Publications

Publikationer rss feed

2019
 

Synthetic Biology of Yeast

Liu, Zihe ; Zhang, Yueping ; Nielsen, Jens
in: Biochemistry, vol: 58, issue: 11, pages: 1511-1520

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.biochem.8b01236

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Identification of genes involved in shea butter biosynthesis from Vitellaria paradoxa fruits through transcriptomics and functional heterologous expression

Wei, Yongjun ; Ji, Boyang ; Siewers, Verena ; Xu, Deyang ; Halkier, Barbara Ann ; Nielsen, Jens
in: Applied Microbiology and Biotechnology, vol: 103, issue: 9, pages: 3727-3736

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/s00253-019-09720-3

 

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13396

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Accelerated H-2 Evolution during Microbial Electrosynthesis with Sporomusa ovata

Tremblay, Pier-Luc ; Faraghiparapari, Neda ; Zhang, Tian
in: Catalysts, vol: 9, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3390/catal9020166

 

A comprehensive metabolic map for production of bio-based chemicals

Lee, Sang Yup ; Kim, Hyun Uk ; Chae, Tong Un ; Cho, Jae Sung ; Kim, Je Woong ; Shin, Jae Ho ; Kim, Dong In ; Ko, Yoo Sung ; Jang, Woo Dae ; Jang, Yu Sin
in: Nature Catalysis, vol: 2, issue: 1, pages: 18-33

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41929-018-0212-4

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A consensus S. cerevisiae metabolic model Yeast8 and its ecosystem for comprehensively probing cellular metabolism

Lu, Hongzhong ; Li, Feiran ; Sánchez, Benjamín J ; Zhu, Zhengming ; Li, Gang ; Domenzain, Iván ; Marcišauskas, Simonas ; Anton, Petre Mihail ; Lappa, Dimitra ; Lieven, Christian ; Beber, Moritz Emanuel ; Sonnenschein, Nikolaus ; Kerkhoven, Eduard J ; Nielsen, Jens
in: Nature Communications, vol: 10, issue: 1, pages: 3586

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-11581-3

 

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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A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae

Zhang, Yueping ; Wang, Juan ; Wang, Zibai ; Zhang, Yiming ; Shi, Shuobo ; Nielsen, Jens ; Liu, Zihe
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-09005-3

 

A High-Throughput Mass Spectrometric Enzyme Activity Assay Enabling the Discovery of Cytochrome P450 Biocatalysts

de Rond, Tristan ; Gao, Jian ; Zargar, Amin ; de Raad, Markus ; Cunha, Jack ; Northen, Trent R. ; Keasling, Jay D.
in: ANGEWANDTE CHEMIE, vol: 58, issue: 30, pages: 10114-10119

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/anie.201901782

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Aledb 1.0: A database of mutations from adaptive laboratory evolution experimentation

Phaneuf, Patrick V. ; Gosting, Dennis ; Palsson, Bernhard O. ; Feist, Adam M.
in: Nucleic acids research, vol: 47, issue: D1, pages: D1164-D1171

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky983

 

Analysis of Pseudomonas putida growth on non-trivial carbon sources using transcriptomics and genome-scale modeling

D'Arrigo, Isotta ; Cardoso, João G. R. ; Rennig, Maja ; Sonnenschein, Nikolaus ; Herrgård, Markus J. ; Long, Katherine S.
in: Environmental Microbiology Reports, vol: 11, issue: 2, pages: 87-97

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1758-2229.12704

 

Antibiotic Lethality Is Impacted by Nutrient Availabilities: New Insights from Machine Learning

Nielsen, Jens
in: CELL, vol: 177, issue: 6, pages: 1373-1374

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cell.2019.05.015

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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

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antiSMASH 5.0: updates to the secondary metabolite genome mining pipeline

Blin, Kai ; Shaw, Simon ; Steinke, Katharina ; Villebro, Rasmus ; Ziemert, Nadine ; Lee, Sang Yup ; Medema, Marnix H ; Weber, Tilmann
in: Nucleic acids research, vol: 87, issue: W2, pages: W81-W87

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gkz310

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A rapid methods development workflow for high-throughput quantitative proteomic applications

Chen, Yan ; Vu, Jonathan ; Thompson, Mitchell G. ; Sharpless, William A. ; Chan, Leanne Jade G. ; Gin, Jennifer W. ; Keasling, Jay D. ; Adams, Paul D. ; Petzold, Christopher J.
in: PLOS ONE, vol: 14, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pone.0211582

