Bibliography

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BioRxiv

1. P Natekar, Z Wang, M Arora, H Hakozaki, J Schöneberg (2023) MitoSpace: Self-supervised deep learning uncovers the semantic landscape of drug-induced latent mitochondrial phenotypes. BioRxiv.

Peer-reviewed Articles

2. W Xia, P Veeragandham, Y Cao, Y Xu, TE Rhyne, J Qian, C-W Hung, P Zhao, Y Jones, H Gao, C Liddle, RT Yu, M Downes, RM Evans, M Rydén, M Wabitsch, Z Wang, H Hakozaki, J Schöneberg, SM Reilly, J Huang,  AR Saltiel (2024) Obesity causes mitochondrial fragmentation and dysfunction in white adipocytes due to RalA activation, Nature Metabolism.

3. Z Wang, P Natekar, C Tea, S Tamir, H Hakozaki, J Schöneberg (2023) MitoTNT: Mitochondrial Temporal Network Tracking for 4D live-cell fluorescence microscopy data, PLOS Computational Biology.

4. G Ortiz-Muñoz, M Brown, CB Carbone, X Pechuan-Jorge, V Rouilly, H Lindberg, AT Ritter, G Raghupathi, Q Sun, T Nicotra, SR Mantri, A Yang, J Doerr, D Nagarkar, S Darmanis, B Haley, S Mariathasan, Y Wang, C Gomez-Roca, CE de Andrea, D Spigel, R Wu, L Delamarre, J Schöneberg, Z Modrusan, R Price, S J Turley, I Mellman, C Moussion (2023) In situ tumour arrays reveal early environmental control of cancer immunity, Nature. 

5. B Andrews, J-B Chang, L Collinson, D Li, E Lundberg, J Mahamid, S Manley, M Mhlanga, A Nakano, J Schöneberg, D Van Valen, T Wu, A Zaritsky (2022) Imaging cell biology, Nature Cell Biology.

6. M Jin, C Shirazinejad, B Wang, A Yan, J Schöneberg, S Upadhyayula, K Xu, DG Drubin (2022) Branched actin networks are organized for asymmetric force production during clathrin-mediated endocytosis in mammalian cells. Nature Communications.

7. C Kaplan, S J Kenny, X Chen, J Schöneberg, E Sitarska, A Diz-Muñoz, M Akamatsu, K Xu, D G Drubin (2022) Load adaptation by endocytic actin networks. Molecular Biology of the Cell.

8. D Serwas, M Akamatsu, A Moayed, K Vegesna, R Vasan, J M Hill, J Schöneberg, K M Davies, P Rangamani, D G Drubin (2022) Mechanistic insights into actin force generation during vesicle formation from cryo-electron tomography. Developmental Cell.

9. Y Markaki, J G Chong, Y Wang, E C Jacobson, C Luong, S YX Tan, J W Jachowicz, M Strehle, D Maestrini, A K Banerjee, B A Mistry, I Dror, F Dossin, J Schöneberg, E Heard, M Guttman, T Chou, K Plath (2021) Xist nucleates local protein gradients to propagate silencing across the X chromosome. Cell.

10. J Schöneberg*, G Raghupathi*, E Betzig, D G Drubin (2019) 3D Deep Convolutional Neural Networks in Lattice Light-Sheet Data Puncta Segmentation. IEEE Proceedings International Conference on Bioinformatics and Biomedicine (BIBM), * equal contribution.

11. Y Sun, J Schöneberg, S Chen, T Jiang, C Kaplan, K Xu, T D Pollard, D G Drubin (2019) Direct comparison of clathrin-mediated endocytosis in budding and fission yeast reveals conserved and evolvable features. eLife, 8:e50749.

12. J Schöneberg, D Dambournet, T-L Liu, R Forster, D Hockemeyer, E Betzig, D G Drubin (2018) 4D cell biology: big data image analytics and lattice light-sheet imaging reveal dynamics of clathrin-mediated endocytosis in stem cell-derived intestinal organoids. Molecular Biology of the Cell, 29(24).

13. J Schöneberg, M R Pavlin*, S Yan*, M Righini, I-H Lee, L-A Carlson, A H Bahrami, D H Goldman, X Ren, G Hummer, C Bustamante and J H Hurley (2018) ATP-dependent force generation and membrane scission by ESCRT-III and Vps4. Science,  362(6421). * equal contribution

14. C Chang*, L N Young*, K L Morris, S v. Bülow, J Schöneberg, H Yamamoto-Imoto, Y Oe, K Yamamoto, S Nakamura, G Stjepanovic, G Hummer, T Yoshimori and J H Hurley (2019) Bidirectional control of autophagy by BECN1 BARA domain dynamics. Molecular Cell,  73(2), 339-353. * equal contribution

15. B M Qureshi, E Behrmann, J Schöneberg, J Loerke, J Bürger, T Mielke, J Giesebrecht, F Noé, T D Lamb, K P Hofmann, C MT Spahn, M Heck (2018) It takes two transducins to activate the cGMP-phosphodiesterase 6 in retinal rods. Open Biology, 8(10).

