Publications

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2020
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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

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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

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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

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Adaptive laboratory evolution of Pseudomonas putida KT2440 improves p-coumaric and ferulic acid catabolism and tolerance

Mohamed, Elsayed Tharwat Tolba ; Werner, Allison Z. ; Salvachúa, Davinia ; Singer, Christine A. ; Szostkiewicz, Kiki ; Rafael Jiménez-Díaz, Manuel ; Eng, Thomas ; Radi, Mohammad S. ; Simmons, Blake A. ; Mukhopadhyay, Aindrila ; Herrgård, Markus J. ; Singer, Steven W. ; Beckham, Gregg T. ; Feist, Adam M.
in: Metabolic Engineering Communications, vol: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1016/j.mec.2020.e00143

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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

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A fluoride-responsive genetic circuit enables in vivo biofluorination in engineered Pseudomonas putida

Calero, Patricia ; Volke, Daniel Christoph ; Lowe, Phillip T ; Gotfredsen, Charlotte Held ; O'Hagan, David ; Nikel, Pablo Ivan
in: Nature Communications, vol: 11, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41467-020-18813-x

 

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

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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

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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

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Antibiotics create a shift from mutualism to competition in human gut communities with a longer-lasting impact on fungi than bacteria

Seelbinder, Bastian ; Chen, Jiarui ; Brunke, Sascha ; Vazquez-Uribe, Ruben ; Santhaman, Rakesh ; Meyer, Anne Christin ; De Oliveira Lino, Felipe Senne ; Chan, Ka Fai ; Loos, Daniel ; Imamovic, Lejla ; Tsang, Chi Ching ; Lam, Rex Pui Kin ; Sridhar, Siddharth ; Kang, Kang ; Hube, Bernhard ; Woo, Patrick Chiu Yat ; Sommer, Morten Otto Alexander ; Panagiotou, Gianni
in: Microbiome, vol: 8, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1186/s40168-020-00899-6

 

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

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ARTS 2.0: feature updates and expansion of the Antibiotic Resistant Target Seeker for comparative genome mining

Mungan, Mehmet Direnç ; Alanjary, Mohammad ; Blin, Kai ; Weber, Tilmann ; Medema, Marnix H. ; Ziemert, Nadine
in: Nucleic acids research, vol: 48, issue: W1, pages: W546-W552

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1093/nar/gkaa374

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A sustainable approach for the green synthesis of silver nanoparticles from Solibacillus isronensis sp. And their application in biofilm inhibition

Singh, Priyanka ; Pandit, Santosh ; Mokkapati, V. R.S.S. ; Garnæs, Jørgen ; Mijakovic, Ivan
in: Molecules, vol: 25, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.3390/molecules25122783

 

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

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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

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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

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Biochemical evidence of both copper chelation and oxygenase activity at the histidine brace

Brander, Søren ; Horvath, Istvan ; Ipsen, Johan Ø ; Peciulyte, Ausra ; Olsson, Lisbeth ; Hernández Rollán, Cristina ; Nørholm, Morten ; Mossin, Susanne ; Leggio, Leila Lo ; Probst, Corinna ; Thiele, Dennis J ; Johansen, Katja S
in: Scientific Reports, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2020     |    DOI: https://doi.org/10.1038/s41598-020-73266-y

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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

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Biosensor Engineering for the Development of Yeast Cell Factories

D'ambrosio, Vasil

Type: Ph.D. thesis

Status: Published     |    Year: 2020