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Bernhard Palsson

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TOP 3
Douglas McCloskey; Bernhard Ø Palsson; Adam M Feist
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
Daniel R Hyduke; Nathan E Lewis; Bernhard Ø Palsson
Analysis of omics data with genome-scale models of metabolism.
Ottar Rolfsson; Manuela Magnusdóttir; Giuseppe Paglia; Bernhard Ø Palsson; Ines Thiele
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.

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All Publications

2013: Douglas McCloskey; Bernhard Ø Palsson; Adam M Feist
Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.
Molecular systems biology 2013;9():661.
2013: Daniel R Hyduke; Nathan E Lewis; Bernhard Ø Palsson
Analysis of omics data with genome-scale models of metabolism.
Molecular bioSystems 2013;9(2):167-74.
2013: Ottar Rolfsson; Manuela Magnusdóttir; Giuseppe Paglia; Bernhard Ø Palsson; Ines Thiele
Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.
The Biochemical journal 2013;449(2):427-35.
2012: Giuseppe Paglia; Bernhard Ø Palsson; Olafur E Sigurjonsson
Systems biology of stored blood cells: can it help to extend the expiration date?
Journal of proteomics 2012;76 Spec No.():163-7.
2012: Weiqi Fu; Olafur Gudmundsson; Gisli Herjolfsson; Sigurdur Brynjolfsson; Adam M Feist; Bernhard Ø Palsson
Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.
Journal of biotechnology 2012;161(3):242-9.
2012: Giuseppe Paglia; Bernhard Ø Palsson; Olafur E Sigurjónsson; Sveinn Guðmundsson; Manuela Magnúsdóttir; Steinunn Thorlacius; Ines Thiele
Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.
Journal of chromatography. B, Analytical technologies in the biomedical and life sciences 2012;898():111-20.
2012: Donghyuk Kim; Harish Nagarajan; Byung-Kwan Cho; Jay Sung Joong Hong; Yu Qiu; Joo-Hyun Seo; Shih-Feng Tsai; Bernhard Ø Palsson
Comparative analysis of regulatory elements between Escherichia coli and Klebsiella pneumoniae by genome-wide transcription start site profiling.
PLoS genetics 2012;8(8):e1002867.
2012: Jeffrey D Orth; Bernhard Ø Palsson
Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.
BMC systems biology 2012;6():30.
2012: Jan Schellenberger; David A Scott; Daniel C Zielinski; Vasiliy Portnoy; Jennifer L Reed; Wing Choi; Sunthosh Madireddi; Andrei L Osterman; Bernhard Ø Palsson
Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.
BMC systems biology 2012;6():9.
2011: Sun-Young Ahn; Kevin T Bush; Ankur Dnyanmote; Satish A Eraly; Tom F Gallegos; Neema Jamshidi; Monica L Mo; Bernhard Ø Palsson; Douglas H Sweet; Wei Wu; Sanjay K Nigam
Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.
The Journal of biological chemistry 2011;286(36):31522-31.
2011: Jan Schellenberger; Ines Thiele; Daniel C Zielinski; Richard Que; Sorena Rahmanian; Aarash Bordbar; Adam M Feist; Ronan Fleming; Daniel R Hyduke; Joseph Kang; Nathan E Lewis; Jeffrey D Orth; Bernhard Ø Palsson
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.
Nature protocols 2011;6(9):1290-307.
2011: Byung-Kwan Cho; Mallory Embree; Stephen A Federowicz; Donghyuk Kim; Young-Seoub Park; Bernhard Ø Palsson
The PurR regulon in Escherichia coli K-12 MG1655.
Nucleic acids research 2011;39(15):6456-64.
2011: M Kenyon Applebee; Tom M Conrad; Andrew R Joyce; Donald W Pettigrew; Bernhard Ø Palsson
Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.
The Journal of biological chemistry 2011;286(26):23150-9.
2011: Jan Schellenberger; Nathan E Lewis; Bernhard Ø Palsson
Elimination of thermodynamically infeasible loops in steady-state metabolic models.
Biophysical journal 2011;100(3):544-53.
2011: Dae-Hee Lee; Christian L Barrett; Adam M Feist; Bernhard Ø Palsson
Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.
