Rodrigo G, Prakash S, Cordero T, Kushwaha M and Jaramillo A "Functionalization of an antisense small RNA", 2016 428(5), pp 889-892, DOI: 10.1016/j.jmb.2015.12.022


Groher F and Suess B "In vitro selection of antibiotic-binding aptamers", Methods, 2016, 106 pp 42-50, DOI: 10.1016/j.ymeth.2016.05.008


Kushwaha M, Rostain W, Prakash S, Duncan JN and Jaramillo A "Using RNA as Molecular Code for Programming Cellular Function", ACS Synthetic Biology, 2016, 5(8), pp 795-809, DOI: 10.1021/acssynbio.5b00297


Skjoedt ML, Snoek T, Kildegaard KR, Arsovska D, Eichenberger M, Goedeche TJ, Rajkumar AS, Zhang J, Kristensen M, Lehka BJ, Siedler S, Borodina I, Jensen MK and Keasling JD "Engineering prokaryotic transcriptional activators as metabolite biosensors in yeast" Nature Chemical Biology, 2016, vol 12 pp 951-958, DOI: 10.1013/nchembio.2177



Eichenberger M, Lehka BJ, Folloy C, Fisher D, Martens S, Simón E and Naesby M "Metabolic engineering of saccharomyces cerevisiae for de novo production of dihydrochalcores with known antioxidant, antidiabetic and sweet tasting properties", Metabolic Engineering, 2015, DOI: 10.1016/j.ymben.2016.10.019


Sommer MOA "Advancing gut microbiome research using cultivtation", Current Opinion in Microbiology, 2015 Vol 27 pp 127-132 DOI: 10.1016/j.mib.2015.08.004


Bonde MR, Kosuri S, Genee HJ, Sarup-Lytzen K, Church GM, Sommer MOA and Wang H "Direct Mutagenesis of thousands of genomic targets using microarray-derived oligonucleotides" ACS Synthetic Biology, 2015, 4 (1) pp 17-22, DOI: 10.1021/sb5001565


Genee HJ, Bali AP, Petersen SD, Sielder S, Bonde MT, Gronenberg LS, Kristensen M, Harrison SJ, Sommer MOA "Functional mining of transporters using synthetic selection" Nature Chemical Biology - DOI: 10.1038/nchembio.2189


Sommer MOAS, Suess B "(Meta-)genome míning for new ribo-regulators" Science Magazine, 352 pp 144-145, 2016, DOI: 10.1126/science. aaf6189


Klausen MS, Sommer MOAS "Principles of Systems Biology, No 2", Cell systems, P 60, 2016


Sommer MOA, "Voices of Biotech" Nature Biotechnology, V.34 NO 3 P. 273 2016, DOI: 10.1038/nbt.3502


Bonde MT, Pedersen M, Klausen MS, Jensen SI, Wulff T, Harrison S, Nielsen AT, Herrgard MJ, Sommer MOAS "Predictable tuning of protein expression in bacteria", Nature Methods, 2016, DOI: 10.1038/NMETH.3727


Ronda C, Pedersen LE, Sommer MOA, Toftgaard Nielsen A#, "CRMAGE: CRISPR Optimized MAGE Recombineering" Scientic Reports, 2016, DOI: 10.1038/srep19452


Rugbjerg P, Genee HJ, Jensen K, Sarup-Lytzen K and Sommer MOA*, "Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals", ACS SyntheticBiology, 2016, DOI: 10.1021/acssynbio.5b00213


Lennen R, Nielsson W, Pedersen M, Bonde MT, Luo H, Herrgard M, Sommer MOA#, "Transient overexpression of DNA adenine methylase enables efficient and mobile genome engineering with reduced off-target effects", Nucleic Acids Research, 2015, DOI: 10.1093/nar/gkv1090


Berens C, Groher F and Suess B, "RNA aptamers as genetic control devices:The potential of riboswitches as synthetic elements for regulating gene expression", Biotechnology Journal, 2015,Vol 10, No 2, 246-257. DOI: 10.1002/biot.201300498


Rodrigo G and Jaramillo A, "RiboMaker: computational design of conformation-based riboregulation", Bioinformatics Vol 30 No 17 2014 pages 2508-2510. DOI: 10.1093/bioinformatics/btu335


Shen S, Rodrigo G, Prakash S, Majer E, Landrain T E, Kirov B, Daros J-A and Jaramillo A, "Dynamic signal processing by ribozyme-mediated RNA Circuits to control gene expression", Nucleic Acids Research, 2015, Vol 43, No 10, pages: 5158-517. DOI: 10.1093/nar/gkv287


