Works matching AU Palsson, Bernhard Ø.

Results: 74

Towards genome-scale signalling network reconstructions.

Published in:

2010

By:

Hyduke, Daniel R.;
Palsson, Bernhard Ø.;
Palsson, Bernhard Ø

Publication type:

journal article

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

Published in:

2011

By:

Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.;
Lovley, Derek R.

Publication type:

Correction Notice

In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.

Published in:

Nature Reviews Microbiology, 2011, v. 9, n. 1, p. 39, doi. 10.1038/nrmicro2456

By:

Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.;
Lovley, Derek R.

Publication type:

Article

Reconstruction of biochemical networks in microorganisms.

Published in:

Nature Reviews Microbiology, 2009, v. 7, n. 2, p. 129, doi. 10.1038/nrmicro1949

By:

Feist, Adam M.;
Herrgård, Markus J.;
Thiele, Ines;
Reed, Jennie L.;
Palsson, Bernhard Ø.

Publication type:

Article

Genome-scale models of microbial cells: evaluating the consequences of constraints.

Published in:

Nature Reviews Microbiology, 2004, v. 2, n. 11, p. 886, doi. 10.1038/nrmicro1023

By:

Price, Nathan D.;
Reed, Jennifer L.;
Palsson, Bernhard Ø.

Publication type:

Article

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

Published in:

Bioinformatics, 2015, v. 31, n. 20, p. 3383, doi. 10.1093/bioinformatics/btv341

By:

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 E.;
Myers, Chris J.;
Le Novère, Nicolas;
Palsson, Bernhard Ø.

Publication type:

Article

GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.

Published in:

Bioinformatics, 2013, v. 29, n. 22, p. 2900, doi. 10.1093/bioinformatics/btt493

By:

Schmidt, Brian J.;
Ebrahim, Ali;
Metz, Thomas O.;
Adkins, Joshua N.;
Palsson, Bernhard Ø.;
Hyduke, Daniel R.

Publication type:

Article

Identification and Engineering of Transporters for Efficient Melatonin Production in Escherichia coli.

Published in:

Frontiers in Microbiology, 2022, p. 1, doi. 10.3389/fmicb.2022.880847

By:

Yang, Lei;
Malla, Sailesh;
Özdemir, Emre;
Kim, Se Hyeuk;
Lennen, Rebecca;
Christensen, Hanne B.;
Christensen, Ulla;
Munro, Lachlan J.;
Herrgård, Markus J.;
Kell, Douglas B.;
Palsson, Bernhard Ø.

Publication type:

Article

Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.

Published in:

Nature Genetics, 2006, v. 38, n. 12, p. 1406, doi. 10.1038/ng1906

By:

Herring, Christopher D.;
Raghunathan, Anu;
Honisch, Christiane;
Patel, Trina;
Applebee, M. Kenyon;
Joyce, Andrew R.;
Albert, Thomas J.;
Blattner, Frederick R.;
van den Boom, Dirk;
Cantor, Charles R.;
Palsson, Bernhard Ø.

Publication type:

Article

Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.

Published in:

Microbial Cell Factories, 2014, v. 13, n. 1, p. 1, doi. 10.1186/1475-2859-13-3

By:

Weiqi Fu;
Paglia, Giuseppe;
Magnúsdóttir, Manuela;
Steinarsdóttir, Elín A;
Gudmundsson, Steinn;
Palsson, Bernhard Ø;
Andrésson, Ólafur S.;
Brynjólfsson, Sigurður

Publication type:

Article

Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.

Published in:

BMC Genomics, 2004, v. 5, p. 1, doi. 10.1186/1471-2164-5-63

By:

Duarte, Natalie C.;
Palsson, Bernhard Ø.;
Pengcheng Fu

Publication type:

Article

expa: a program for calculating extreme pathways in biochemical reaction networks.

Published in:

Bioinformatics, 2005, v. 21, n. 8, p. 1739

By:

Bernhard Ø. Palsson

Publication type:

Article

Cumulative Number of Cell Divisions as a Meaningful Timescale for Adaptive Laboratory Evolution of Escherichia coli.