 

Are we there yet? How and when specific biotechnologies will improve human health

O'Day, Elizabeth ; Hosta-Rigau, Leticia ; Oyarzún, Diego A. ; Okano, Hideyuki ; de Lorenzo, Víctor ; von Kameke, Conrad ; Alsafar, Habiba ; Cao, Cong ; Chen, Guo-Qiang ; Ji, Weizhi ; Roberts, Richard J. ; Ronaghi, Mostafa ; Yeung, Karen ; Zhang, Feng ; Lee, Sang Yup
in: Biotechnology Journal, vol: 14, issue: 1, pages: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800195

 

A robotic platform to screen aqueous two-phase systems for overcoming inhibition in enzymatic reactions

Bussamra, Bianca Consorti ; Gomes, Joana Castro ; Freitas, Sindelia ; Mussatto, Solange I. ; da Costa, Aline Carvalho ; van der Wielen, Luuk ; Ottens, Marcel
in: Bioresource Technology, vol: 280, pages: 37-50

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biortech.2019.01.136

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A Systematic Investigation of the Malignant Functions and Diagnostic Potential of the Cancer Secretome

Robinson, Jonathan L. ; Feizi, Amir ; Uhlén, Mathias ; Nielsen, Jens
in: Cell Reports, vol: 26, issue: 10, pages: 2622-2635

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.celrep.2019.02.025

 

A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action

Yang, Jason H ; Wright, Sarah N ; Hamblin, Meagan ; McCloskey, Douglas ; Alcantar, Miguel A ; Schrübbers, Lars ; Lopatkin, Allison J ; Satish, Sangeeta ; Nili, Amir ; Palsson, Bernhard O ; Walker, Graham C ; Collins, James J
in: CELL

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.cell.2019.04.016

 

Biochemistry, genetics and biotechnology of glycerol utilization in Pseudomonas species

Poblete-Castro, Ignacio ; Wittmann, Christoph ; Nikel, Pablo Ivan
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13400

 

BiP Inducer X: An ER Stress Inhibitor for Enhancing Recombinant Antibody Production in CHO Cell Culture

Kwang Ha, Tae ; Hansen, Anders H ; Kildegaard, Helene Faustrup ; Min Lee, Gyun
in: Biotechnology Journal

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201900130

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BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data

Lachance, Jean Christophe ; Lloyd, Colton J. ; Monk, Jonathan M. ; Yang, Laurence ; Sastry, Anand V. ; Seif, Yara ; Palsson, Bernhard O. ; Rodrigue, Sébastien ; Feist, Adam M. ; King, Zachary A. ; Jacques, Pierre Étienne
in: PLOS Computational Biology, vol: 15, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1006971

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Breaking the state-of-the-art in the chemical industry with new-to-Nature products via synthetic microbiology

Martinelli, Laura ; Nikel, Pablo Ivan
in: Microbial Biotechnology, vol: 12, issue: 2, pages: 187-190

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13372

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Building a global alliance of biofoundries

Hillson, Nathan ; Caddick, Mark ; Cai, Yizhi ; Carrasco, Jose A. ; Chang, Matthew Wook ; Curach, Natalie C. ; Bell, David J. ; Le Feuvre, Rosalind ; Friedman, Douglas C. ; Fu, Xiongfei ; Gold, Nicholas D. ; Herrgård, Markus J. ; Holowko, Maciej B. ; Johnson, James R. ; Johnson, Richard A. ; Keasling, Jay D. ; Kitney, Richard I. ; Kondo, Akihiko ; Liu, Chenli ; Martin, Vincent J.J. ; Menolascina, Filippo ; Ogino, Chiaki ; Patron, Nicola J. ; Pavan, Marilene ; Poh, Chueh Loo ; Pretorius, Isak S. ; Rosser, Susan J. ; Scrutton, Nigel S. ; Storch, Marko ; Tekotte, Hille ; Travnik, Evelyn ; Vickers, Claudia E. ; Yew, Wen Shan ; Yuan, Yingjin ; Zhao, Huimin ; Freemont, Paul S.
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-10079-2

 

Cellular responses to reactive oxygen species are predicted from molecular mechanisms

