Vasily Zaburdaev

2024

• Angeloni M., van Doeveren T., Lindner S., Volland P., Schmelmer J., Foersch S., Matek C., Stöhr R., Geppert CI., Heers H., Wach S., Taubert H., Sikic D., Wullich B., van Leenders GJ., Zaburdaev V., Eckstein M., Hartmann A., Boormans JL., Ferrazzi F., Bahlinger V.:
  A deep-learning workflow to predict upper tract urothelial carcinoma protein-based subtypes from H&E slides supporting the prioritization of patients for molecular testing
  In: Journal of Pathology: Clinical Research 10 (2024), Article No.: e12369
  ISSN: 2056-4538
  DOI: 10.1002/2056-4538.12369
• Firooz S., Reddy BD., Zaburdaev V., Steinmann P.:
  Mean zero artificial diffusion for stable finite element approximation of convection in cellular aggregate formation
  In: Computer Methods in Applied Mechanics and Engineering 419 (2024), p. 116649
  ISSN: 0045-7825
  DOI: 10.1016/j.cma.2023.116649
• Möckel C., Beck T., Kaliman S., Abuhattum S., Kim K., Kolb J., Wehner D., Zaburdaev V., Guck J.:
  Estimation of the mass density of biological matter from refractive index measurements
  In: Biophysical Reports (2024), p. 100156
  ISSN: 2667-0747
  DOI: 10.1016/j.bpr.2024.100156

2022

• Abuhattum S., Kuan HS., Müller P., Guck J., Zaburdaev V.:
  Unbiased retrieval of frequency-dependent mechanical properties from noisy time-dependent signals
  In: Biophysical Reports 2 (2022), Article No.: 100054
  ISSN: 2667-0747
  DOI: 10.1016/j.bpr.2022.100054
• Firooz S., Kaessmair S., Zaburdaev V., Javili A., Steinmann P.:
  On continuum modeling of cell aggregation phenomena
  In: Journal of the Mechanics and Physics of Solids 167 (2022), Article No.: 105004
  ISSN: 0022-5096
  DOI: 10.1016/j.jmps.2022.105004
• Poenisch W., Zaburdaev V.:
  A Pili-Driven Bacterial Turbine
  In: Frontiers in Physics 10 (2022)
  ISSN: 2296-424X
  DOI: 10.3389/fphy.2022.875687
• Tran MP., Chatterjee R., Dreher Y., Fichtler J., Jahnke K., Hilbert L., Zaburdaev V., Göpfrich K.:
  A DNA Segregation Module for Synthetic Cells
  In: Small (2022)
  ISSN: 1613-6829
  DOI: 10.1002/smll.202202711
• Vurnek D., Amon L., Buttazzo L., Lehmann C., Zaburdaev V., Dudziak D.:
  Spatial, structural and density determinants of DC:T cell interaction under immunostimulatory conditions
  In: EUROPEAN JOURNAL OF IMMUNOLOGY, HOBOKEN: 2022

2021

• Anchang CG., Xu C., Raimondo MG., Atreya R., Maier A., Schett G., Zaburdaev V., Rauber S., Ramming A.:
  The potential of omics technologies for the treatment of immune‐mediated inflammatory diseases
  In: International Journal of Molecular Sciences 22 (2021), Article No.: 7506
  ISSN: 1422-0067
  DOI: 10.3390/ijms22147506
• Clopes J., Shin J., Jahnel M., Grill SW., Zaburdaev V.:
  Thermal fluctuations assist mechanical signal propagation in coiled-coil proteins
  In: Physical Review E 104 (2021)
  ISSN: 2470-0045
  DOI: 10.1103/PhysRevE.104.054403
• Hilbert L., Sato Y., Kuznetsova K., Bianucci T., Kimura H., Jülicher F., Honigmann A., Zaburdaev V., Vastenhouw NL.:
  Transcription organizes euchromatin via microphase separation
  In: Nature Communications 12 (2021), Article No.: 1360
  ISSN: 2041-1723
  DOI: 10.1038/s41467-021-21589-3
• Kuan HS., Poenisch W., Juelicher F., Zaburdaev V.:
  Continuum Theory of Active Phase Separation in Cellular Aggregates
  In: Physical Review Letters 126 (2021)
  ISSN: 0031-9007
  DOI: 10.1103/PhysRevLett.126.018102
• Noa A., Kuan HS., Aschmann V., Zaburdaev V., Hilbert L.:
  The hierarchical packing of euchromatin domains can be described as multiplicative cascades
  In: PLoS Computational Biology 17 (2021), Article No.: e1008974
  ISSN: 1553-734X
  DOI: 10.1371/journal.pcbi.1008974
• Pancholi A., Klingberg TG., Zhang W., Prizak R., Mamontova I., Noa A., Sobucki M., Kobitski AY., Nienhaus GU., Zaburdaev V., Hilbert L.:
  RNA polymerase II clusters form in line with surface condensation on regulatory chromatin
  In: Molecular Systems Biology 17 (2021), Article No.: e10272
  ISSN: 1744-4292
  DOI: 10.15252/msb.202110272

