Publications

Publikationer rss feed

2019
 

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 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

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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

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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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1111/1751-7915.13372

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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

 

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

 

Construction of mini-chemostats for high-throughput strain characterization

Bergenholm, David ; Liu, Guodong ; Hansson, David ; Nielsen, Jens
in: Biotechnology and Bioengineering

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2019     |    DOI: https://doi.org/10.1002/bit.26931

 

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

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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

 

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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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

 

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

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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

 

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

 

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

Type: Journal article (Peer reviewed)

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

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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

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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

 

Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System

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: 233-242

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.06.005

 

Advances and opportunities in biomass conversion technologies and biorefineries for the development of a bio-based economy

Yamakawa, Celina K. ; Qin, Fen ; Mussatto, Solange I.
in: Biomass and Bioenergy, vol: 119, pages: 54-60

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.biombioe.2018.09.007

 

Advances in analytical tools for high throughput strain engineering

Marcellin, Esteban ; Nielsen, Lars Keld
in: Current Opinion in Biotechnology, vol: 54, pages: 33-40

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.copbio.2018.01.027

 

Advances in synthetic biology of oleaginous yeast Yarrowia lipolytica for producing non-native chemicals

Darvishi, Farshad ; Ariana, Mehdi ; Marella, Eko Roy ; Borodina, Irina
in: Applied Microbiology and Biotechnology, vol: 102, issue: 14, pages: 5925-5938

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s00253-018-9099-x

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Advancing biotechnology with CRISPR/Cas9: recent applications and patent landscape

Ferreira, Raphael ; David, Florian ; Nielsen, Jens
in: Journal of Industrial Microbiology and Biotechnology, vol: 45, issue: 7, pages: 467-480

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s10295-017-2000-6

 

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2018     |    DOI: https://doi.org/10.1111/jcal.12335

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A laboratory device to automatically measure growth of cell culture non-invasively

van der Helm, Eric ; Redl, Stephanie Maria Anna
Patent no.: WO2018096143 , Date: 2018-05-31

Type: Patent

Status: Published     |    Year: 2018

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A method for improved glycerol utilization in yeast

Strucko, Tomas ; Förster, Jochen ; Zirngibl, Katharina (Inventor) ; Patil, Kiran Raosaheb
Patent no.: WO2018127572 , Date: 2018-07-12

Type: Patent

Status: Published     |    Year: 2018

 

An Adaptive Laboratory Evolution Method to Accelerate Autotrophic Metabolism

Zhang, Tian ; Tremblay, Pier-Luc
part of: Synthetic Metabolic Pathways, pages: 149-161, 2018, Springer

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_10

 

Anaerobic digestion process: technological aspects and recent developments

Náthia-Neves, G. ; Berni, M. ; Dragone, G. ; Mussatto, S. I. ; Forster-Carneiro, T.
in: International Journal of Environmental Science and Technology, vol: 15, issue: 9, pages: 2033-2046

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s13762-018-1682-2

 

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

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2018     |    DOI: https://doi.org/10.1111/1758-2229.12704

 

An Expanded Heterologous GAL Promoter Collection for Diauxie-Inducible Expression in Saccharomyces cerevisiae

Peng, Bingyin ; Wood, Rebecca J. ; Nielsen, Lars K. ; Vickers, Claudia E.
in: A C S Synthetic Biology, vol: 7, issue: 2, pages: 748-751

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1021/acssynbio.7b00355

 

An Online Compendium of CHO RNA-Seq Data Allows Identification of CHO Cell Line-specific Transcriptomic Signatures

Singh, Ankita ; Kildegaard, Helene F. ; Andersen, Mikael R.
in: Biotechnology Journal, vol: 13, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/biot.201800070

 

An Orthogonal and pH-Tunable Sensor-Selector for Muconic Acid Biosynthesis in Yeast

Snoek, Tim ; Romero-Suarez, David ; Zhang, Jie ; Ambri, Francesca ; Skjoedt, Mette L. ; Sudarsan, Suresh ; Jensen, Michael K. ; Keasling, Jay D.
in: A C S Synthetic Biology, vol: 7, issue: 4, pages: 995-1003

Type: Letter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1021/acssynbio.7b00439

 

