Ghent University Academic Bibliography

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Simple and efficient modification of Golden Gate design standards and parts using oligo stitching

Jonas De Saeger (UGent) , Mattias Vermeersch (UGent) , Christophe Gaillochet (UGent) and Thomas B. Jacobs (UGent)

(2022) ACS SYNTHETIC BIOLOGY. 11(6). p.2214-2220
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Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Lien De Wannemaeker (UGent) , Indra Bervoets and Marjan De Mey (UGent)

(2022) BIOTECHNOLOGY ADVANCES. 60.
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- PhD Thesis
Finding the metabolic sweet spot : exploring post-transcriptional regulation and pathway balancing in yeast

Yatti De Nijs (UGent)

(2022)
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- C3
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Discovery and structure elucidation of novel alkaloids from marine actinobacteria

Jeltien Rombaut (UGent) , Anne-Sofie De Rop (UGent) , Thomas Willems (UGent) , Marilyn De Graeve (UGent) , Lynn Vanhaecke (UGent) , Paco Hulpiau, Sofie De Maeseneire (UGent) , Maarten De Mol (UGent) and Wim Soetaert (UGent)

(2022) Annual Symposium of the Belgian Society for Microbiology, Abstracts.
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Engineering transcriptional regulation in Escherichia coli using an archaeal TetR-family transcription factor

David Sybers, Amber Joka Bernauw, Diala El Masri, Hassan Ramadan Maklad, Daniel Charlier, Marjan De Mey (UGent) , Indra Bervoets and Eveline Peeters

(2022) GENE. 809.
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- Book Chapter
ProD : a tool for predictive design of tailored promoters in Escherichia coli

Friederike Mey (UGent) , Jim Clauwaert (UGent) , Maarten Van Brempt, Michiel Stock (UGent) , Jo Maertens (UGent) , Willem Waegeman (UGent) and Marjan De Mey (UGent)

(2022) Prokaryotic gene regulation : methods and protocols. In Methods in Molecular Biology 2516. p.51-59
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Unlocking the potential of non-model bacteria : a cross-bacterial gene expression toolbox

Cara Deal (UGent) , Lien De Wannemaeker (UGent) , Brecht De Paepe (UGent) , Antoni Planas and Marjan De Mey (UGent)

(2022) National Symposium for Applied Biological Sciences, 26th, Abstracts.
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A universal and orthogonal translation initiation module enabling standardized gene expression across the bacterial domain

Lien De Wannemaeker (UGent) , Jo Maertens (UGent) , Indra Bervoets and Marjan De Mey (UGent)

(2022) Innovation for Biomanufacturing, Abstracts.
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Biosensor-driven, model-based optimization of the orthogonally expressed naringenin biosynthesis pathway

Maarten Van Brempt, Andries Peeters (UGent) , Dries Duchi (UGent) , Lien De Wannemaeker (UGent) , Jo Maertens (UGent) , Brecht De Paepe (UGent) and Marjan De Mey (UGent)

(2022) MICROBIAL CELL FACTORIES. 21(1).
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Engineering a highly sensitive biosensor for abscisic acid in mammalian cells

Seo Woo Kim (UGent) , Kûbra Alci (UGent) , Femke Van Gaever (UGent) , Yasmine Driege (UGent) , Keylla Bicalho (UGent) , Geert Goeminne (UGent) , Claude Libert (UGent) , Alain Goossens (UGent) , Rudi Beyaert (UGent) and Jens Staal (UGent)

(2022) FEBS LETTERS. 596(19). p.2576-2590
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New synthetic biology tools for the thermoacidophilic Archaeon Sulfolobus acidocaldarius

Andries Peeters (UGent) , Pauline Pijpstra, David Sybers, Brecht De Paepe (UGent) , Eveline Peeters and Marjan De Mey (UGent)

(2022) National Symposium for Applied Biological Sciences, 26th, Abstracts.
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Novel alkaloids from marine actinobacteria : discovery and characterization