16. M G Lin, J Schöneberg, C W Davies, X Ren, and J H Hurley (2018) The dynamic Atg13-free conformation of the Atg1 EAT domain is required for phagophore expansion, Molecular Biology of the Cell, 29(10).

17. J Schöneberg*, M Lehmann*, A Ullrich, Y Posor, W-T Lo, G Lichtner, J Schmoranzer, Volker Haucke, Frank Noé. (2017) Lipid-mediated PX-BAR domain recruitment couples local membrane constriction to endocytic vesicle fission. Nature Communications. * equal contribution

18. F Paul*, C Wehmeyer*, E T Abualrous, H Wu, M D Crabtree, J Schöneberg, J Clarke, C Freund, T R Weikl, Frank Noé, (2017) Protein-peptide association kinetics beyond the seconds timescale from atomistic simulations. Nature Communications, accepted. *equal contribution

19. M Gunkel*, J Schöneberg*, W Alkhaldi, S Irsen, F Noé, U B Kaupp and A Al-Amoudi, (2015) Higher-order architecture of rhodopsin in intact photoreceptor controls phototransduction kinetics. Structure, 23(4):628-38. * equal contribution

20. A Ullrich, MA Böhme, J Schöneberg, H Depner, SJ Sigrist, F Noé (2015) Dynamical organization of syntaxin-1A at the presynaptic active zone. PLoS Comput. Biol., 11(9), e1004407.

21. J Biedermann, A Ullrich, J Schöneberg and F Noé, (2015) ReaDDyMM: fast particle-based reaction-diffusion simulations using graphical processing units. Biophysical Journal,108(3):457-61.

22. J Schöneberg, M Heck, KP Hofmann, F Noé,  (2014) Explicit spatiotemporal simulation of receptor-G protein coupling in rod cell disk membranes. Biophysical Journal, 107(5): 1042-1053.

23. J Schöneberg and F Noé (2013) ReaDDy - a software for particle based reaction diffusion dynamics in crowded cellular environments. PLOS One, 8(9): e74261.

24. Y Posor, M Eichhorn-Gruenig, D Puchkov, J Schöneberg, A Ullrich, A Lampe, R Müller, S Zarbakhsh, F Gulluni, E Hirsch, M Krauss, C Schultz, J Schmoranzer, F Noé and V Haucke (2013) Spatiotemporal control of endocytosis by phosphatidylinositol-3,4-bisphosphate. Nature, 499(7457): 233-237.

Software

1.  pyLattice (J Schöneberg, 2017-present): Python/Jupyter, MATLAB | Big data analytics package for lattice light-sheet data. Published and applied in [3]. Have a look at the pyLattice tutorials and keep an eye out on the deep learning module [1].

2. Confleezers (J Schöneberg, 2016-2018): Python/Jupyter | Data analysis package for the Confleezers microscope and membrane nanotube pulling. Published and applied in [4].

3. GUV_Tracking_Quantification (J Schöneberg, 2017/2018): Python/Jupyter | Quantification tool for fluorescence intensity GUV membranes and binding proteins. Published in and applied in [4, 5].

4. ReaDDy (J Schöneberg, and Frank Noé, 2012-2016): Java, 70k LOC, GPU accellerated | High-performance particle-based reaction-diffusion simulation engine for crowded cellular environments. Published in [14,12], applied in [15,13,11,10,8]. 

Reviews

1. J Schöneberg*, I-H Lee*, JH Iwasa, JH Hurley (2016) Reverse-topology membrane scission by the ESCRT proteins. Nature Reviews Molecular and Cell Biology. * equal contribution

2. J Schöneberg, A Ullrich, F Noé,  (2014) Simulation tools for particle-based reaction-diffusion dynamics in continuous space. BMC Biophysics, 7(11). 

Book Chapters

1. R Vasan, M S Akamatsu, J Schöneberg, and P Rangamani (2018) Intracellular membrane trafficking: modeling local movements in cells. Cell Movement: Modeling and Applications. Springer. 

Assists

1. M Akamatsu, R Vasan, D Serwas, M Ferrin, P Rangamani, D G Drubin (2019) Principles of self-organization and load adaptation by the actin cytoskeleton during clathrin-mediated endocytosis. bioRxiv 678797

2. A L Stubbs and C W Stubbs (2016) Spectral discrimination in color blind animals via chromatic aberration and pupil shape, PNAS 113 (29);

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