Publications

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2019
 

A gender matching effect in learning with pedagogical agents in an immersive virtual reality science simulation

Makransky, Guido ; Wismer, Philip ; Mayer, Richard E.
in: Journal of Computer Assisted Learning, vol: 35, issue: 3, pages: 349-358

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/jcal.12335

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Antibiotic Treatment Drives the Diversification of the Human Gut Resistome

Li, Jun ; Rettedal, Elizabeth A ; van der Helm, Eric ; Ellabaan, Mostafa M Hashim ; Panagiotou, Gianni ; Sommer, Morten Otto Alexander
in: Genomics, Proteomics and Bioinformatics, vol: 17, issue: 1, pages: 39-51

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.gpb.2018.12.003

 

Characterization of Hypermutator Pseudomonas aeruginosa Isolates from Patients with Cystic Fibrosis in Australia

Rees, Vanessa Emily ; Deveson Lucas, Deanna S. ; López-Causapé, Carla ; Huang, Yuling ; Kotsimbos, Tom ; Bulitta, Jürgen B. ; Rees, Murray C. ; Barugahare, Adele ; Peleg, Anton Y. ; Nation, Roger L. ; Oliver, Antonio ; Boyce, John D. ; Landersdorfer, Cornelia B.
in: Antimicrobial Agents and Chemotherapy, pages: e02538-18

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1128/AAC.02538-1

 

Classification and enzyme kinetics of formate dehydrogenases for biomanufacturing via CO2 utilization

Nielsen, Christian Førgaard ; Lange, Lene ; Meyer, Anne S.
in: Biotechnology Advances

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biotechadv.2019.06.007

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Collateral sensitivity constrains resistance evolution of the CTX-M-15 β-lactamase

Rosenkilde, Carola Elisa Heesemann ; Munck, Christian ; Porse, Andreas ; Linkevicius, Marius ; Andersson, Dan I. ; Sommer, Morten Otto Alexander
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-08529-y

 

Discovery and Characterization of Cas9 Inhibitors Disseminated across Seven Bacterial Phyla

Vazquez-Uribe, Ruben ; van der Helm, Eric ; Misiakou, Maria-Anna ; Lee, Sang-Woo ; Kol, Stefan ; Sommer, Morten Otto Alexander
in: Cell Host & Microbe, vol: 25, issue: 2, pages: 233-241

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.chom.2019.01.003

 

Lack of the major multifunctional catalase KatA in P.aeruginosa accelerates evolution of antibiotic resistance in ciprofloxacin-treated biofilms

Ahmed, Marwa N ; Porse, Andreas ; Abdelsamad, Ahmed ; Sommer, Morten Otto Alexander ; Høiby, Niels ; Ciofu, Oana
in: Antimicrobial Agents and Chemotherapy

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1128/AAC.00766-19

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Mining, analyzing, and integrating viral signals from metagenomic data

Zheng, Tingting ; Li, Jun ; Ni, Yueqiong ; Kang, Kang ; Misiakou, Maria-Anna ; Imamovic, Lejla ; Chow, Billy K C ; Rode, Anne A ; Bytzer, Peter ; Sommer, Morten Otto Alexander ; Panagiotou, Gianni
in: Microbiome, vol: 7, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s40168-019-0657-y

 

NetSurfP-2.0: Improved prediction of protein structural features by integrated deep learning

Klausen, Michael Schantz ; Jespersen, Martin Closter ; Nielsen, Henrik ; Jensen, Kamilla Kjærgaard ; Jurtz, Vanessa Isabell ; Sønderby, Casper Kaae ; Sommer, Morten Otto Alexander ; Winther, Ole ; Nielsen, Morten ; Petersen, Bent ; Marcatili, Paolo
in: Proteins: Structure, Function, and Bioinformatics, vol: 87, issue: 6, pages: 520-527

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/prot.25674

 

Overcoming genetic heterogeneity in industrial fermentations

Rugbjerg, Peter ; Sommer, Morten Otto Alexander
in: Nature Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41587-019-0171-6

 

Publisher Correction: Shared strategies for β-lactam catabolism in the soil microbiome

