Bernhard Palsson

Bernhard Palsson

CEO

DTU BIOSUSTAIN
Novo Nordisk Foundation Center for Biosustainability

Danmarks Tekniske Universitet

Kemitorvet

Bygning 220, rum 527F

2800 Kgs. Lyngby

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2019
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Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration

Anand, Amitesh ; Chen, Ke ; Yang, Laurence ; Sastry, Anand V. ; Olson, Connor A. ; Poudel, Saugat ; Seif, Yara ; Hefner, Ying ; Phaneuf, Patrick V. ; Xu, Sibei ; Szubin, Richard ; Feist, Adam ; Palsson, Bernhard
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 116, issue: 50, pages: 25287-25292

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1073/pnas.1909987116

 

Adaptive laboratory evolution of Escherichia coli under acid stress

Du, Bin ; Olson, Connor A. ; Sastry, Anand V ; Fang, Xin ; Phaneuf, Patrick V. ; Chen, Ke ; Wu, Muyao ; Szubin, Richard ; Xu, Sibei ; Gao, Ye ; Hefner, Ying ; Feist, Adam M ; Palsson, Bernhard O
in: Microbiology

Type: Journal article (Peer reviewed)

Status: Accepted/In press     |    År: 2019     |    DOI: https://doi.org/10.1099/mic.0.000867

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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     |    År: 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, vol: 177, issue: 6, pages: 1649-1661.e9

Type: Journal article (Peer reviewed)

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

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Expanding the uses of genome-scale models with protein structures

Mih, Nathan ; Palsson, Bernhard O.
in: Molecular Systems Biology, vol: 15, issue: 11

Type: Comment/debate (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.15252/msb.20188601

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Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli

Du, Bin ; Yang, Laurence ; Lloyd, Colton J. ; Fang, Xin ; Palsson, Bernhard
in: PLOS Computational Biology, vol: 15, issue: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1007525

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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     |    År: 2019     |    DOI: https://doi.org/10.1371/journal.pcbi.1007066

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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     |    År: 2019     |    DOI: https://doi.org/10.7554/eLife.45379

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Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome

Hwang, Soonkyu ; Lee, Namil ; Jeong, Yujin ; Lee, Yongjae ; Kim, Woori ; Cho, Suhyung ; Palsson, Bernhard O ; Cho, Byung-Kwan
in: Nucleic acids research, vol: 47, issue: 12, pages: 6114-6129

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1093/nar/gkz471

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Profiling the effect of nafcillin on HA-MRSA D712 using bacteriological and physiological media

Rajput, Akanksha ; 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. ; Knight, Rob ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Scientific Data, vol: 6, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1038/s41597-019-0331-z

 

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     |    År: 2019     |    DOI: https://doi.org/10.1038/s41564-018-0340-2

 

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus

Machado, Henrique ; Weng, Liam L. ; Dillon, Nicholas ; Seif, Yara ; Holland, Michelle ; Pekar, Jonathan E. ; Monk, Jonathan M. ; Nizet, Victor ; Palsson, Bernhard O. ; Feist, Adam M.
in: Applied and Environmental Microbiology, vol: 85, issue: 21, pages: 1-13

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1128/aem.01773-19

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Synthetic biology tools for novel secondary metabolite discovery in streptomyces

Lee, Namil ; Hwang, Soonkyu ; Lee, Yongjae ; Cho, Suhyung ; Palsson, Bernhard
in: Journal of Microbiology and Biotechnology, vol: 29, issue: 5, pages: 667-686

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.4014/jmb.1904.04015

 

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology

Sandberg, Troy E. ; Salazar, Michael J ; Weng, Liam L ; Palsson, Bernhard O ; Feist, Adam M
in: Metabolic Engineering, vol: 56, pages: 1-16

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1016/j.ymben.2019.08.004

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The Transcription Unit Architecture of Streptomyces lividans TK24

Lee, Yongjae ; Lee, Namil ; Jeong, Yujin ; Hwang, Soonkyu ; Kim, Woori ; Cho, Suhyung ; Palsson, Bernhard O. ; Cho, Byung-Kwan
in: Frontiers in Microbiology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.3389/fmicb.2019.02074

