References

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

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 pagehttps://doi.org/10.1007/s00401-023-02537-5call_made

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 pagehttps://doi.org/10.1016/j.isci.2023.106055call_made

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 pagehttps://doi.org/10.1002/advs.202300812call_made

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 pagehttps://doi.org/10.1038/s41467-023-36863-9call_made

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 pagehttps://doi.org/10.1016/j.devcel.2023.04.013call_made

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 pagehttps://doi.org/10.1016/j.ymben.2023.03.001call_made

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 pagehttps://doi.org/10.1038/s41589-023-01281-xcall_made

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 pagehttps://doi.org/10.1101/2023.05.15.540681call_made

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

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 pagehttps://doi.org/10.1101/2023.10.09.561492call_made

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 pagehttps://doi.org/10.1002/adhm.202202506call_made

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 pagehttps://doi.org/10.1038/s41467-023-39015-1call_made

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

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 pagehttps://doi.org/10.1038/s41467-023-37760-xcall_made

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

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 pagehttps://doi.org/10.1039/d2lc00840hcall_made

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

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 pagehttps://doi.org/10.1016/j.stemcr.2023.04.008call_made

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 pagehttps://doi.org/10.1002/btpr.3312call_made

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 pagehttps://doi.org/10.1093/nar/gkad600call_made

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

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 pagehttps://doi.org/10.1002/advs.202205752call_made

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 pagehttps://doi.org/10.1101/2023.02.22.529503call_made

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

2022

25           Ahmed, N. et al. Blood stem cell PU.1 upregulation is a consequence of differentiation without fast autoregulation. J Exp Med 219 (2022). external pagehttps://doi.org/10.1084/jem.20202490call_made

26           Altamura, R., Doshi, J. & Benenson, Y. Rational design and construction of multi-copy biomanufacturing islands in mammalian cells. Nucleic Acids Res 50, 561-578 (2022). external pagehttps://doi.org/10.1093/nar/gkab1214call_made

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

28           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. Metab Eng 69, 98-111 (2022). external pagehttps://doi.org/10.1016/j.ymben.2021.10.014call_made

29           Castellanos-Rueda, R. et al. speedingCARs: accelerating the engineering of CAR T cells by signaling domain shuffling and single-cell sequencing. Nat Commun 13, 6555 (2022). external pagehttps://doi.org/10.1038/s41467-022-34141-8call_made

30           Dettinger, P. et al. Open-source personal pipetting robots with live-cell incubation and microscopy compatibility. Nat Commun 13, 2999 (2022). external pagehttps://doi.org/10.1038/s41467-022-30643-7call_made

31           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 (2022). external pagehttps://doi.org/10.1016/j.softx.2022.101160call_made

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

33           Haellman, V. et al. dCas9-mediated dysregulation of gene expression in human induced pluripotent stem cells during primitive streak differentiation. Metab Eng 73, 70-81 (2022). external pagehttps://doi.org/10.1016/j.ymben.2022.06.003call_made

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

35           Lust, K. et al. Single-cell analyses of axolotl telencephalon organization, neurogenesis, and regeneration. Science 377, eabp9262 (2022). external pagehttps://doi.org/10.1126/science.abp9262call_made

36           Manioglu, S. et al. Antibiotic polymyxin arranges lipopolysaccharide into crystalline structures to solidify the bacterial membrane. Nat Commun 13, 6195 (2022). external pagehttps://doi.org/10.1038/s41467-022-33838-0call_made

37           Neumeier, D. et al. Profiling the specificity of clonally expanded plasma cells during chronic viral infection by single-cell analysis. Eur J Immunol 52, 297-311 (2022). external pagehttps://doi.org/10.1002/eji.202149331call_made

38           Neumeier, D. et al. Phenotypic determinism and stochasticity in antibody repertoires of clonally expanded plasma cells. Proc Natl Acad Sci U S A 119, e2113766119 (2022). external pagehttps://doi.org/10.1073/pnas.2113766119call_made

39           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, e2202566 (2022). external pagehttps://doi.org/10.1002/smll.202202566call_made

40           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 pagehttps://doi.org/10.1016/j.cell.2022.08.024call_made

41           Vetter, R. & Iber, D. Precision of morphogen gradients in neural tube development. Nat Commun 13, 1145 (2022). external pagehttps://doi.org/10.1038/s41467-022-28834-3call_made

