Int&in: a machine learning-based web server for active split site identification in inteins
https://intein.biologie.uni-freiburg.de/
M. Schmitz, J. B. Ballestin, J. Liang, F. Tomas, L. Freist, K. Voigt, B. Di Ventura, M. A. Öztürk
Protein Science, 2024
https://doi.org/10.1002/pro.4985
iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation
https://non-canonical-aas.biologie.uni-freiburg.de/
L.-S. Icking, A. M. Riedlberger, F. Krause, J. Widder, A. S. Frederiksen, F. Stockert, M. Spädt, N. Edel, D. Armbruster, G. Forlani, S. Franchini, P. Kaas, B. M. Kırpat Konak, F. Krier, M. Lefebvre, D. Mazraeh, J. Ranniger, J. Gerstenecker, P. Gescher, K. Voigt, P. Salavei, N. Gensch, B. Di Ventura, M. A. Öztürk
Nucleic Acids Research, 2023
https://doi.org/10.1093/nar/gkad1090
Fabrication of embedded microfluidic chips with single micron resolution using two-photon lithography
M. Luitz, B. M. Kırpat Konak, A. Sherbaz, R. Prediger, N. Nekoonam, B. Di Ventura, F. Kotz-Helmer, B. E. Rapp
Advanced Materials Technologies, 2023
https://doi.org/10.1002/admt.202300667
Requirements for mammalian promoters to decode transcription factor dynamics
E. B. Antwi, Y. Marrakchi, Ö. Cicek, T. Brox, B. Di Ventura
Nucleic Acids Research, 2023
https://doi.org/10.1093/nar/gkad273
Identification of functional Npu DnaE and gp41-1 inteins split in three fragments
D. Weis, N. Palanisamy, J.B. Ballestin, M.A. Öztürk, B. Di Ventura
bioRxiv, 2023
https://doi.org/10.1101/2023.01.30.526203
ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina
https://reversedock.biologie.uni-freiburg.de/
F. Krause, K. Voigt, B. Di Ventura, M. A. Öztürk
Frontiers in Molecular Biosciences, 2023
https://doi.org/10.3389/fmolb.2023.1243970
Analysis of slow-cycling variants of the light-inducible nuclear protein export system LEXY in mammalian cells
G. Forlani, E. B. Antwi, D. Weis, M. A. Öztürk, B. A. W. Queck, D. Brecht, B. Di Ventura
ACS Synthetic Biology, 2022
https://doi.org/10.1021/acssynbio.2c00232
Synthetic microbiology applications powered by light
D. Mazraeh, B. Di Ventura
Current Opinion in Microbiology, 2022
https://doi.org/10.1016/j.mib.2022.102158
Temporal control of the integrated stress response by a stochastic molecular switch
P. Klein, S. M. Kallenbeger, H. Rorth, K. Roth, T. B. N. Ly-Hartig, V. Magg, J. Aleš, S. R. Talemi, Y. Qiang, S. Wolf, O. Oleksiuk, R. Kurilov, B. Di Ventura, R. Bartenschlager, R. Eils, K. Rohr, F. A. Hamprecht, T. Höfer, O. T. Fackler, G. Stoecklin, A. Ruggieri
Science Advances, 2022
https://doi.org/10.1126/sciadv.abk2022
patcHwork: A user friendly pH sensitivity analysis web-server for protein sequences and structures.