Crofts, Terence S. ; Wang, Bin ; Spivak, Aaron ; Gianoulis, Tara A. ; Forsberg, Kevin J. ; Gibson, Molly K. ; Johnsky, Lauren A. ; Broomall, Stacey M. ; Rosenzweig, C. Nicole ; Skowronski, Evan W. ; Gibbons, Henry S. ; Sommer, Morten O. A. ; Dantas, Gautam
in: Nature Chemical Biology

Type: Comment/debate (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41589-018-0208-z

 

Rapid diagnosis of lung infections

Prodan, Andrei ; Sommer, Morten Otto Alexander ; Nieuwdorp, Max
in: Nature Biotechnology, vol: 37, issue: 7, pages: 725-726

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41587-019-0174-3

 

Systematic Evaluation of Site-Specific Recombinant Gene Expression for Programmable Mammalian Cell Engineering

Pristovšek, Nuša ; Nallapareddy, Saranya ; Grav, Lise Marie ; Hefzi, Hooman ; Lewis, Nathan E. ; Rugbjerg, Peter ; Hansen, Henning Gram ; Lee, Gyun Min ; Andersen, Mikael Rørdam ; Kildegaard, Helene Faustrup
in: ACS Synthetic Biology, vol: 8, issue: 4, pages: 758-774

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.8b00453

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The resistome of important human pathogens

Munck, Christian ; Ellabaan, Mostafa M Hashim ; Klausen, Michael Schantz ; Sommer, Morten Otto Alexander
in: bioRxiv

Type: Journal article (Peer reviewed)

Status: Submitted     |    Year: 2019     |    DOI: https://doi.org/10.1101/140194

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Wiring cell growth to product formation

Buerger, Josi ; Gronenberg, Luisa S ; Genee, Hans Jasper ; Sommer, Morten Otto Alexander
in: Current Opinion in Biotechnology, vol: 59, pages: 85-92

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.copbio.2019.02.014

2018
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A synthetic medium to simulate sugarcane molasses

Senne de Oliveira Lino, Felipe ; Basso, Thiago Olitta ; Sommer, Morten Otto Alexander
in: Biotechnology for Biofuels, vol: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s13068-018-1221-x

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Bacterial cells with improved tolerance to diacids

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2018091525 , Date: 2018-05-24

Type: Patent

Status: Published     |    Year: 2018

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Biochemical mechanisms determine the functional compatibility of heterologous genes

Porse, Andreas ; Schou, Thea S. ; Munck, Christian ; Ellabaan, Mostafa M. H. ; Sommer, Morten O. A.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41467-018-02944-3

 

Bluephage: A rapid method for the detection of somatic coliphages used as indicators of fecal pollution in water

Muniesa, M. ; Balleste, E. ; Imamovic, Lejla ; Pascual-Benito, M. ; Toribio-Avedillo, D. ; Lucena, F. ; Blanch, A. R. ; Jofre, J.
in: Water Research, vol: 128, pages: 10-19

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.watres.2017.10.030

 

Combination of Three Methods to Reduce Glucose Metabolic Rate for improving N-Acetylglucosamine Production in Saccharomyces cerevisiae

Lee, Sang-Woo ; Lee, Bo-Young ; Oh, Min-Kyu
in: Journal of Agricultural and Food Chemistry, vol: 66, issue: 50, pages: 13191-13198

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1021/acs.jafc.8b04291

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Complete Genome Sequence of Escherichia coli Strain WG5

Imamovic, Lejla ; Misiakou, Maria-Anna ; van der Helm, Eric ; Panagiotou, Gianni ; Muniesa, Maite ; Sommer, Morten Otto Alexander
in: Genome Announcements, vol: 6, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1128/genomeA.01403-17

 

CRISPR-Cas antimicrobials

Vazquez-Uribe, Ruben

Type: Ph.D. thesis

Status: Published     |    Year: 2018

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Dependency of Heterochromatin Domains on Replication Factors

Jahn, Leonie Johanna ; Mason, Bethany ; Brøgger, Peter ; Toteva, Tea ; Nielsen, Dennis Kim ; Thon, Genevieve
in: G3: Genes, Genomes, Genetics (Bethesda), vol: 8, issue: 2, pages: 477-489

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1534/g3.117.300341

 

Directed Evolution of Membrane Transport Using Synthetic Selections

Bali, Anne Pihl ; Genee, Hans J. ; Sommer, Morten O. A.
in: A C S Synthetic Biology, vol: 7, issue: 3, pages: 789-793