2020

• Adame-Arana O., Weber CA., Zaburdaev V., Prost J., Jülicher F.:
  Liquid Phase Separation Controlled by pH
  In: Biophysical Journal (2020)
  ISSN: 0006-3495
  DOI: 10.1016/j.bpj.2020.07.044
• Kaptan D., Penkov S., Zhang X., Gade VR., Raghuraman BK., Galli R., Sampaio JL., Haase R., Koch E., Shevchenko A., Zaburdaev V., Kurzchalia T.:
  Exogenous ethanol induces a metabolic switch that prolongs the survival of Caenorhabditis elegans dauer larva and enhances its resistance to desiccation
  In: Aging Cell (2020)
  ISSN: 1474-9718
  DOI: 10.1111/acel.13214
• Luhr JJ., Alex N., Amon L., Krater M., Kubankova M., Sezgin E., Lehmann C., Heger L., Heidkamp GF., Smith AS., Zaburdaev V., Böckmann R., Levental I., Dustin ML., Eggeling C., Dudziak D., Guck J.:
  Maturation of Monocyte-Derived DCs Leads to Increased Cellular Stiffness, Higher Membrane Fluidity, and Changed Lipid Composition
  In: Frontiers in Immunology 11 (2020), Article No.: 590121
  ISSN: 1664-3224
  DOI: 10.3389/fimmu.2020.590121
• Mazaheri M., Ehrig J., Shkarin A., Zaburdaev V., Sandoghdar V.:
  Ultrahigh-Speed Imaging of Rotational Diffusion on a Lipid Bilayer
  In: Nano Letters 20 (2020), p. 7213-7219
  ISSN: 1530-6984
  DOI: 10.1021/acs.nanolett.0c02516
• Taylor RW., Holler C., Mahmoodabadi RG., Küppers M., Mirzaalian Dastjerdi H., Zaburdaev V., Schambony A., Sandoghdar V.:
  High-Precision Protein-Tracking With Interferometric Scattering Microscopy
  In: Frontiers in Cell and Developmental Biology 8 (2020), Article No.: 590158
  ISSN: 2296-634X
  DOI: 10.3389/fcell.2020.590158

2019

• Huang W., Zaburdaev V.:
  The shape of pinned forced polymer loops
  In: Soft Matter 15 (2019), p. 1785-1792
  ISSN: 1744-683X
  DOI: 10.1039/c8sm02357c
• Kuan HS., Juelicher F., Zaburdaev V.:
  Bacterial colonies as active droplets - from single cells to continuum theory
  Joint 12th EBSA European Biophysics Congress / 10th IUPAP International Conference on Biological Physics (ICBP) (Madrid, July 20, 2019 - July 24, 2019)
  In: EUROPEAN BIOPHYSICS JOURNAL WITH BIOPHYSICS LETTERS, NEW YORK: 2019
• Passucci G., Brasch ME., Henderson JH., Zaburdaev V., Manning ML.:
  Identifying the mechanism for superdiffusivity in mouse fibroblast motility
  In: PLoS Computational Biology 15 (2019)
  ISSN: 1553-734X
  DOI: 10.1371/journal.pcbi.1006732
• Poenisch W., Weber CA., Zaburdaev V.:
  How bacterial cells and colonies move on solid substrates
  In: Physical Review E 99 (2019), Article No.: 042419
  ISSN: 2470-0045
  DOI: 10.1103/PhysRevE.99.042419
• Sato Y., Hilbert L., Oda H., Wan Y., Heddleston JM., Chew TL., Zaburdaev V., Keller P., Lionnet T., Vastenhouw N., Kimura H.:
  Histone H3K27 acetylation precedes active transcription during zebrafish zygotic genome activation as revealed by live-cell analysis
  In: Development 146 (2019)
  ISSN: 1477-9129
  DOI: 10.1242/dev.179127
• Weber A., Bahrs M., Alirezaeizanjani Z., Zhang X., Beta C., Zaburdaev V.:
  Rectification of Bacterial Diffusion in Microfluidic Labyrinths
  In: Frontiers in Physics 7 (2019), Article No.: 148
  ISSN: 2296-424X
  DOI: 10.3389/fphy.2019.00148