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The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function

Ghatak, Sankha ; King, Zachary A ; Sastry, Anand ; Palsson, Bernhard O
in: Nucleic acids research, vol: 47, issue: 5, pages: 2446-2454

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2019     |    DOI: https://doi.org/10.1093/nar/gkz030

2018
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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     |    År: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.05.012

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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     |    År: 2018     |    DOI: https://doi.org/10.1016/j.ymben.2018.06.005

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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     |    År: 2018     |    DOI: https://doi.org/10.1186/s12915-018-0555-y

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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     |    År: 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     |    År: 2018     |    DOI: https://doi.org/10.1371/journal.pone.0197272

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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     |    År: 2018     |    DOI: https://doi.org/10.1371/journal.pcbi.1006302

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Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli

Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam M. ; Palsson, Bernhard O. ; Antoniewicz, Maciek R.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 1, pages: 222-227

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1073/pnas.1716056115

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Escher-FBA: a web application for interactive flux balance analysis

Rowe, Elliot ; Palsson, Bernhard O. ; King, Zachary A.
in: BMC Systems Biology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1186/s12918-018-0607-5

 

Estimating Metabolic Equilibrium Constants: Progress and Future Challenges

Du, Bin ; Zielinski, Daniel C. ; Palsson, Bernhard O.
in: Trends in Biochemical Sciences, vol: 43, issue: 12, pages: 960-969

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1016/j.tibs.2018.09.009

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Evolution of gene knockout strains of E-coli reveal regulatory architectures governed by metabolism

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1038/s41467-018-06219-9

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Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits

Seif, Yara ; Kavvas, Erol ; Lachance, Jean-Christophe ; Yurkovich, James T. ; Nuccio, Sean-Paul ; Fang, Xin ; Catoiu, Edward ; Raffatellu, Manuela ; Palsson, Bernhard O. ; Monk, Jonathan M.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1038/s41467-018-06112-5

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Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.3389/fmicb.2018.01793

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Identification of growth-coupled production strains considering protein costs and kinetic variability

Dinh, Hoang V. ; King, Zachary A. ; Palsson, Bernhard O. ; Feist, Adam M.
in: Metabolic Engineering Communications, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1016/j.mec.2018.e00080

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Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa

Fang, Xin ; Monk, Jonathan M. ; Mih, Nathan ; Du, Bin ; Sastry, Anand V. ; Kavvas, Erol ; Seif, Yara ; Smarr, Larry ; Palsson, Bernhard O.
in: B M C Systems Biology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1186/s12918-018-0587-5

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Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models

Heckmann, David ; Lloyd, Colton J. ; Mih, Nathan ; Ha, Yuanchi ; Zielinski, Daniel C. ; Haiman, Zachary B. ; Desouki, Abdelmoneim Amer ; Lercher, Martin J. ; Palsson, Bernhard O.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1038/s41467-018-07652-6

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Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient

Fang, Xin ; Monk, Jonathan M. ; Nurk, Sergey ; Akseshina, Margarita ; Zhu, Qiyun ; Gemmell, Christopher ; Gianetto-Hill, Connor ; Leung, Nelly ; Szubin, Richard ; Sanders, Jon ; Beck, Paul L. ; Li, Weizhong ; Sandborn, William J. ; Gray-Owen, Scott D. ; Knight, Rob ; Allen-Vercoe, Emma ; Palsson, Bernhard O. ; Smarr, Larry
in: Frontiers in Microbiology, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.3389/fmicb.2018.02559

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Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates

Heckmann, David ; Zielinski, Daniel C. ; Palsson, Bernhard O.
in: Nature Communications, vol: 9

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1038/s41467-018-07649-1

 

Modeling the multi-scale mechanisms of macromolecular resource allocation

Yang, Laurence ; Yurkovich, James T ; King, Zachary A ; Palsson, Bernhard O
in: Current opinion in Microbiology, vol: 45, pages: 8-15

