Publications

Browse our scientific output, from foundational promoter mapping studies to recent advances in AI-driven gene regulation and engineering.

2025

Totlani K, Khan EA, Ahmed H, Lale R, Stokke BT. Integrated microdroplet workflow for high-throughput cell-free transcription in double emulsion picoreactors. bioRxiv
Khan EA, Rückert-Reed C, Dahiya GS, Tietze L, Fages-Lartaud M, Busche T, Kalinowski J, Shingler V, Lale R. High-resolution mapping of Sigma Factor DNA Binding Sequences using Artificial Promoters, RNA aptamers and Deep Sequencing. Nucleic Acids Research.
Blanch-Asensio M, Tadimarri VS, Martinez RP, Dahiya GS, Lale R, Sankaran S. Encapsulation-enhanced switchable protein release from engineered probiotic lactobacilli. Journal of Controlled Release.
Wong CFA, Zhang S, Tietze L , Dahiya GS , Lale R. Engineering Artificial 5' Regulatory Sequences for Thermostable Protein Expression in the Extremophile Thermus thermophilus. bioRxiv. (Accepted in OUP Synthetic Biology)

2023

Dahiya GS, Bakken TI, Fages-Lartaud M, Lale R. From Context to Code: Rational De Novo DNA Design and Predicting Cross-Species DNA Functionality Using Deep Learning Transformer Models. bioRxiv.
Dannert C, Mardal I, Lale R, Stokke BT, Dias RS. DNA condensation by peptide-conjugated PAMAM dendrimers. Influence of peptide charge. ACS Omega.

2022

Lale R, Tietze L, Fages-Lartaud M, Nesje J, Onsager I, Engelhardt K, Wong CFA, Akan M, Hummel N, Kalinowski J, Rückert C, Hohmann-Marriott MF. A universal approach to gene expression engineering. Synthetic Biology.
Fages-Lartaud M, Prone W, Mueller Y, Lale R. Method for engineering artificial bidirectional promoters.) Research Square.
Fages-Lartaud M, Tietze L, Elie F, Lale R, Hohmann-Marriott MF. mCherry contains a fluorescent protein isoform that interferes with its reporter function. Frontiers in Bioengineering and Biotechnology - Synthetic Biology.
Tietze L, Mangold A, Hoff M, Lale R. Identification and cross-characterisation of artificial promoters and 5' untranslated regions in Vibrio natriegens. Frontiers in Bioengineering and Biotechnology - Synthetic Biology.

2021

Wong CFA, Bhujbal SV, van Vliet L, Guo C, Sletmoen M, Stokke BT, Hollfelder F, Lale R. A Titratable Cell Lysis-on-Demand System for Droplet-Compartmentalised Ultrahigh-Throughput Screening in Functional Metagenomics and Directed Evolution. ACS Synthetic Biology.
Tietze L, Lale R. Importance of the 5′ Regulatory Region to Bacterial Synthetic Biology Applications. Microbial Biotechnology.

2020

Bhujbal SV, Dekov M, Ottesen V, Dunker K, Lale R, Sletmoen M. Effect of design geometry, exposure energy, cytophilic molecules, cell type and load in fabrication of single-cell arrays using micro-contact printing. Scientific Reports.
Le SB, Onsager I, Lorentzen JA, Lale R. Dual UTR–A novel 5' untranslated region design for synthetic biology applications. Synthetic Biology.

2019

Le SB, Onsager I, Lorentzen JA, Lale R. Dual UTR–A novel 5' untranslated region design for synthetic biology applications. bioRxiv.
Lale R, Tietze L, Nesje J, Onsager I, Engelhardt K, Wong CFA, Akan M, Hummel N, Kalinowski J, Rückert C, Hohmann-Marriott MF. A universal method for gene expression engineering. bioRxiv.

2018

Schneider O, Simic N, Aachmann F, Rückert C, Kristiansen K, Kalinowski J, Jiang Y, Wang L, Jiang C, Lale R, Zotchev S. Genome Mining of Streptomyces sp. YIM 130001 Isolated from Lichen Affords New Thiopeptide Antibiotic. Frontiers in Microbiology.

2017

Ramisetty SK, Langlette P, Lale R, Dias RdS. In vitro studies of DNA condensation by bridging protein in a crowding environment. International Journal of Biological Macromolecules.
Vogel AIM, Lale R, Hohmann-Marriott MF. Streamlining recombination-mediated genetic engineering by validating three neutral integration sites in Synechococcus sp. PCC 7002. Journal of Biological Engineering.
Lewin A, Lale R, Wentzel A. Expression Platforms for Functional Metagenomics – Emerging technology options beyond Escherichia coli. Functional Metagenomics: Tools and Applications. Springer.