2018

• Abuhattum S., Kim K., Franzmann TM., Esslinger A., Midtvedt D., Schluessler R., Kuan HS., Alberti S., Zaburdaev V., Guck J., Möllmert S.:
  Intracellular Mass Density Increase Is Accompanying but Not Sufficient for Stiffening and Growth Arrest of Yeast Cells
  In: Frontiers in Bioscience 6 (2018)
  ISSN: 1093-9946
  DOI: 10.3389/fphy.2018.00131
• Huang W., Lin YT., Froemberg D., Shin J., Juelicher F., Zaburdaev V.:
  Exactly solvable dynamics of forced polymer loops
  In: New Journal of Physics 20 (2018)
  ISSN: 1367-2630
  DOI: 10.1088/1367-2630/aae8f0
• Krivonosov MI., Zaburdaev V., Denisov SV., Ivanchenko MV.:
  Genetic noise mechanism for power-law switching in bacterial flagellar motors
  In: Journal of Physics A: Mathematical and Theoretical 51 (2018)
  ISSN: 1751-8113
  DOI: 10.1088/1751-8121/aac543
• Poenisch W., Eckenrode KB., Alzurqa K., Nasrollahi H., Weber C., Zaburdaev V., Biais N.:
  Pili mediated intercellular forces shape heterogeneous bacterial microcolonies prior to multicellular differentiation
  In: Scientific Reports 8 (2018)
  ISSN: 2045-2322
  DOI: 10.1038/s41598-018-34754-4
• Poenisch W., Zaburdaev V.:
  Relative distance between tracers as a measure of diffusivity within moving aggregates
  In: European Physical Journal B 91 (2018)
  ISSN: 1434-6028
  DOI: 10.1140/epjb/e2017-80347-5
• Schluessler R., Abuhattum S., Cojoc G., Beck T., Reichel F., Kim K., Schuermann M., Mueller P., Czarske J., Zaburdaev V., Franzmann T., Alberti S., Guck J.:
  Biophysical Techniques for the Study of Phase Transitions in Protein Droplets and Cells
  In: Biophysical Journal 114 (2018), p. 204A-204A
  ISSN: 0006-3495

