Publications

A chromosome-scale genome assembly of Rauvolfia tetraphylla facilitates the identification of the complete ajmaline biosynthetic pathway

Lezin, Enzo ; Carqueijeiro, Inês ; Cuello, Clément ; Durand, Mickael ; Jansen, Hans J ; Vergès, Valentin ; Williams, Caroline Birer ; Oudin, Audrey ; De Bernonville, Thomas Duge ; Petrignet, Julien ; Celton, Noémie ; St-Pierre, Benoit ; Papon, Nicolas ; Sun, Chao ; Dirks, Ron P ; O'Connor, Sarah Ellen ; Jensen, Michael Krogh ; Besseau, Sébastien ; Courdavault, Vincent
in: Plant Communications

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1016/j.xplc.2023.100784

A comparative study of protein structure prediction tools for challenging targets

Kalogeropoulos, Konstantinos ; Bohn, Markus-Frederik ; Jenkins, David E. ; Ledergerber, Jann ; Sørensen, Christoffer V. ; Hofmann, Nils ; Wade, Jack ; Fryer, Thomas ; Nguyen, Giang Thi Tuyet ; auf dem Keller, Ullrich ; Laustsen, Andreas H. ; Jenkins, Timothy P.
in: Toxicon, vol: 238

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.toxicon.2023.107559

A comparative study of the performance of E. coli and K. phaffii for expressing α-cobratoxin

Damsbo, Anna ; Rimbault, Charlotte ; Burlet, Nick J. ; Vlamynck, Anneline ; Bisbo, Ida ; Belfakir, Selma B. ; Laustsen, Andreas H. ; Rivera-de-Torre, Esperanza
in: Toxicon, vol: 239

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.toxicon.2024.107613

Adaptive Evolution of Pseudomonas aeruginosa in Human Airways Shows Phenotypic Convergence Despite Diverse Patterns of Genomic Changes

Espaillat, Akbar ; Colque, Claudia Antonella ; Rago, Daniela ; Rosa, Ruggero La ; Molin, Søren ; Johansen, Helle Krogh
in: Molecular Biology and Evolution, vol: 41, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1093/molbev/msae022

Adaptive laboratory evolution reveals general and specific chemical tolerance mechanisms and enhances biochemical production

Lennen, Rebecca M. ; Jensen, Kristian ; Mohammed, Elsayed T. ; Malla, Sailesh ; Börner, Rosa A. ; Chekina, Ksenia ; Özdemir, Emre ; Bonde, Ida ; Koza, Anna ; Maury, Jérôme ; Pedersen, Lasse E. ; Schöning, Lars Y. ; Sonnenschein, Nikolaus ; Palsson, Bernhard O. ; Sommer, Morten O. A. ; Feist, Adam M. ; Nielsen, Alex T. ; Herrgård, Markus J.
in: bioRxiv

Type: Journal article

Status: Submitted | Year: 2024 | DOI: https://doi.org/10.1101/634105

A data-driven approach for timescale decomposition of biochemical reaction networks

Akbari, Amir ; Haiman, Zachary B. ; Palsson, Bernhard O.
in: mSystems, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1128/msystems.01001-23

A General and Convenient Peptide Self-Assembling Mechanism for Developing Supramolecular Versatile Nanomaterials Based on The Biosynthetic Hybrid Amyloid-Resilin Protein

Wu, Junjun ; Zhou, Lin ; Peng, Hu ; Wang, Zhaojun ; Wang, Zhaoshi ; Keasling, Jay D ; Liu, Shike ; Zhou, Guanghong ; Ding, Shijie ; Wang, Qiong ; Wang, Xuejian ; Chen, Xinxiu ; Lang, Yifei ; Xia, Mo ; Guan, Xin ; Dong, Mingsheng ; Zhou, Jingwen ; Chen, Jian
in: Advanced Materials, vol: 36, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1002/adma.202304364

A Hitchhiker’s guide to CRISPR editing tools in bacteria

Krink, Nicolas ; Nikel, Pablo Iván ; Beisel, Chase L.
in: EMBO Reports, vol: 25, pages: 1694 - 1699

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1038/s44319-024-00086-w

A molecular toolkit of cross-feeding strains for engineering synthetic yeast communities

Peng, Huadong ; Darlington, Alexander P.S. ; South, Eric J. ; Chen, Hao Hong ; Jiang, Wei ; Ledesma-Amaro, Rodrigo
in: Nature Microbiology, vol: 9, issue: 3, pages: 848-863

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1038/s41564-023-01596-4

Anaerobic glucose uptake in Pseudomonas putida KT2440 in a bioelectrochemical system

Pause, Laura ; Weimer, Anna ; Wirth, Nicolas T. ; Nguyen, Anh Vu ; Lenz, Claudius ; Kohlstedt, Michael ; Wittmann, Christoph ; Nikel, Pablo I. ; Lai, Bin ; Krömer, Jens O.
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1111/1751-7915.14375

A novel strategy for extraction of intracellular poly(3-hydroxybutyrate) from engineered Pseudomonas putida using deep eutectic solvents: Comparison with traditional biobased organic solvents