Anne-Sofie De Rop (UGent) , Jeltien Rombaut (UGent) , Thomas Willems (UGent) , Marilyn De Graeve (UGent) , Lynn Vanhaecke (UGent) , Paco Hulpiau, Sofie De Maeseneire (UGent) , Maarten De Mol (UGent) and Wim Soetaert (UGent)

(2021) MARINE DRUGS. 20(1).
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- Miscellaneous
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The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike Mey (UGent) , Jim Clauwaert (UGent) , Kirsten Van Huffel (UGent) , Willem Waegeman (UGent) and Marjan De Mey (UGent)

(2021)
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Improving the performance of machine learning models for biotechnology : the quest for deus ex machina

Friederike Mey (UGent) , Jim Clauwaert (UGent) , Kirsten Van Huffel (UGent) , Willem Waegeman (UGent) and Marjan De Mey (UGent)

(2021) BIOTECHNOLOGY ADVANCES. 53.
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Engineering metabolism in nicotiana species : a promising future

Franciso Javier Molina Hidalgo (UGent) , Marta Vazquez-Vilar, Lucio D'Andrea, Olivia C. Demurtas, Paul Fraser, Giovanni Giuliano, Ralph Bock, Diego Orzáez and Alain Goossens (UGent)

(2021) TRENDS IN BIOTECHNOLOGY. 39(9). p.901-913
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Synthetic biology as a technoscience : the case of minimal genomes and essential genes

Massimiliano Simons (UGent)

(2021) STUDIES IN HISTORY AND PHILOSOPHY OF SCIENCE. 85. p.127-136
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A toolbox for digitally enhanced teaching in synthetic biology

Liv Teresa Muth (UGent) , Liam Richard Jenkins Sánchez (UGent) , Silke Claus (UGent) , José Manuel Salvador López (UGent) and Inge Van Bogaert (UGent)

(2021) FEMS MICROBIOLOGY LETTERS. 368(17).
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The diversity of engineering in synthetic biology

Massimiliano Simons (UGent)

(2020) NANOETHICS. 14(1). p.71-91
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A VersaTile driven platform for rapid hit-to-lead development of engineered lysins

Hans Gerstmans, Dennis Grimon (UGent) , Diana Gutierrez Fernandez (UGent) , Cédric Lood, Ana Rodríguez, Vera van Noort, Jeroen Lammertyn, Rob Lavigne and Yves Briers (UGent)

(2020) SCIENCE ADVANCES. 6(23).
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Off-target glycans encountered along the synthetic biology route toward humanized N-glycans in Pichia pastoris

Bram Laukens, Pieter Jacobs, Katelijne Gheysen, José Martins (UGent) , Charlot De Wachter (UGent) , Paul Ameloot (UGent) , Willy Morelle, Jurgen Haustraete (UGent) , Jean-Christophe Renauld, Bart Samyn (UGent) , et al.

(2020) BIOTECHNOLOGY AND BIOENGINEERING. 117(8). p.2479-2488
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Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis

Sandra Kozak, Yehudi Bloch (UGent) , Steven De Munck, Aleksandra Mikula, Isabel Bento, Savvas Savvides (UGent) and Rob Meijers

(2020) ACTA CRYSTALLOGRAPHICA SECTION D-STRUCTURAL BIOLOGY. 76. p.1244-1255
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Synthetic protein scaffolds for the colocalisation of co-acting enzymes

Julie Vanderstraeten (UGent) and Yves Briers (UGent)

(2020) BIOTECHNOLOGY ADVANCES. 44.
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Quality control and statistical evaluation of combinatorial DNA libraries using nanopore sequencing

Cédric Lood, Hans Gerstmans, Yves Briers (UGent) , Vera van Noort and Rob Lavigne

(2020) BIOTECHNIQUES. 69(5). p.379-383
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- Conference Paper
- C3
Unlocking the bacterial domain for industrial biotechnology applications using orthogonal parts and tools

Lien De Wannemaeker (UGent) , Monica Texido, Béné Amery (UGent) , Jo Maertens (UGent) , Indra Bervoets and Marjan De Mey (UGent)