Hassall J, MacDonald P, Cordero T, Rostain W and Jaramillo A, "Design and Characterization of Topological Small RNAs", Methods and Protocols, Methods in Molecular Biology,2015, Vol 1316, DOI: 10.1007/978.1.4939.2730.2


van der Helm E, Geertz-Hansen HM, Genee HJ, Malla S and Sommer MOA, "deFUME: Dynamic exploration

of functional metagenomic sequencing data", BioMed Central Research Notes, 2015, Vol 8, No 1,DOI: 10.1186/s131104-015-1281-y


Rugbjerg P, Myling-Petersen N, Sommer MOA, "Flexible metabolic pathway construction using modular and divisible selection gene regulators", Metabolic Engineering, 2015 doi: 10.1016/j.ymben.2015.08.004


Rugbjerg P, Knuf C, Förster J, Sommer MOA, "Recombination-stable multimeric green fluorescent protein for characterization of weak promoter outputs in Saccharomyces cerevisiae", FEMS Yeast Research, 2015, DOI: 10.1093/femsyr/fov085


Vogel M, Suess B, "Label-Free Determination of the Dissociation Constant of Small Molecule-Aptamer Interaction by Isothermal

Titration Calorimetry", Methods in Molecular Biology, 2016, vol 1380 pages 113-125, DOI: 10.1007/978-1-4939-3197-2


Schmidt A, Kachonowski K, Vedelaar S, Ahrne E, Volkmer B, Callipo L, Knoops K, Bauer M, Aebersold A, Heinemann M, "The quantitative and condition-dependent Escherichia coli proteome", Nature Biotechnology, DOI: 10.1038/nbt.3418


Schneider C, Suess B, "Identification of RNA aptamers with riboswitching properties", Elsevier, DOI: 10.1016/j.ymeth.2015.12.001


Cardinale S, Tueros F G, Sommer MOAS, "Genetic-Metabolic Coupling for Targeted Metabolic Engineering", Cell reports, DOI: 10.1016/j.cvelrep.2017.07.015


Lehning CE, Siedler S, Ellabaan MHH, Sommer MOAS "Assessing glycolytic flux alterations resulting from gentic perturbations in E-coli using a biosensor", Metabolic Engineering, DOI: 10.1016/j.ymben.2017.07.002


Siedler S, Khantri NK, Zsohar A, Kjaerboelling I, Vogt M, Hammar P, Nielsen CF, Marienhagen J, Sommer MOAS Joensson NK

"Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production", ACS Synthetic Biology, DOI: 10.1021/acssynbio.7b00009


Lheka BJ, Eichenberg M, Bjoern-Yoshimoto EW, Vanegas KG, Juijs N, Jensen NB, Dyekjaer JD, Jenssen H, Simon E, Naesby M, “Improving heterologous production of phenylpropanoids in Saccharomyces cerevisiae by tackling an unwanted side reaction of Tsc13, an endogenous double bond reductase”, FEM Yeast Research, DOI: 10.1093/femsyr/fox004


Rodrigo G, Majer E, Praksh S, Daros JA, Jaramillo A, Poyatos JF “Exploring the Dynamics and Mutational Landscape of Riboregulation with a Minimal Synthetic Circuit in Living Cells”, Biophysical Journal, DOI: 10.1016/j.bpj.2015.07.021


Broedel AK, Jaramillo, A Isalan M “Intracellular directed evolution of proteins from combinatorial libraries based on conditional phage replication”, Nature Protocols, DOI: 10.1038/nprot.2017.084


Broedel AK, Jaramillo A, Isalan M “Engineering orthogonal dual transcription factors for multi-input synthetic promoters", Nature Communications, DOI: 10.1038/ncomms13858


Schneider C, Bronstein L, Diemer J, Koeppl H, Suess B “ROC’n’Ribo: Characterizing a Riboswitching Expression System by Modeling Single-Cell Data”, ACS Synthetic Biology, DOI: 10.1021/acssynbio.6b00322


Rugbjerg P, Myling-Petersen N, Porse A, Sarup-Lytzen K, Sommer MOA “Diverse genetic error modes constrain large-scale bio-based production”, Nature Communications, DOI: 10.1038/s41467-018-03232-w


Rugbjerg P, Sarup-Lytzen K, Nagy M, Sommer MOA “Synthetic addiction extends the productive life time of engineered Escherichia coli populations”, Proceedings of the National Academy of Sciences of the United States, DOI: 10.1073/pnas.1718622115


Please use this citation when you publish any articles in relation to the Promys project:


“The XX’s (name of person) research leading to these results has received funding from the European Union Seventh Framework Programme (FP7-KBBE-2013-7-single-stage) under grant agreement no. 613745, Promys.”