Yang, Laurence ; Mih, Nathan ; Anand, Amitesh ; Park, Joon Ho ; Tan, Justin ; Yurkovich, James T. ; Monk, Jonathan M. ; Lloyd, Colton J. ; Sandberg, Troy E. ; Seo, Sang Woo ; Kim, Donghyuk ; Sastry, Anand V. ; Phaneuf, Patrick ; Gao, Ye ; Broddrick, Jared T. ; Chen, Ke ; Heckmann, David ; Szubin, Richard ; Hefner, Ying ; Feist, Adam M. ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 116, issue: 28, pages: 14368-14373

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1073/pnas.1905039116

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Changing substrate specificity and iteration of amino acid chain elongation in glucosinolate biosynthesis through targeted mutagenesis of Arabidopsis methylthioalkylmalate synthase 1

Petersen, Annette ; Gram Hansen, Lea ; Mirza, Nadia ; Crocoll, Christoph ; Mirza, Osman ; Halkier, Barbara Ann
in: Bioscience Reports, vol: 39, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1042/BSR20190446

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Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media

Poudel, Saugat ; Tsunemoto, Hannah ; Meehan, Michael ; Szubin, Richard ; Olson, Connor A. ; Lamsa, Anne ; Seif, Yara ; Dillon, Nicholas ; Vrbanac, Alison ; Sugie, Joseph ; Dahesh, Samira ; Monk, Jonathan M. ; Dorrestein, Pieter C. ; Pogliano, Joseph ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Scientific Data, vol: 6, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41597-019-0051-4

 

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

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Chasing bacterial chassis for metabolic engineering: a perspective review from classical to non-traditional microorganisms

Calero, Patricia ; Nikel, Pablo I.
in: Microbial Biotechnology, vol: 12, issue: 1, pages: 98-124

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13292

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Chromophore pre-maturation for improved speed and sensitivity of split-GFP monitoring of protein secretion

Lundqvist, Magnus ; Thalén, Niklas ; Volk, Anna Luisa ; Hansen, Henning Gram ; von Otter, Eric ; Nygren, Per-Åke ; Uhlén, Mathias ; Rockberg, Johan
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-018-36559-x

 

Cocktails of human monoclonal IgG antibodies capable of neutralizing dendrotoxin-mediated neurotoxicity of black mamba venom in vivo

Laustsen, Andreas H. ; Karatt-Vellatt, Aneesh ; Masters, Edward W. ; Arias, Ana Silvia ; Pus, Urska ; Knudsen, Cecilie ; Oscoz, Saioa ; Slavny, Peter ; Griffiths, Daniel T. ; Luther, Alice M. ; Leah, Rachael A. ; Lindholm, Majken ; Lomonte, Bruno ; Mar a Guti rrez, Jos ; McCafferty, John
in: Toxicon, vol: 159, issue: Supp. 1, pages: S5-S6
Presented at:
19th EU-IST Congress 2018

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.toxicon.2018.11.331

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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

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Combating viral contaminants in CHO cells by engineering innate immunity

Chiang, Austin W.T. ; Li, Shangzhong ; Kellman, Benjamin P. ; Chattopadhyay, Gouri ; Zhang, Yaqin ; Kuo, Chih Chung ; Gutierrez, Jahir M. ; Ghazi, Faezeh ; Schmeisser, Hana ; Ménard, Patrice ; Petersen Bjørn, Sara ; Voldborg, Bjørn Gunnar ; Rosenberg, Amy S. ; Puig, Montserrat ; Lewis, Nathan E.
in: Scientific Reports, vol: 9, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41598-019-45126-x

 

Combined Rapid Injection NMR and Simulation Approach to Probe Redox-Dependent Pathway Control in Living Cells

Jensen, Pernille Rose ; Matos, Marta ; Sonnenschein, Nikolaus ; Meier, Sebastian
in: Analytical Chemistry, vol: 91, issue: 8, pages: 5395-5402

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acs.analchem.9b00660

 

Combining Pro-peptide Engineering and Multisite Saturation Mutagenesis to Improve the Catalytic Potential of Keratinase

Su, Chang ; Gong, Jin Song ; Sun, Yu Xin ; Qin, Jiufu ; Zhai, Shen ; Li, Heng ; Li, Hui ; Lu, Zhen Ming ; Xu, Zheng Hong ; Shi, Jin Song
in: A C S Synthetic Biology, vol: 8, issue: 2, pages: 425-433

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.8b00442

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Comparative Transcriptome Analysis Shows Conserved Metabolic Regulation during Production of Secondary Metabolites in Filamentous Fungi

