Publications

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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, 2011

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, 2011

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, 2011

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, 2011

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, 2011

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, 2011

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, 2011

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, 2011

Type: Journal article (Peer reviewed)

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

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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

 

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, 2011

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, 2011

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, 2012

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, 2011

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, 2012

Type: Letter (Peer reviewed)

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

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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, 2011

Type: Journal article (Peer reviewed)

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

 

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, pages: 11, 2011

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    Year: 2018     |    DOI: https://doi.org/10.1002/biot.201800195

 

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, 2011

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, 2011

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, 2011

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