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1021/acssynbio.7b00407

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Diverse genetic error modes constrain large-scale bio-based production

Rugbjerg, Peter ; Myling-Petersen, Nils ; Porse, Andreas ; Sarup-Lytzen, Kira ; Sommer, Morten Otto Alexander
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41467-018-03232-w

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Drug-Driven Phenotypic Convergence Supports Rational Treatment Strategies of Chronic Infections

Imamovic, Lejla ; Ellabaan, Mostafa Mostafa Hashim ; Dantas Machado, Ana Manuel ; Citterio, Linda ; Wulff, Tune ; Molin, Søren ; Johansen, Helle Krogh ; Sommer, Morten Otto Alexander
in: CELL, vol: 172, issue: 1-2, pages: 121-134

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.cell.2017.12.012

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Enhanced Metabolite Productivity of Escherichia coli Adapted to Glucose M9 Minimal Medium

Rugbjerg, Peter ; Feist, Adam M. ; Sommer, Morten Otto Alexander
in: Frontiers in Bioengineering and Biotechnology, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3389/fbioe.2018.00166

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Evolution of antibiotic resistance in biofilm and planktonic P. aeruginosa populations exposed to sub-inhibitory levels of ciprofloxacin

Ahmed, Marwa N. ; Porse, Andreas ; Sommer, Morten Otto Alexander ; Høiby, Niels ; Ciofu, Oana
in: Antimicrobial Agents and Chemotherapy, vol: 62, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1128/AAC.00320-18

 

Parts Characterization for Tunable Protein Expression

Klausen, Michael Schantz ; Sommer, Morten Otto Alexander
part of: Synthetic Metabolic Pathways, pages: 3-14, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_1

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Pharmacogenomics of GPCR Drug Targets

Hauser, Alexander Sebastian ; Chavali, Sreenivas ; Masuho, Ikuo ; Jahn, Leonie Johanna ; Martemyanov, Kirill ; Gloriam, David E. ; Babu, Madan
in: CELL, vol: 172, issue: 1-2, pages: 41-54

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.cell.2017.11.033

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Shared strategies for β-lactam catabolism in the soil microbiome

Crofts, Terence S. ; Wang, Bin ; Spivak, Aaron ; Gianoulis, Tara A. ; Forsberg, Kevin J. ; Gibson, Molly K. ; Johnsky, Lauren A. ; Broomall, Stacey M. ; Rosenzweig, C. Nicole ; Skowronski, Evan W. ; Gibbons, Henry S. ; Sommer, Morten O. A. ; Dantas, Gautam
in: Nature Chemical Biology, vol: 14, pages: 556-564

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41589-018-0052-1

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Synthetic addiction extends the productive life time of engineered Escherichia coli populations

Rugbjerg, Peter ; Sarup-Lytzen, Kira ; Nagy, Mariann ; Sommer, Morten Otto Alexander
in: Proceedings of the National Academy of Sciences of the United States of America

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1718622115

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The Environmental Exposures and Inner- and Intercity Traffic Flows of the Metro System May Contribute to the Skin Microbiome and Resistome

Kang, Kang ; Ni, Yueqiong ; Li, Jun ; Imamovic, Lejla ; Sarkar, Chinmoy ; Kobler, Marie Danielle ; Heshiki, Yoshitaro ; Zheng, Tingting ; Kumari, Sarika ; Wong, Jane Ching Yan ; Archna, Anand ; Wong, Cheong Wai Martin ; Dingle, Caroline ; Denizen, Seth ; Baker, David Michael ; Sommer, Morten Otto Alexander ; Webster, Christopher John ; Panagiotou, Gianni
in: Cell Reports, vol: 24, issue: 5, pages: 1190-1202

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.celrep.2018.06.109

 

The evolving interface between synthetic biology and functional metagenomics

van der Helm, Eric ; Genee, Hans J. ; Sommer, Morten O. A.
in: Nature Chemical Biology, vol: 14, issue: 8, pages: 752-759

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41589-018-0100-x

2017
 

High throughput in vivo protease inhibitor selection platform

Van Der Helm, Eric ; Sommer,, Morten
Patent no.: WO2017186854, Date: 2017-11-02

Type: Patent

Status: Published     |    Year: 2017

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Bacterial cells with improved tolerance to polyols

