References

The use of the SCF's ressources and the contribution of its staff members has been acknowledged in many papers or resulted in co-authorships of such publications.

List of publications that used the resources of the SCF during the last three years:

2024

1 Borrelli, C. et al. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 632, 411-418 (2024). external page https://doi.org/10.1038/s41586-024-07715-3

2 Erlach, L. et al. Evaluating predictive patterns of antigen-specific B cells by single-cell transcriptome and antibody repertoire sequencing. Cell Systems 15, 1295-1303.e1295 (2024). external page https://doi.org/https://doi.org/10.1016/j.cels.2024.11.005

3 Hu, G., Huang, J. & Fussenegger, M. Toward Photosynthetic Mammalian Cells through Artificial Endosymbiosis. Small 20, e2310310 (2024). external page https://doi.org/10.1002/smll.202310310

4 Kapetanovic, E. et al. Engineered allogeneic T cells decoupling T-cell-receptor and CD3 signalling enhance the antitumour activity of bispecific antibodies. Nature Biomedical Engineering (2024). external page https://doi.org/10.1038/s41551-024-01255-x

5 Kasuba, K. C. et al. Mechanical stimulation and electrophysiological monitoring at subcellular resolution reveals differential mechanosensation of neurons within networks. Nat Nanotechnol 19, 825-833 (2024). external page https://doi.org/10.1038/s41565-024-01609-1

6 Kumar, S., Beyer, H. M., Chen, M., Zurbriggen, M. D. & Khammash, M. Image-guided optogenetic spatiotemporal tissue patterning using μPatternScope. Nature Communications 15, 10469 (2024). external page https://doi.org/10.1038/s41467-024-54351-6

7 Kurmashev, A. et al. Transwell‐Based Microfluidic Platform for High‐Resolution Imaging of Airway Tissues. Advanced Materials Technologies (2024). external page https://doi.org/10.1002/admt.202400326

8 Nguyen, O. T. P., Misun, P. M., Hierlemann, A. & Lohasz, C. A Versatile Intestine-on-Chip System for Deciphering the Immunopathogenesis of Inflammatory Bowel Disease. Adv Healthc Mater 13, e2302454 (2024). external page https://doi.org/10.1002/adhm.202302454

9 Schirmacher, D. et al. aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images. PLoS Comput Biol 20, e1012361 (2024). external page https://doi.org/10.1371/journal.pcbi.1012361

10 Svanberg, S., Hirth, E., Mitsiadis, T. A. & Dittrich, P. S. "Periodontal ligament-on-chip" as a Novel Tool for Studies on the Physiology and Pathology of Periodontal Tissues. Adv Healthc Mater, e2303942 (2024). external page https://doi.org/10.1002/adhm.202303942

11 Zenk, F. et al. Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems. Nature Neuroscience 27, 1376-1386 (2024). external page https://doi.org/10.1038/s41593-024-01652-0

2023

1 Agrafiotis, A. et al. Persistent virus-specific and clonally expanded antibody-secreting cells respond to induced self-antigen in the CNS. Acta Neuropathol 145, 335-355 (2023). external page https://doi.org/10.1007/s00401-023-02537-5

2 Agrafiotis, A. et al. Generation of a single-cell B cell atlas of antibody repertoires and transcriptomes to identify signatures associated with antigen specificity. iScience 26, 106055 (2023). external page https://doi.org/10.1016/j.isci.2023.106055

3 Ahn, S., Sharma, U., Kasuba, K. C., Strohmeyer, N. & Muller, D. J. Engineered Biomimetic Fibrillar Fibronectin Matrices Regulate Cell Adhesion Initiation, Migration, and Proliferation via alpha5beta1 Integrin and Syndecan-4 Crosstalk. Adv Sci (Weinh) 10, e2300812 (2023). external page https://doi.org/10.1002/advs.202300812

4 Anastassov, S., Filo, M., Chang, C. H. & Khammash, M. A cybergenetic framework for engineering intein-mediated integral feedback control systems. Nat Commun 14, 1337 (2023). external page https://doi.org/10.1038/s41467-023-36863-9

5 Arekatla, G. et al. Optogenetic manipulation identifies the roles of ERK and AKT dynamics in controlling mouse embryonic stem cell exit from pluripotency. Dev Cell 58, 1022-1036 e1024 (2023). external page https://doi.org/10.1016/j.devcel.2023.04.013

6 Benisch, M., Benzinger, D., Kumar, S., Hu, H. & Khammash, M. Optogenetic closed-loop feedback control of the unfolded protein response optimizes protein production. Metab Eng 77, 32-40 (2023). external page https://doi.org/10.1016/j.ymben.2023.03.001