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1016/j.mib.2018.01.002

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Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions

McCloskey, Douglas ; Xu, Sibei ; Sandberg, Troy E. ; Brunk, Elizabeth ; Hefner, Ying ; Szubin, Richard ; Feist, Adam M. ; Palsson, Bernhard O.
in: Applied and Environmental Microbiology, vol: 84, issue: 19

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1128/AEM.00823-18

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Recon3D enables a three-dimensional view of gene variation in human metabolism

Brunk, Elizabeth ; Sahoo, Swagatika ; Zielinski, Daniel C. ; Altunkaya, Ali ; Dräger, Andreas ; Mih, Nathan ; Gatto, Francesco ; Nilsson, Avlant ; Preciat Gonzalez, German Andres ; Aurich, Maike Kathrin ; Prlic, Andreas ; Sastry, Anand ; Danielsdottir, Anna D. ; Heinken, Almut ; Noronha, Alberto ; Rose, Peter W. ; Burley, Stephen K. ; Fleming, Ronan M.T. ; Nielsen, Jens ; Thiele, Ines ; Palsson, Bernhard O.
in: Nature Biotechnology, vol: 36, issue: 3, pages: 272-281

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1038/nbt.4072

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Reframing gene essentiality in terms of adaptive flexibility

Guzmán, Gabriela I. ; Olson, Connor A. ; Hefner, Ying ; Phaneuf, Patrick V. ; Catoiu, Edward ; Crepaldi, Lais B. ; Micas, Lucas Goldschmidt ; Palsson, Bernhard O. ; Feist, Adam M.
in: BMC Systems Biology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1186/s12918-018-0653-z

 

Revealing key determinants of clonal variation in transgene expression in recombinant CHO cells using targeted genome editing

Lee, Jae Seong ; Park, Jin Hyoung ; Kwang Ha, Tae ; Samoudi, Mojtaba ; Lewis, Nathan E. ; Palsson, Bernhard O. ; Kildegaard, Helene Faustrup ; Min Lee, Gyun
in: A C S Synthetic Biology, vol: 7, issue: 12, pages: 2867-2878

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1021/acssynbio.8b00290

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Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655

Gao, Ye ; Yurkovich, James T. ; Seo, Sang Woo ; Kabimoldayev, Ilyas ; Dräger, Andreas ; Chen, Ke ; Sastry, Anand V. ; Fang, Xin ; Mih, Nathan ; Yang, Laurence ; Eichner, Johannes ; Cho, Byung-Kwan ; Kim, Donghyuk ; Palsson, Bernhard O.
in: Nucleic acids research, vol: 46, issue: 20, pages: 10682–10696

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1093/nar/gky752

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Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP

Kim, Donghyuk ; Seo, Sang Woo ; Gao, Ye ; Nam, Hojung ; Guzman, Gabriela I. ; Cho, Byung-Kwan ; Palsson, Bernhard O.
in: Nucleic acids research, vol: 46, issue: 6, pages: 2901-2917

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1093/nar/gky069

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Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice

Du, Bin ; Zielinski, Daniel C. ; Monk, Jonathan M. ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 115, issue: 44, pages: 11339-11344

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1073/pnas.1805367115

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Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions

Kavvas, Erol S. ; Seif, Yara ; Yurkovich, James T. ; Norsigian, Charles ; Poudel, Saugat ; Greenwald, William W. ; Ghatak, Sankha ; Palsson, Bernhard O. ; Monk, Jonathan M.
in: B M C Systems Biology, vol: 12

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2018     |    DOI: https://doi.org/10.1186/s12918-018-0557-y

2017
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A Model for Designing Adaptive Laboratory Evolution Experiments

LaCroix, Ryan A. ; Palsson, Bernhard O. ; Feist, Adam M. ; Kivisaar, Maia (Editor)
in: Applied and Environmental Microbiology, vol: 83, issue: 8

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1128/AEM.03115-16

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Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function