Nielsen, Jens ; Prigent, Sylvain ; Grijseels, Sietske ; Workman, Mhairi ; Ji, Boyang
in: mSystems, vol: 4, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1128/mSystems.00012-19

 

Complete biosynthesis of cannabinoids and their unnatural analogues in yeast

Luo, Xiaozhou ; Reiter, Michael A. ; d’Espaux, Leo ; Wong, Jeff ; Denby, Charles M. ; Lechner, Anna ; Zhang, Yunfeng ; Grzybowski, Adrian T. ; Harth, Simon ; Lin, Weiyin ; Lee, Hyunsu ; Yu, Changhua ; Shin, John ; Deng, Kai ; Benites, Veronica T. ; Wang, George ; Baidoo, Edward E.K. ; Chen, Yan ; Dev, Ishaan ; Petzold, Christopher J. ; Keasling, Jay D.
in: Nature, vol: 567, issue: 7746, pages: 123-126

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41586-019-0978-9

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Computational methods for microbial cell factory engineering aided by evolution

Jensen, Kristian

Type: Ph.D. thesis

Status: Published     |    Year: 2019

 

Construction of mini-chemostats for high-throughput strain characterization

Bergenholm, David ; Liu, Guodong ; Hansson, David ; Nielsen, Jens
in: Biotechnology and Bioengineering, vol: 116, issue: 5, pages: 1029-1038

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/bit.26931

 

Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0

Heirendt, Laurent ; Arreckx, Sylvain ; Pfau, Thomas ; Mendoza, Sebastian N. ; Richelle, Anne ; Heinken, Almut ; Haraldsdottir, Hulda S. ; Wachowiak, Jacek ; Keating, Sarah M. ; Vlasov, Vanja ; Magnusdottir, Stefania ; Ng, Chiam Yu ; Preciat, German ; Zagare, Alise ; Chan, Siu Hung Joshua ; Aurich, Maike K. ; Clancy, Catherine M. ; Modamio, Jennifer ; Sauls, John T. ; Noronha, Alberto ; Bordbar, Aarash ; Cousins, Benjamin ; El Assal, Diana C. ; Valcarcel, Luis V. ; Apaolaza, Inigo ; Ghaderi, Susan ; Ahookhosh, Masoud ; Ben Guebila, Marouen ; Kostromins, Andrejs ; Sompairac, Nicolas ; Le, Hoai M. ; Ma, Ding ; Sun, Yuekai ; Wang, Lin ; Yurkovich, James T. ; Oliveira, Miguel A. P. ; Vuong, Phan T. ; El Assal, Lemmer P. ; Kuperstein, Inna ; Zinovyev, Andrei ; Hinton, H. Scott ; Bryant, William A. ; Aragon Artacho, Francisco J. ; Planes, Francisco J. ; Stalidzans, Egils ; Maass, Alejandro ; Vempala, Santosh ; Hucka, Michael ; Saunders, Michael A. ; Maranas, Costas D. ; Lewis, Nathan E. ; Sauter, Thomas ; Palsson, Bernhard O. ; Thiele, Ines ; Fleming, Ronan M. T.
in: Nature Protocols, vol: 14, issue: 3, pages: 639-702

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41596-018-0098-2

 

CRISPR/Cas9 as a Genome Editing Tool for Targeted Gene Integration in CHO Cells

Sergeeva, Daria ; Manuel Camacho Zaragoza, Jose ; Lee, Jae Seong ; Kildegaard, Helene Faustrup
part of: CRISPR Gene Editing, pages: 213-232, 2019

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-9170-9_13

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CRISPR/Cas9-RNAi system for combinatorial metabolic engineering of Saccharomyces cerevisiae

Kildegaard, Kanchana Rueksomtawin ; Ribeiro Ramos Tramontin, Larissa ; Chekina, Ksenia ; Li, Mingji ; Goedecke, Tobias Justus ; Kristensen, Mette ; Borodina, Irina
in: Yeast, vol: 36, issue: 5, pages: 237-247

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/yea.3390

 

CRISPR/Cas-based genome engineering in natural product discovery

Tong, Yaojun ; Weber, Tilmann ; Lee, Sang Yup
in: Natural Product Reports

Type: Review (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1039/C8NP00089A

 

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

 

Dynamic investigation and modeling of the nitrogen co-metabolism in Methylococcus capsulatus (Bath)