2016

Beal J, Haddock-Angelli T, Gershater M, de Mora K, Lizarazo M, Hollenhorst J, et al. Reproducibility of fluorescent expression from engineered biological constructs in E. coli. PLOS ONE.
Arnfinnsdottir, NB., Bjørkøy, A., Lale, R., Sletmoen, M. Heterogeneity in GFP expression in isogenic populations of P. putida KT2440 investigated using flow cytometry and bacterial microarrays. RSC Advances.
Moghadam MM, Albersmeier A,Winkler A, Cimmino L, Rise K, Hohmann-Marriott FM, Kalinowski J, Rückert C, Wentzel A, Lale, R. Isolation and genome sequencing of four Arctic marine Psychrobacter strains exhibiting multicopper oxidase activity. BMC Genomics.

2015

Bjerga, GE, Lale, R., Williamson, A. Engineering low-temperature expression systems for heterologous expression of cold-adapted enzymes. Bioengineered.
Arnfinnsdottir, NB., Ottesen, V., Lale, R., Sletmoen, M. The design of simple bacterial microarrays. Development towards immobilizing single living bacteria on predefined micro-sized spots on patterned surfaces. PLOS ONE.

2014

Petrov, V., Balasubramaniam, S., Lale, R., Moltchanov, D., Lio’, P., Koucheryavy, Y. Forward and Reverse Coding for Chromosome Transfer in Bacterial Nanonetworks. Nano Communication Networks.
Strand, TA., Lale, R., Degnes, KF., Lando, M. and Valla, S. A new and improved host-independent plasmid system for RK2-based conjugal transfer. PLOS ONE.
DNA Cloning and Assembly Methods. Methods in Molecular Biology, editors Rahmi Lale and Svein Valla. Volume 1116, XI, 303 p. Springer Protocols, Humana Press.
Røkke, G., Korvald, E., Pahr, J., Øyås, O., and Lale, R. BioBrick assembly standards and techniques and associated software tools. DNA Cloning and Assembly Methods. Methods in Molecular Biology, editors Lale, R. and Valla, S. Volume 1116, 2014, pp 1-24 Springer Protocols, Humana Press.

2013

Zwick, F., Lale, R. and Valla, S. Regulation of the expression level of transcription factor XylS reveals new functional insight into its induction mechanism at the Pm promoter. BMC Microbiology. 13: 262
Zwick, F., Lale, R. and Valla, S. Combinatorial engineering for heterologous gene expression. Bioengineered.
Balzer, S., Kucharova, V., Megerle, J., Lale, R., Brautaset, T., Valla, S. A comparative analysis of the properties of regulated promoter systems commonly used for recombinant gene expression in Escherichia coli. Microbial Cell Factories, 12:26.

2012

Zwick, F., Lale, R. and Valla, S. Strong stimulation of recombinant protein production in Escherichia coli by combining stimulatory expression control elements in the expression cassette. Microbial Cell Factories, 11:133.
Almaas, E., Bruheim, P., Lale, R. and Valla, S. Dynamics and robustness of metabolic networks: A systems biology review of Escherichia coli metabolism. Systems Microbiology: Current Topics and Applications. ISBN: 978-1-908230-02-7.

2011

Aakvik, T., Lale, R., Liles, M. and Valla, S. Metagenomic libraries for functional screening, Ch 22. Handbook of Molecular Microbial Ecology I: Metagenomics and Complementary Approaches. Ed. de Bruijn, F.J.
Lale, R., Brautaset, T.and Valla, S. Broad-host-range plasmid vectors for gene expression in bacteria. Methods in Molecular Biology. 765, Part 3, 327-343.
Lale, R., Berg, L., Stüttgen, F., Netzer, R., Stafsnes, M., Brautaset, T., Aune, T.E.V. and Valla. S. Continuous control of the flow in biochemical pathways through 5'-UTR sequence modifications in mRNA expressed from the broad-host-range Pm promoter. Applied and Environmental Microbiology. 77: 2648-2655.

2010

Aune, T. E. V., Bakke, I., Drabløs, F., Lale, R., Brautaset, T. and Valla, S. Directed evolution of the transcription factor XylS for development of improved expression systems. Microbial Biotechnology. 3:1, 38–47.

2009

Berg, L., Lale, R., Bakke, I., Burroughs, N. and Valla, S. The expression of recombinant genes in Escherichia coli can be strongly stimulated at the transcript production level by mutating the DNA-region corresponding to the 5'-untranslated part of mRNA. Microbial Biotechnology. 2(3), 379-389.
Brautaset, T., Lale, R. and Valla, S. Positively regulated bacterial expression systems. Microbial Biotechnology. 2 (1), 15-30.

2008

Bar, N. S. and Lale, R. Modeling and control of the protein synthesis process in eukaryotic cells. 47th IEEE Proceedings: Conference on Decision and Control (CDC) 179-184.