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

2021

43           Angelici, B., Shen, L., Schreiber, J., Abraham, A. & Benenson, Y. An AAV gene therapy computes over multiple cellular inputs to enable precise targeting of multifocal hepatocellular carcinoma in mice. Science Translational Medicine 13, eabh4456 (2021). external pagehttps://doi.org/doi:10.1126/scitranslmed.abh4456call_made

44           Becker, K., Meyer, A., Roberts, T. M. & Panke, S. Plasmid replication based on the T7 origin of replication requires a T7 RNAP variant and inactivation of ribonuclease H. Nucleic Acids Res 49, 8189-8198 (2021). external pagehttps://doi.org/10.1093/nar/gkab596call_made

45           Boos, J. A. et al. Microfluidic Co-Culture Platform to Recapitulate the Maternal-Placental-Embryonic Axis. Adv Biol (Weinh) 5, e2100609 (2021). external pagehttps://doi.org/10.1002/adbi.202100609call_made

46           Conrad, L. et al. The biomechanical basis of biased epithelial tube elongation in lung and kidney development. Development 148 (2021). external pagehttps://doi.org/10.1242/dev.194209call_made

47           Duncombe, T. A., Ponti, A., Seebeck, F. P. & Dittrich, P. S. UV-Vis Spectra-Activated Droplet Sorting for Label-Free Chemical Identification and Collection of Droplets. Anal Chem 93, 13008-13013 (2021). external pagehttps://doi.org/10.1021/acs.analchem.1c02822call_made

48           Gokce, F., Ravaynia, P. S., Modena, M. M. & Hierlemann, A. What is the future of electrical impedance spectroscopy in flow cytometry? Biomicrofluidics 15, 061302 (2021). external pagehttps://doi.org/10.1063/5.0073457call_made

49           Gurtner, A. et al. Single-cell RNA sequencing unveils intestinal eosinophil development and specialization. bioRxiv, 2021.2010.2027.466053 (2021). external pagehttps://doi.org/10.1101/2021.10.27.466053call_made

50           Hausmann, A. et al. Intercrypt sentinel macrophages tune antibacterial NF-kappaB responses in gut epithelial cells via TNF. J Exp Med 218 (2021). external pagehttps://doi.org/10.1084/jem.20210862call_made

51           Juskova, P., Schmitt, S., Armbrecht, L. & Dittrich, P. S. Microbial factories: monitoring vitamin B(2) production by Escherichia coli in microfluidic cultivation chambers. Lab Chip 21, 4071-4080 (2021). external pagehttps://doi.org/10.1039/d1lc00621ecall_made

52           Juskova, P. et al. Real-Time Respiration Changes as a Viability Indicator for Rapid Antibiotic Susceptibility Testing in a Microfluidic Chamber Array. ACS Sens 6, 2202-2210 (2021). external pagehttps://doi.org/10.1021/acssensors.1c00020call_made

53           Napiorkowska, M., Pestalozzi, L., Panke, S., Held, M. & Schmitt, S. High-Throughput Optimization of Recombinant Protein Production in Microfluidic Gel Beads. Small 17, e2005523 (2021). external pagehttps://doi.org/10.1002/smll.202005523call_made

54           Nguyen, O. T. P. et al. An Immunocompetent Microphysiological System to Simultaneously Investigate Effects of Anti-Tumor Natural Killer Cells on Tumor and Cardiac Microtissues. Front Immunol 12, 781337 (2021). external pagehttps://doi.org/10.3389/fimmu.2021.781337call_made

55           Nikoloff, J. M., Saucedo-Espinosa, M. A., Kling, A. & Dittrich, P. S. Identifying extracellular vesicle populations from single cells. Proc Natl Acad Sci U S A 118 (2021). external pagehttps://doi.org/10.1073/pnas.2106630118call_made

56           Stucki, A., Juskova, P., Nuti, N., Schmitt, S. & Dittrich, P. S. Synchronized Reagent Delivery in Double Emulsions for Triggering Chemical Reactions and Gene Expression. Small Methods 5, e2100331 (2021). external pagehttps://doi.org/10.1002/smtd.202100331call_made

57           Yermanos, A. et al. Single-cell immune repertoire and transcriptome sequencing reveals that clonally expanded and transcriptionally distinct lymphocytes populate the aged central nervous system in mice. Proc Biol Sci 288, 20202793 (2021). external pagehttps://doi.org/10.1098/rspb.2020.2793call_made