Yang, Jason H. ; Bhargava, Prerna ; McCloskey, Douglas ; Mao, Ning ; Palsson, Bernhard ; Collins, James J.
in: Cell Host & Microbe, vol: 22, pages: 757-765

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.chom.2017.10.020

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A Padawan Programmer's Guide to Developing Software Libraries

Yurkovich, James T. ; Yurkovich, Benjamin J. ; Dräger, Andreas ; Palsson, Bernhard O. ; King, Zachary A.
in: Cell Systems, vol: 5, issue: 5, pages: 431-437

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.cels.2017.08.003

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Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics

Bordbar, Aarash ; Yurkovich, James T. ; Paglia, Giuseppe ; Rolfsson, Ottar ; Sigurjónsson, Olafur E. ; Palsson, Bernhard
in: Scientific Reports, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1038/srep46249

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Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring

Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam M. ; Palsson, Bernhard O ; Antoniewicz, Maciek R.
in: Metabolic Engineering, vol: 44, pages: 100-107

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.ymben.2017.09.012

 

Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities

Fang, Xin ; Sastry, Anand ; Mih, Nathan ; Kim, Donghyuk ; Tan, Justin ; Yurkovich, James T. ; Lloyd, Colton J. ; Gao, Ye ; Yang, Laurence ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 114, issue: 38, pages: 10286-10291

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1073/pnas.1702581114

 

iML1515, a knowledgebase that computes Escherichia coli traits

Monk, Jonathan M. ; Lloyd, Colton J. ; Brunk, Elizabeth ; Mih, Nathan ; Sastry, Anand ; King, Zachary ; Takeuchi, Rikiya ; Nomura, Wataru ; Zhang, Zhen ; Mori, Hirotada ; Feist, Adam M. ; Palsson, Bernhard O.
in: Nature Biotechnology, vol: 35, issue: 10, pages: 904-908

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1038/nbt.3956

 

Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies

Sandberg, Troy E. ; Lloyd, Colton J. ; Palsson, Bernhard O. ; Feist, Adam M. ; Kivisaar, Maia (Editor)
in: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol: 83, issue: 13

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1128/AEM.00410-17

 

Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion

King, Zachary A. ; O'Brien, Edward J. ; Feist, Adam M. ; Palsson, Bernhard O.
in: Metabolic Engineering, vol: 39, pages: 220–227

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.ymben.2016.12.004

 

Machine learning in computational biology to accelerate high-throughput protein expression

Sastry, Anand ; Monk, Jonathan M. ; Tegel, Hanna ; Uhlén, Mathias ; Palsson, Bernhard ; Rockberg, Johan ; Brunk, Elizabeth
in: Bioinformatics, vol: 33, issue: 16, pages: 2487-2495

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1093/bioinformatics/btx207

 

Metabolic Models of Protein Allocation Call for the Kinetome

Nilsson, Avlant ; Nielsen, Jens ; Palsson, Bernhard
in: Cell Systems, vol: 5, issue: 6, pages: 538-541

Type: Comment/debate (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.cels.2017.11.013

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Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression

Ma, Ding ; Yang, Laurence ; Fleming, Ronan M. T. ; Thiele, Ines ; Palsson, Bernhard ; Saunders, Michael A.
in: Scientific Reports, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1038/srep40863

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Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655

Seo, Sang Woo ; Gao, Ye ; Kim, Donghyuk ; Szubin, Richard ; Yang, Jina ; Cho, Byung-Kwan ; Palsson, Bernhard O.
in: Scientific Reports, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1038/s41598-017-02110-7

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The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli

Aziz, Ramy K. ; Monk, Jonathan M. ; Andrews, Kathleen A. ; Nhan, Jenny ; Khaw, Valerie L. ; Wong, Hesper ; Palsson, Bernhard O. ; Charusanti, Pep
in: Microbiological Research, vol: 194, pages: 47-52

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1016/j.micres.2016.10.006

 

Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation

Chen, Ke ; Gao, Ye ; Mih, Nathan ; O'Brien, Edward J. ; Yang, Laurence ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 114, issue: 43, pages: 11548-11553