Petersen, Leander A. H. ; Lieven, Christian ; Nandy, Subir K. ; Villadsen, John ; Jørgensen, Sten B. ; Christensen, Ib ; Gernaey, Krist V.
in: Biotechnology and Bioengineering

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1002/bit.27113

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DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression

Yang, Laurence ; Ebrahim, Ali ; Lloyd, Colton J. ; Saunders, Michael A. ; Palsson, Bernhard
in: BMC Systems Biology, vol: 13, issue: 2

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12918-018-0675-6

 

Effects of overexpression of STB5 in Saccharomyces cerevisiae on fatty acid biosynthesis, physiology and transcriptome

Bergman, Alexandra ; Vitay, Dóra ; Hellgren, John ; Chen, Yun ; Nielsen, Jens ; Siewers, Verena
in: FEMS Yeast Research, vol: 19, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/femsyr/foz027

 

Efficient and Precise Genome Editing in Shewanella with Recombineering and CRISPR/Cas9-Mediated Counter-Selection

Corts, Anna D ; Thomason, Lynn C ; Gill, Ryan T ; Gralnick, Jeffrey A
in: ACS Synthetic Biology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.9b00188

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Engineered Reversal of Function in Glycolytic Yeast Promoters

Rajkumar, Arun S. ; Özdemir, Emre ; Lis, Alicia V. ; Schneider, Konstantin ; Qin, Jiufu ; Jensen, Michael K. ; Keasling, Jay D.
in: ACS Synthetic Biology, vol: 8, issue: 6, pages: 1462-1468

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.9b00027

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Engineering glucose metabolism of escherichia coli under nitrogen starvation

Chubukov, Victor ; Desmarais, John James ; Wang, George ; Chan, Leanne Jade G. ; Baidoo, Edward E.K. ; Petzold, Christopher J. ; Keasling, Jay D. ; Mukhopadhyay, Aindrila
in: n p j Systems Biology and Applications, vol: 3, issue: 1

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1038/npjsba.2016.35

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Engineering Saccharomyces cerevisiae cells for production of fatty acid-derived biofuels and chemicals

Hu, Yating ; Zhu, Zhiwei ; Nielsen, Jens ; Siewers, Verena
in: Biology Open, vol: 9, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1098/rsob.190049

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Enzyme promiscuity shapes adaptation to novel growth substrates

Guzmán, Gabriela I. ; Sandberg, Troy E. ; LaCroix, Ryan A. ; Nyerges, Ákos ; Papp, Henrietta ; de Raad, Markus ; King, Zachary A. ; Hefner, Ying ; Northen, Trent R. ; Notebaart, Richard A. ; Pál, Csaba ; Palsson, Bernhard O. ; Papp, Balázs ; Feist, Adam M.
in: Molecular Systems Biology, vol: 15, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.15252/msb.20188462

 

Evolutionary approaches for engineering industrially-relevant phenotypes in bacterial cell factories

Fernandez-Cabezon, Lorena ; Cros, Antonin ; Nikel, Pablo Ivan
in: Biotechnology Journal

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800439

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Evolutionary highways to persistent bacterial infection

Bartell, Jennifer ; Sommer, Lea M. ; Haagensen, Janus Anders Juul ; Loch, Anne ; Espinosa Portero, Rocio ; Molin, Søren ; Johansen, Helle Krogh
in: Nature Communications, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-08504-7

 

Evolving metabolism of 2,4-dinitrotoluene triggers SOS-independent diversification of host cells

Akkaya, Özlem ; Nikel, Pablo I. ; Pérez-Pantoja, Danilo ; de Lorenzo, Víctor
in: Environmental Microbiology, vol: 21, issue: 1, pages: 314-326

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1462-2920.14459

 

FadR-Based Biosensor-Assisted Screening for Genes Enhancing Fatty Acyl-CoA Pools in Saccharomyces cerevisiae

Dabirian, Yasaman ; Gonçalves Teixeira, Paulo ; Nielsen, Jens ; Siewers, Verena ; David, Florian
in: ACS Synthetic Biology, vol: 8, issue: 8, pages: 1788-1800

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.9b00118

 

Filamentous bacteriophages are associated with chronic Pseudomonas lung infections and antibiotic resistance in cystic fibrosis

