Klermund, J., Bernard, B. E., Kolb, S., Warmuth, L., Andrieux, G., Miller, G., Jiménez-Muñoz, M., Theis, F. J., Boerries, M., Busch, D. H., Cathomen, T. & Schumann, K., 17 Dec 2024, In: Cell Reports Medicine. 5, 12, 101846.

Research output: Contribution to journal › Article › peer-review

Open Access

Multi-modal generative modeling for joint analysis of single-cell T cell receptor and gene expression data

Drost, F., An, Y., Bonafonte-Pardàs, I., Dratva, L. M., Lindeboom, R. G. H., Haniffa, M., Teichmann, S. A., Theis, F., Lotfollahi, M. & Schubert, B., Dec 2024, In: Nature Communications. 15, 1, 5577.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Multiplexing cortical brain organoids for the longitudinal dissection of developmental traits at single-cell resolution

Caporale, N., Castaldi, D., Rigoli, M. T., Cheroni, C., Valenti, A., Stucchi, S., Lessi, M., Bulgheresi, D., Trattaro, S., Pezzali, M., Vitriolo, A., Lopez-Tobon, A., Bonfanti, M., Ricca, D., Schmid, K. T., Heinig, M., Theis, F. J., Villa, C. E. & Testa, G., 2024, (Accepted/In press) In: Nature Methods. 69.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Panpipes: a pipeline for multiomic single-cell and spatial transcriptomic data analysis

Curion, F., Rich-Griffin, C., Agarwal, D., Ouologuem, S., Rue-Albrecht, K., May, L., Garcia, G. E. L., Heumos, L., Thomas, T., Lason, W., Sims, D., Theis, F. J. & Dendrou, C. A., Dec 2024, In: Genome Biology. 25, 1, 181.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Polyploidisation pleiotropically buffers ageing in hepatocytes

Yin, K., Büttner, M., Deligiannis, I. K., Strzelecki, M., Zhang, L., Talavera-López, C., Theis, F., Odom, D. T. & Martinez-Jimenez, C. P., Aug 2024, In: Journal of Hepatology. 81, 2, p. 289-302 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Probe set selection for targeted spatial transcriptomics

Kuemmerle, L. B., Luecken, M. D., Firsova, A. B., Barros de Andrade e Sousa, L., Straßer, L., Mekki, I. I., Campi, F., Heumos, L., Shulman, M., Beliaeva, V., Hediyeh-Zadeh, S., Schaar, A. C., Mahbubani, K. T., Sountoulidis, A., Balassa, T., Kovacs, F., Horvath, P., Piraud, M., Ertürk, A. & Samakovlis, C. & 1 others, Theis, F. J., Dec 2024, In: Nature Methods. 21, 12, p. 2260-2270 11 p., 4307.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

scTab: Scaling cross-tissue single-cell annotation models

Fischer, F., Fischer, D. S., Mukhin, R., Isaev, A., Biederstedt, E., Villani, A. C. & Theis, F. J., Dec 2024, In: Nature Communications. 15, 1, 6611.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Sfrp1 inhibits lung fibroblast invasion during transition to injury-induced myofibroblasts

Mayr, C. H., Sengupta, A., Asgharpour, S., Ansari, M., Pestoni, J. C., Ogar, P., Angelidis, I., Liontos, A., Rodriguez-Castillo, J. A., Lang, N. J., Strunz, M., Porras-Gonzalez, D., Gerckens, M., De Sadeleer, L. J., Oehrle, B., Viteri-Alvarez, V., Fernandez, I. E., Tallquist, M., Irmler, M. & Beckers, J. & 13 others, Eickelberg, O., Stoleriu, G. M., Behr, J., Kneidinger, N., Wuyts, W. A., Wasnick, R. M., Yildirim, A. Ö., Ahlbrecht, K., Morty, R. E., Samakovlis, C., Theis, F. J., Burgstaller, G. & Schiller, H. B., 1 Feb 2024, In: European Respiratory Journal. 63, 2, 2301326.

Research output: Contribution to journal › Article › peer-review

Open Access

20 Scopus citations

Shared inflammatory glial cell signature after stab wound injury, revealed by spatial, temporal, and cell-type-specific profiling of the murine cerebral cortex

Koupourtidou, C., Schwarz, V., Aliee, H., Frerich, S., Fischer-Sternjak, J., Bocchi, R., Simon-Ebert, T., Bai, X., Sirko, S., Kirchhoff, F., Dichgans, M., Götz, M., Theis, F. J. & Ninkovic, J., Dec 2024, In: Nature Communications. 15, 1, 2866.