PloS one 2011;6(10):e26172.
2011: Jeffrey D Orth; Tom M Conrad; Adam M Feist; Joshua A Lerman; Jessica Na; Hojung Nam; Bernhard Ø Palsson
A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.
Molecular systems biology 2011;7():535.
2011: Roger L Chang; Weiqi Fu; Lila Ghamsari; Tong Hao; Erik F Y Hom; Ani Manichaikul; Bernhard Ø Palsson; Kourosh Salehi-Ashtiani; Yun Shen; Santhanam Balaji; Jason A Papin
Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.
Molecular systems biology 2011;7():518.
2011: Tom M Conrad; Nathan E Lewis; Bernhard Ø Palsson
Microbial laboratory evolution in the era of genome-scale science.
Molecular systems biology 2011;7():509.
2011: Radhakrishnan Mahadevan; Bernhard Ø Palsson; Derek R Lovley
In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.
Nature reviews. Microbiology 2011;9(1):39-50.
2010: Nathan E Lewis; Gunnar Schramm; Aarash Bordbar; Jan Schellenberger; Michael P Andersen; Jeffrey K Cheng; Nilam Patel; Alex Yee; Randall A Lewis; Roland Eils; Rainer König; Bernhard Ø Palsson
Large-scale in silico modeling of metabolic interactions between cell types in the human brain.
Nature biotechnology 2010;28(12):1279-85.
2010: Tom M Conrad; Michael Frazier; Andrew R Joyce; Byung-Kwan Cho; Eric M Knight; Nathan E Lewis; Robert Landick; Bernhard Ø Palsson
RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.
Proceedings of the National Academy of Sciences of the United States of America 2010;107(47):20500-5.
2010: Pep Charusanti; Tom M Conrad; Eric M Knight; Karthik Venkataraman; Nicole L Fong; Bin Xie; Yuan Gao; Bernhard Ø Palsson
Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.
PLoS genetics 2010;6(11):e1001186.
2010: Aarash Bordbar; Nathan E Lewis; Jan Schellenberger; Bernhard Ø Palsson; Neema Jamshidi
Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.
Molecular systems biology 2010;6():422.
2010: Jeffrey D Orth; Bernhard Ø Palsson
Systematizing the generation of missing metabolic knowledge.
Biotechnology and bioengineering 2010;107(3):403-12.
2010: Vasiliy A Portnoy; David A Scott; Nathan E Lewis; Yekaterina Tarasova; Andrei L Osterman; Bernhard Ø Palsson
Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.
Applied and environmental microbiology 2010;76(19):6529-40.
2010: Yu Qiu; Byung-Kwan Cho; Young Seoub Park; Derek Lovley; Bernhard Ø Palsson; Karsten Zengler
Structural and operational complexity of the Geobacter sulfurreducens genome.
Genome research 2010;20(9):1304-11.
2010: Nathan E Lewis; Kim K Hixson; Tom M Conrad; Joshua A Lerman; Pep Charusanti; Ashoka D Polpitiya; Joshua N Adkins; Gunnar Schramm; Samuel O Purvine; Daniel Lopez-Ferrer; Karl K Weitz; Roland Eils; Rainer König; Richard D Smith; Bernhard Ø Palsson
Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.
Molecular systems biology 2010;6():390.
2010: Dae-Hee Lee; Bernhard Ø Palsson
Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.
Applied and environmental microbiology 2010;76(13):4158-68.
2010: Ines Thiele; Ronan M T Fleming; Aarash Bordbar; Jan Schellenberger; Bernhard Ø Palsson
Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.
Biophysical journal 2010;98(10):2072-81.
2010: Adam M Feist; Daniel C Zielinski; Jeffrey D Orth; Jan Schellenberger; Markus J Herrgard; Bernhard Ø Palsson
Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.
Metabolic engineering 2010;12(3):173-86.
2010: Ines Thiele; Bernhard Ø Palsson
Reconstruction annotation jamborees: a community approach to systems biology.
Molecular systems biology 2010;6():361.
2010: Daniel R Hyduke; Bernhard Ø Palsson
Towards genome-scale signalling network reconstructions.
Nature reviews. Genetics 2010;11(4):297-307.