Lennen, Rebecca ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander ; Feist, Adam ; Tharwat Tolba Mohamed, Elsayed
Patent no.: WO2017211883, Date: 2017-12-14

Type: Patent

Status: Published     |    Year: 2017

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A family of microbial lysine transporter polypeptides

Malla, Sailesh ; Sommer, Morten Otto Alexander ; van der Helm, Eric ; Wieschalka, Stefan (Inventor) ; Förster, Jochen
Patent no.: WO2017085241, Date: 2017-05-26

Type: Patent

Status: Published     |    Year: 2017

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A system for improved production titers in fermentations

Rugbjerg, Peter ; Sarup-Lytzen, Kira ; Sommer, Morten Otto Alexander
Patent no.: WO2017055360, Date: 2017-04-06

Type: Patent

Status: Published     |    Year: 2017

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Assessing glycolytic flux alterations resulting from genetic perturbations in E. coli using a biosensor

Lehning, Christina Eva ; Siedler, Solvej ; Ellabaan, Mostafa M Hashim ; Sommer, Morten Otto Alexander
in: Metabolic Engineering, vol: 42, pages: 194-202

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.ymben.2017.07.002

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A versatile one-step CRISPR-Cas9 based approach to plasmid-curing

Lauritsen, Ida ; Porse, Andreas ; Sommer, Morten Otto Alexander ; Nørholm, Morten
in: Microbial Cell Factories, vol: 16

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1186/s12934-017-0748-z

 

Controlling Citrate Synthase Expression by CRISPR/Cas9 Genome Editing for n-Butanol Production in Escherichia coli

Heo, Min-Ji ; Jung, Hwi-Min ; Um, Jaeyong ; Lee, Sang-Woo ; Oh, Min-Kyu
in: A C S Synthetic Biology, vol: 6, issue: 2, pages: 182–189

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1021/acssynbio.6b00134

 

Development of a Bacterial Biosensor for Rapid Screening of Yeast p-Coumaric Acid Production

Siedler, Solvej ; Khatri, Narendar K. ; Zsohar, Andrea ; Kjærbølling, Inge ; Vogt, Michael ; Hammar, Petter ; Nielsen, Christian Førgaard ; Marienhagen, Jan ; Sommer, Morten Otto Alexander ; Joensson, Haakan N.
in: A C S Synthetic Biology, vol: 6, issue: 10, pages: 1860-1869

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1021/acssynbio.7b00009

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Draft Genome Sequences of Three β-Lactam-Catabolizing Soil Proteobacteria

Crofts, Terence S. ; Wang, Bin ; Spivak, Aaron ; Gianoulis, Tara A. ; Forsberg, Kevin J. ; Gibson, Molly K. ; Johnsky, Lauren A. ; Broomall, Stacey M. ; Rosenzweig, C. Nicole ; Skowronski, Evan W. ; Gibbons, Henry S. ; Sommer, Morten Otto Alexander ; Dantas, Gautam
in: Genome Announcements, vol: 5, issue: 32

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1128/genomeA.00653-17

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Dynamic Rearrangement of Cell States Detected by Systematic Screening of Sequential Anticancer Treatments

Koplev, Simon ; Longden, James ; Ferkinghoff-Borg, Jesper ; Blicher Bjerregård, Mathias ; Cox, Thomas R. ; Erler, Janine T. ; Pedersen, Jesper T. ; Voellmy, Franziska ; Sommer, Morten Otto Alexander ; Linding, Rune
in: Cell Reports, vol: 20, issue: 12, pages: 2784-2791

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.celrep.2017.08.095

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Genetic-Metabolic Coupling for Targeted Metabolic Engineering

Cardinale, Stefano ; Tueros Farfan, Felipe Gonzalo ; Sommer, Morten Otto Alexander
in: Cell Reports, vol: 20, issue: 5, pages: 1029-1037

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1016/j.celrep.2017.07.015

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Genome Dynamics of Escherichia coli during Antibiotic Treatment: Transfer, Loss, and Persistence of Genetic Elements In situ of the Infant Gut

Porse, Andreas ; Gumpert, Heidi ; Kubicek-Sutherland, Jessica Z. ; Karami, Nahid ; Adlerberth, Ingegerd ; Wold, Agnes E. ; Andersson, Dan I. ; Sommer, Morten Otto Alexander
in: Frontiers in Cellular and Infection Microbiology, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.3389/fcimb.2017.00126

 

Prediction of antibiotic resistance: time for a new preclinical paradigm?