https://patchwork.biologie.uni-freiburg.de/index.php
M. Schmitz, A. Schultze, R. Vanags, K. Voigt, B. Di Ventura and M. A. Öztürk
Nucleic Acids Research, 2022
https://doi.org/10.1093/nar/gkac252
Experimental characterization of in silico red-shift predicted iLOVL470T/Q489K and iLOVV392K/F410V/A426S mutants
P. Wehler, D. Armbruster, A. Günter, E. Schleicher B. Di Ventura, M. A. Öztürk
ACS Omega, 2022
https://doi.org/10.1021/acsomega.2c01283
Deterministic lateral displacement microfluidic chip for minicell purification
A. Sherbaz, B. M. K. Konak, P. Pezeshkpour, B. Di Ventura, B. E. Rapp
Micromachines, 2022
https://doi.org/10.3390/mi13030365
Synthetic biology landscape and community in Germany
N. Krink, A. Löchner, H. Cooper, C. Beisel, B. Di Ventura, German Association for Synthetic Biology – GASB e.V
Biotechnology Notes, 2021
https://doi.org/10.1016/j.biotno.2021.12.001
The rise of molecular optogenetics
B. Di Ventura and W. Weber
Advanced Biology, 2021
https://doi.org/10.1002/adbi.202100776
Light express
G. Forlani and B. Di Ventura
Current Opinion in Systems Biology, 2021
https://doi.org/10.1016/j.coisb.2021.100356
finDr: A web server for in silico D-peptide ligand identification
https://findr.biologie.uni-freiburg.de/
H. Engel, F. Guischard, F. Krause, J. Nandy, P. Kaas, N. Höfflin, M. Köhn, N. Kilb, K. Voigt, S. Wolf, T. Aslan, F. Baezner, S. Hahne, C. Ruckes, J. Weygant, A. Zinina, E. B. Akmeriç, E. B. Antwi, D. Dombrovskij, P. Franke, K. L. Lesch, N. Vesper, D. Weis, N. Gensch, B. Di Ventura and M. A. Öztürk
Synthetic and Systems Biotechnology, 2021
https://doi.org/10.1016/j.synbio.2021.11.004
A novel nanobody precisely visualizes phosphorylated histone H2AX in living cancer cells under drug-induced replication stress
E. Moeglin, D. Desplancq, A. Stoessel, C. Massute, J. Ranniger, A. G. McEwen, G. Zeder-Lutz, M. Oulad-Abdelghani, M. Chiper, P. Lafaye, B. Di Ventura, P. Didier, A. Poterszman and E. Weiss
Cancers, 2021
https://www.mdpi.com/2072-6694/13/13/3317
Expanding the SiMPl plasmid toolbox for use with spectinomycin/streptomycin
N. Palanisamy, J. Ballestin Ballestin and B. Di Ventura
ACS Omega, 2021
https://doi.org/10.1021/acsomega.1c00649
The active repertoire of Escherichia coli peptidoglycan amidases varies with physiochemical environment
E. Mueller, A. G. Iken, M. A. Öztürk, M. Winkle, M. Schmitz, W. Vollmer, B. Di Ventura and P. A. Levin
Molecular Microbiology, 2021
https://doi.org/10.1111/mmi.14711
Engineering AraC to make it responsive to light instead of arabinose
E. Romano, A. Baumschlager, E. B. Akmeriç, N. Palanisamy, M. Houmani, G. Schmidt, M. A. Öztürk, L. Ernst, M. Khammash and B. Di Ventura
Nature Chemical Biology, 2021
https://doi.org/10.1038/s41589-021-00787-6
A light way for nuclear cell biologists
G. Forlani and B. Di Ventura
The Journal of Biochemistry, 2020
doi:10.1093/jb/mvaa139
Recovering the imperfect: Cell Segmentation in the presence of dynamically localized proteins
Ö. Cicek, Y. Marrakchi, E. B. Antwi, B. Di Ventura and T. Brox
Interpretable and Annotation-Efficient Learning for Medical Image Computing, 2020
https://doi.org/10.1007/978-3-030-61166-8_9
Optogenetic control of nucleocytoplasmic protein transport
D. Weis and B. Di Ventura
Photoswitching Proteins: Methods and Protocols, Methods in Molecular Biology, 2020
https://doi.org/10.1007/978-1-0716-0755-8_8
C-terminal eYFP fusion impairs Escherichia coli MinE function
N. Palanisamy, M. A. Öztürk, E. B. Akmeric and B. Di Ventura
Open Biology, 2020
https://doi.org/10.1098/rsob.200010
Split intein-mediated selection of cells containing two plasmids using a single antibiotic