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1073/pnas.1705524114

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Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion

van Wijk, Xander M. ; Döhrmann, Simon ; Hallstrom, Bjorn ; Li, Shangzhong ; Voldborg, Bjørn Gunnar ; Meng, Brandon X. ; McKee, Karen K. ; van Kuppevelt, Toin H. ; Yurchenco, Peter D. ; Palsson, Bernhard ; Lewis, Nathan ; Nizet, Victor ; Esko, Jeffrey D.
in: mBio, vol: 8, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2017     |    DOI: https://doi.org/10.1128/mBio.02128-16

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Why microbes will rule the world – and our industries

Lykke, Anne Wärme ; Palsson, Bernhard ; Nielsen, Jens
in: Biozoom, vol: 2017, issue: 2, pages: 4-5

Type: Journal article

Status: Published     |    År: 2017

2016
 

A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism

Hefzi, Hooman ; Ang, Kok Siong ; Hanscho, Michael ; Bordbar, Aarash ; Ruckerbauer, David ; Lakshmanan, Meiyappan ; Orellana, Camila A. ; Baycin-Hizal, Deniz ; Huang, Yingxiang ; Ley, Daniel ; Martinez, Veronica S. ; Kyriakopoulos, Sarantos ; Jiménez, Natalia E. ; Zielinski, Daniel C. ; Quek, Lake-Ee ; Wulff, Tune ; Arnsdorf, Johnny ; Li, Shangzhong ; Lee, Jae Seong ; Paglia, Giuseppe ; Loira, Nicolas ; Spahn, Philipp N. ; Pedersen, Lasse Ebdrup ; Gutierrez, Jahir M. ; King, Zachary A. ; Lund, Anne Mathilde ; Nagarajan, Harish ; Thomas, Alex ; Abdel-Haleem, Alyaa M. ; Zanghellini, Juergen ; Kildegaard, Helene Faustrup ; Voldborg, Bjørn Gunnar ; Gerdtzen, Ziomara P. ; Betenbaugh, Michael J. ; Palsson, Bernhard ; Andersen, Mikael Rørdam ; Nielsen, Lars K. ; Borth, Nicole ; Lee, Dong-Yup ; Lewis, Nathan E.
in: Cell Systems, vol: 3, issue: 5, pages: 434-443

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.10.020

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BiGG Models: A platform for integrating, standardizing and sharing genome-scale models

King, Zachary A. ; Lu, Justin ; Dräger, Andreas ; Miller, Philip ; Federowicz, Stephen ; Lerman, Joshua A. ; Ebrahim, Ali ; Palsson, Bernhard ; Lewis, Nathan
in: Nucleic acids research, vol: 44, pages: D515-D522

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1093/nar/gkv1049

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Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow

Brunk, Elizabeth ; George, Kevin W. ; Alonso-Gutierrez, Jorge ; Tjompson, Mitchell ; Baidoo, Edward ; Wang, George ; Petzold, Christopher J. ; McCloskey , Douglas ; Monk, Jonathan ; Yang, Laurence ; O’Brien, Edward J. ; Batth , Tanveer S. ; Garcia Martin, Hector ; Feist, Adam ; Adams, Paul D. ; Keasling , Jay D. ; Palsson, Bernhard ; Soon Lee, Taek
in: Cell Systems, vol: 2, issue: 5, pages: 335-346

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.04.004

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Evaluation of rate law approximations in bottom-up kinetic models of metabolism

Du, Bin ; Zielinski, Daniel C. ; Kavvas, Erol S. ; Draeger, Andreas ; Tan, Justin ; Zhang, Zhen ; Ruggiero, Kayla E. ; Arzumanyan, Garri A. ; Palsson, Bernhard
in: BMC Systems Biology, vol: 10

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1186/s12918-016-0283-2

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Evolution of E. coli on [U-13C] Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology

Sandberg, Troy E. ; Long, Christopher P. ; Gonzalez, Jacqueline E. ; Feist, Adam ; Antoniewicz, Maciek R. ; Palsson, Bernhard
in: P L o S One, vol: 11, issue: 3