Published in:

PLoS ONE, 2011, v. 6, n. 10, p. 1, doi. 10.1371/journal.pone.0026172

By:

Dae-Hee Lee;
Feist, Adam M.;
Barrett, Christian L.;
Palsson, Bernhard Ø.

Publication type:

Article

De Novo Assembly of the Complete Genome of an Enhanced Electricity-Producing Variant of Geobacter sulfurreducens Using Only Short Reads.

Published in:

PLoS ONE, 2010, v. 5, n. 6, p. 1, doi. 10.1371/journal.pone.0010922

By:

Nagarajan, Harish;
Butler, Jessica E.;
Klimes, Anna;
Yu Qiu;
Zengler, Karsten;
Ward, Joy;
Young, Nelson D.;
Methe', Barbara A.;
Palsson, Bernhard Ø.;
Lovley, Derek R.;
Barrett, Christian L.

Publication type:

Article

Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.

Published in:

BMC Microbiology, 2005, v. 5, p. 8, doi. 10.1186/1471-2180-5-8

By:

Becker, Scott A.;
Palsson, Bernhard Ø

Publication type:

Article

Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.

Published in:

Molecular Systems Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1038/msb.2013.52

By:

O'Brien, Edward J;
Lerman, Joshua A;
Chang, Roger L;
Hyduke, Daniel R;
Palsson, Bernhard Ø

Publication type:

Article

Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.

Published in:

Molecular Systems Biology, 2013, v. 9, n. 1, p. 1, doi. 10.1038/msb.2013.18

By:

McCloskey, Douglas;
Palsson, Bernhard Ø;
Feist, Adam M

Publication type:

Article

Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.52

By:

Chang, Roger L;
Ghamsari, Lila;
Manichaikul, Ani;
Hom, Erik F Y;
Balaji, Santhanam;
Fu, Weiqi;
Shen, Yun;
Hao, Tong;
Palsson, Bernhard Ø;
Salehi‐Ashtiani, Kourosh;
Papin, Jason A

Publication type:

Article

Microbial laboratory evolution in the era of genome-scale science.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.42

By:

Conrad, Tom M;
Lewis, Nathan E;
Palsson, Bernhard Ø

Publication type:

Article

A comprehensive genome-scale reconstruction of Escherichia coli metabolism—2011.

Published in:

Molecular Systems Biology, 2011, v. 7, n. 1, p. 1, doi. 10.1038/msb.2011.65

By:

Orth, Jeffrey D;
Conrad, Tom M;
Na, Jessica;
Lerman, Joshua A;
Nam, Hojung;
Feist, Adam M;
Palsson, Bernhard Ø

Publication type:

Article

Reconstruction annotation jamborees: a community approach to systems biology.

Published in:

Molecular Systems Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1038/msb.2010.15

By:

Thiele, Ines;
Palsson, Bernhard Ø

Publication type:

Article

Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.

Published in:

Molecular Systems Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1038/msb.2010.68

By:

Bordbar, Aarash;
Lewis, Nathan E;
Schellenberger, Jan;
Palsson, Bernhard Ø;
Jamshidi, Neema

Publication type:

Article

Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.

Published in:

Molecular Systems Biology, 2010, v. 6, n. 1, p. 1, doi. 10.1038/msb.2010.47

By:

Lewis, Nathan E;
Hixson, Kim K;
Conrad, Tom M;
Lerman, Joshua A;
Charusanti, Pep;
Polpitiya, Ashoka D;
Adkins, Joshua N;
Schramm, Gunnar;
Purvine, Samuel O;
Lopez‐Ferrer, Daniel;
Weitz, Karl K;
Eils, Roland;
König, Rainer;
Smith, Richard D;
Palsson, Bernhard Ø

Publication type:

Article

Applications of genome-scale metabolic reconstructions.

Published in:

Molecular Systems Biology, 2009, v. 5, n. 1, p. 320, doi. 10.1038/msb.2009.77

By:

Oberhardt, Matthew A;
Palsson, Bernhard Ø;
Papin, Jason A

Publication type:

Article

Formulating genome-scale kinetic models in the post-genome era.