Sommer, Morten Otto Alexander ; Munck, Christian ; Toft-Kehler, Rasmus Vendler ; Andersson, Dan I.
in: Nature Reviews. Microbiology, vol: 15, pages: 689-696

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1038/nrmicro.2017.75

 

PROMYS – Programming synthetic networks for bio-based production of value chemicals – FP7 project

Sommer, Morten Otto Alexander
in: Impact, issue: 3, pages: 45-47

Type: Journal article

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.21820/23987073.2017.3.45

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Rapid resistome mapping using nanopore sequencing

van der Helm, Eric ; Imamovic, Lejla ; Ellabaan, Mostafa M Hashim ; van Schaik, Willem ; Koza, Anna ; Sommer, Morten Otto Alexander
in: Nucleic acids research, vol: 45, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1093/nar/gkw1328

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Transfer and persistence of a multi-drug resistance plasmid in situ of the infant gut microbiota in the absence of antibiotic treatment

Gumpert, Heidi ; Kubicek-Sutherland, Jessica Z. ; Porse, Andreas ; Karami, Nahid ; Munck, Christian ; Linkevicius, Marius ; Adlerberth, Ingegerd ; Wold, Agnes E. ; Andersson, Dan I. ; Sommer, Morten Otto Alexander
in: Frontiers in Microbiology, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.3389/fmicb.2017.01852

 

Whole-Genome Sequencing of Bacterial Pathogens: the Future of Nosocomial Outbreak Analysis

Quainoo, Scott ; Coolen, Jordy P. M. ; van Hijum, Sacha A. F. T. ; Huynen, Martijn A. ; Melchers, Willem J. G. ; van Schaik, Willem ; Wertheim, Heiman F. L.
in: Clinical Microbiology Reviews, vol: 30, issue: 4, pages: 1015-1063

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2017     |    DOI: https://doi.org/10.1128/CMR.00016-17

2016
 

Adaptive responses to cefotaxime treatment in ESBL-producing Escherichia coli and the possible use of significantly regulated pathways as novel secondary targets

Møller, Thea S. B. ; Rau, Martin Holm ; Bonde, Charlotte S ; Sommer, Morten Otto Alexander ; Guardabassi, Luca ; Olsen, John E
in: Journal of Antimicrobial Chemotherapy, vol: 71, issue: 9, pages: 2449-2459

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1093/jac/dkw198

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An Integrated Genomics Framework for System-Level Cell Factory Design

Cardinale, Stefano ; Ye, Lumeng ; Sommer, Morten Otto Alexander
Presented at:
An Integrated Genomics Framework for System-Level Cell Factory Design

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2016

 

Biosynthesis of 2-phenylethanol from glucose with genetically engineered Kluyveromyces marxianus

Lee, Sang-Woo ; Oh, Min-Kuy
in: Biotechnology and Bioengineering (Print), vol: 113, issue: 11, pages: 2524-2528

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1002/bit.26014

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Cell Factory Stability and Genetic Circuits for Improved Strain Development

Rugbjerg, Peter

Type: Ph.D. thesis

Status: Published     |    Year: 2016

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Collateral sensitivity cycling of antibiotics for cystic fibrosis airway

Sommer, L.M. ; Imamovic, Lejla ; Pressler, Tacjana ; Sommer, Morten Otto Alexander ; Molin, Søren ; Johansen, Helle Krogh
in: Journal of Cystic Fibrosis, vol: 15, issue: Suppl. 1, pages: 583

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/S1569-1993(16)30365-4

 

Copper tolerant ecotypes of Heliscus lugdunensis differ in their ecological function and growth

Quainoo, Scott ; Seena, Sahadevan ; Graça, Manuel A.S.
in: Science of the Total Environment, vol: 544, pages: 168-174

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.scitotenv.2015.11.119

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CRMAGE: CRISPR Optimized MAGE Recombineering

Ronda, Carlotta ; Pedersen, Lasse Ebdrup ; Sommer, Morten Otto Alexander ; Nielsen, Alex Toftgaard
in: Scientific Reports, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/srep19452

