Publications

Absolute yeast mitochondrial proteome quantification reveals trade-off between biosynthesis and energy generation during diauxic shift

Di Bartolomeo, Francesca ; Malina, Carl ; Campbell, Kate ; Mormino, Maurizio ; Fuchs, Johannes ; Vorontsov, Egor ; Gustafsson, Claes M. ; Nielsen, Jens
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 117, issue: 13, pages: 7524-7535

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1073/pnas.1918216117

Accelerated genome engineering of Pseudomonas putida by I-SceI-mediated recombination and CRISPR-Cas9 counterselection

Wirth, Nicolas ; Kozaeva, Ekaterina ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 233-249

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1111/1751-7915.13396

Adaptation of hydroxymethylbutenyl diphosphate reductase enables volatile isoprenoid production

Bongers, Mareike ; Perez-Gil, Jordi ; Hodson, Mark P. ; Schrübbers, Lars ; Wulff, Tune ; Sommer, Morten Oa ; Nielsen, Lars K. ; Vickers, Claudia E.
in: eLife, vol: 9

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.7554/elife.48685

Adaptive laboratory evolution of Escherichia coli under acid stress

Du, Bin ; Olson, Connor A. ; Sastry, Anand V ; Fang, Xin ; Phaneuf, Patrick V. ; Chen, Ke ; Wu, Muyao ; Szubin, Richard ; Xu, Sibei ; Gao, Ye ; Hefner, Ying ; Feist, Adam M ; Palsson, Bernhard O
in: Microbiology, vol: 166, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1099/mic.0.000867

Addressing environmental sustainability of biochemicals

Ögmundarson, Ólafur ; Herrgård, Markus J. ; Forster, Jochen ; Hauschild, Michael Zwicky ; Fantke, Peter
in: Nature Sustainability, vol: 3, pages: 167-174

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41893-019-0442-8

An atlas of human metabolism

Robinson, Jonathan L. ; Kocabaş, Pınar ; Wang, Hao ; Cholley, Pierre Etienne ; Cook, Daniel ; Nilsson, Avlant ; Anton, Mihail ; Ferreira, Raphael ; Domenzain, Iván ; Billa, Virinchi ; Limeta, Angelo ; Hedin, Alex ; Gustafsson, Johan ; Kerkhoven, Eduard J. ; Svensson, L. Thomas ; Palsson, Bernhard O. ; Mardinoglu, Adil ; Hansson, Lena ; Uhlén, Mathias ; Nielsen, Jens
in: Science Signaling, vol: 13, issue: 624

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1126/scisignal.aaz1482

An autoinducible trp-T7 expression system for production of proteins and biochemicals in Escherichia coli

Landberg, Jenny ; Mundhada, Hemanshu ; Nielsen, Alex Toftgaard
in: Biotechnology and Bioengineering, vol: 117, issue: 5, pages: 1513-1524

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1002/bit.27297

An expanded CRISPRi toolbox for tunable control of gene expression in Pseudomonas putida

Batianis, Christos ; Kozaeva, Ekaterina ; Damalas, Stamatios G. ; Martín-Pascual, María ; Volke, Daniel Christoph ; Nikel, Pablo Ivan ; Martins dos Santos, Vitor A.P.
in: Microbial Biotechnology, vol: 13, issue: 2, pages: 368-385

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1111/1751-7915.13533

Antibiotic resistance: turning evolutionary principles into clinical reality

Andersson, Dan I ; Balaban, Nathalie Q ; Baquero, Fernando ; Courvalin, Patrice ; Glaser, Philippe ; Gophna, Uri ; Kishony, Roy ; Molin, Søren ; Tønjum, Tone
in: FEMS Microbiology Reviews

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1093/femsre/fuaa001

ArsH protects Pseudomonas putida from oxidative damage caused by exposure to arsenic

Páez-Espino, A. David ; Nikel, Pablo Ivan ; Chavarría, Max ; de Lorenzo, Víctor
in: Environmental Microbiology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1111/1462-2920.14991

A single-host fermentation process for the production of flavor lactones from non-hydroxylated fatty acids

Marella, Eko Roy ; Dahlin, Jonathan ; Dam, Marie Inger ; ter Horst, Jolanda ; Christensen, Hanne Bjerre ; Sudarsan, Suresh ; Wang, Guokun ; Holkenbrink, Carina ; Borodina, Irina
in: Metabolic Engineering

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1016/j.ymben.2019.08.009

A teaching protocol demonstrating the use of EasyClone and CRISPR/Cas9 for metabolic engineering of Saccharomyces cerevisiae and Yarrowia lipolytica

Milne, Nicholas ; Ribeiro Ramos Tramontin, Larissa ; Borodina, Irina
in: FEMS Yeast Research, vol: 20, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1093/femsyr/foz062

Attenuating apoptosis in Chinese hamster ovary cells for improved biopharmaceutical production

