Bernhard Palsson

Bernhard Palsson

CEO

DTU BIOSUSTAIN
Novo Nordisk Foundation Center for Biosustainability

Technical University of Denmark

Kemitorvet

Building 220, room 527F

2800 Kgs. Lyngby

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2019
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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

 

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

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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

 

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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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

 

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

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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

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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

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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