2010: Jeffrey D Orth; Ines Thiele; Bernhard Ø Palsson
What is flux balance analysis?
Nature biotechnology 2010;28(3):245-8.
2010: Neema Jamshidi; Bernhard Ø Palsson
Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.
Biophysical journal 2010;98(2):175-85.
2010: Roger L Chang; Li Xie; Lei Xie; Philip Bourne; Bernhard Ø Palsson
Drug off-target effects predicted using structural analysis in the context of a metabolic network model.
PLoS computational biology 2010;6(9):e1000938.
2010: Harish Nagarajan; Jessica E Butler; Anna Klimes; Yu Qiu; Karsten Zengler; Joy Ward; Nelson D Young; Barbara A Methé; Bernhard Ø Palsson; Derek R Lovley; Christian L Barrett
De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.
PloS one 2010;5(6):e10922.
2010: Ines Thiele; Bernhard Ø Palsson
A protocol for generating a high-quality genome-scale metabolic reconstruction.
Nature protocols 2010;5(1):93-121.
2009: Byung-Kwan Cho; Karsten Zengler; Yu Qiu; Young Seoub Park; Eric M Knight; Christian L Barrett; Yuan Gao; Bernhard Ø Palsson
The transcription unit architecture of the Escherichia coli genome.
Nature biotechnology 2009;27(11):1043-9.
2009: Neema Jamshidi; Bernhard Ø Palsson
Flux-concentration duality in dynamic nonequilibrium biological networks.
Biophysical journal 2009;97(5):L11-3.
2009: Byung-Kwan Cho; Bernhard Ø Palsson
Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect.
Molecular cell 2009;35(3):255-6.
2009: Byung-Kwan Cho; Bernhard Ø Palsson
Probing the basis for genotype-phenotype relationships.
Nature methods 2009;6(8):565-6.
2009: Erwin Gianchandani; Andrew R Joyce; Bernhard Ø Palsson; Jason A Papin
Functional states of the genome-scale Escherichia coli transcriptional regulatory system.
PLoS computational biology 2009;5(6):e1000403.
2009: Nathan E Lewis; Byung-Kwan Cho; Eric M Knight; Bernhard Ø Palsson
Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.
Journal of bacteriology 2009;191(11):3437-44.
2009: Ines Thiele; Neema Jamshidi; Ronan Fleming; Bernhard Ø Palsson
Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.
PLoS computational biology 2009;5(3):e1000312.
2009: Jan Schellenberger; Bernhard Ø Palsson
Use of randomized sampling for analysis of metabolic networks.
The Journal of biological chemistry 2009;284(9):5457-61.
2009: Fan Li; Ines Thiele; Neema Jamshidi; Bernhard Ø Palsson
Identification of potential pathway mediation targets in Toll-like receptor signaling.
PLoS computational biology 2009;5(2):e1000292.
2009: Adam M Feist; Markus J Herrgård; Ines Thiele; Jennifer L Reed; Bernhard Ø Palsson
Reconstruction of biochemical networks in microorganisms.
Nature reviews. Microbiology 2009;7(2):129-43.
2009: Matthew A Oberhardt; Bernhard Ø Palsson; Jason A Papin
Applications of genome-scale metabolic reconstructions.
Molecular systems biology 2009;5():320.
2009: Neema Jamshidi; Bernhard Ø Palsson
Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.
BMC systems biology 2009;3():44.
2009: Monica L Mo; Bernhard Ø Palsson; Markus J Herrgård
Connecting extracellular metabolomic measurements to intracellular flux states in yeast.
BMC systems biology 2009;3():37.
2009: Christian L Barrett; Markus J Herrgard; Bernhard Ø Palsson
Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.
BMC systems biology 2009;3():30.
2009: Martin Sigurdsson; Neema Jamshidi; Jon J Jonsson; Bernhard Ø Palsson
Genome-scale network analysis of imprinted human metabolic genes.
Epigenetics : official journal of the DNA Methylation Society 2009;4(1):43-6.
2009: Monica L Mo; Bernhard Ø Palsson
Understanding human metabolic physiology: a genome-to-systems approach.
Trends in biotechnology 2009;27(1):37-44.