Burgener, Elizabeth B. ; Sweere, Johanna M. ; Bach, Michelle S. ; Secor, Patrick R. ; Haddock, Naomi ; Jennings, Laura K. ; Marvig, Rasmus Lykke ; Johansen, Helle Krogh ; Rossi, Elio ; Cao, Xiou ; Tian, Lu ; Nedelec, Laurence ; Molin, Søren ; Bollyky, Paul L. ; Milla, Carlos E.
in: Science Translational Medicine, vol: 11, issue: 488

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1126/scitranslmed.aau9748

 

Fructo-oligosaccharides (FOS) production by fungal submerged culture using aguamiel as a low-cost by-product

Muñiz-Márquez, Diana B. ; Teixeira, José A. ; Mussatto, Solange I. ; Contreras-Esquivel, Juan C. ; Rodríguez-Herrera, Raúl ; Aguilar, Cristóbal N.
in: L W T- Food Science and Technology, vol: 102, pages: 75-79

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.lwt.2018.12.020

 

Functional implementation of a linear glycolysis for sugar catabolism in Pseudomonas putida

Sánchez-Pascuala, Alberto ; Fernandez-Cabezon, Lorena ; de Lorenzo, Víctor ; Nikel, Pablo Ivan
in: Metabolic Engineering, vol: 54, pages: 200-211

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2019.04.005

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Generation of an E. coli platform strain for improved sucrose utilization using adaptive laboratory evolution

Mohamed, Elsayed Tharwat Tolba ; Mundhada, Hemanshu ; Landberg, Jenny Marie ; Cann, Isaac ; Mackie, Roderick I. ; Nielsen, Alex Toftgaard ; Herrgard, Markus J. ; Feist, Adam M.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1165-2

 

Genetic engineering approaches to improve post-translational modification of biopharmaceuticals in different production platforms

Amann, Thomas ; Schmieder, Valerie ; Kildegaard, Helene Faustrup ; Borth, Nicole ; Andersen, Mikael Rørdam
in: Biotechnology and Bioengineering

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1002/bit.27101

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Genome editing of lactic acid bacteria: opportunities for food, feed, pharma and biotech

Börner, Rosa A. ; Kandasamy, Vijayalakshmi ; Axelsen, Amalie M. ; Nielsen, Alex T. ; Bosma, Elleke F.
in: F E M S Microbiology Letters, vol: 366, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/femsle/fny291

 

Genome-Scale Metabolic Reconstruction of Actinomycetes for Antibiotics Production

Mohite, Omkar Satyavan ; Weber, Tilmann ; Kim, Hyun Uk ; Lee, Sang Yup
in: Biotechnology Journal, vol: 14, issue: 1

Type: Review (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1002/biot.201800377

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Genome-wide systematic identification of methyltransferase recognition and modification patterns

Jensen, Torbjørn Ølshøj ; Tellgren-Roth, Christian ; Redl, Stephanie Maria Anna ; Maury, Jérôme ; Baallal Jacobsen, Simo Abdessamad ; Pedersen, Lasse Ebdrup ; Nielsen, Alex Toftgaard
in: Nature Communications, vol: 10, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41467-019-11179-9

 

Green synthesis of silver nanoparticles using acacia lignin, their cytotoxicity, catalytic, metal ion sensing capability and antibacterial activity

Aadil, Keshaw R. ; Pandey, Neha ; Mussatto, Solange I. ; Jha, Harit
in: Journal of Environmental Chemical Engineering, vol: 7, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.jece.2019.103296

 

Harnessing human monoclonal antibodies for neutralisation of dendrotoxins in a murine model

Knudsen, Cecilie ; Arias, Ana Silvia ; Lomonte, Bruno ; Mar a Guti rrez, Jos ; Puš, rška ; Oscoz, Saioa ; Masters, Edward W. ; Luther, Alice M. ; Griffiths, Daniel T. ; Olesen, Majken L. ; Leah, Rachael A ; Slavny, Peter ; Karatt-Vellatt, Aneesh ; McCafferty, John ; Laustsen, Andreas H.
in: Toxicon, vol: 159, issue: Supp. 1, pages: S14
Presented at:
19th EU-IST Congress 2018

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.toxicon.2018.11.363

 

Harnessing phage display technology for generating fully human IgG antibodies that neutralise elapid neurotoxins