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Development of biotechnological tools for modulating an industrial microbiome

Senne de Oliveira Lino, Felipe ; Cardinale, Stefano ; Molin, Søren ; Sommer, Morten Otto Alexander
Presented at:
Novo Nordisk Foundation Cluster Days 2016

Type: Poster (Peer reviewed)

Status: Published     |    Year: 2016

 

Functional mining of transporters using synthetic selections

Genee, Hans Jasper ; Bali, Anne Pihl ; Petersen, Søren Dalsgård ; Siedler, Solvej ; Bonde, Mads ; Gronenberg, Luisa S. ; Kristensen, Mette ; Harrison, Scott James ; Sommer, Morten Otto Alexander
in: Nature Chemical Biology

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/nchembio.2189

 

Heterogeneity in phage induction enables the survival of the lysogenic population

Imamovic, Lejla ; Ballesté, Elisenda ; Martínez-Castillo, Alexandre ; García-Aljaro, Cristina ; Muniesa, Maite
in: Environmental Microbiology

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2016     |    DOI: https://doi.org/10.1111/1462-2920.13151

 

Improved production of N-acetylglucosamine in Saccharomyces cerevisiae by reducing glycolytic flux

Lee, Sang-Woo ; Oh, Min-Kuy
in: Biotechnology and Bioengineering (Print), vol: 113, issue: 11, pages: 2524-2528

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1002/bit.26014

 

(Meta-)genome mining for new ribo-regulators

Sommer, Morten Otto Alexander ; Suess, Beatrix
in: Science Magazine, vol: 352, issue: 6282, pages: 144-145

Type: Journal article

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1126/science.aaf6189

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Molecular Buffers Permit Sensitivity Tuning and Inversion of Riboswitch Signals

Rugbjerg, Peter ; Genee, Hans Jasper ; Jensen, Kristian ; Sarup-Lytzen, Kira ; Sommer, Morten Otto Alexander
in: A C S Synthetic Biology, vol: 5, issue: 7, pages: 632-638

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1021/acssynbio.5b00213

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Oral supplementation of healthy adults with 2'-O-fucosyllactose and lacto-N-neotetraose is well tolerated and shifts the intestinal microbiota

Elison, Emma ; Vigsnæs, Louise K. ; Rindom Krogsgaard, Laura ; Rasmussen, Julie ; Sørensen, Nikolaj ; McConnell, Bruce ; Hennet, Thierry ; Sommer, Morten Otto Alexander ; Bytzer, Peter
in: The British Journal of Nutrition, vol: 116, pages: 1356-1368

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1017/S0007114516003354

 

Predictable tuning of protein expression in bacteria

Bonde, Mads ; Pedersen, Margit ; Klausen, Michael Schantz ; Ingemann Jensen, Sheila ; Wulff, Tune ; Harrison, Scott James ; Nielsen, Alex Toftgaard ; Herrgard, Markus ; Sommer, Morten Otto Alexander
in: Nature Methods, vol: 13, pages: 233-236

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2016     |    DOI: https://doi.org/10.1038/nmeth.3727

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Principles of Systems Biology, No. 2

Klausen, Michael Schantz ; Sommer, Morten Otto Alexander
in: Cell Systems, vol: 2, issue: 2, pages: 60-61

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.02.008

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Relation between tetR and tetA expression in tetracycline resistant Escherichia coli

Møller, Thea S. B. ; Overgaard, Martin ; Nielsen, Søren S. ; Bortolaia, Valeria ; Sommer, Morten Otto Alexander ; Guardabassi, Luca ; Olsen, John E.
in: B M C Microbiology, vol: 16, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1186/s12866-016-0649-z

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Simulating Serial-Target Antibacterial Drug Synergies Using Flux Balance Analysis

Krueger, Andrew S. ; Munck, Christian ; Dantas, Gautam ; Church, George M. ; Galagan, James ; Lehár, Joseph ; Sommer, Morten Otto Alexander
in: P L o S One, vol: 11, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1371/journal.pone.0147651

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Sponge Microbiota are a Reservoir of Functional Antibiotic Resistance Genes