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1371/journal.pone.0151130

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Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution

Utrilla, José ; O'Brien, Edward J. ; Chen, Ke ; McCloskey, Douglas ; Cheung , Jacky ; Wang , Harris ; Armenta-Medina , Dagoberto ; Feist, Adam ; Palsson, Bernhard
in: Cell, vol: 2, pages: 260-271

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.04.003

 

MID Max: LC–MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications

McCloskey, Douglas ; Young, Jamey D. ; Xu, Sibei ; Palsson, Bernhard ; Feist, Adam
in: Analytical Chemistry, vol: 88, issue: 2, pages: 1362–1370

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1021/acs.analchem.5b03887

 

Modeling Method for Increased Precision and Scope of Directly Measurable Fluxes at a Genome-Scale

McCloskey, Douglas ; Young, Jamey D. ; Xu, Sibei ; Palsson, Bernhard ; Feist, Adam
in: Analytical chemistry, vol: 88, issue: 7, pages: 3844-3852

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1021/acs.analchem.5b04914

  PDF

Multi-omic data integration enables discovery of hidden biological regularities

Ebrahim, Ali ; Brunk, Elizabeth ; Tan, Justin ; O'Brien, Edward J. ; Kim, Donghyuk ; Szubin, Richard ; Lerman, Joshua A. ; Lechner, Anna ; Sastry, Anand ; Bordbar, Aarash ; Feist, Adam ; Palsson, Bernhard
in: Nature Communications, vol: 7

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1038/ncomms13091

  PDF

Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes

Monk, Jonathan M ; Koza, Anna ; Campodonico, Miguel A ; Machado, Daniel ; Seoane, Jose Miguel ; Palsson, Bernhard ; Herrgard, Markus ; Feist, Adam
in: Cell Systems, vol: 3, issue: 3, pages: 238-251

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1016/j.cels.2016.08.013

  PDF

Principles of proteome allocation are revealed using proteomic data and genome-scale models

Yang, Laurence ; Yurkovich, James T. ; Lloyd, Colton J. ; Ebrahim, Ali ; Saunders, Michael A. ; Palsson, Bernhard
in: Scientific Reports, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1038/srep36734

  PDF

Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments

O'Brien, Edward J. ; Utrilla, Jose ; Palsson, Bernhard
in: P L o S Computational Biology (Online), vol: 12, issue: 6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1371/journal.pcbi.1004998

 

Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow

Golabgir, Aydin ; Gutierrez, Jahir M. ; Hefzi, Hooman ; Li, Shangzhong ; Palsson, Bernhard ; Herwig, Christoph ; Lewis, Nathan
in: Biotechnology Advances, vol: 34, issue: 5, pages: 621-633

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1016/j.biotechadv.2016.02.011

  PDF

solveME: fast and reliable solution of nonlinear ME models

Yang, Laurence ; Ma, Ding ; Ebrahim, Ali ; Lloyd, Colton J. ; Saunders, Michael A. ; Palsson, Bernhard
in: B M C Bioinformatics, vol: 17, issue: 1

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2016     |    DOI: https://doi.org/10.1186/s12859-016-1240-1

2015
 

A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites

McCloskey, Douglas ; Gangoiti, Jon A. ; Palsson, Bernhard O. ; Feist, Adam M.
in: Metabolomics, vol: 11, issue: 5, pages: 1338-1350

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1007/s11306-015-0790-y

 

A streamlined ribosome profiling protocol for the characterization of microorganisms

Latif, Haythem ; Szubin, Richard ; Tan, Justin ; Brunk, Elizabeth ; Lechner, Anna ; Zengler, Karsten ; Palsson, Bernhard O.
in: BioTechniques, vol: 58, issue: 6, pages: 329-332

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.2144/000114302

 

Computing the functional proteome

O'Brien, Edward J. ; Palsson, Bernhard
in: Current Opinion in Biotechnology, vol: 34, pages: 125-134

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1016/j.copbio.2014.12.017

  PDF

Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli

Seo, Sang Woo ; Kim, Donghyuk ; O'Brien, Edward J. ; Szubin, Richard ; Palsson, Bernhard O.
in: Nature Communications, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1038/ncomms8970

  PDF

Do genome-scale models need exact solvers or clearer standards?