Research output: Contribution to journal › Article › peer-review

Open Access

7 Scopus citations

Small data methods in omics: the power of one

Johnston, K. G., Grieco, S. F., Nie, Q., Theis, F. J. & Xu, X., Sep 2024, In: Nature Methods. 21, 9, p. 1597-1602 6 p.

Research output: Contribution to journal › Article › peer-review

SpatialData: an open and universal data framework for spatial omics

Marconato, L., Palla, G., Yamauchi, K. A., Virshup, I., Heidari, E., Treis, T., Vierdag, W. M., Toth, M., Stockhaus, S., Shrestha, R. B., Rombaut, B., Pollaris, L., Lehner, L., Vöhringer, H., Kats, I., Saeys, Y., Saka, S. K., Huber, W., Gerstung, M. & Moore, J. & 2 others, Theis, F. J. & Stegle, O., 2024, (Accepted/In press) In: Nature Methods.

Research output: Contribution to journal › Article › peer-review

Open Access

20 Scopus citations

Transformers in single-cell omics: a review and new perspectives

Szałata, A., Hrovatin, K., Becker, S., Tejada-Lapuerta, A., Cui, H., Wang, B. & Theis, F. J., Aug 2024, In: Nature Methods. 21, 8, p. 1430-1443 14 p.

Research output: Contribution to journal › Article › peer-review

7 Scopus citations

2023

An integrated cell atlas of the lung in health and disease

Lung Biological Network Consortium, Jun 2023, In: Nature Medicine. 29, 6, p. 1563-1577 15 p.

Research output: Contribution to journal › Article › peer-review

Open Access

192 Scopus citations

A reversible state of hypometabolism in a human cellular model of sporadic Parkinson’s disease

Schmidt, S., Stautner, C., Vu, D. T., Heinz, A., Regensburger, M., Karayel, O., Trümbach, D., Artati, A., Kaltenhäuser, S., Nassef, M. Z., Hembach, S., Steinert, L., Winner, B., Jürgen, W., Jastroch, M., Luecken, M. D., Theis, F. J., Westmeyer, G. G., Adamski, J. & Mann, M. & 4 others, Hiller, K., Giesert, F., Vogt Weisenhorn, D. M. & Wurst, W., Dec 2023, In: Nature Communications. 14, 1, 7674.

Research output: Contribution to journal › Article › peer-review

Open Access

8 Scopus citations

Best practices for single-cell analysis across modalities

Single-cell Best Practices Consortium, Aug 2023, In: Nature Reviews Genetics. 24, 8, p. 550-572 23 p.

Research output: Contribution to journal › Article › peer-review

Open Access

248 Scopus citations

Biologically informed deep learning to query gene programs in single-cell atlases

Lotfollahi, M., Rybakov, S., Hrovatin, K., Hediyeh-zadeh, S., Talavera-López, C., Misharin, A. V. & Theis, F. J., Feb 2023, In: Nature Cell Biology. 25, 2, p. 337-350 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

41 Scopus citations

CIARA: a cluster-independent algorithm for identifying markers of rare cell types from single-cell sequencing data

Lubatti, G., Stock, M., Iturbide, A., Ruiz Tejada Segura, M. L., Riepl, M., Tyser, R. C. V., Danese, A., Colomé-Tatché, M., Theis, F. J., Srinivas, S., Torres-Padilla, M. E. & Scialdone, A., Jun 2023, In: Development (Cambridge). 150, 11, dev201264.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Delineating mouse β-cell identity during lifetime and in diabetes with a single cell atlas

Hrovatin, K., Bastidas-Ponce, A., Bakhti, M., Zappia, L., Büttner, M., Salinno, C., Sterr, M., Böttcher, A., Migliorini, A., Lickert, H. & Theis, F. J., Sep 2023, In: Nature Metabolism. 5, 9, p. 1615-1637 23 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Distinct molecular profiles of skull bone marrow in health and neurological disorders