Versluis, Dennis ; de Evgrafov, Mari Cristina Rodriguez ; Sommer, Morten Otto Alexander ; Sipkema, Detmer ; Smidt, Hauke ; van Passel, Mark W. J.
in: Frontiers in Microbiology, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.3389/fmicb.2016.01848

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Survival and evolution of a large multidrug resistance plasmid in new clinical bacterial hosts

Porse, Andreas ; Schønning, Kristian ; Munck, Christian ; Sommer, Morten Otto Alexander
in: Molecular Biology and Evolution, vol: 33, issue: 11, pages: 2860-2873

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1093/molbev/msw163

 

Transcriptional interactions suggest niche segregation among microorganisms in the human gut

Plichta, Damian Rafal ; Juncker, Agnieszka ; dos Santos, Marcelo Bertalan Quintanilha ; Rettedal, Elizabeth ; Gautier, Laurent ; Varela, Encarna ; Manichanh, Chaysavanh ; Fouqueray, Charlène ; Levenez, Florence ; Nielsen, Trine ; Doré, Joël ; MacHado, Ana Manuel Dantas ; de Evgrafov, Mari Cristina Rodriguez ; Hansen, Torben ; Jørgensen, Torben ; Bork, Peer ; Guarner, Francisco ; Pedersen, Oluf ; , ; Sommer, Morten Otto Alexander ; Ehrlich, S. Dusko ; Sicheritz-Pontén, Thomas ; Brunak, Søren ; Nielsen, Henrik Bjørn
in: Nature Microbiology, vol: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/nmicrobiol.2016.152

 

Voices of biotech

Amit, Ido ; Baker, David ; Barker, Roger ; Berger, Bonnie ; Bertozzi, Carolyn ; Bhatia, Sangeeta ; Biffi, Alessandra ; Demichelis, Francesca ; Doudna, Jennifer ; Dowdy, Steven F. ; Sommer, Morten Otto Alexander ; Zhang, Tian
in: Nature Biotechnology, vol: 34, issue: 3, pages: 270-275

Type: Contribution to newspaper - Feature article

Status: Published     |    Year: 2016     |    DOI: https://doi.org/10.1038/nbt.3502

2015
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Improved biosensor-based detection system

Rugbjerg, Peter ; Genee, Hans Jasper ; Sommer, Morten Otto Alexander
Patent no.: WO2015044456, Date: 2015-04-02

Type: Patent

Status: Published     |    Year: 2015

 

Advancing gut microbiome research using cultivation

Sommer, Morten OA
in: Current opinion in Microbiology, vol: 27, pages: 127-132

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.mib.2015.08.004

 

A synthetic suicide riboswitch for the high-throughput screening of metabolite production in Saccharomyces cerevisiae

Lee, Sang-Woo ; Oh, Min-Kuy
in: Metabolic Engineering, vol: 28, pages: 143-150

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2015.01.004

 

BaeSR, Involved in Envelope Stress Response, Protects against Lysogenic Conversion by Shiga Toxin 2-Encoding Phages

Imamovic, Lejla ; Martínez-Castillo, Alexandre ; Benavides, Carmen ; Muniesa, Maite
in: Infection and Immunity, vol: 83, issue: 4, pages: 1451-1457

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1128/IAI.02916-14

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Biosensor-based genome screening platform for the production of Biosynthetic Precursors and coFactors in E. coli.

Cardinale, Stefano ; Ye, Lumeng ; Sommer, Morten
part of: Book of Abstracts. DTU's Sustain Conference 2015, 2015, Technical University of Denmark, Lyngby
Presented at:
DTU Sustain Conference 2015

Type: Conference abstract in proceedings (Peer reviewed)

Status: Published     |    Year: 2015

 

Changing the way science is taught through gamified laboratories

Bonde, Mads ; Makransky, G. ; Wandall, J. ; Larsen, Mette Voldby ; Morsing, M. ; Jarmer, Hanne Østergaard ; Lopez-Cordoba, A. ; Sommer, Morten Otto Alexander
part of: EDULEARN15 Proceedings, pages: 6697-6703, 2016
Presented at:
The 7th International Conference on Education and New Learning Technologies

Type: Article in proceedings (Peer reviewed)

Status: Published     |    Year: 2015

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CTX-M-1 β-lactamase expression in Escherichia coli is dependent on cefotaxime concentration, growth phase and gene location.