(2020) 5th Applied Synthetic Biology in Europe meeting (ASBE V), Abstracts.
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- Conference Paper
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The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Friederike Mey (UGent) , Jim Clauwaert (UGent) , Kirsten Van Huffel (UGent) , Willem Waegeman (UGent) and Marjan De Mey (UGent)

(2020) 5th Applied Synthetic Biology in Europe meeting (ASBE V), Abstracts.
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Engineering a minimal cloning vector from a pUC18 plasmid backbone with an extended multiple cloning site

Jens Staal (UGent) , Kûbra Alci (UGent) , Wouter De Schamphelaire (UGent) , Martine Vanhoucke (UGent) and Rudi Beyaert (UGent)

(2019) BIOTECHNIQUES. 66(6). p.254-259
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- PhD Thesis
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A study of different co-localization strategies for the production of flavonoids in Saccharomyces cerevisiae

Tom Delmulle (UGent)

(2019)
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A sigma factor toolbox for orthogonal gene expression in Escherichia coli

Indra Bervoets, Maarten Van Brempt, Katleen Van Nerom, Bob Van Hove, Jo Maertens (UGent) , Marjan De Mey (UGent) and Daniel Charlier

(2018) NUCLEIC ACIDS RESEARCH. 46(4). p.2133-2144
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Expanding the portfolio of synthetic biology tools in Saccharomyces cerevisiae for the optimization of heterologous production pathways at the transcriptional and translational level

Thomas Decoene

(2018)
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Development of N-acetylneuraminic acid responsive biosensors based on the transcriptional regulator NanR

Gert Peters (UGent) , Brecht De Paepe (UGent) , Lien De Wannemaeker (UGent) , Dries Duchi (UGent) , Jo Maertens (UGent) , Jeroen Lammertyn and Marjan De Mey (UGent)

(2018) BIOTECHNOLOGY AND BIOENGINEERING. 115(7). p.1855-1865
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Standardization in synthetic biology : an engineering discipline coming of age

Thomas Decoene, Brecht De Paepe (UGent) , Jo Maertens (UGent) , Pieter Coussement (UGent) , Gert Peters (UGent) , Sofie De Maeseneire (UGent) and Marjan De Mey (UGent)

(2018) CRITICAL REVIEWS IN BIOTECHNOLOGY. 38(5). p.647-656
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Challenges in the microbial production of flavonoids

Tom Delmulle (UGent) , Sofie De Maeseneire (UGent) and Marjan De Mey (UGent)

(2018) PHYTOCHEMISTRY REVIEWS. 17(2). p.229-247
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- Miscellaneous
- open access
Engineering a minimal cloning vector from a pUC18 plasmid backbone with an extended multiple cloning site

Jens Staal (UGent) , Wouter De Schamphelaire (UGent) and Rudi Beyaert (UGent)

(2018) PREPRINTS.
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Small-molecule-based regulation of RNA-delivered circuits in mammalian cells

Tyler E Wagner, Jacob R Becraft, Katie Bodner, Brian Teague, Xin Zhang, Amanda Woo, Ely Porter, Bremy Alburquerque, Brian Dobosh, Oliwia Andries (UGent) , et al.

(2018) NATURE CHEMICAL BIOLOGY. 14(11). p.1043-1050
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- Journal Article
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Hidden antibiotics : where to uncover?

Maarten De Mol (UGent) , Nico Snoeck, Sofie De Maeseneire (UGent) and Wim Soetaert (UGent)

(2018) BIOTECHNOLOGY ADVANCES. 36(8). p.2201-2218
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Recursive DNA assembly using protected oligonucleotide duplex assisted cloning (PODAC)

Bob Van Hove, Chiara Guidi (UGent) , Lien De Wannemaeker (UGent) , Jo Maertens (UGent) and Marjan De Mey (UGent)

(2017) ACS SYNTHETIC BIOLOGY. 6(6). p.943-949
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Biotechnology and the bioeconomy : towards inclusive and sustainable industrial development