Karatt-Vellatt, Aneesh ; Laustsen, Andreas Hougaard ; Masters, Edward W. ; Oscoz, Saioa ; Pus, Urska ; Knudsen, Cecilie ; Slavny, Peter ; Luther, Alice M. ; Leah, Rachael A. ; Grifiths, Daniel T. ; Olesen, Majken L. ; Lomonte, Bruno ; Gutiérrez, José María ; McCafferty, John
in: Toxicon, vol: 158, issue: Suppl. 1, pages: s18-s18

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.toxicon.2018.10.068

 

Harnessing xylose pathways for biofuels production

Li, Xiaowei ; Chen, Yun ; Nielsen, Jens
in: Current Opinion in Biotechnology, vol: 57, pages: 56-65

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.copbio.2019.01.006

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Heterologous phosphoketolase expression redirects flux towards acetate, perturbs sugar phosphate pools and increases respiratory demand in Saccharomyces cerevisiae

Bergman, Alexandra ; Hellgren, John ; Moritz, Thomas ; Siewers, Verena ; Nielsen, Jens ; Chen, Yun
in: Microbial Cell Factories, vol: 18, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1072-6

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High-Performance Biocomputing in Synthetic Biology-Integrated Transcriptional and Metabolic Circuits

Goni-Moreno, Angel ; Nikel, Pablo Ivan
in: Frontiers in Bioengineering and Biotechnology, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fbioe.2019.00040

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Meta synthetic biology: controlling the evolution of engineered living systems

Nørholm, Morten H. H.
in: Microbial Biotechnology, vol: 12, issue: 1, pages: 35-37

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13350

 

Improving recombinant bone morphogenetic protein-4 (BMP-4) production by autoregulatory feedback loop removal using BMP receptor-knockout CHO cell lines

Kim, Che Lin ; Min Lee, Gyun
in: Metabolic Engineering, vol: 52, pages: 57-67

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2018.11.003

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Improving Reproducibility in Synthetic Biology

Jessop-Fabre, Mathew M. ; Sonnenschein, Nikolaus
in: Frontiers in Bioengineering and Biotechnology, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fbioe.2019.00018

 

Increased carbon dioxide reduction to acetate in a microbial electrosynthesis reactor with a reduced graphene oxide-coated copper foam composite cathode

Aryal, Nabin ; Wan, Lulu ; Overgaard, Marc Hvid ; Stoot, Adam C. ; Chen, Yiming ; Tremblay, Pier Luc ; Zhang, Tian
in: Bioelectrochemistry, vol: 128, pages: 83-93

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.bioelechem.2019.03.011

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Increasing jojoba-like wax ester production in Saccharomyces cerevisiae by enhancing very long-chain, monounsaturated fatty acid synthesis

Wenning, Leonie ; Ejsing, Christer S. ; David, Florian ; Sprenger, Richard R. ; Nielsen, Jens ; Siewers, Verena
in: Microbial Cell Factories, vol: 18, issue: 49

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-019-1098-9

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Integration of enzymatic data in Bacillus subtilis genome-scale metabolic model improves phenotype predictions and enables in silico design of poly-γ-glutamic acid production strains

Massaiu, Ilaria ; Pasotti, Lorenzo ; Sonnenschein, Nikolaus ; Rama, Erlinda ; Cavaletti, Matteo ; Magni, Paolo ; Calvio, Cinzia ; Herrgård, Markus J.
in: Microbial Cell Factories, vol: 18

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12934-018-1052-2

 

Integration of subcritical water pretreatment and anaerobic digestion technologies for valorization of açai processing industries residues

Maciel-Silva, Francisco W. ; Mussatto, Solange I. ; Forster-Carneiro, Tânia
in: Journal of Cleaner Production, vol: 228, pages: 1131-1142

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.jclepro.2019.04.362

 

Isolation and physicochemical characterization of different lignin streams generated during the second-generation ethanol production process

Castro, Rafael C.A. ; Ferreira, Isabela S. ; Roberto, Inês C. ; Mussatto, Solange I.
in: International Journal of Biological Macromolecules, vol: 129, pages: 497-510

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ijbiomac.2019.01.148

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Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism

Cheng, Chuankai ; O'Brien, Edward J. ; McCloskey, Douglas ; Utrilla, Jose ; Olson, Connor ; LaCroix, Ryan A. ; Sandberg, Troy E. ; Feist, Adam M. ; Palsson, Bernhard O. ; King, Zachary A.
in: PLOS Computational Biology, vol: 15, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1007066

 

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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Life Cycle Assessment of chosen Biochemicals and Bio-based polymers