Ebrahim, A. ; Almaas, E. ; Bauer, E. ; Bordbar, A. ; Burgard, A. P. ; Chang, R. L. ; Drager, A. ; Famili, I. ; Feist, A. M. ; Fleming, R. M. ; Fong, S. S. ; Hatzimanikatis, V. ; Herrgard, M. J. ; Holder, A. ; Hucka, M. ; Hyduke, D. ; Jamshidi, N. ; Lee, Sang Yup ; Le Novere, N. ; Lerman, J. A. ; Lewis, Nathan ; Ma, D. ; Mahadevan, R. ; Maranas, C. ; Nagarajan, H. ; Navid, A. ; Nielsen, Jens ; Nielsen, L. K. ; Nogales, J. ; Noronha, A. ; Pal, C. ; Palsson, Bernhard ; Papin, J. A. ; Patil, Kiran R. ; Price, N. D. ; Reed, J. L. ; Saunders, M. ; Senger, R. S. ; Sonnenschein, Nikolaus ; Sun, Yuekai ; Thiele, I.
in: Molecular Systems Biology, vol: 11, issue: 10

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.15252/msb.20156157

  PDF

Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655

Seo, Sang Woo ; Kim, Donghyuk ; Szubin, Richard ; Palsson, Bernhard O.
in: Cell Reports, vol: 12, issue: 8, pages: 1289-1299

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1016/j.celrep.2015.07.043

 

How to set up collaborations between academia and industrial biotech companies

Pronk, Jack T. ; Lee, Sang Yup ; Lievense, Jeff ; Pierce, John ; Palsson, Bernhard ; Uhlén, Mathias ; Nielsen, Jens
in: Nature Biotechnology, vol: 33, issue: 3, pages: 237-240

Type: Comment/debate (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1038/nbt.3171

  PDF

JSBML 1.0: providing a smorgasbord of options to encode systems biology models

Rodriguez, Nicolas ; Thomas, Alex ; Watanabe, Leandro ; Vazirabad, Ibrahim Y. ; Kofia, Victor ; Gómez, Harold F. ; Mittag, Florian ; Matthes, Jakob ; Rudolph, Jan ; Wrzodek, Finja ; Netz, Eugen ; Diamantikos, Alexander ; Eichner, Johannes ; Keller, Roland ; Wrzodek, Clemens ; Fröhlich, Sebastian ; Lewis, Nathan ; Myers, Chris J. ; Le Novère, Nicolas ; Palsson, Bernhard ; Hucka, Michael ; Dräger, Andreas
in: Bioinformatics, vol: 31, issue: 20, pages: 3383-6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1093/bioinformatics/btv341

  PDF

Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC

Aziz, Ramy K. ; Khaw, Valerie L. ; Monk, Jonathan M. ; Brunk, Elizabeth ; Lewis, Robert ; Loh, Suh I. ; Mishra, Arti ; Nagle, Amrita A. ; Satyanarayana, Chitkala ; Dhakshinamoorthy, Saravanakumar ; Luche, Michele ; Kitchen, Douglas B. ; Andrews, Kathleen A. ; Palsson, Bernhard Ø ; Charusanti, Pep
in: Frontiers in Microbiology, vol: 6

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.3389/fmicb.2015.00958

 

Model-driven discovery of underground metabolic functions in Escherichia coli

Guzmán, Gabriela I. ; Utrilla, José ; Nurk, Sergey ; Brunk, Elizabeth ; Monk, Jonathan M. ; Ebrahim, Ali ; Palsson, Bernhard O. ; Feist, Adam M.
in: Proceedings of the National Academy of Sciences, vol: 112, issue: 3, pages: 929-934

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1073/pnas.1414218112

 

