Publications

Publikationer rss feed

2019
 

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

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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

 

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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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

 

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

 

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1002/prot.25674

 

Pretreatment of switchgrass by steam explosion in a semi-continuous pre-pilot reactor

Bonfiglio, Fernando ; Cagno, Matías ; Rey, Fabiana ; Torres, Marina ; Böthig, Silvia ; Menéndez, Pilar ; Mussatto, Solange I.
in: Biomass and Bioenergy, vol: 121, pages: 41-47

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biombioe.2018.12.013

 

Protocols for RecET-based markerless gene knockout and integration to express heterologous biosynthetic gene clusters in Pseudomonas putida

Choi, Kyeong Rok ; Lee, Sang Yup
in: Microbial Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13374

 

Pseudogene repair driven by selection pressure applied in experimental evolution

Anand, Amitesh ; Olson, Connor A. ; Yang, Laurence ; Sastry, Anand V. ; Catoiu, Edward ; Choudhary, Kumari Sonal ; Phaneuf, Patrick V. ; Sandberg, Troy E. ; Xu, Sibei ; Hefner, Ying ; Szubin, Richard ; Feist, Adam ; Palsson, Bernhard
in: Nature Microbiology, vol: 4, issue: 3, pages: 386-389

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1038/s41564-018-0340-2

 

Sequence-based classification of type II polyketide synthase biosynthetic gene clusters for antiSMASH

Villebro, Rasmus ; Shaw, Simon ; Blin, Kai ; Weber, Tilmann
in: Journal of Industrial Microbiology and Biotechnology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1007/s10295-018-02131-9

 

Simultaneous quantification of multiple bacterial metabolites using surface-enhanced Raman scattering

Morelli, Lidia ; Centorbi, Francesca Alessandra ; Ilchenko, Oleksii ; Jendresen, Christian Bille ; Demarchi, Danilo ; Nielsen, Alex Toftgaard ; Zor, Kinga ; Boisen, Anja
in: Analyst

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1039/C8AN02128G

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SLIMEr: probing flexibility of lipid metabolism in yeast with an improved constraint-based modeling framework

Sanchez, Benjamin J. ; Li, Feiran ; Kerkhoven, Eduard J. ; Nielsen, Jens
in: BMC Systems Biology, vol: 13, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1186/s12918-018-0673-8

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Structural Analysis of the Hanks-Type Protein Kinase YabT From Bacillus subtilis Provides New Insights in its DNA-Dependent Activation

Shi, Lei ; Cavagnino, Andrea ; Rabefiraisana, Jean-Luc ; Lazar, Noureddine ; Li de la Sierra-Gallay, Inés ; Ochsenbein, Francoise ; Valerio-Lepiniec, Marie ; Urvoas, Agathe ; Minard, Philippe ; Mijakovic, Ivan ; Nessler, Sylvie
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.3389/fmicb.2018.03014

 

Synthetic biology and metabolic engineering of actinomycetes for natural product discovery

Palazzotto, Emilia ; Tong, Yaojun ; Lee, Sang Yup ; Weber, Tilmann
in: Biotechnology Advances

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1016/j.biotechadv.2019.03.005

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The antiSMASH database version 2: a comprehensive resource on secondary metabolite biosynthetic gene clusters

Blin, Kai ; Pascal Andreu, Victòria ; de Los Santos, Emmanuel L C ; Del Carratore, Francesco ; Lee, Sang Yup ; Medema, Marnix H. ; Weber, Tilmann
in: Nucleic Acids Research, vol: 47, issue: D1, pages: D625–D630

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1093/nar/gky1060

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The Synthetic Microbiology Caucus: from abstract ideas to turning microbes into cellular machines and back

Huang, Wei E. ; Nikel, Pablo I.
in: Microbial Biotechnology, vol: 12, issue: 1, pages: 5-7

Type: Editorial (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13337

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Understanding metabolite transport gives an upper hand in strain development

Borodina, Irina
in: Microbial Biotechnology, vol: 12, issue: 1, pages: 69-70

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13347

2018
 

Selecting of a cytochrome P450cam SeSaM library with 3-chloroindole and endosulfan – Identification of mutants that dehalogenate 3-chloroindole

Kammoonah, Shaima ; Prasad, Brinda ; Balaraman, Priyadarshini ; Mundhada, Hemanshu ; Schwaneberg, Ulrich ; Plettner, Erika
in: Biochimica et Biophysica Acta - Proteins and Proteomics, vol: 1866, issue: 1, pages: 68-79

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.bbapap.2017.09.006

 

A Capture-SELEX Strategy for Multiplexed Selection of RNA Aptamers Against Small Molecules

Lauridsen, Lasse Holm ; Doessing, Holger B. ; Long, Katherine S. ; Nielsen, Alex Toftgaard
part of: Synthetic Metabolic Pathways, pages: 291-306, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_18

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Accelerated and Rational Design of Improved CHO Cell Factories

Grav, Lise Marie

Type: Ph.D. thesis

Status: Published     |    Year: 2018

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A combinatorial approach to synthetic transcription factor-promoter combinations for yeast strain engineering

Dossani, Zain Y. ; Apel, Amanda Reider ; Szmidt-Middleton, Heather ; Hillson, Nathan J. ; Deutsch, Samuel ; Keasling, Jay D. ; Mukhopadhyay, Aindrila
in: Yeast, vol: 35, issue: 3, pages: 273-280

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/yea.3292

 

Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Metabolic Engineering, vol: 48, pages: 82-93

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.05.012