Kolabas, Z. I., Kuemmerle, L. B., Perneczky, R., Förstera, B., Ulukaya, S., Ali, M., Kapoor, S., Bartos, L. M., Büttner, M., Caliskan, O. S., Rong, Z., Mai, H., Höher, L., Jeridi, D., Molbay, M., Khalin, I., Deligiannis, I. K., Negwer, M., Roberts, K. & Simats, A. & 65 others, Carofiglio, O., Todorov, M. I., Horvath, I., Ozturk, F., Hummel, S., Biechele, G., Zatcepin, A., Unterrainer, M., Gnörich, J., Roodselaar, J., Shrouder, J., Khosravani, P., Tast, B., Richter, L., Díaz-Marugán, L., Kaltenecker, D., Lux, L., Chen, Y., Zhao, S., Rauchmann, B. S., Sterr, M., Kunze, I., Stanic, K., Kan, V. W. Y., Besson-Girard, S., Katzdobler, S., Palleis, C., Schädler, J., Paetzold, J. C., Liebscher, S., Hauser, A. E., Gokce, O., Lickert, H., Steinke, H., Benakis, C., Braun, C., Martinez-Jimenez, C. P., Buerger, K., Albert, N. L., Höglinger, G., Levin, J., Haass, C., Kopczak, A., Dichgans, M., Havla, J., Kümpfel, T., Kerschensteiner, M., Schifferer, M., Simons, M., Liesz, A., Krahmer, N., Bayraktar, O. A., Franzmeier, N., Plesnila, N., Erener, S., Puelles, V. G., Delbridge, C., Bhatia, H. S., Hellal, F., Elsner, M., Bechmann, I., Ondruschka, B., Brendel, M., Theis, F. J. & Erturk, A., 17 Aug 2023, In: Cell. 186, 17, p. 3706-3725.e29

Research output: Contribution to journal › Article › peer-review

Open Access

45 Scopus citations

Early life adversity shapes social subordination and cell type-specific transcriptomic patterning in the ventral hippocampus

Kos, A., Lopez, J. P., Bordes, J., de Donno, C., Dine, J., Brivio, E., Karamihalev, S., Luecken, M. D., Almeida-Correa, S., Gasperoni, S., Dick, A., Miranda, L., Büttner, M., Stoffel, R., Flachskamm, C., Theis, F. J., Schmidt, M. V. & Chen, A., Dec 2023, In: Science Advances. 9, 48, eadj3793.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Epicardioid single-cell genomics uncovers principles of human epicardium biology in heart development and disease

Meier, A. B., Zawada, D., De Angelis, M. T., Martens, L. D., Santamaria, G., Zengerle, S., Nowak-Imialek, M., Kornherr, J., Zhang, F., Tian, Q., Wolf, C. M., Kupatt, C., Sahara, M., Lipp, P., Theis, F. J., Gagneur, J., Goedel, A., Laugwitz, K. L., Dorn, T. & Moretti, A., Dec 2023, In: Nature Biotechnology. 41, 12, p. 1787-1800 14 p.

Research output: Contribution to journal › Article › peer-review

Open Access

26 Scopus citations

Explainable machine learning for profiling the immunological synapse and functional characterization of therapeutic antibodies

Shetab Boushehri, S., Essig, K., Chlis, N. K., Herter, S., Bacac, M., Theis, F. J., Glasmacher, E., Marr, C. & Schmich, F., Dec 2023, In: Nature Communications. 14, 1, 7888.

Research output: Contribution to journal › Article › peer-review

Open Access

4 Scopus citations

Ex vivo tissue perturbations coupled to single-cell RNA-seq reveal multilineage cell circuit dynamics in human lung fibrogenesis

Lang, N. J., Gote-Schniering, J., Porras-Gonzalez, D., Yang, L., De Sadeleer, L. J., Jentzsch, R. C., Shitov, V. A., Zhou, S., Ansari, M., Agami, A., Mayr, C. H., Kashani, B. H., Chen, Y., Heumos, L., Pestoni, J. C., Molnar, E. S., Geeraerts, E., Anquetil, V., Saniere, L. & Wögrath, M. & 12 others, Gerckens, M., Lehmann, M., Yildirim, A. Ö., Hatz, R., Kneidinger, N., Behr, J., Wuyts, W. A., Stoleriu, M. G., Luecken, M. D., Theis, F. J., Burgstaller, G. & Schiller, H. B., 2023, In: Science Translational Medicine. 15, 725, eadh0908.