2008: Byung-Kwan Cho; Christian L Barrett; Eric M Knight; Young Seoub Park; Bernhard Ø Palsson
Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.
Proceedings of the National Academy of Sciences of the United States of America 2008;105(49):19462-7.
2008: Vasiliy A Portnoy; Markus J Herrgård; Bernhard Ø Palsson
Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.
Applied and environmental microbiology 2008;74(24):7561-9.
2008: Joungmin Lee; Hongseok Yun; Adam M Feist; Bernhard Ø Palsson; Sang Yup Lee
Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.
Applied microbiology and biotechnology 2008;80(5):849-62.
2008: Tomer Shlomi; Moran N Cabili; Markus J Herrgård; Bernhard Ø Palsson; Eytan Ruppin
Network-based prediction of human tissue-specific metabolism.
Nature biotechnology 2008;26(9):1003-10.
2008: M Kenyon Applebee; Markus J Herrgård; Bernhard Ø Palsson
Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.
Journal of bacteriology 2008;190(14):5087-94.
2008: Adam M Feist; Bernhard Ø Palsson
The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.
Nature biotechnology 2008;26(6):659-67.
2008: Byung-Kwan Cho; Eric M Knight; Christian L Barrett; Bernhard Ø Palsson
Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.
Genome research 2008;18(6):900-10.
2008: Scott A Becker; Bernhard Ø Palsson
Context-specific metabolic networks are consistent with experiments.
PLoS computational biology 2008;4(5):e1000082.
2008: Juan Nogales; Bernhard Ø Palsson; Ines Thiele
A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.
BMC systems biology 2008;2():79.
2008: Neema Jamshidi; Bernhard Ø Palsson
Top-down analysis of temporal hierarchy in biochemical reaction networks.
PLoS computational biology 2008;4(9):e1000177.
2008: Andrew R Joyce; Bernhard Ø Palsson
Predicting gene essentiality using genome-scale in silico models.
Methods in molecular biology (Clifton, N.J.) 2008;416():433-57.
2008: Byung-Kwan Cho; Eric M Knight; Bernhard Ø Palsson
Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.
Methods in molecular biology (Clifton, N.J.) 2008;439():131-45.
2008: Neema Jamshidi; Bernhard Ø Palsson
Formulating genome-scale kinetic models in the post-genome era.
Molecular systems biology 2008;4():171.
2008: Scott A Becker; Bernhard Ø Palsson
Three factors underlying incorrect in silico predictions of essential metabolic genes.
BMC systems biology 2008;2():14.
2007: Tomer Shlomi; Markus Herrgard; Vasiliy Portnoy; Efrat Naim; Bernhard Ø Palsson; Roded Sharan; Eytan Ruppin
Systematic condition-dependent annotation of metabolic genes.
Genome research 2007;17(11):1626-33.
2007: Osbaldo Resendis-Antonio; Jennifer L Reed; Sergio Encarnación; Julio Collado-Vides; Bernhard Ø Palsson
Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.
PLoS computational biology 2007;3(10):1887-95.
2007: You-Kwan Oh; Bernhard Ø Palsson; Sung M Park; Christophe H Schilling; Radhakrishnan Mahadevan
Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.
The Journal of biological chemistry 2007;282(39):28791-9.
2007: Monica L Mo; Neema Jamshidi; Bernhard Ø Palsson
A genome-scale, constraint-based approach to systems biology of human metabolism.
Molecular bioSystems 2007;3(9):598-603.
2007: Byung-Kwan Cho; Pep Charusanti; Markus J Herrgård; Bernhard Ø Palsson
Microbial regulatory and metabolic networks.
Current opinion in biotechnology 2007;18(4):360-4.
2007: Qiang Hua; Andrew R Joyce; Bernhard Ø Palsson; Stephen S Fong
Metabolic characterization of Escherichia coli strains adapted to growth on lactate.
Applied and environmental microbiology 2007;73(14):4639-47.
2007: Megan J Anderson; Byron DeLaBarre; Anu Raghunathan; Bernhard Ø Palsson; Axel T Brunger; Stephen R Quake
Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.
Biochemistry 2007;46(19):5722-31.
2007: Thuy D Vo; W N Paul Lee; Bernhard Ø Palsson
Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.