Didion, Yannick Patrice ; Vargas, Maria Victoria Gracia Alvan ; Tjaslma, Tjalling Gijsbert ; Woodley, John ; Nikel, Pablo Ivan ; Malankowska, Magdalena ; Su, Ziran ; Pinelo, Manuel
in: Separation and Purification Technology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1016/j.seppur.2024.126465

Antibacterial applications of biologically synthesized Pichia pastoris silver nanoparticles

More, Pragati Rajendra ; Shinde, Surbhi ; Cao, Zhejiang ; Zhang, Jian ; Pandit, Santosh ; De Filippis, Anna ; Mijakovic, Ivan ; Galdiero, Massimiliano
in: Heliyon, vol: 10, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.heliyon.2024.e25664

Antibody-dependent enhancement of toxicity of myotoxin II from Bothrops asper

Sørensen, Christoffer V. ; Fernández, Julián ; Christina Adams, Anna ; Wildenauer, Helen H. K. ; Schoffelen, Sanne ; Ledsgaard, Line ; Pucca, Manuela B. ; Fiebig, Michael ; Cerni, Felipe A. ; Tulika, Tulika ; Voldborg, Bjørn G. ; Karatt-Vellat, Aneesh ; Morth, J. Preben ; Ljungars, Anne ; Grav, Lise M. ; Lomonte, Bruno ; Laustsen, Andreas H.
in: Nature Communications, vol: 15

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1038/s41467-023-42624-5

An Untargeted Metabolomics Strategy to Identify Substrates of Known and Orphan E. coli Transporters

Radi, Mohammad ; Munro, Lachlan Jake ; Rago, Daniela ; Kell, Douglas
in: Membranes, vol: 14, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.3390/membranes14030070

A Perspective on How Fibrinaloid Microclots and Platelet Pathology May be Applied in Clinical Investigations

Pretorius, Etheresia ; Kell, Douglas B.
in: Seminars in Thrombosis and Hemostasis

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1055/s-0043-1774796

Are we under- or overreacting to climate change?

von Bülow, Catharina Wolff
in: Journal of Risk and Uncertainty

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024

Argonaute and Dicer are essential for communication between Trichoderma atroviride and fungal hosts during mycoparasitism

Enriquez-Felix, Eli Efrain ; Pérez-Salazar, Camilo ; Rico-Ruiz, José Guillermo ; de Carvalho, Ana Calheiros ; Cruz-Morales, Pablo ; Villalobos-Escobedo, José Manuel ; Herrera-Estrella, Alfredo
in: Microbiology Spectrum, vol: 12, issue: 4

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1128/spectrum.03165-23

Automating relative and absolute environmental sustainability assessments of bio-based products

Meramo, Samir ; Pasutto, Eleonora ; Sukumara, Sumesh
in: Bioresource Technology, vol: 394

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.biortech.2023.130196

Bad to the bone? - Genomic analysis of Enterococcus isolates from diverse environments reveals that most are safe and display potential as food fermentation microorganisms

Tadesse, Belay Tilahun ; Svetlicic, Ema ; Zhao, Shuangqing ; Berhane, Nega ; Jers, Carsten ; Solem, Christian ; Mijakovic, Ivan
in: Microbiological Research, vol: 283

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.micres.2024.127702

Biosynthesis of the Azoxy Compound Azodyrecin from Streptomyces mirabilis P8-A2

Maleckis, Matiss ; Wibowo, Mario ; Gren, Tetiana ; Jarmusch, Scott A ; Sterndorff, Eva B. ; Booth, Thomas ; Henriksen, Nathalie N. S. E. ; Whitford, Christopher M. ; Jiang, Xinglin ; Jørgensen, Tue S. ; Ding, Ling ; Weber, Tilmann
in: ACS chemical biology, vol: 19, issue: 3, pages: 641-653

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1021/acschembio.3c00632

Bio-upcycling of even and uneven medium-chain-length diols and dicarboxylates to polyhydroxyalkanoates using engineered Pseudomonas putida

Ackermann, Yannic S. ; de Witt, Jan ; Mezzina, Mariela P. ; Schroth, Christoph ; Polen, Tino ; Nikel, Pablo I. ; Wynands, Benedikt ; Wierckx, Nick
in: Microbial Cell Factories, vol: 23, issue: 1

Type: Journal article (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1186/s12934-024-02310-7

Can biotechnology lead the way toward a sustainable pharmaceutical industry?

Etit, Deniz ; Meramo, Samir ; Ögmundarson, Ólafur ; Jensen, Michael K. ; Sukumara, Sumesh
in: Current Opinion in Biotechnology, vol: 87

Type: Review (Peer reviewed)

Status: Published | Year: 2024 | DOI: https://doi.org/10.1016/j.copbio.2024.103100

Carbene chemistry for unnatural biosynthesis

Huang, Jing ; Keasling, Jay D.
in: Science China Life Sciences

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1007/s11427-023-2470-5

Characterization and Diversification of AraC/XylS Family Regulators Guided by Transposon Sequencing

Pearson, Allison N ; Incha, Matthew R ; Ho, Cindy N ; Schmidt, Matthias ; Roberts, Jacob B ; Nava, Alberto A ; Keasling, Jay D
in: ACS Synthetic Biology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2024 | DOI: https://doi.org/10.1021/acssynbio.3c00441