7 Bertschi, A., Wang, P., Galvan, S., Teixeira, A. P. & Fussenegger, M. Combinatorial protein dimerization enables precise multi-input synthetic computations. Nat Chem Biol 19, 767-777 (2023). external page https://doi.org/10.1038/s41589-023-01281-x

8 Borrelli, C. et al. In vivo screening of tumor-hepatocyte interactions identifies Plexin B2 as a gatekeeper of liver metastasis. bioRxiv, 2023.2005.2015.540681 (2023). external page https://doi.org/10.1101/2023.05.15.540681

9 Fleck, J. S. et al. Inferring and perturbing cell fate regulomes in human brain organoids. Nature 621, 365-372 (2023). external page https://doi.org/10.1038/s41586-022-05279-8

10 Frei, L. et al. Deep learning-guided selection of antibody therapies with enhanced resistance to current and prospective SARS-CoV-2 Omicron variants. bioRxiv, 2023.2010.2009.561492 (2023). external page https://doi.org/10.1101/2023.10.09.561492

11 Gokce, F. et al. Microphysiological Drug-Testing Platform for Identifying Responses to Prodrug Treatment in Primary Leukemia. Adv Healthc Mater 12, e2202506 (2023). external page https://doi.org/10.1002/adhm.202202506

12 Guha Ray, P., Maity, D., Huang, J., Zulewski, H. & Fussenegger, M. A versatile bioelectronic interface programmed for hormone sensing. Nat Commun 14, 3151 (2023). external page https://doi.org/10.1038/s41467-023-39015-1

13 He, Z. et al. An integrated transcriptomic cell atlas of human neural organoids. bioRxiv, 2023.2010.2005.561097 (2023). external page https://doi.org/10.1101/2023.10.05.561097

14 Huber, M., Casares-Arias, J., Fassler, R., Muller, D. J. & Strohmeyer, N. In mitosis integrins reduce adhesion to extracellular matrix and strengthen adhesion to adjacent cells. Nat Commun 14, 2143 (2023). external page https://doi.org/10.1038/s41467-023-37760-x

15 Jain, A. et al. Morphodynamics of human early brain organoid development. bioRxiv, 2023.2008.2021.553827 (2023). external page https://doi.org/10.1101/2023.08.21.553827

16 Kling, A., Dirscherl, L. & Dittrich, P. S. Laser-assisted protein micropatterning in a thermoplastic device for multiplexed prostate cancer biomarker detection. Lab Chip 23, 534-541 (2023). external page https://doi.org/10.1039/d2lc00840h

17 Lin, H.-C. et al. Human neuron subtype programming through combinatorial patterning with scRNA-seq readouts. bioRxiv, 2023.2012.2012.571318 (2023). external page https://doi.org/10.1101/2023.12.12.571318

18 Reimann, A. et al. Embryonic stem cell ERK, AKT, plus STAT3 response dynamics combinatorics are heterogeneous but NANOG state independent. Stem Cell Reports 18, 1295-1307 (2023). external page https://doi.org/10.1016/j.stemcr.2023.04.008

19 Strittmatter, T. et al. Mechano-regulation of Wnt/beta-Catenin signaling to control paraxial versus lateral mesoderm lineage bifurcation. Biotechnol Prog 39, e3312 (2023). external page https://doi.org/10.1002/btpr.3312

20 Teixeira, A. P., Xue, S., Huang, J. & Fussenegger, M. Evolution of molecular switches for regulation of transgene expression by clinically licensed gluconate. Nucleic Acids Res 51, e85 (2023). external page https://doi.org/10.1093/nar/gkad600

21 Wahle, P. et al. Multimodal spatiotemporal phenotyping of human retinal organoid development. Nat Biotechnol 41, 1765-1775 (2023). external page https://doi.org/10.1038/s41587-023-01747-2

22 Wei, W., Cardes, F., Hierlemann, A. & Modena, M. M. 3D In Vitro Blood-Brain-Barrier Model for Investigating Barrier Insults. Adv Sci (Weinh) 10, e2205752 (2023). external page https://doi.org/10.1002/advs.202205752

23 Yokoyama, F., Kling, A. & Dittrich, P. S. Capturing and Detecting of Extracellular Vesicles Derived from Single <em>Escherichia coli</em> Mother Cells. bioRxiv, 2023.2002.2022.529503 (2023). external page https://doi.org/10.1101/2023.02.22.529503

24 Zilbauer, M. et al. A Roadmap for the Human Gut Cell Atlas. Nat Rev Gastroenterol Hepatol 20, 597-614 (2023). external page https://doi.org/10.1038/s41575-023-00784-1

2022

1 Aznauryan, E. et al. Discovery and validation of human genomic safe harbor sites for gene and cell therapies. Cell Reports Methods 2, 100154 (2022). external page https://doi.org/https://doi.org/10.1016/j.crmeth.2021.100154