Molecular genetics and metabolism 2007;91(1):15-22.
2007: Natalie C Duarte; Scott A Becker; Neema Jamshidi; Ines Thiele; Monica L Mo; Thuy D Vo; Rohith Srivas; Bernhard Ø Palsson
Global reconstruction of the human metabolic network based on genomic and bibliomic data.
Proceedings of the National Academy of Sciences of the United States of America 2007;104(6):1777-82.
2007: Christopher D Herring; Bernhard Ø Palsson
An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.
BMC genomics 2007;8():274.
2007: Adam M Feist; Christopher S Henry; Jennifer L Reed; Markus Krummenacker; Andrew R Joyce; Peter D Karp; Linda J Broadbelt; Vassily Hatzimanikatis; Bernhard Ø Palsson
A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.
Molecular systems biology 2007;3():121.
2007: Neema Jamshidi; Thuy D Vo; Bernhard Ø Palsson
In silico analysis of SNPs and other high-throughput data.
Methods in molecular biology (Clifton, N.J.) 2007;366():267-85.
2007: Neema Jamshidi; Bernhard Ø Palsson
Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.
BMC systems biology 2007;1():26.
2007: Scott A Becker; Adam M Feist; Monica L Mo; Gregory Hannum; Bernhard Ø Palsson; Markus J Herrgard
Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.
Nature protocols 2007;2(3):727-38.
2007: Andrew R Joyce; Bernhard Ø Palsson
Toward whole cell modeling and simulation: comprehensive functional genomics through the constraint-based approach.
Progress in drug research. Fortschritte der Arzneimittelforschung. Progrès des recherches pharmaceutiques 2007;64():265, 267-309.
2007: Thuy D Vo; Bernhard Ø Palsson
Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.
American journal of physiology. Cell physiology 2007;292(1):C164-77.
2006: Thuy D Vo; Bernhard Ø Palsson
Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.
Biotechnology and bioengineering 2006;95(5):972-83.
2006: Qiang Hua; Andrew R Joyce; Stephen S Fong; Bernhard Ø Palsson
Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.
Biotechnology and bioengineering 2006;95(5):992-1002.
2006: Christopher D Herring; Anu Raghunathan; Christiane Honisch; Trina Patel; M Kenyon Applebee; Andrew R Joyce; Thomas J Albert; Frederick R Blattner; Dirk van den Boom; Charles R Cantor; Bernhard Ø Palsson
Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.
Nature genetics 2006;38(12):1406-12.
2006: Andrew R Joyce; Jennifer L Reed; Aprilfawn White; Robert Edwards; Andrei Osterman; Tomoya Baba; Hirotada Mori; Scott A Lesely; Bernhard Ø Palsson; Sanjay Agarwalla
Experimental and computational assessment of conditionally essential genes in Escherichia coli.
Journal of bacteriology 2006;188(23):8259-71.
2006: Jennifer L Reed; Trina R Patel; Keri H Chen; Andrew R Joyce; Margaret K Applebee; Christopher D Herring; Olivia T Bui; Eric M Knight; Stephen S Fong; Bernhard Ø Palsson
Systems approach to refining genome annotation.
Proceedings of the National Academy of Sciences of the United States of America 2006;103(46):17480-4.
2006: Christian L Barrett; Tae Yong Kim; Hyun Uk Kim; Bernhard Ø Palsson; Sang Yup Lee
Systems biology as a foundation for genome-scale synthetic biology.
Current opinion in biotechnology 2006;17(5):488-92.
2006: Erwin Gianchandani; Jason A Papin; Nathan Price; Andrew R Joyce; Bernhard Ø Palsson
Matrix formalism to describe functional states of transcriptional regulatory systems.
PLoS computational biology 2006;2(8):e101.
2006: Byung-Kwan Cho; Eric M Knight; Bernhard Ø Palsson
Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.
Microbiology (Reading, England) 2006;152(Pt 8):2207-19.
2006: Markus J Herrgård; Stephen S Fong; Bernhard Ø Palsson
Identification of genome-scale metabolic network models using experimentally measured flux profiles.
PLoS computational biology 2006;2(7):e72.
2006: Nathan Price; Ines Thiele; Bernhard Ø Palsson
Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.