Henry, Matthew N. ; MacDonald, Michael A. ; Orellana, Camila A. ; Gray, Peter P. ; Gillard, Marianne ; Baker, Kym ; Nielsen, Lars K. ; Marcellin, Esteban ; Mahler, Stephen ; Martínez, Verónica S.
in: Biotechnology and Bioengineering, vol: 17, issue: 4, pages: 1187-1203

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1002/bit.27269

Awakening dormant glycosyltransferases in CHO cells with CRISPRa

Julie la Cour Karottki, Karen ; Hefzi, Hooman ; Xiong, Kai ; Shamie, Isaac ; Hansen, Anders Holmgaard ; Li, Songyuan ; Pedersen, Lasse Ebdrup ; Li, Shangzhong ; Lee, Jae Seong ; Min Lee, Gyun ; Kildegaard, Helene Faustrup ; Lewis, Nathan E.
in: Biotechnology and Bioengineering, vol: 117, issue: 2, pages: 593-598

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1002/bit.27199

A workflow for generating multi-strain genome-scale metabolic models of prokaryotes

Norsigian, Charles J. ; Fang, Xin ; Seif, Yara ; Monk, Jonathan M. ; Palsson, Bernhard O.
in: Nature Protocols, vol: 15, issue: 1, pages: 1-14

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1038/s41596-019-0254-3

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree

Norsigian, Charles J. ; Pusarla, Neha ; McConn, John Luke ; Yurkovich, James T. ; Dräger, Andreas ; Palsson, Bernhard O. ; King, Zachary
in: Nucleic acids research, vol: 48, issue: 1, pages: D402-D406

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1093/nar/gkz1054

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Poblete-Castro, Ignacio ; Wittmann, Christoph ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 13, issue: 1, pages: 32-53

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1111/1751-7915.13400

Biosensor Engineering for the Development of Yeast Cell Factories

D'ambrosio, Vasil

Type: Ph.D. thesis

Status: Published | Year: 2020

Biotransformation of 2,4-dinitrotoluene in a phototrophic co-culture of engineered Synechococcus elongatus and Pseudomonas putida

Fedeson, Derek T. ; Saake, Pia ; Calero, Patricia ; Nikel, Pablo Ivan ; Ducat, Daniel C.
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1111/1751-7915.13544

Building blocks are synthesized on demand during the yeast cell cycle

Campbell, Kate ; Westholm, Jakub ; Kasvandik, Sergo ; Di Bartolomeo, Francesca ; Mormino, Maurizio ; Nielsen, Jens
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 117, issue: 14, pages: 7575-7583

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1073/pnas.1919535117

Cold-Resistant Heterotrophic Ammonium and Nitrite-Removing Bacteria Improve Aquaculture Conditions of Rainbow Trout (Oncorhynchus mykiss)

Neissi, Alireza ; Rafiee, Gholamreza ; Farahmand, Hamid ; Rahimi, Shadi ; Mijakovic, Ivan
in: Microbial Ecology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1007/s00248-020-01498-6

Combining Environmental and Economic Performance for Bioprocess Optimization

Ögmundarson, Ólafur ; Sukumara, Sumesh ; Herrgård, Markus J. ; Fantke, Peter
in: Trends in Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press | Year: 2020 | DOI: https://doi.org/10.1016/j.tibtech.2020.04.011

Complete Genome Sequences of 13 Bacillus subtilis Soil Isolates for Studying Secondary Metabolite Diversity

Kiesewalter, Heiko T. ; Lozano-Andrade, Carlos N. ; Maróti, Gergely ; Snyder, Dan ; Cooper, Vaughn S. ; Jørgensen, Tue Sparholt ; Weber, Tilmann ; Kovács, Ákos T.
in: Microbiology Resource Announcements, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1128/mra.01406-19

Cow's milk allergy prevention and treatment by heat-treated whey - a study in Brown Norway rats

Graversen, Katrine Bækby ; Ravn Ballegaard, Anne-Sofie ; Kræmer, Louise H ; Hornslet, Sofie Emilie ; Sørensen, Laila V ; Christoffersen, Heidi F. ; Jacobsen, Lotte N. ; Untersmayr, Eva ; Smit, Joost J ; Bøgh, Katrine Lindholm
in: Clinical and Experimental Allergy, vol: 50, issue: 6, pages: 708-721

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.1111/cea.13587

CRISPR/Cas9 recombineering-mediated deep mutational scanning of essential genes in Escherichia coli

Choudhury, Alaksh ; Fenster, Jacob A. ; Fankhauser, Reilly G. ; Kaar, Joel L. ; Tenaillon, Olivier ; Gill, Ryan T.
in: Molecular Systems Biology, vol: 16, issue: 3

Type: Journal article (Peer reviewed)

Status: Published | Year: 2020 | DOI: https://doi.org/10.15252/msb.20199265

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