2017

• Boothe T., Hilbert L., Heide M., Berninger L., Huttner WB., Zaburdaev V., Vastenhouw NL., Myers EW., Drechsel DN., Rink JC.:
  A tunable refractive index matching medium for live imaging cells, tissues and model organisms
  In: eLife 6 (2017)
  ISSN: 2050-084X
  DOI: 10.7554/eLife.27240
• Fouxon I., Denisov S., Zaburdaev V., Barkai E.:
  Limit theorems for Levy walks in d dimensions: rare and bulk fluctuations
  In: Journal of Physics A: Mathematical and Theoretical 50 (2017)
  ISSN: 1751-8113
  DOI: 10.1088/1751-8121/aa5f6d
• Hilbert L., Sato Y., Kimura H., Honigmann A., Zaburdaev V., Vastenhouw N.:
  Transcription Locally Disperses Chromatin and Thereby Organizes the Global Architecture of Interphase Nuclei
  In: Biophysical Journal 112 (2017), p. 211A-211A
  ISSN: 0006-3495
  DOI: 10.1016/j.bpj.2016.11.1164
• Hilbert L., Sato Y., Kimura H., Julicher F., Honigmann A., Zaburdaev V., Vastenhouw N.:
  Interphase chromatin is adaptively folded by ongoing transcription and RNA accumulation.
  In: Molecular Biology of the Cell 28 (2017)
  ISSN: 1059-1524
• Joseph SR., Palfy M., Hilbert L., Kumar M., Karschau J., Zaburdaev V., Shevchenko A., Vastenhouw NL.:
  Competition between histone and transcription factor binding regulates the onset of transcription in zebrafish embryos
  In: eLife 6 (2017)
  ISSN: 2050-084X
  DOI: 10.7554/eLife.23326
• Poenisch W., Weber CA., Juckeland G., Biais N., Zaburdaev V.:
  Multiscale modeling of bacterial colonies: how pili mediate the dynamics of single cells and cellular aggregates
  In: New Journal of Physics 19 (2017)
  ISSN: 1367-2630
  DOI: 10.1088/1367-2630/aa5483
• Shin J., Cherstvy AG., Kim WK., Zaburdaev V.:
  Elasticity-based polymer sorting in active fluids: a Brownian dynamics study
  In: Physical Chemistry Chemical Physics 19 (2017), p. 18338-18347
  ISSN: 1463-9076
  DOI: 10.1039/c7cp02947k
• Strelnikova N., Sauter N., Guizar-Sicairos M., Gollner M., Diaz A., Delivani P., Chacon M., Tolic IM., Zaburdaev V., Pfohl T.:
  Live cell X-ray imaging of autophagic vacuoles formation and chromatin dynamics in fission yeast
  In: Scientific Reports 7 (2017)
  ISSN: 2045-2322
  DOI: 10.1038/s41598-017-13175-9

2016

• Fitz V., Shin J., Ehrlich C., Farnung L., Cramer P., Zaburdaev V., Grill SW.:
  Nucleosomal arrangement affects single-molecule transcription dynamics
  In: Proceedings of the National Academy of Sciences of the United States of America 113 (2016), p. 12733-12738
  ISSN: 0027-8424
  DOI: 10.1073/pnas.1602764113
• Hilbert L., Zaburdaev V., Vastenhouw N.:
  Subnuclear Spatial Structuring of Chromatin and Polymerase II during Transcription Activation of the Zebrafish Zygotic Genome
  In: Biophysical Journal 110 (2016), p. 232A-233A
  ISSN: 0006-3495
• Iomin A., Zaburdaev V., Pfohl T.:
  Reaction front propagation of actin polymerization in a comb-reaction system
  In: Chaos Solitons & Fractals 92 (2016), p. 115-122
  ISSN: 0960-0779
  DOI: 10.1016/j.chaos.2016.09.011
• Munder MC., Midtvedt D., Franzmann T., Nueske E., Otto O., Herbig M., Ulbricht E., Mueller P., Taubenberger A., Maharana S., Malinovska L., Richter D., Guck J., Zaburdaev V., Alberti S.:
  A pH-driven transition of the cytoplasm from a fluid- to a solid-like state promotes entry into dormancy
  In: eLife 5 (2016)
  ISSN: 2050-084X
  DOI: 10.7554/eLife.09347
• Zaburdaev V., Fouxon I., Denisov S., Barkai E.:
  Superdiffusive Dispersals Impart the Geometry of Underlying Random Walks
  In: Physical Review Letters 117 (2016)
  ISSN: 0031-9007
  DOI: 10.1103/PhysRevLett.117.270601