Biophysical journal 2006;90(11):3919-28.
2006: Christian L Barrett; Bernhard Ø Palsson
Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.
PLoS computational biology 2006;2(5):e52.
2006: Markus J Herrgård; Baek-Seok Lee; Vasiliy Portnoy; Bernhard Ø Palsson
Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.
Genome research 2006;16(5):627-35.
2006: Stephen S Fong; Annik Nanchen; Bernhard Ø Palsson; Uwe Sauer
Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.
The Journal of biological chemistry 2006;281(12):8024-33.
2006: Neema Jamshidi; Bernhard Ø Palsson
Systems biology of the human red blood cell.
Blood cells, molecules & diseases 2006;36(2):239-47.
2006: Andrew R Joyce; Bernhard Ø Palsson
The model organism as a system: integrating 'omics' data sets.
Nature reviews. Molecular cell biology 2006;7(3):198-210.
2006: Radhakrishnan Mahadevan; D R Bond; J E Butler; A Esteve-Nuñez; M V Coppi; Bernhard Ø Palsson; Christophe H Schilling; D R Lovley
Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.
Applied and environmental microbiology 2006;72(2):1558-68.
2006: Jennifer L Reed; Iman Famili; Ines Thiele; Bernhard Ø Palsson
Towards multidimensional genome annotation.
Nature reviews. Genetics 2006;7(2):130-41.
2006: Neema Jamshidi; Bernhard Ø Palsson
Systems biology of SNPs.
Molecular systems biology 2006;2():38.
2006: Adam M Feist; Johannes Scholten; Bernhard Ø Palsson; Fred J Brockman; Trey Ideker
Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.
Molecular systems biology 2006;2():2006.0004.
2006: Christian L Barrett; Nathan Price; Bernhard Ø Palsson
Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.
BMC bioinformatics 2006;7():132.
2006: Scott A Becker; Nathan Price; Bernhard Ø Palsson
Metabolite coupling in genome-scale metabolic networks.
BMC bioinformatics 2006;7():111.
2006: Timothy Allen; Nathan Price; Andrew R Joyce; Bernhard Ø Palsson
Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.
PLoS computational biology 2006;2(1):e2.
2005: Christian L Barrett; Christopher D Herring; Jennifer L Reed; Bernhard Ø Palsson
The global transcriptional regulatory network for metabolism in Escherichia coli exhibits few dominant functional states.
Proceedings of the National Academy of Sciences of the United States of America 2005;102(52):19103-8.
2005: Stephen S Fong; Andrew R Joyce; Bernhard Ø Palsson
Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.
Genome research 2005;15(10):1365-72.
2005: Elie G Hanania; Annabeth Fieck; Janine Stevens; Leon J Bodzin; Bernhard Ø Palsson; Manfred R Koller
Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.
Biotechnology and bioengineering 2005;91(7):872-6.
2005: Stephen S Fong; Anthony P Burgard; Christopher D Herring; Eric M Knight; Frederick R Blattner; Costas D Maranas; Bernhard Ø Palsson
In silico design and adaptive evolution of Escherichia coli for production of lactic acid.
Biotechnology and bioengineering 2005;91(5):643-8.
2005: Stephen S Fong; Andrew R Joyce; Bernhard Ø Palsson
The econometrics of evolution.
Nature chemical biology 2005;1(4):191-2.
2005: Christopher D Herring; Marni Raffaelle; Timothy Allen; Elenita I Kanin; Robert Landick; Aseem Z Ansari; Bernhard Ø Palsson
Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.
Journal of bacteriology 2005;187(17):6166-74.
2005: Ines Thiele; Thuy D Vo; Nathan Price; Bernhard Ø Palsson
Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.
Journal of bacteriology 2005;187(16):5818-30.
2005: Steven L Bell; Bernhard Ø Palsson
Expa: a program for calculating extreme pathways in biochemical reaction networks.
Bioinformatics (Oxford, England) 2005;21(8):1739-40.
2005: Ines Thiele; Nathan Price; Thuy D Vo; Bernhard Ø Palsson
Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.
The Journal of biological chemistry 2005;280(12):11683-95.