Yvonne Lokko, Marc Heijde (UGent) , Karl Schebesta, Philippe Scholtès, Marc Van Montagu (UGent) and Mauro Giacca

(2017) NEW BIOTECHNOLOGY. 40. p.5-10
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A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules

James Reed, Michael J Stephenson, Karel Miettinen (UGent) , Bastiaan Brouwer, Aymeric Leveau, Paul Brett, Rebecca JM Goss, Alain Goossens (UGent) , Maria A O'Connell and Anne Osbourn

(2017) METABOLIC ENGINEERING. 42. p.185-193
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- Miscellaneous
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Plants for human health : greening biotechnology and synthetic biology

Tessa Moses (UGent) and Alain Goossens (UGent)

(2017) JOURNAL OF EXPERIMENTAL BOTANY. 68(15). p.4009-4011
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- C3
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Towards predictable 5’-UTRs in Saccharomyces cerevisiae

Thomas Decoene, Gert Peters (UGent) , Sofie De Maeseneire (UGent) and Marjan De Mey (UGent)

(2017) Synthetic Biology, 7th International meeting, Abstracts.
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The algal revolution

Juliet Brodie, Cheong Xin Chan, Olivier De Clerck (UGent) , J Mark Cock, Susana M Coelho, Claire Gachon, Arthur R Grossman, Thomas Mock, John A Raven, Alison G Smith, et al.

(2017) TRENDS IN PLANT SCIENCE. 22(8). p.726-738
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Constructing artificial CRISPR guide RNA arrays using methylated oligonucleotides

Bob Van Hove, Lien De Wannemaeker (UGent) , Jo Maertens (UGent) and Marjan De Mey (UGent)

(2016) Applied Synthetic Biology in Europe, 3rd Meeting, Abstract. p.62-62
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- C3
Spanning the boundaries: expanding the cross-bacterial toolbox

David Bauwens

(2016) NEW BIOTECHNOLOGY. 33(suppl.). p.S184-S184
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Not just PCR: using modified oligonucleotides for recursive cloning

Bob Van Hove, Chiara Guidi (UGent) , Lien De Wannemaeker (UGent) , Jo Maertens (UGent) and Marjan De Mey (UGent)

(2016) NEW BIOTECHNOLOGY. 33(suppl.). p.S65-S66
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Recursive cloning for the assembly of biosynthetic pathways and artificial CRISPR arrays

Bob Van Hove, Lien De Wannemaeker (UGent) , Chiara Guidi (UGent) , Jo Maertens (UGent) and Marjan De Mey (UGent)

(2016) SEED : Synthetic Biology: Engineering, Evolution and Design, Conference program book. p.89-89
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Engineering transcription in S. cerevisiae through random assembly of an UAS library

Thomas Decoene, Nathalie Cuypers, Marjan De Mey (UGent) and Sofie De Maeseneire (UGent)

(2016) Genome Engineering and Synthetic Biology: Tools and Technologies, Program book.
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Creating a ready-to-use sigma factor toolbox for pathway control

Maarten Van Brempt, Indra Bervoets, Jo Maertens (UGent) , Daniel Charlier and Marjan De Mey (UGent)

(2016) Genome Engineering and Synthetic Biology: Tools and Technologies, Program book.
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- Conference Paper
- C3
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Iterative cloning using a methylation protected oligonucleotide duplex

Bob Van Hove, Chiara Guidi (UGent) , Jo Maertens (UGent) and Marjan De Mey (UGent)

(2016) Genome Engineering and Synthetic Biology: Tools and Technologies, Program book.
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- C3
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Protein expression modulation in S. cerevisiae through random assembly of an UAS library

Thomas Decoene, Nathalie Cuypers, Marjan De Mey (UGent) and Sofie De Maeseneire (UGent)

(2016) Yeasterday, Abstracts.
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Putting RNA to work: translating RNA fundamentals into biotechnological engineering practice