N. Palanisamy, A. Degen, A. Morath, J. Ballestin Ballestin, C. Juraske, M. A. Öztürk, G. A. Sprenger, J. W. Youn, W. W. Schamel and B. Di Ventura
Nature Communications, 2019
doi:10.1038/s41467-019-12911-1
Optogenetic repressors of gene expression in yeasts using light-controlled nuclear localization
S. H. Geller, E. B. Antwi, B. Di Ventura and M. N. McClean
Cellular and Molecular Bioengineering, 2019
doi:10.1007/s12195-019-00598-9
Context-dependent activity of A domains in the tyrocidine synthetase
A. Degen, F. Mayerthaler, H. D. Mootz and B. Di Ventura
Scientific Reports, 2019
doi:10.1038/s41598-019-41492-8
Switchable inteins for conditional protein splicing
B. Di Ventura and H.D. Mootz
Biological Chemistry, 2019
https://doi.org/10.1515/hsz-2018-0309
Optogenetic control of nuclear protein import in living cells using Light-Inducible Nuclear Localization Signals (LINuS)
P. Wehler, D. Niopek, R. Eils and B. Di Ventura
Current Protocols in Chemical Biology, 2016
https://doi.org/10.1002/cpch.4
Optogenetic control of nuclear protein export
D. Niopek, P. Wehler, J. Roensch, R. Eils and B. Di Ventura
Nature Communications, 2016
doi:10.1038/ncomms10624
Go in! Go out! Inducible control of nuclear localization
B. Di Ventura and B. Kuhlman
Current Opinion in Chemical Biology, 2016
doi:10.1016/j.cbpa.2016.06.009
Backbone circularization of Bacillus subtilis family 11 xylanase increases its thermostability and its resistance against aggregation
M. C. Waldhauer, S. N. Schmitz, C. Ahlmann-Eltze, J. G. Gleixner, C. C. Schmelas, A. G. Huhn, C. Bunne, M. Buscher, M. Horn, N. Klughammer,J. Kreft, E. Schafer, P. A. Bayer, S. G. Kramer, J. Neugebauer, P. Wehler, M. P. Mayer, R. Eils and B. Di Ventura
Molecular BioSystems, 2015
doi:10.1039/c5mb00341e
Engineering light-inducible nuclear localization signals for precise spatiotemporal control of protein dynamics in living cells
D. Niopek, D. Benzinger, J. Roensch, T. Draebing, P. Wehler, R. Eils and B. Di Ventura
Nature Communications, 2014
doi:10.1038/ncomms5404
Creating functional engineered variants of the single-module non-ribosomal peptide synthetase IndC by T domain exchange
R. Beer, K. Herbst, N. Ignatiadis, I. Kats, L. Adlung, H. Meyer, D. Niopek, T. Christiansen, F. Georgi, N. Kurzawa, J. Meichsner, S. Rabe, A. Riedel, J. Sachs, J. Schessner, F. Schmidt, P. Walch, K. Niopek, T. Heinemann, R. Eils and B. Di Ventura
Molecular BioSystems, 2014
doi:10.1039/c3mb70594c
Chromosome segregation by the Escherichia coli Min system
B. Di Ventura, B. Knecht, H. Andreas, W. J. Godinez, M. Fritsche, K. Rohr, W. Nickel, D. W. Heermann and V. Sourjik
Molecular Systems Biology, 2013
https://doi.org/10.1038/msb.2013.44
Self-organized partitioning of dynamically localized proteins in bacterial cell division
B. Di Ventura and V. Sourjik
Molecular Systems Biology, 2011
doi:10.1038/msb.2010.111
Reconstitution of Mdm2-dependent post-translational modifications of p53 in yeast
B. Di Ventura, C. Funaya, C. Antony, M. Knop and L. Serrano
PLoS One, 2008
https://doi.org/10.1371/journal.pone.0001507
From in vivo to in silico biology and back
B. Di Ventura, C. Lemerle, K. Michalodimitrakis and L. Serrano
Nature, 2006
doi:10.1038/nature05127
Space as the final frontier in stochastic simulations of biological systems
C. Lemerle, B. Di Ventura and L. Serrano
FEBS Letters, 2005
doi:10.1016/j.febslet.2005.02.009
SmartCell,a framework to simulate cellular processes that combines stochastic approximation with diffusion and localisation: analysis of simple networks
M. Ander, P. Beltrao, B. Di Ventura, J. Ferkinghoff-Borg, M. Foglierini,A. Kaplan, C. Lemerle, I. Tomas-Oliveira and L. Serrano
Systematic Biology, 2004
https://doi.org/10.1049/sb:20045017