Next-generation genome-scale models for metabolic engineering

King, Zachary A. ; Lloyd, Colton J. ; Feist, Adam M. ; Palsson, Bernhard O.
in: Current Opinion in Biotechnology, vol: 35, pages: 23-29

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1016/j.copbio.2014.12.016

 

Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics

Bordbar, Aarash ; McCloskey, Douglas ; Zielinski, Daniel C ; Sonnenschein, Nikolaus ; Jamshidi, Neema ; Palsson, Bernhard
in: Cell Systems, vol: 1, issue: 4, pages: 283-292

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1016/j.cels.2015.10.003

  PDF

SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks

Draeger, Andreas ; Zielinski, Daniel C. ; Keller, Roland ; Rall, Matthias ; Eichner, Johannes ; Palsson, Bernhard O. ; Zell, Andreas
in: B M C Systems Biology, vol: 9, issue: 68

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1186/s12918-015-0212-9

 

Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data

Yang, Laurence ; Tan, Justin ; O'Brien, Edward J. ; Monk, Jonathan M. ; Kim, Donghyuk ; Li, Howard J. ; Charusanti, Pep ; Ebrahim, Ali ; Lloyd, Colton J. ; Yurkovich, James T. ; Du, Bin ; Draeger, Andreas ; Thomas, Alex ; Sun, Yuekai ; Saunders, Michael A. ; Palsson, Bernhard O.
in: Proceedings of the National Academy of Sciences of the United States of America, vol: 112, issue: 34, pages: 10810-10815

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1073/pnas.1501384112

  PDF

The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli

Cho, Suhyung ; Cho, Yoo-Bok ; Kang, Taek Jin ; Kim, Sun Chang ; Palsson, Bernhard ; Cho, Byung-Kwan
in: Nucleic acids research, vol: 43, issue: 6, pages: 3079-3088

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1093/nar/gkv150

 

Use of Adaptive Laboratory Evolution To Discover Key Mutations Enabling Rapid Growth of Escherichia coli K-12 MG1655 on Glucose Minimal Medium

LaCroix, Ryan A. ; Sandberg, Troy E. ; O'Brien, Edward J. ; Utrilla, Jose ; Ebrahim, Ali ; Guzman, Gabriela I. ; Szubin, Richard ; Palsson, Bernhard ; Feist, Adam
in: APPLIED AND ENVIRONMENTAL MICROBIOLOGY, vol: 81, issue: 1, pages: 17-30

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1128/AEM.02246-14

  PDF

Using Genome-scale Models to Predict Biological Capabilities

O’Brien, Edward J. ; Monk, Jonathan M. ; Palsson, Bernhard O.
in: CELL, vol: 161, issue: 5, pages: 971-987

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2015     |    DOI: https://doi.org/10.1016/j.cell.2015.05.019

2014
 

A model‐driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K‐12 MG1655 that is biochemically and thermodynamically consistent

McCloskey, Douglas ; Gangoiti, Jon A. ; King, Zachary A. ; Naviaux, Robert K. ; Barshop, Bruce A. ; Palsson, Bernhard ; Feist, Adam
in: Biotechnology and Bioengineering, vol: 111, issue: 4, pages: 803-815

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2014     |    DOI: https://doi.org/10.1002/bit.25133

 

Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli

Seo, Sang Woo ; Kim, Donghyuk ; Latif, Haythem ; O'Brien, Edward J. ; Szubin, Richard ; Palsson, Bernhard
in: Nature Communications, vol: 5

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2014     |    DOI: https://doi.org/10.1038/ncomms5910

  PDF

Determining the Control Circuitry of Redox Metabolism at the Genome-Scale

Federowicz, Stephen ; Kim, Donghyuk ; Ebrahim, Ali ; Lerman, Joshua ; Nagarajan, Harish ; Cho, Byung-kwan ; Zengler, Karsten ; Palsson, Bernhard
in: P L o S Genetics, vol: 10, issue: 4

Type: Journal article (Peer reviewed)

Status: Published     |    År: 2014     |    DOI: https://doi.org/10.1371/journal.pgen.1004264