2 Bahls, M. O., Platz, L., Morgado, G., Schmidt, G. W. & Panke, S. Directed evolution of biofuel-responsive biosensors for automated optimization of branched-chain alcohol biosynthesis. Metabolic Engineering 69, 98-111 (2022). external page https://doi.org/https://doi.org/10.1016/j.ymben.2021.10.014

3 Castellanos-Rueda, R. et al. speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing. Nature Communications 13, 6555 (2022). external page https://doi.org/10.1038/s41467-022-34141-8

4 Dettinger, P. et al. Open-source personal pipetting robots with live-cell incubation and microscopy compatibility. Nature Communications 13, 2999 (2022). external page https://doi.org/10.1038/s41467-022-30643-7

5 Duncombe, T. A., Ponti, A. & Dittrich, P. S. SpectraSorter: Ocean Insight spectrometer software application for high-throughput full-spectrum UV–VIS analysis and triggered sorting. SoftwareX 19, 101160 (2022). external page https://doi.org/https://doi.org/10.1016/j.softx.2022.101160

6 Ehling, R. A. et al. SARS-CoV-2 reactive and neutralizing antibodies discovered by single-cell sequencing of plasma cells and mammalian display. Cell Reports 38, 110242 (2022). external page https://doi.org/https://doi.org/10.1016/j.celrep.2021.110242

7 Haellman, V. et al. dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation. Metabolic Engineering 73, 70-81 (2022). external page https://doi.org/https://doi.org/10.1016/j.ymben.2022.06.003

8 He, Z. et al. Lineage recording in human cerebral organoids. Nature Methods 19, 90-99 (2022). external page https://doi.org/10.1038/s41592-021-01344-8

9 Lust, K. et al. Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration. Science 377, eabp9262 (2022). external page https://doi.org/doi:10.1126/science.abp9262

10 Manioglu, S. et al. Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane. Nature Communications 13, 6195 (2022). external page https://doi.org/10.1038/s41467-022-33838-0

11 Neumeier, D. et al. Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis. European Journal of Immunology 52, 297-311 (2022). external page https://doi.org/https://doi.org/10.1002/eji.202149331

12 Neumeier, D. et al. Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells. Proceedings of the National Academy of Sciences 119, e2113766119 (2022). external page https://doi.org/doi:10.1073/pnas.2113766119

13 Stefanov, B.-A., Mansouri, M., Charpin-El Hamri, G. & Fussenegger, M. Sunlight-Controllable Biopharmaceutical Production for Remote Emergency Supply of Directly Injectable Therapeutic Proteins. Small 18, 2202566 (2022). external page https://doi.org/https://doi.org/10.1002/smll.202202566

14 Taft, J. M. et al. Deep mutational learning predicts ACE2 binding and antibody escape to combinatorial mutations in the SARS-CoV-2 receptor-binding domain. Cell 185, 4008-4022.e4014 (2022). external page https://doi.org/https://doi.org/10.1016/j.cell.2022.08.024

15 Vetter, R. & Iber, D. Precision of morphogen gradients in neural tube development. Nature Communications 13, 1145 (2022). external page https://doi.org/10.1038/s41467-022-28834-3

16 Wehling, A. et al. Combining single-cell tracking and omics improves blood stem cell fate regulator identification. Blood 140, 1482-1495 (2022). external page https://doi.org/10.1182/blood.2022016880

2021

1 Borrelli, C. et al. In vivo interaction screening reveals liver-derived constraints to metastasis. Nature 632, 411-418 (2024). external page https://doi.org/10.1038/s41586-024-07715-3

3 Hu, G., Huang, J. & Fussenegger, M. Toward Photosynthetic Mammalian Cells through Artificial Endosymbiosis. Small 20, e2310310 (2024). external page https://doi.org/10.1002/smll.202310310

10 Schirmacher, D. et al. aiSEGcell: User-friendly deep learning-based segmentation of nuclei in transmitted light images. PLOS Computational Biology 20, e1012361 (2024). external page https://doi.org/10.1371/journal.pcbi.1012361

11 Svanberg, S., Hirth, E., Mitsiadis, T. A. & Dittrich, P. S. "Periodontal ligament-on-chip" as a Novel Tool for Studies on the Physiology and Pathology of Periodontal Tissues. Adv Healthc Mater, e2303942 (2024). external page https://doi.org/10.1002/adhm.202303942

12 Zenk, F. et al. Single-cell epigenomic reconstruction of developmental trajectories from pluripotency in human neural organoid systems. Nature Neuroscience 27, 1376-1386 (2024). external page https://doi.org/10.1038/s41593-024-01652-0