Published in:

Molecular Systems Biology, 2008, v. 4, n. 1, p. 1, doi. 10.1038/msb.2008.8

By:

Jamshidi, Neema;
Palsson, Bernhard Ø

Publication type:

Article

A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.

Published in:

Molecular Systems Biology, 2007, v. 3, n. 1, p. 121, doi. 10.1038/msb4100155

By:

Feist, Adam M;
Henry, Christopher S;
Reed, Jennifer L;
Krummenacker, Markus;
Joyce, Andrew R;
Karp, Peter D;
Broadbelt, Linda J;
Hatzimanikatis, Vassily;
Palsson, Bernhard Ø

Publication type:

Article

Systems biology of SNPs.

Published in:

Molecular Systems Biology, 2006, v. 2, n. 1, p. E1, doi. 10.1038/msb4100077

By:

Jamshidi, Neema;
Palsson, Bernhard Ø

Publication type:

Article

Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.

Published in:

Molecular Systems Biology, 2006, v. 2, n. 1, p. E1, doi. 10.1038/msb4100046

By:

Feist, Adam M;
Scholten, Johannes C M;
Palsson, Bernhard Ø;
Brockman, Fred J;
Ideker, Trey

Publication type:

Article

Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.

Published in:

Biotechnology & Bioengineering, 2004, v. 86, n. 3, p. 317, doi. 10.1002/bit.20011

By:

Wiback, Sharon J.;
Mahadevan, Radhakrishnan;
Palsson, Bernhard Ø.

Publication type:

Article

Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.

Published in:

Biotechnology & Bioengineering, 2000, v. 71, n. 4, p. 286, doi. 10.1002/1097-0290(2000)71:4<286::AID-BIT1018>3.0.CO;2-R

By:

Schilling, Christophe H.;
Edwards, Jeremy S.;
Letscher, David;
Palsson, Bernhard Ø.

Publication type:

Article

Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data.

Published in:

Biotechnology & Bioengineering, 1996, v. 52, n. 1, p. 24, doi. 10.1002/(SICI)1097-0290(19961005)52:1<24::AID-BIT3>3.0.CO;2-0

By:

Peng, Ching-An;
Koller, Manfred R.;
Palsson, Bernhard Ø.

Publication type:

Article

Membrane adsorption characteristics determine the kinetics of flow-through transductions.

Published in:

Biotechnology & Bioengineering, 1996, v. 51, n. 3, p. 260, doi. 10.1002/(SICI)1097-0290(19960805)51:3<260::AID-BIT2>3.0.CO;2-B

By:

Chuck, Alice S.;
Palsson, Bernhard Ø.

Publication type:

Article

Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions.

Published in:

Biotechnology & Bioengineering, 1996, v. 50, n. 5, p. 505, doi. 10.1002/(SICI)1097-0290(19960605)50:5<505::AID-BIT4>3.0.CO;2-J

By:

Koller, Manfred R.;
Manchel, Ilana;
Palsson, Mahshid A.;
Maher, Robert J.;
Palsson, Bernhard Ø.

Publication type:

Article

Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.

Published in:

Biotechnology & Bioengineering, 1996, v. 50, n. 5, p. 479, doi. 10.1002/(SICI)1097-0290(19960605)50:5<479::AID-BIT2>3.0.CO;2-C

By:

Peng, Ching-An;
Palsson, Bernhard Ø.

Publication type:

Article

High-density algal photobioreactors using light-emitting diodes.

Published in:

Biotechnology & Bioengineering, 1994, v. 44, n. 10, p. 1161, doi. 10.1002/bit.260441002

By:

Lee, Choul-Gyun;
Palsson, Bernhard Ø.

Publication type:

Article

Metabolic Reconstruction and Modeling of Nitrogen Fixation in Rhizobium etli.

Published in:

PLoS Computational Biology, 2007, v. 3, n. 10, p. e192, doi. 10.1371/journal.pcbi.0030192

By:

Resendis-Antonio, Osbaldo;
Reed, Jennifer L.;
Encarnación, Sergio;
Collado-Vides, Julio;
Palsson, Bernhard Ø.

Publication type:

Article

Identification of Genome-Scale Metabolic Network Models Using Experimentally Measured Flux Profiles.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 7, p. e72, doi. 10.1371/journal.pcbi.0020072

By:

Herrgård, Markus J.;
Fong, Stephen S.;
Palsson, Bernhard Ø.

Publication type:

Article

Long-Range Periodic Patterns in Microbial Genomes Indicate Significant Multi-Scale Chromosomal Organization.

Published in:

PLoS Computational Biology, 2006, v. 2, n. 1, p. e2, doi. 10.1371/journal.pcbi.0020002

By:

Allen, Timothy E.;
Price, Nathan D.;
Joyce, Andrew R.;
Palsson, Bernhard Ø.

Publication type:

Article

Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.

Published in:

Biotechnology Letters, 2003, v. 25, n. 5, p. 435, doi. 10.1023/A:1022497310798

By:

Raghunathan, Anuradha;
Palsson, Bernhard Ø.

Publication type:

Article

What is flux balance analysis?

Published in:

Nature Biotechnology, 2010, v. 28, n. 3, p. 245, doi. 10.1038/nbt.1614

By:

Orth, Jeffrey D.;
Palsson, Bernhard Ø.

Publication type:

Article

The transcription unit architecture of the Escherichia coli genome.

Published in:

Nature Biotechnology, 2009, v. 27, n. 11, p. 1043, doi. 10.1038/nbt.1582

By:

Byung-Kwan Cho;
Zengler, Karsten;
Yu Qiu;
Young Seoub Park;
Knight, Eric M.;
Barrett, Christian L.;
Yuan Gao;
Palsson, Bernhard Ø.

Publication type:

Article

Network-based prediction of human tissue-specific metabolism.

Published in:

Nature Biotechnology, 2008, v. 26, n. 9, p. 1003, doi. 10.1038/nbt.1487

By:

Shlomi, Tomer;
Cabili, Moran N;
Herrgård, Markus J;
Palsson, Bernhard Ø;
Ruppin, Eytan

Publication type:

Article

The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.

Published in:

Nature Biotechnology, 2008, v. 26, n. 6, p. 659, doi. 10.1038/nbt1401

By:

Feist, Adam M;
Palsson, Bernhard Ø

Publication type:

Article

Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.

Published in:

BMC Systems Biology, 2012, v. 6, n. 1, p. 30, doi. 10.1186/1752-0509-6-30

By:

Orth, Jeffrey D.;
Palsson, Bernhard Ø

Publication type:

Article

A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.

Published in:

BMC Systems Biology, 2010, v. 4, p. 140, doi. 10.1186/1752-0509-4-140

By:

Sigurdsson, Martin I.;
Jamshidi, Neema;
Steingrimsson, Eirikur;
Thiele, Ines;
Palsson, Bernhard Ø.

Publication type:

Article

Connecting extracellular metabolomic measurements to intracellular flux states in yeast.

Published in:

BMC Systems Biology, 2009, v. 3, p. 1, doi. 10.1186/1752-0509-3-37

By:

Mo, Monica L.;
Palsson, Bernhard Ø.;
Herrgård, Markus J.

Publication type:

Article

A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.

Published in:

BMC Systems Biology, 2008, v. 2, p. 1, doi. 10.1186/1752-0509-2-79

By:

Nogales, Juan;
Palsson, Bernhard ø.;
Thiele, Ines

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2015, p. 1, doi. 10.3389/fmicb.2015.00958

By:

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

Publication type:

Article

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

Published in:

Frontiers in Microbiology, 2015, p. 1

By:

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

Publication type:

Article

Drug Off-Target Effects Predicted Using Structural Analysis in the Context of a Metabolic Network Model.

Published in:

PLoS Computational Biology, 2010, v. 6, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000938

By:

Chang, Roger L.;
Li Xie;
Lei Xie;
Bourne, Philip E.;
Palsson, Bernhard Ø.

Publication type:

Article