2024
A data-driven active learning approach to reusing ML solutions in scientific applications. Hamideh Hajiabadi, Christopher Gerking, Lennart Hilbert, Anne Koziolek; Journal of Systems and Software, 111986, 2024
Photon-Efficient Aberration Correction for 3D-STED Imaging of Thick Biological Specimens Using Sensorless Adaptive Optics. Siqing Dai, Andrei Kobitski, Amirhossein Barati Sedeh, Süheyla Eroğlu-Kayıkçı, Lennart Hilbert, Gerd Ulrich Nienhaus; ACS Photonics, 3c01558, 2024
2023
Stimulated emission double depletion nanoscopy with background correction at the single-pixel level. Amirhossein Barati Sedeh, Andrei Kobitski, Siqing Dai, Süheyla Eroğlu-Kayıkçı, Karin Nienhaus, Lennart Hilbert, Gerd Ulrich Nienhaus; Optics Letters, 502001, 2023
Synchronization of oscillatory growth prepares fungal hyphae for fusion. Valentin Wernet, Marius Kriegler, Vojtěch Kumpošt, Ralf Mikut, Lennart Hilbert, Reinhard Fischer; eLife, 83310, 2023
Transcriptional clusters follow a conserved condensation-dispersal sequence during stem cell differentiation. Tim Klingberg*, Irina Wachter*, Agnieszka Pancholi, Yomna Gohar, Priya Kumar, Marcel Sobucki, Elisa Kämmer, Süheyla Eroğlu-Kayikçi, Sylvia Erhardt, Carmelo Ferrai, Vasily Zaburdaev, Lennart Hilbert**; bioRxiv preprint, 2023 (*equal contribution, **corresponding author)
Amphiphiles formed from synthetic DNA-nanomotifs mimic the step-wise dispersal of transcriptional clusters in the cell nucleus. Xenia Tschurikow*, Aaron Gadzekpo*, Mai P. Tran, Rakesh Chatterjee, Marcel Sobucki, Vasily Zaburdaev, Kerstin Göpfrich, Lennart Hilbert**; Nano Letters, 3c01301, 2023 (*equal contribution, **corresponding author)
Noise facilitates entrainment of a population of uncoupled limit cycle oscillators. Vojtěch Kumpošt, Lennart Hilbert*, Ralf Mikut*; Journal of the Royal Society Interface, 20(198):20220781, 2023 (*co-corresponding authors)
2022
Deep-learning microscopy image reconstruction with quality control reveals second-scale rearrangements in RNA polymerase II clusters. Hamideh Hajiabadi*, Irina Mamontova*, Roshan Prizak, Agnieszka Pancholi, Anne Koziolek**, Lennart Hilbert**; PNAS Nexus, 1(3):pgac065, 2022 (*equal contribution, **joint supervision)
A DNA segregation module for synthetic cells. Mai P Tran, Rakesh Chatterjee, Yannik Dreher, Julius Fichtler, Kevin Jahnke, Lennart Hilbert, Vasily Zaburdaev, Kerstin Göpfrich; Small, Online Early, 2022; Link to bioRxiv preprint
Clustered transposon insertion via formation of chromatin loops. Roshan Prizak*, Lennart Hilbert*; bioRxiv preprint, 2022 (*co-corresponding authors)
2021
RNA polymerase II clusters form in line with surface condensation on regulatory chromatin.
A stochastic oscillator model simulates the entrainment of vertebrate cellular clocks by light. Vojtěch Kumpošt, Daniela Vallone, Srinivas Babu Gondi, Nicholas S Foulkes*, Ralf Mikut*, Lennart Hilbert*; Scientific Reports 11:14497, 2021 (*co-corresponding authors)
The hierarchical packing of euchromatin domains can be described as multiplicative cascades. Amra Noa, Hui-Shun Kuan, Vera Aschmann, Vasily Zaburdaev, Lennart Hilbert; PLOS Computational Biology 17(5):e1008974, 2021
Transcription organizes euchromatin via microphase separation. 2021 (*equal contribution, **shared supervision)
2019
Spreading of perturbations in myosin group kinetics along actin filaments.