Ögmundarson, Ólafur

Type: Ph.D. thesis

Status: Published     |    Year: 2019

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Linking genetic, metabolic, and phenotypic diversity among Saccharomyces cerevisiae strains using multi-omics associations

Kang, Kang ; Bergdahl, Basti ; Machado, Daniel ; Dato, Laura ; Han, Ting-Li ; Li, Jun ; Villas-Boas, Silas ; Herrgård, Markus J ; Förster, Jochen ; Panagiotou, Gianni
in: GigaScience, vol: 8, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/gigascience/giz015

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Lipid engineering combined with systematic metabolic engineering of Saccharomyces cerevisiae for high-yield production of lycopene

Ma, Tian ; Shi, Bin ; Ye, Ziling ; Li, Xiaowei ; Liu, Min ; Chen, Yun ; Xia, Jiang ; Nielsen, Jens ; Deng, Zixin ; Liu, Tiangang
in: Metabolic Engineering, vol: 52, pages: 134-142

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2018.11.009

 

Liquid chromatography and mass spectrometry analysis of isoprenoid intermediates in Escherichia coli

Baidoo, Edward E.K. ; Wang, George ; Joshua, Chijioke J. ; Benites, Veronica Teixeira ; Keasling, Jay D.
part of: Microbial Metabolomics, pages: 209-224, 2019, Humana Press, New York

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1007/978-1-4939-8757-3_11

 

Machine Learning Applied to Predicting Microorganism Growth Temperatures and Enzyme Catalytic Optima

Li, Gang ; Rabe, Kersten S. ; Nielsen, Jens ; Engqvist, Martin K.M.
in: ACS Synthetic Biology, vol: 8, issue: 6, pages: 1411-1420

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1021/acssynbio.9b00099

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Massively parallel fitness profiling reveals multiple novel enzymes in Pseudomonas putida lysine metabolism

Thompson, Mitchell G. ; Blake-Hedges, Jacquelyn M. ; Cruz-Morales, Pablo ; Barajas, Jesus F. ; Curran, Samuel C. ; Eiben, Christopher B. ; Harris, Nicholas C. ; Benites, Veronica T. ; Gin, Jennifer W. ; Sharpless, William A. ; Twigg, Frederick F. ; Skyrud, Will ; Krishna, Rohith N. ; Pereira, Jose Henrique ; Baidoo, Edward E.K. ; Petzold, Christopher J. ; Adams, Paul D. ; Arkin, Adam P. ; Deutschbauer, Adam M. ; Keasling, Jay D.
in: mBio, vol: 10, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1128/mBio.02577-18

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Metagenomic analysis of bile salt biotransformation in the human gut microbiome

Das, Promi ; Marcišauskas, Simonas ; Ji, Boyang ; Nielsen, Jens
in: BMC Genomics, vol: 20

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12864-019-5899-3

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Metagenomic analysis of microbe-mediated vitamin metabolism in the human gut microbiome

Das, Promi ; Babaei, Parizad ; Nielsen, Jens
in: BMC Genomics, vol: 20

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12864-019-5591-7

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Minimal cells, maximal knowledge

Lachance, Jean Christophe ; Rodrigue, Sébastien ; Palsson, Bernhard O.
in: eLife, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.7554/eLife.45379

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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

 

Mitigating Clonal Variation in Recombinant Mammalian Cell Lines

Lee, Jae Seong ; Kildegaard, Helene Faustrup ; Lewis, Nathan E ; Min Lee, Gyun
in: Trends in Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.tibtech.2019.02.007

 

Modelling approaches for studying the microbiome

Kumar, Manish ; Ji, Boyang ; Zengler, Karsten ; Nielsen, Jens
in: Nature Microbiology, vol: 4, issue: 8, pages: 1253-1267

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41564-019-0491-9

 

Monoclonal human IgGs capable of neutralizing elapid neurotoxins in vivo

Pus, Urska ; Laustsen, Andreas Hougaard ; Karatt-Vellatt, Aneesh ; Griffiths, Daniel T. ; Oscoz, Saioa ; Andersen, Mikael Rørdam ; Harrison, Robert ; Casewell, Nicholas ; Lomonte, Bruno ; McCafferty, John ; Gutiérrez, José María
in: Toxicon, vol: 158, issue: Suppl. 1, pages: S44-S44

Type: Conference abstract in journal (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.toxicon.2018.10.154