Anti-biofilm effects of gold and silver nanoparticles synthesized by the Rhodiola rosea rhizome extracts

Singh, Priyanka ; Pandit, Santosh ; Beshay, Mariam ; Mokkapati, V. R. S. S. ; Garnæs, Jørgen ; Olsson, Mikael Emil ; Sultan, Abida ; Mackevica, Aiga ; Mateiu, Ramona Valentina ; Lütken, Henrik ; Daugaard, Anders Egede ; Baun, Anders ; Mijakovic, Ivan
in: Artificial Cells, Nanomedicine and Biotechnology, vol: 46, issue: sup3, pages: S886-S899

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1080/21691401.2018.1518909

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Antimicrobial Effects of Biogenic Nanoparticles

Singh, Priyanka ; Garg, Abhroop ; Pandit, Santosh ; Mokkapati, V. R. S. S. ; Mijakovic, Ivan
in: Nanomaterials, vol: 8, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.3390/nano8121009

 

A Post-translational Metabolic Switch Enables Complete Decoupling of Bacterial Growth from Biopolymer Production in Engineered Escherichia coli

Durante-Rodríguez, Gonzalo ; de Lorenzo, Víctor ; Nikel, Pablo I.
in: A C S Synthetic Biology, vol: 7, issue: 11, pages: 2686-2697

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1021/acssynbio.8b00345

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A Pseudomonas putida efflux pump acts on short-chain alcohols

Basler, Georg ; Thompson, Mitchell ; Tullman-Ercek, Danielle ; Keasling, Jay
in: Biotechnology for Biofuels, vol: 11, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s13068-018-1133-9

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Arylalkylamine n-acetyltransferase and uses thereof

Luo, Hao
Patent no.: WO2018108966 , Date: 2018-06-21

Type: Patent

Status: Published     |    Year: 2018

 

Assembly and Multiplex Genome Integration of Metabolic Pathways in Yeast Using CasEMBLR

Jakočiūnas, Tadas ; Jensen, Emil D. ; Jensen, Michael Krogh ; Keasling, Jay D.
part of: Synthetic Metabolic Pathways, pages: 185-201, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_12

 

Assessing carbon source-dependent phenotypic variability in Pseudomonas putida

Nikel, Pablo Ivan ; de Lorenzo, Victor
part of: Cellular Heterogeneity. Methods in Molecular Biology., pages: 287-301, 2018, Humana Press, New York

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7680-5_16

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A synbio approach for selection of highly expressed gene variants in Gram-positive bacteria

Ferro, Roberto ; Rennig, Maja ; Hernández Rollán, Cristina ; Daley, Daniel O. ; Nørholm, Morten H H
in: Microbial Cell Factories, vol: 17, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12934-018-0886-y

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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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A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0

Santos-Zavaleta, Alberto ; Sanchez-Perez, Mishael ; Salgado, Heladia ; Velazquez-Ramirez, David A. ; Gama-Castro, Socorro ; Tierrafria, Victor H. ; Busby, Stephen J. W. ; Aquino, Patricia ; Fang, Xin ; Palsson, Bernhard O. ; Galagan, James E. ; Collado-Vides, Julio
in: B M C Biology, vol: 16

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s12915-018-0555-y

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BacHBerry:: BACterial Hosts for production of Bioactive phenolics from bERRY fruits

