Hernández-Arriaga AM, Campano C, Rivero-Buceta V, Prieto MA. 2022. When microbial biotechnology meets material engineering. Microbial Biotechnology,


Vigasova D, Nemergut M, Liskova B, Damborsky J. 2021 Multi-pathogen infections and Alzheimer's disease. Microbial Cell Factories,

Khan RT, Musil M, Stourac J, Damborsky J, Bednar D. 2021. Fully Automated Ancestral Sequence Reconstruction using FireProtASR. Current Protocols,

Orsi E, Claassens NJ, Nikel PI, Lindner SN. 2021. Growth-coupled selection of synthetic modules to accelerate cell factory development. Nature Communications,

Griffith CM, Walvekar AS, Linster CL. 2021. Approaches for completing metabolic networks through metabolite damage and repair discovery. Current Opinion in Systems Biology,

Cros A, Alfaro-Espinoza G, De Maria A, Wirth NT, Nikel PI. 2021. Synthetic metabolism for biohalogenation. Current Opinion in Biotechnology,

Marques SM, Planas-Iglesias J, Damborsky J. 2021. Web-based tools for computational enzyme design. Current Opinion in Structural Biology,

Musil M, Khan RT, Beier A, Stourac J, Konegger H, Damborsky J, Bednar D. 2021. FireProtASR: A Web Server for Fully Automated Ancestral Sequence Reconstruction. Briefings in Bioinformatics,

Hon J, Marusiak M, Martinek T, Kunka A, Zendulka J, Bednar D, Damborsky J. 2021. SoluProt: Prediction of Soluble Protein Expression in Escherichia coli. Bioinformatics,

Markova K, Kunka A, Chmelova K, Havlasek M, Babkova P, Marques SM, Vasina M, Planas-Iglesias J, Chaloupkova R, Bednar D, Prokop Z, Damborsky J, and Marek M. 2021. Computational Enzyme Stabilization Can Affect Folding Energy Landscapes and Lead to Catalytically Enhanced Domain-Swapped Dimers. ACS Catalysis,

Pinto GP, Vavra O, Marques SM, Filipovic J, Bednar D, Damborsky J. 2021. Screening of world approved drugs against highly dynamical spike glycoprotein of SARS-CoV-2 using CaverDock and machine learning. Computational and Structural Biotechnology Journal,

Pérez-Pantoja D, Nikel PI, Chavarría M, de Lorenzo V. 2021. Transcriptional control of 2,4-dinitrotoluene degradation in Burkholderia sp. R34 bears a regulatory patch that eases pathway evolution. Environmental Microbiology,


Mezzina MP, Manoli MT, Prieto MA, Nikel Pl. 2020. Engineering Native and Synthetic Pathways in Pseudomonas putida for the Production of Tailored Polyhydroxyalkanoates. Biotechnology Journal,

Lammens EM, Nikel PI, Lavigne R. 2020. Exploring the synthetic biology potential of bacteriophages for engineering non-model bacteria. Nature Communications,

Dockalova V, Sanchez-Carnerero EM, Dunajova Z, Palao E, Slanska M, Buryska T, Damborsky J, Klán P, Prokop Z. 2020. Fluorescent substrates for haloalkane dehalogenases: Novel probes for mechanistic studies and protein labeling. Computational and Structural Biotechnology Journal,

Nieto-Domínguez M, Nikel PI. Markova K, Chmelova K, Marques SM, Carpentier P, Bednar D, Damborsky J, Marek M. 2020. Decoding the intricate network of molecular interactions of a hyperstable engineered biocatalyst. Chemical Science,

Marek M, Chaloupkova R, Prudnikova T, Sato Y, Rezacova P, Nagata Y, Kuta Smatanova I, Damborsky J. 2020. Structural and catalytic effects of surface loop-helix transplantation within haloalkane dehalogenase family. Computational and Structural Biotechnology Journal,

Chmelova K, Sebestova E, Liskova V, Beier A, Bednar D, Prokop Z, Chaloupkova R, Damborsky J. A 2020. Haloalkane Dehalogenase from Saccharomonospora viridis Strain DSM 43017, a Compost Bacterium with Unusual Catalytic Residues, Unique (S)-Enantiopreference, and High Thermostability. Applied and Environmental Microbiology,

Markakis K, Lowe PT, Davison-Gates L, O'Hagan D, Rosser SJ, Elfick A. 2020. An Engineered E. coli Strain for Direct in Vivo Fluorination. ChemBioChem,

Calero P, Volke DC, Lowe PT et al. 2020. A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida. Nature Communications,

Nieto-Domínguez M, Nikel PI. 2020. Intersecting Xenobiology and Neometabolism To Bring Novel Chemistries to Life. ChemBioChem,

Babkova P, Dunajova Z, Chaloupkova R, Damborsky J, Bednar D, Marek M. 2020. Structures of hyperstable ancestral haloalkane dehalogenases show restricted conformational dynamics. Computational and Structural Biotechnology Journal,

Batianis C, Kozaeva E, Damalas SG, Martín‐Pascual M, Volke DC, Nikel PI, Martins dos Santos VAP. 2020. An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida. Microbial Biotechnology,

Schmidt M, Budisa N. 2020. Alternative Biofacts – Life as we don’t (yet) know it.
Chapter in the book "Art as We Don’t Know It". PDF

Volke DC, Friis L, Wirth NT, Turlin J, Nikel PI. 2020. Synthetic control of plasmid replication enables target- and self-curing of vectors and expedites genome engineering of Pseudomonas putida. Metabolic Engineering Communications,

Vavra O, Filipovic J, Plhak J, Bednar D, Marques SM, Brezovsky J, Stourac J, Matyska L, Damborsky J. 2019. CaverDock: a molecular docking-based tool to analyse ligand transport through protein tunnels and channels. Bioinformatics,

Beier A, Damborsky J, Prokop Z. 2019. Transhalogenation Catalysed by Haloalkane Dehalogenases Engineered to Stop Natural Pathway at Intermediate. Advanced Synthesis and Catalysis,

Demko M, Chrást L, Dvořák P, Damborský J, Šafránek D. 2019. Computational Modelling of Metabolic Burden and Substrate Toxicity in Escherichia coli Carrying a Synthetic Metabolic Pathway. Microorganisms.

Arce‐Rodríguez A, Volke DC,  Bense S,  Häussler S,  Nike PI. 2019. Non‐invasive, ratiometric determination of intracellular pH in Pseudomonas species using a novel genetically encoded indicator. Microbial Biotechnology Vol.12(4): 799-813.

 Evolutionary Approaches for Engineering Industrially Relevant Phenotypes in Bacterial Cell Factories. Biotechnology Journal.

Wirth NT, Kozaeva E, Nikel PI, 2019. Accelerated genome engineering of Pseudomonas putida by I‐SceI―mediated recombination and CRISPR‐Cas9 counterselection.  Microbial Biotechnology.
Volke DC, Turlin J, Mol V, Nikel PI, 2019. Physical decoupling of XylS/Pm regulatory elements and conditional proteolysis enable precise control of gene expression in Pseudomonas putida. Microbial Biotechnology.

Martinelli L, Nikel PI. 2019. Breaking the state‐of‐the‐art in the chemical industry with new‐to‐Nature products via synthetic microbiology. Microbial Biotechnology. Vol. 12(2): 187-190.