Super-resolution imaging of densely packed DNA in nuclei of zebrafish embryos using stimulated emission double depletion microscopy. Weichun Zhang, Amra Noa, Karin Nienhaus, Lennart Hilbert*, G. Ulrich Nienhaus*; Journal of Physics D: Applied Physics 52:414001, 2019 (*co-corresponding authors)
Quantitative measurements of chromatin modification dynamics during zygotic genome activation. Yuko Sato, Lennart Hilbert, Haruka Oda, Yinan Wan, John M Heddleston, Teng-Leong Chew, Vasily Zaburdaev, Philipp Keller, Timothee Lionnet, Nadine Vastenhouw, Hiroshi Kimura; Development 146, 2019
2017 and before
A tunable refractive index matching medium for live imaging cells, tissues and model organisms. Tobias Boothe, Lennart Hilbert, Michael Heide, Lea Berninger, Wieland B Huttner, Vasily Zaburdaev, Nadine L Vastenhouw, Eugene W Myers, David N Drechsel, Jochen C Rink; eLife 27240, 2017
Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos. Shai R Joseph, Máté Pálfy, Lennart Hilbert, Mukesh Kumar, Jens Karschau, Vasily Zaburdaev, Andrej Shevchenko, Nadine L Vastenhouw; eLife 23326, 2017
Computational Study of Synchrony in Fields and Microclusters of Ephaptically Coupled Neurons. Richard G Stacey*, Lennart Hilbert*, Thomas Quail; Journal of Neurophysiology, 113:3229-3241, 2015 (*equal contribution)
Phosphate and ADP Differently Inhibit Coordinated Smooth Muscle Myosin Groups. Lennart Hilbert, Zsombor Balassy, Nedjma B Zitouni, Michael C Mackey, Anne-Marie Lauzon; Biophysical Journal 108(3):622-631, 2015
Molecular Mechanical Differences between Isoforms of Contractile Actin in the Presence of Isoforms of Smooth Muscle Tropomyosin. Lennart Hilbert, Genevieve Bates, Horia N Roman, Jenna L Blumenthal, Nedjma B Zitouni, Apolinary Sobieszek, Michael C Mackey, Anne-Marie Lauzon; PLOS Computational Biology 9(10):e1003273, 2013
The Kinetics of Mechanically Coupled Myosins Exhibit Group Size Dependent Regimes. Lennart Hilbert, Shivaram Cumarasamy, Nedjma B Zitouni, Michael C Mackey, Anne-Marie Lauzon; Biophysical Journal 105(6):1466-1474, 2013
Unphosphorylated calponin enhances the binding force of unphosphorylated myosin to actin. Horia N Roman, Nedjma B Zitouni, Linda Kachmar, Gijs Ijpma, Lennart Hilbert, Oleg Matusovskiy, Andrea Benedetti, Apolinary Sobieszek, Anne-Marie Lauzon; Biochimica et Biophysica Acta (BBA) – General Subjects 1830(10):4634-4641, 2013
Stress-induced hypermutation as a physical property of life, a force of natural selection and its role in four thought experiments. Lennart Hilbert; Physical Biology 10(2):026001, 2013
Pre-Power-Stroke Cross-Bridges Contribute to Force Transients during Imposed Shortening in Isolated Muscle Fibers. Fabio C Minozzo, Lennart Hilbert, Dilson E Rassier; PLOS ONE 7(1):e29356, 2012
Small delay, big waves: a minimal delayed negative feedback model captures Escherichia coli single cell SOS kinetics. Lennart Hilbert, David Albrecht, Michael C Mackey; Molecular Biosystems 7(9):2599-2607, 2011