Dudnik, Alexey ; Almeida, A. Filipa ; Andrade, Ricardo ; Avila, Barbara ; Bañados, Pilar ; Barbay, Diane ; Bassard, Jean Etienne ; Benkoulouche, Mounir ; Bott, Michael ; Braga, Adelaide ; Breitel, Dario ; Brennan, Rex ; Bulteau, Laurent ; Chanforan, Celine ; Costa, Inês ; Costa, Rafael S. ; Doostmohammadi, Mahdi ; Faria, Nuno ; Feng, Chengyong ; Fernandes, Armando ; Ferreira, Patricia ; Ferro, Roberto ; Foito, Alexandre ; Freitag, Sabine ; Garcia, Gonçalo ; Gaspar, Paula ; Godinho-Pereira, Joana ; Hamberger, Björn ; Hartmann, András ; Heider, Harald ; Jardim, Carolina ; Julien-Laferriere, Alice ; Kallscheuer, Nicolai ; Kerbe, Wolfgang ; Kuipers, Oscar P. ; Li, Shanshan ; Love, Nicola ; Marchetti-Spaccamela, Alberto ; Marienhagen, Jan ; Martin, Cathie ; Mary, Arnaud ; Mazurek, Vincent ; Meinhart, Camillo ; Sevillano, David Méndez ; Menezes, Regina ; Naesby, Michael ; Nørholm, Morten H.H. ; Okkels, Finn T. ; Oliveira, Joana ; Ottens, Marcel ; Parrot, Delphine ; Pei, Lei ; Rocha, Isabel ; Rosado-Ramos, Rita ; Rousseau, Caroline ; Sagot, Marie France ; Dos Santos, Claudia Nunes ; Schmidt, Markus ; Shelenga, Tatiana ; Shepherd, Louise ; Silva, Ana Rita ; da Silva, Marcelo Henriques ; Simon, Olivier ; Stahlhut, Steen Gustav ; Solopova, Ana ; Sorokin, Artem ; Stewart, Derek ; Stougie, Leen ; Su, Shang ; Thole, Vera ; Tikhonova, Olga ; Trick, Martin ; Vain, Philippe ; Veríssimo, André ; Vila-Santa, Ana ; Vinga, Susana ; Vogt, Michael ; Wang, Liangsheng ; Wang, Lijin ; Wei, Wei ; Youssef, Sandra ; Neves, Ana Rute ; Forster, Jochen
in: Phytochemistry Reviews, vol: 17, issue: 2, pages: 291-326

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/s11101-017-9532-2

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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

 

Bacterial Genome Editing Strategy for Control of Transcription and Protein Stability

Lauritsen, Ida ; Martinez, Virginia ; Ronda, Carlotta ; Nielsen, Alex Toftgaard ; Nørholm, Morten H. H.
part of: Synthetic Metabolic Pathways, pages: 27-37, 2018

Type: Book chapter (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1007/978-1-4939-7295-1_3

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Baicalein reduces oxidative stress in CHO cell cultures and improves recombinant antibody productivity

Kwang Ha, Tae ; Hansen, Anders Holmgaard ; Kol, Stefan ; Kildegaard, Helene Faustrup ; Min Lee, Gyun
in: Biotechnology Journal, vol: 13, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/biot.201700425

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Balanced trafficking between the ER and the Golgi apparatus increases protein secretion in yeast

Bao, Jichen ; Huang, Mingtao ; Petranovic, Dina ; Nielsen, Jens
in: A M B Express, vol: 8

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s13568-018-0571-x

 

Barriers and opportunities in bio-based production of hydrocarbons

Zhou, Yongjin J. ; Kerkhoven, Eduard J. ; Nielsen, Jens
in: Nature Energy, vol: 3, issue: 11, pages: 925-935

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41560-018-0197-x

 

Basics of genome-scale metabolic modeling and applications on C1-utilization

Kabimoldayev, Ilyas ; Nguyen, Anh Duc ; Yang, Laurence ; Park, Sunghoon ; Lee, Eun Yeol ; Kim, Donghyuk
in: FEMS MICROBIOLOGY LETTERS, vol: 365, issue: 20

Type: Review (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1093/femsle/fny241

 

Biochemical Characterization of β-Amino Acid Incorporation in Fluvirucin B2 Biosynthesis

Barajas, Jesus F. ; Zargar, Amin ; Pang, Bo ; Benites, Veronica T. ; Gin, Jennifer ; Baidoo, Edward E. K. ; Petzold, Christopher J. ; Hillson, Nathan J. ; Keasling, Jay D.
in: Chembiochem, vol: 19, issue: 13, pages: 1391-1395

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/cbic.201800169

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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

 

Bioconda: sustainable and comprehensive software distribution for the life sciences

Grüning , Björn ; Dale, Ryan ; Sjödin, Andreas ; Chapman, Brad A. ; Rowe, Jillian ; Tomkins-Tinch, Christopher H. ; Valieris, Renan ; Köster, Johannes ; Blin, Kai ; Haudgaard, Mathias ; Kratz, Arne ; Junge, Alexander ; Knudsen, Michael
in: Nature Methods, vol: 15, pages: 475-476

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/s41592-018-0046-7

 