2015

• Froemberg D., Schmiedeberg M., Barkai E., Zaburdaev V.:
  Asymptotic densities of ballistic Levy walks
  In: Physical Review E 91 (2015), Article No.: 022131
  ISSN: 2470-0045
  DOI: 10.1103/PhysRevE.91.022131
• Lin YT., Froemberg D., Huang W., Delivani P., Chacon M., Tolic IM., Juelicher F., Zaburdaev V.:
  Pulled Polymer Loops as a Model for the Alignment of Meiotic Chromosomes
  In: Physical Review Letters 115 (2015)
  ISSN: 0031-9007
  DOI: 10.1103/PhysRevLett.115.208102
• Munder MC., Midtvedt D., Franzmann TM., Nueske E., Malinovska L., Otto O., Ulbricht E., Zaburdaev V., Alberti S., Guck J.:
  A sol-gel transition of the cytoplasm driven by adaptive intracellular pH changes promotes entry into dormancy.
  In: Molecular Biology of the Cell 26 (2015)
  ISSN: 1059-1524
• Taktikos J., Lin YT., Stark H., Biais N., Zaburdaev V.:
  Pili-Induced Clustering of N-gonorrhoeae Bacteria
  In: PLoS ONE 10 (2015)
  ISSN: 1932-6203
  DOI: 10.1371/journal.pone.0137661
• Theves M., Taktikos J., Zaburdaev V., Stark H., Beta C.:
  Random walk patterns of a soil bacterium in open and confined environments
  In: EPL - Europhysics Letters 109 (2015)
  ISSN: 0295-5075
  DOI: 10.1209/0295-5075/109/28007
• Weber CA., Lin YT., Biais N., Zaburdaev V.:
  Formation and dissolution of bacterial colonies
  In: Physical Review E 92 (2015)
  ISSN: 1539-3755
  DOI: 10.1103/PhysRevE.92.032704
• Zaburdaev V., Denisov S., Klafter J.:
  Levy walks
  In: Reviews of Modern Physics 87 (2015), p. 483-530
  ISSN: 0034-6861
  DOI: 10.1103/RevModPhys.87.483

2014

• Zaburdaev V., Biais N., Schmiedeberg M., Eriksson J., Jonsson AB., Sheetz MP., Weitz DA.:
  Uncovering the Mechanism of Trapping and Cell Orientation during Neisseria gonorrhoeae Twitching Motility
  In: Biophysical Journal 107 (2014), p. 1523-1531
  ISSN: 0006-3495
  DOI: 10.1016/j.bpj.2014.07.061

2013

• Taktikos J., Stark H., Zaburdaev V.:
  How the Motility Pattern of Bacteria Affects Their Dispersal and Chemotaxis
  In: PLoS ONE 8 (2013)
  ISSN: 1932-6203
  DOI: 10.1371/journal.pone.0081936
• Theves M., Taktikos J., Zaburdaev V., Stark H., Beta C.:
  A Bacterial Swimmer with Two Alternating Speeds of Propagation
  In: Biophysical Journal 105 (2013), p. 1915-1924
  ISSN: 0006-3495
  DOI: 10.1016/j.bpj.2013.08.047
• Wilking JN., Zaburdaev V., De Volder M., Losick R., Brenner MP., Weitz DA.:
  Liquid transport facilitated by channels in Bacillus subtilis biofilms
  In: Proceedings of the National Academy of Sciences of the United States of America 110 (2013), p. 848-852
  ISSN: 0027-8424
  DOI: 10.1073/pnas.1216376110
• Zaburdaev V., Denisov S., Haenggi P.:
  Space-Time Velocity Correlation Function for Random Walks
  In: Physical Review Letters 110 (2013)
  ISSN: 0031-9007
  DOI: 10.1103/PhysRevLett.110.170604

2012

• Denisov SV., Zaburdaev V., Haenggi P.:
  Lévy walks with velocity fluctuations
  In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85 (2012), Article No.: 031148
  ISSN: 1550-2376
  DOI: 10.1103/PhysRevE.85.031148
• Eule S., Zaburdaev V., Friedrich R., Geisel T.:
  Langevin description of superdiffusive Lévy processes
  In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 86 (2012), Article No.: 041134
  ISSN: 1550-2376
  DOI: 10.1103/PhysRevE.86.041134
• Taktikos J., Zaburdaev V., Stark H.:
  Collective dynamics of model microorganisms with chemotactic signaling
  In: Physical Review E - Statistical, Nonlinear, and Soft Matter Physics 85 (2012), Article No.: 051901
  ISSN: 1550-2376
  DOI: 10.1103/PhysRevE.85.051901

2009

• Schmiedeberg M., Zaburdaev V., Stark H.:
  On moments and scaling regimes in anomalous random walks
  In: Journal of Statistical Mechanics-Theory and Experiment (2009)
  ISSN: 1742-5468
  DOI: 10.1088/1742-5468/2009/12/P12020

2008

• Zaburdaev V., Schmiedeberg M., Stark H.:
  Random walks with random velocities
  In: Physical Review E 78 (2008)
  ISSN: 2470-0045
  DOI: 10.1103/PhysRevE.78.011119