2005: Iman Famili; Radhakrishnan Mahadevan; Bernhard Ø Palsson
k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.
Biophysical journal 2005;88(3):1616-25.
2005: Jason A Papin; Tony Hunter; Bernhard Ø Palsson; Shankar Subramaniam
Reconstruction of cellular signalling networks and analysis of their properties.
Nature reviews. Molecular cell biology 2005;6(2):99-111.
2005: Markus J Herrgård; Bernhard Ø Palsson
Untangling the web of functional and physical interactions in yeast.
Journal of biology 2005;4(2):5.
2005: Scott A Becker; Bernhard Ø Palsson
Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.
BMC microbiology 2005;5():8.
2005: Radhakrishnan Mahadevan; Bernhard Ø Palsson
Properties of metabolic networks: structure versus function.
Biophysical journal 2005;88(1):L07-9.
2004: Christiane Honisch; Anu Raghunathan; Charles R Cantor; Bernhard Ø Palsson; Dirk van den Boom
High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.
Genome research 2004;14(12):2495-502.
2004: Jason A Papin; Jennifer L Reed; Bernhard Ø Palsson
Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.
Trends in biochemical sciences 2004;29(12):641-7.
2004: Nathan Price; Jennifer L Reed; Bernhard Ø Palsson
Genome-scale models of microbial cells: evaluating the consequences of constraints.
Nature reviews. Microbiology 2004;2(11):886-97.
2004: Bernhard Ø Palsson
Two-dimensional annotation of genomes.
Nature biotechnology 2004;22(10):1218-9.
2004: Nathan Price; Jan Schellenberger; Bernhard Ø Palsson
Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.
Biophysical journal 2004;87(4):2172-86.
2004: Stephen S Fong; Bernhard Ø Palsson
Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.
Nature genetics 2004;36(10):1056-8.
2004: Manfred R Koller; Elie G Hanania; Janine Stevens; Timothy M Eisfeld; Glenn C Sasaki; Annabeth Fieck; Bernhard Ø Palsson
High-throughput laser-mediated in situ cell purification with high purity and yield.
Cytometry. Part A : the journal of the International Society for Analytical Cytology 2004;61(2):153-61.
2004: Thuy D Vo; Harvey J Greenberg; Bernhard Ø Palsson
Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.
The Journal of biological chemistry 2004;279(38):39532-40.
2004: Natalie C Duarte; Bernhard Ø Palsson; Pengcheng Fu
Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.
BMC genomics 2004;5():63.
2004: Jennifer L Reed; Bernhard Ø Palsson
Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.
Genome research 2004;14(9):1797-805.
2004: Jason A Papin; Jörg Stelling; Nathan Price; Steffen Klamt; Stefan Schuster; Bernhard Ø Palsson
Comparison of network-based pathway analysis methods.
Trends in biotechnology 2004;22(8):400-5.
2004: Jason A Papin; Bernhard Ø Palsson
The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.
Biophysical journal 2004;87(1):37-46.
2004: Natalie C Duarte; Markus J Herrgård; Bernhard Ø Palsson
Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.
Genome research 2004;14(7):1298-309.
2004: Sharon J Wiback; Iman Famili; Harvey J Greenberg; Bernhard Ø Palsson
Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.
Journal of theoretical biology 2004;228(4):437-47.
2004: Markus J Herrgård; Bernhard Ø Palsson
Flagellar biosynthesis in silico: building quantitative models of regulatory networks.
Cell 2004;117(6):689-90.
2004: Markus W Covert; Eric M Knight; Jennifer L Reed; Markus J Herrgard; Bernhard Ø Palsson
Integrating high-throughput and computational data elucidates bacterial networks.
Nature 2004;429(6987):92-6.
2004: Sharon J Wiback; Radhakrishnan Mahadevan; Bernhard Ø Palsson
Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.
Biotechnology and bioengineering 2004;86(3):317-31.
2004: Jason A Papin; Bernhard Ø Palsson
Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk.
Journal of theoretical biology 2004;227(2):283-97.
2004: Markus J Herrgård; Markus W Covert; Bernhard Ø Palsson
Reconstruction of microbial transcriptional regulatory networks.
Current opinion in biotechnology 2004;15(1):70-7.