Research output: Contribution to journal › Article › peer-review

Open Access

19 Scopus citations

Gene Expression–Based Molecular Test as Diagnostic Aid for the Differential Diagnosis of Psoriasis and Eczema in Formalin-Fixed and Paraffin-Embedded Tissue, Microbiopsies, and Tape Strips

Fischer, F., Doll, A., Uereyener, D., Roenneberg, S., Hillig, C., Weber, L., Hackert, V., Meinel, M., Farnoud, A., Seiringer, P., Thomas, J., Anand, P., Graner, L., Schlenker, F., Zengerle, R., Jonsson, P., Jargosch, M., Theis, F. J., Schmidt-Weber, C. B. & Biedermann, T. & 7 others, Howell, M., Reich, K., Eyerich, K., Menden, M., Garzorz-Stark, N., Lauffer, F. & Eyerich, S., Aug 2023, In: Journal of Investigative Dermatology. 143, 8, p. 1461-1469.e5

Research output: Contribution to journal › Article › peer-review

Open Access

6 Scopus citations

Human pluripotent stem cell fate trajectories toward lung and hepatocyte progenitors

Ori, C., Ansari, M., Angelidis, I., Olmer, R., Martin, U., Theis, F. J., Schiller, H. B. & Drukker, M., 17 Nov 2023, In: iScience. 26, 11, 108205.

Research output: Contribution to journal › Article › peer-review

Open Access

Learning consistent subcellular landmarks to quantify changes in multiplexed protein maps

Spitzer, H., Berry, S., Donoghoe, M., Pelkmans, L. & Theis, F. J., Jul 2023, In: Nature Methods. 20, 7, p. 1058-1069 12 p.

Research output: Contribution to journal › Article › peer-review

Open Access

10 Scopus citations

Longitudinal Effects of 1-Year Smoking Cessation on Human Bronchial Epithelial Transcriptome

National Heart, Lung, and Blood Institute LungMAP Consortium, Jul 2023, In: Chest. 164, 1, p. 85-89 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

2 Scopus citations

Modeling intercellular communication in tissues using spatial graphs of cells

Fischer, D. S., Schaar, A. C. & Theis, F. J., Mar 2023, In: Nature Biotechnology. 41, 3, p. 332-336 5 p.

Research output: Contribution to journal › Article › peer-review

Open Access

71 Scopus citations

Multi-omics regulatory network inference in the presence of missing data

Henao, J. D., Lauber, M., Azevedo, M., Grekova, A., Theis, F., List, M., Ogris, C. & Schubert, B., 1 Sep 2023, In: Briefings in Bioinformatics. 24, 5, bbad309.

Research output: Contribution to journal › Article › peer-review

Open Access

3 Scopus citations

Population-level integration of single-cell datasets enables multi-scale analysis across samples

De Donno, C., Hediyeh-Zadeh, S., Moinfar, A. A., Wagenstetter, M., Zappia, L., Lotfollahi, M. & Theis, F. J., Nov 2023, In: Nature Methods. 20, 11, p. 1683-1692 10 p.

Research output: Contribution to journal › Article › peer-review

Open Access

16 Scopus citations

Predicting cellular responses to complex perturbations in high-throughput screens

Lotfollahi, M., Klimovskaia Susmelj, A., De Donno, C., Hetzel, L., Ji, Y., Ibarra, I. L., Srivatsan, S. R., Naghipourfar, M., Daza, R. M., Martin, B., Shendure, J., McFaline-Figueroa, J. L., Boyeau, P., Wolf, F. A., Yakubova, N., Günnemann, S., Trapnell, C., Lopez-Paz, D. & Theis, F. J., 12 Jun 2023, In: Molecular Systems Biology. 19, 6, e11517.

Research output: Contribution to journal › Article › peer-review

Open Access

53 Scopus citations

Progressive disruption of hematopoietic architecture from clonal hematopoiesis to MDS

Buck, M. C., Bast, L., Hecker, J. S., Rivière, J., Rothenberg-Thurley, M., Vogel, L., Wang, D., Andrä, I., Theis, F. J., Bassermann, F., Metzeler, K. H., Oostendorp, R. A. J., Marr, C. & Götze, K. S., 18 Aug 2023, In: iScience. 26, 8, 107328.

Research output: Contribution to journal › Article › peer-review

Open Access

1 Scopus citations

Chair of Mathematical Modelling of Biological Systems

Research output

Search results