Di Ventura Lab


Int&in: a machine learning-based web server for active split site identification in inteins
M. Schmitz, J. B. Ballestin, J. Liang, F. Tomas, L. Freist, K. Voigt, B. Di Ventura, M. A. Öztürk
Protein Science, 2024

iNClusive: a database collecting useful information on non-canonical amino acids and their incorporation into proteins for easier genetic code expansion implementation
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

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

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

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

ReverseDock: a web server for blind docking of a single ligand to multiple protein targets using AutoDock Vina
F. Krause, K. Voigt, B. Di Ventura, M. A. Öztürk
Frontiers in Molecular Biosciences, 2023

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

Synthetic microbiology applications powered by light
D. Mazraeh, B. Di Ventura
Current Opinion in Microbiology, 2022

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

patcHwork: A user friendly pH sensitivity analysis web-server for protein sequences and structures.
M. Schmitz, A. Schultze, R. Vanags, K. Voigt, B. Di Ventura and M. A. Öztürk
Nucleic Acids Research, 2022

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

Deterministic lateral displacement microfluidic chip for minicell purification
A. Sherbaz, B. M. K. Konak, P. Pezeshkpour, B. Di Ventura, B. E. Rapp
Micromachines, 2022

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

The rise of molecular optogenetics
B. Di Ventura and W. Weber
Advanced Biology, 2021

Light express
G. Forlani and B. Di Ventura
Current Opinion in Systems Biology, 2021

finDr: A web server for in silico D-peptide ligand identification
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


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

Expanding the SiMPl plasmid toolbox for use with spectinomycin/streptomycin
N. Palanisamy, J. Ballestin Ballestin and B. Di Ventura
ACS Omega, 2021

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

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

A light way for nuclear cell biologists
G. Forlani and B. Di Ventura
The Journal of Biochemistry, 2020

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

Optogenetic control of nucleocytoplasmic protein transport
D. Weis and B. Di Ventura
Photoswitching Proteins: Methods and Protocols, Methods in Molecular Biology, 2020

C-terminal eYFP fusion impairs Escherichia coli MinE function
N. Palanisamy, M. A. Öztürk, E. B. Akmeric and B. Di Ventura
Open Biology, 2020

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

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

Context-dependent activity of A domains in the tyrocidine synthetase
A. Degen, F. Mayerthaler, H. D. Mootz and B. Di Ventura
Scientific Reports, 2019

Switchable inteins for conditional protein splicing 
B. Di Ventura and H.D. Mootz
Biological Chemistry, 2019

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

Optogenetic control of nuclear protein export
D. Niopek, P. Wehler, J. Roensch, R. Eils and B. Di Ventura
Nature Communications, 2016

Go in! Go out! Inducible control of nuclear localization
B. Di Ventura and B. Kuhlman
Current Opinion in Chemical Biology, 2016

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

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

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

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

Self-organized partitioning of dynamically localized proteins in bacterial cell division
B. Di Ventura and V. Sourjik
Molecular Systems Biology, 2011

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

From in vivo to in silico biology and back
B. Di Ventura, C. Lemerle, K. Michalodimitrakis and L. Serrano
Nature, 2006

Space as the final frontier in stochastic simulations of biological systems
C. Lemerle, B. Di Ventura and L. Serrano
FEBS Letters, 2005

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