Gert Peters (UGent) , Pieter Coussement (UGent) , Jo Maertens (UGent) , Jeroen Lammertyn and Marjan De Mey (UGent)

(2015) BIOTECHNOLOGY ADVANCES. 33(8). p.1829-1844

Simple and efficient modification of Golden Gate design standards and parts using oligo stitching

Unlocking the bacterial domain for industrial biotechnology applications using universal parts and tools

Finding the metabolic sweet spot : exploring post-transcriptional regulation and pathway balancing in yeast

Discovery and structure elucidation of novel alkaloids from marine actinobacteria

Engineering transcriptional regulation in Escherichia coli using an archaeal TetR-family transcription factor

ProD : a tool for predictive design of tailored promoters in Escherichia coli

Unlocking the potential of non-model bacteria : a cross-bacterial gene expression toolbox

A universal and orthogonal translation initiation module enabling standardized gene expression across the bacterial domain

Biosensor-driven, model-based optimization of the orthogonally expressed naringenin biosynthesis pathway

Engineering a highly sensitive biosensor for abscisic acid in mammalian cells

New synthetic biology tools for the thermoacidophilic Archaeon Sulfolobus acidocaldarius

Novel alkaloids from marine actinobacteria : discovery and characterization

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Improving the performance of machine learning models for biotechnology : the quest for deus ex machina

Engineering metabolism in nicotiana species : a promising future

Synthetic biology as a technoscience : the case of minimal genomes and essential genes

A toolbox for digitally enhanced teaching in synthetic biology

The diversity of engineering in synthetic biology

A VersaTile driven platform for rapid hit-to-lead development of engineered lysins

Off-target glycans encountered along the synthetic biology route toward humanized N-glycans in Pichia pastoris

Homogeneously N-glycosylated proteins derived from the GlycoDelete HEK293 cell line enable diffraction-quality crystallogenesis

Synthetic protein scaffolds for the colocalisation of co-acting enzymes

Quality control and statistical evaluation of combinatorial DNA libraries using nanopore sequencing

Unlocking the bacterial domain for industrial biotechnology applications using orthogonal parts and tools

The quest for deus ex machina : harnessing the power of machine learning for synthetic biology

Engineering a minimal cloning vector from a pUC18 plasmid backbone with an extended multiple cloning site

A study of different co-localization strategies for the production of flavonoids in Saccharomyces cerevisiae

A sigma factor toolbox for orthogonal gene expression in Escherichia coli

Expanding the portfolio of synthetic biology tools in Saccharomyces cerevisiae for the optimization of heterologous production pathways at the transcriptional and translational level

Development of N-acetylneuraminic acid responsive biosensors based on the transcriptional regulator NanR

Standardization in synthetic biology : an engineering discipline coming of age

Challenges in the microbial production of flavonoids

Engineering a minimal cloning vector from a pUC18 plasmid backbone with an extended multiple cloning site

Small-molecule-based regulation of RNA-delivered circuits in mammalian cells

Hidden antibiotics : where to uncover?

Recursive DNA assembly using protected oligonucleotide duplex assisted cloning (PODAC)

Biotechnology and the bioeconomy : towards inclusive and sustainable industrial development

A translational synthetic biology platform for rapid access to gram-scale quantities of novel drug-like molecules

Plants for human health : greening biotechnology and synthetic biology

Towards predictable 5’-UTRs in Saccharomyces cerevisiae

The algal revolution

Constructing artificial CRISPR guide RNA arrays using methylated oligonucleotides

Spanning the boundaries: expanding the cross-bacterial toolbox

Not just PCR: using modified oligonucleotides for recursive cloning

Recursive cloning for the assembly of biosynthetic pathways and artificial CRISPR arrays

Engineering transcription in S. cerevisiae through random assembly of an UAS library

Creating a ready-to-use sigma factor toolbox for pathway control

Iterative cloning using a methylation protected oligonucleotide duplex

Protein expression modulation in S. cerevisiae through random assembly of an UAS library

Putting RNA to work: translating RNA fundamentals into biotechnological engineering practice