Kjeldsen, Thea S. B. ; Overgaard, Martin ; Nielsen, Søren S. ; Bortolaia, Valeria ; Jelsbak, Lotte ; Sommer, Morten Otto Alexander ; Guardabassi, Luca ; Olsen, John E.
in: Journal of Antimicrobial Chemotherapy, vol: 70, issue: 1, pages: 62-70

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1093/jac/dku332

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deFUME: Dynamic exploration of functional metagenomic sequencing data

van der Helm, Eric ; Geertz-Hansen, Henrik Marcus ; Genee, Hans Jasper ; Malla, Sailesh ; Sommer, Morten Otto Alexander
in: BMC Research Notes, vol: 8, issue: 328, pages: 328

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1186/s13104-015-1281-y

 

Direct Mutagenesis of Thousands of Genomic Targets using Microarray-derived Oligonucleotides

Bonde, Mads ; Kosuri, Sriram ; Genee, Hans Jasper ; Sarup-Lytzen, Kira ; Church, George M. ; Sommer, Morten ; Wang, Harris H.
in: A C S Synthetic Biology, vol: 4, issue: 1, pages: 17-22

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1021/sb5001565

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Extended spectrum beta-lactamase-producing Escherichia coli forms filaments as an initial response to cefotaxime treatment

Kjeldsen, Thea S. B. ; Sommer, Morten Otto Alexander ; Olsen, John E.
in: B M C Microbiology, vol: 15, issue: 63

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1186/s12866-015-0399-3

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Flexible metabolic pathway construction using modular and divisible selection gene regulators

Rugbjerg, Peter ; Myling-Petersen, Nils ; Sommer, Morten Otto Alexander
in: Metabolic Engineering, vol: 31, pages: 189-197

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1016/j.ymben.2015.08.004

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Limited dissemination of the wastewater treatment plant core resistome

Munck, Christian ; Albertsen, Mads ; Telke, Amar ; Ellabaan, Mostafa M Hashim ; Nielsen, Per Halkjær ; Sommer, Morten Otto Alexander
in: Nature Communications, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1038/ncomms9452

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LYRA, a webserver for lymphocyte receptor structural modeling.

Klausen, Michael Schantz ; Anderson, Mads Valdemar ; Jespersen, Martin Closter ; Nielsen, Morten ; Marcatili, Paolo
in: Nucleic Acids Research, vol: 43, issue: W1, pages: W349-W355

Type: Journal article (Peer reviewed)

Status: E-pub ahead of print     |    Year: 2015     |    DOI: https://doi.org/10.1093/nar/gkv535

 

Production of Industrially Relevant Isoprenoid Compounds in Engineered Microbes

Vickers, Claudia E. ; Behrendorff, James B. Y. H. ; Bongers, Mareike ; Brennan, Timothy C. R. ; Bruschi, Michele ; Nielsen, Lars K.
part of: Microorganisms in Biorefineries, pages: 303-334, 2015, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1007/978-3-662-45209-7_11

 

Protocols for the Production and Analysis of Isoprenoids in Bacteria and Yeast

Vickers, Claudia E. ; Bongers, Mareike ; F. Bydder, Sarah ; Chrysanthopoulos, Panagiotis ; Hodson, Mark P.
part of: Hydrocarbon and Lipid Microbiology Protocols, pages: 23-52, 2015, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1007/8623_2015_107

 

Software-Supported USER Cloning Strategies for Site-Directed Mutagenesis and DNA Assembly

Genee, Hans Jasper ; Bonde, Mads Tvillinggaard ; Bagger, Frederik Otzen ; Jespersen, Jakob Berg ; Sommer, Morten O. A. ; Wernersson, Rasmus ; Olsen, Lars Rønn
in: A C S Synthetic Biology, vol: 4, issue: 3, pages: 342-349

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1021/sb500194z

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Systems analysis of methylerythritol-phosphate pathway flux in E.coli

Bongers, Mareike ; Chrysanthopoulos, Panagiotis K. ; Behrendorff, James B. Y. H. ; Hodson, Mark P. ; Vickers, Claudia E. ; Nielsen, Lars K.
in: Microbial Cell Factories, vol: 14

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2015     |    DOI: https://doi.org/10.1186/s12934-015-0381-7