2004: Bernhard Ø Palsson
In silico biotechnology. Era of reconstruction and interrogation.
Current opinion in biotechnology 2004;15(1):50-1.
2004: Anu Raghunathan; Nathan Price; Michael Galperin; Kira S Makarova; Samuel O Purvine; Alex F Picone; Tim Cherny; Tao Xie; Thomas J Reilly; Robert munson; Ryan E Tyler; Brian Akerley; Arnold L. Smith; Bernhard Ø Palsson; Eugene Kolker
In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.
Omics : a journal of integrative biology 2004;8(1):25-41.
2003: Markus W Covert; Iman Famili; Bernhard Ø Palsson
Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology?
Biotechnology and bioengineering 2003;84(7):763-72.
2003: Nathan Price; Jennifer L Reed; Jason A Papin; Sharon J Wiback; Bernhard Ø Palsson
Network-based analysis of metabolic regulation in the human red blood cell.
Journal of theoretical biology 2003;225(2):185-94.
2003: Iman Famili; Jochen Forster; Jens Nielsen; Bernhard Ø Palsson
Saccharomyces cerevisiae phenotypes can be predicted by using constraint-based analysis of a genome-scale reconstructed metabolic network.
Proceedings of the National Academy of Sciences of the United States of America 2003;100(23):13134-9.
2003: Stephen S Fong; Jennifer Y Marciniak; Bernhard Ø Palsson
Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.
Journal of bacteriology 2003;185(21):6400-8.
2003: Timothy Allen; Markus J Herrgård; Mingzhu Liu; Yu Qiu; Jeremy D Glasner; Frederick R Blattner; Bernhard Ø Palsson
Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.
Journal of bacteriology 2003;185(21):6392-9.
2003: Markus J Herrgård; Markus W Covert; Bernhard Ø Palsson
Reconciling gene expression data with known genome-scale regulatory network structures.
Genome research 2003;13(11):2423-34.
2003: Sharon J Wiback; Radhakrishnan Mahadevan; Bernhard Ø Palsson
Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.
Journal of theoretical biology 2003;224(3):313-24.
2003: Iman Famili; Bernhard Ø Palsson
Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.
Journal of theoretical biology 2003;224(1):87-96.
2003: Eugene Kolker; Samuel O Purvine; Michael Galperin; Sergey Stolyar; David R Goodlett; Alexey I Nesvizhskii; Andrew Keller; Tao Xie; Jimmy K Eng; Eugene Yi; Leroy Hood; Alex F Picone; Tim Cherny; Brian C Tjaden; Andrew F Siegel; Thomas J Reilly; Kira S Makarova; Bernhard Ø Palsson; Arnold L. Smith
Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.
Journal of bacteriology 2003;185(15):4593-602.
2003: Iman Famili; Bernhard Ø Palsson
The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.
Biophysical journal 2003;85(1):16-26.
2003: Jason A Papin; Nathan Price; Sharon J Wiback; David A Fell; Bernhard Ø Palsson
Metabolic pathways in the post-genome era.
Trends in biochemical sciences 2003;28(5):250-8.
2003: Bernhard Ø Palsson; Nathan Price; Jason A Papin
Development of network-based pathway definitions: the need to analyze real metabolic networks.
Trends in biotechnology 2003;21(5):195-8.
2003: Jennifer L Reed; Bernhard Ø Palsson
Thirteen years of building constraint-based in silico models of Escherichia coli.
Journal of bacteriology 2003;185(9):2692-9.
2003: Markus W Covert; Bernhard Ø Palsson
Constraints-based models: regulation of gene expression reduces the steady-state solution space.
Journal of theoretical biology 2003;221(3):309-25.
2003: Nathan Price; Jason A Papin; Christophe H Schilling; Bernhard Ø Palsson
Genome-scale microbial in silico models: the constraints-based approach.
Trends in biotechnology 2003;21(4):162-9.
2003: Anu Raghunathan; Bernhard Ø Palsson
Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.
Biotechnology letters 2003;25(5):435-41.
2003: Jochen Förster; Iman Famili; Patrick Fu; Bernhard Ø Palsson; Jens Nielsen
Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.
Genome research 2003;13(2):244-53.
2003: Nathan Price; