Works by 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

Systematizing the generation of missing metabolic knowledge.

Published in:

Biotechnology & Bioengineering, 2010, v. 107, n. 3, p. 403, doi. 10.1002/bit.22844

By:

Orth, Jeffrey D.;
Palsson, Bernhard Ø.

Publication type:

Article

Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.

Published in:

Biotechnology & Bioengineering, 2006, v. 95, n. 5, p. 992, doi. 10.1002/bit.21073

By:

Hua, Qiang;
Joyce, Andrew R.;
Fong, Stephen S.;
Palsson, Bernhard Ø.

Publication type:

Article

Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.

Published in:

Biotechnology & Bioengineering, 2005, v. 91, n. 7, p. 872, doi. 10.1002/bit.20559

By:

Hanania, Elie G.;
Fieck, Annabeth;
Stevens, Janine;
Bodzin, Leon J.;
Palsson, Bernhard Ø.;
Koller, Manfred R.

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

Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.

Published in:

Scientific Reports, 2014, p. 1, doi. 10.1038/srep03925

By:

Thomas, Alex;
Rahmanian, Sorena;
Bordbar, Aarash;
Palsson, Bernhard Ø.;
Jamshidi, Neema

Publication type:

Article

Genome-Scale Metabolic Model of Xanthomonas phaseoli pv. manihotis : An Approach to Elucidate Pathogenicity at the Metabolic Level.

Published in:

Frontiers in Genetics, 2020, v. 11, p. N.PAG, doi. 10.3389/fgene.2020.00837

By:

Botero, David;
Monk, Jonathan;
Rodríguez Cubillos, María Juliana;
Rodríguez Cubillos, Andrés;
Restrepo, Mariana;
Bernal-Galeano, Vivian;
Reyes, Alejandro;
González Barrios, Andrés;
Palsson, Bernhard Ø.;
Restrepo, Silvia;
Bernal, Adriana

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

The PurR regulon in Escherichia coli K-12 MG1655.

Published in:

Nucleic Acids Research, 2011, v. 39, n. 15, p. 6456, doi. 10.1093/nar/gkr307

By:

Cho, Byung-Kwan;
Federowicz, Stephen A.;
Embree, Mallory;
Park, Young-Seoub;
Kim, Donghyuk;
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

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

Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by GenomeWide Transcription Start Site Profiling.

Published in:

PLoS Genetics, 2012, v. 8, n. 8, p. 1, doi. 10.1371/journal.pgen.1002867

By:

Donghyuk Kim;
Sung-Joong Hong, Jay;
Yu Qiu;
Harish Nagarajan;
Joo-Hyun Seo;
Byung-Kwan Cho;
Shih-Feng Tsai;
Palsson, Bernhard Ø

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

The model organism as a system: integrating 'omics' data sets.

Published in:

Nature Reviews Molecular Cell Biology, 2006, v. 7, n. 3, p. 198, doi. 10.1038/nrm1857

By:

Joyce, Andrew R.;
Palsson, Bernhard Ø

Publication type:

Article

Comparison of metal‐bound and unbound structures of aminopeptidase B proteins from Escherichia coli and Yersinia pestis.

Published in:

Protein Science: A Publication of the Protein Society, 2020, v. 29, n. 7, p. 1618, doi. 10.1002/pro.3876

By:

Minasov, George;
Lam, Matthew R.;
Rosas‐Lemus, Monica;
Sławek, Joanna;
Woinska, Magdalena;
Shabalin, Ivan G.;
Shuvalova, Ludmilla;
Palsson, Bernhard Ø.;
Godzik, Adam;
Minor, Wladek;
Satchell, Karla J. F.

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

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

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

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

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

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

Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.

Published in:

Nature Communications, 2013, v. 4, n. 11, p. 2809, doi. 10.1038/ncomms3809

By:

Nagarajan, Harish;
Embree, Mallory;
Rotaru, Amelia-Elena;
Shrestha, Pravin M.;
Feist, Adam M.;
Palsson, Bernhard Ø;
Lovley, Derek R.;
Zengler, Karsten

Publication type:

Article

BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.

Published in:

BMC Bioinformatics, 2010, v. 11, p. 213, doi. 10.1186/1471-2105-11-213

By:

Schellenberger, Jan;
Park, Junyoung O.;
Conrad, Tom M.;
Palsson, Bernhard Ø.

Publication type:

Article

Metabolite coupling in genome-scale metabolic networks.

Published in:

BMC Bioinformatics, 2006, v. 7, p. 111, doi. 10.1186/1471-2105-7-111

By:

Becker, Scott A;
Price, Nathan D;
Palsson, Bernhard Ø

Publication type:

Article

Effects of Dissolved Oxygen on Hybridoma Cell Growth, Metabolism, and Antibody Production Kinetics in Continuous Culture.

Published in:

Biotechnology Progress, 1990, v. 6, n. 6, p. 437, doi. 10.1021/bp00006a006

By:

Ozturk, Sadettin S.;
Palsson, Bernhard Ø

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

Functional States of the Genome-Scale Escherichia Coli Transcriptional Regulatory System.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 6, p. 1, doi. 10.1371/journal.pcbi.1000403

By:

Gianchandani, Erwin P.;
Joyce, Andrew R.;
Palsson, Bernhard Ø.;
Papin, Jason A.

Publication type:

Article

Genome-Scale Reconstruction of Escherichia coli's Transcriptional and Translational Machinery: A Knowledge Base, Its Mathematical Formulation, and Its Functional Characterization.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 3, p. 1, doi. 10.1371/journal.pcbi.1000312

By:

Thiele, Ines;
Jamshidi, Neema;
Fleming, Ronan M. T.;
Palsson, Bernhard Ø.

Publication type:

Article

Identification of Potential Pathway Mediation Targets in Toll-like Receptor Signaling.

Published in:

PLoS Computational Biology, 2009, v. 5, n. 2, p. 1, doi. 10.1371/journal.pcbi.1000292

By:

Fan Li;
Thiele, Ines;
Jamshidi, Neema;
Palsson, Bernhard Ø.

Publication type:

Article

Top-Down Analysis of Temporal Hierarchy in Biochemical Reaction Networks.

Published in:

PLoS Computational Biology, 2008, v. 4, n. 9, p. 1, doi. 10.1371/journal.pcbi.1000177

By:

Jamshidi, Neema;
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

Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase–Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.

Published in:

Frontiers in Cellular & Infection Microbiology, 2019, v. 9, p. N.PAG, doi. 10.3389/fcimb.2019.00161

By:

Norsigian, Charles J.;
Attia, Heba;
Szubin, Richard;
Yassin, Aymen S.;
Palsson, Bernhard Ø.;
Aziz, Ramy K.;
Monk, Jonathan M.

Publication type:

Article

A treasure trove of 1034 actinomycete genomes.

Published in:

Nucleic Acids Research, 2024, v. 52, n. 13, p. 7487, doi. 10.1093/nar/gkae523

By:

Jørgensen, Tue Sparholt;
Mohite, Omkar S;
Sterndorff, Eva B;
Alvarez-Arevalo, Maria;
Blin, Kai;
Booth, Thomas J;
Charusanti, Pep;
Faurdal, David;
Hansen, Troels Ø;
Nuhamunada, Matin;
Mourched, Anna-Sophie;
Palsson, Bernhard Ø;
Weber, Tilmann

Publication type:

Article

Probing the basis for genotype-phenotype relationships.

Published in:

Nature Methods, 2009, v. 6, n. 8, p. 565, doi. 10.1038/nmeth0809-565

By:

Byung-Kwan Cho;
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