Bioengineering triacetic acid lactone production in Yarrowia lipolytica for pogostone synthesis

Yu, James ; Landberg, Jenny Marie ; Shavarebi, Farbod ; Bilanchone, Virginia ; Okerlund, Adam ; Wanninayake, Umayangani ; Zhao, Le ; Kraus, George ; Sandmeyer, Suzanne
in: Biotechnology and Bioengineering, vol: 115, issue: 9, pages: 2383-2388

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1002/bit.26733

 

BSG Refinery: Recycling protein and amino acids from brewer´s spent grains

Mussatto, Solange I.
Presented at:
ECO-BIO 2018

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2018

  PDF

CasPER, a method for directed evolution in genomic contexts using mutagenesis and CRISPR/Cas9

Jakočiūnas, Tadas ; Pedersen, Lasse E. ; Lis, Alicia V. ; Jensen, Michael K. ; Keasling, Jay D.
in: Metabolic Engineering, vol: 48, pages: 288-296

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.07.001

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Centrifugal microfluidic platform for optical monitoring and treatment of biofilms

Serioli, Laura ; Severini, Giaele ; Laksafoss, Trygvi Z. ; Haagensen, Janus A. J. ; Sørensen, Mads P. ; Molin, Søren ; Johansen, Helle K. ; Zor, Kinga ; Boisen, Anja
Presented at:
44th International Conference on Micro and NanoEngineering

Type: Conference abstract for conference (Peer reviewed)

Status: Published     |    Year: 2018

 

Challenges in modeling the human gut microbiome

Babaei, Parizad ; Shoaie, Saeed ; Ji, Boyang ; Nielsen, Jens
in: Nature Biotechnology, vol: 36, issue: 8, pages: 682-686

Type: Comment/debate (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1038/nbt.4213

  PDF

Changes in lipid metabolism convey acid tolerance in Saccharomyces cerevisiae

Guo, Zhong-peng ; Khoomrung, Sakda ; Nielsen, Jens ; Olsson, Lisbeth
in: Biotechnology for Biofuels, vol: 11

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1186/s13068-018-1295-5

 

Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow

Brunk, Elizabeth ; Chang, Roger L. ; Xia, Jing ; Hefzi, Hooman ; Yurkovich, James T. ; Kim, Donghyuk ; Buckmiller, Evan ; Wang, Harris H. ; Cho, Byung-Kwan ; Yang, Chen ; Palsson, Bernhard O. ; Church, George M. ; Lewis, Nathan E.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 43, pages: 11096-11101

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1073/pnas.1811971115

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ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions

Latif, Haythem ; Federowicz, Stephen ; Ebrahim, Ali ; Tarasova, Janna ; Szubin, Richard ; Utrilla, Jose ; Zengler, Karsten ; Palsson, Bernhard O.
in: P L o S One, vol: 13, issue: 5

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1371/journal.pone.0197272

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ClusterCAD: a computational platform for type I modular polyketide synthase design

Eng, Clara H. ; Backman, Tyler W. H. ; Bailey, Constance B. ; Magnan, Christophe ; Martin, Hector Garcia ; Katz, Leonard ; Baldi, Pierre ; Keasling, Jay D.
in: Nucleic Acids Research, vol: 46, issue: D1, pages: D509-D515

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1093/nar/gkx893

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COBRAme: A computational framework for genome-scale models of metabolism and gene expression

Lloyd, Colton J. ; Ebrahim, Ali ; Yang, Laurence ; King, Zachary A. ; Catoiu, Edward ; O'Brien, Edward J. ; Liu, Joanne K. ; Polsson, Bernhard O.
in: P L o S Computational Biology (Online), vol: 14, issue: 7

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1371/journal.pcbi.1006302

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Combination of phage and Gram-positive bacterial display of human antibody repertoires enables isolation of functional high affinity binders

Hu, Francis Jingxin ; Volk, Anna-Luisa ; Persson, Helena ; Säll, Anna ; Borrebaeck, Carl ; Uhlén, Mathias ; Rockberg, Johan
in: New Biotechnology, vol: 45, pages: 80-88

Type: Journal article (Peer reviewed)

Status: Published     |    Year: 2018     |    DOI: https://doi.org/10.1016/j.nbt.2017.07.011

 

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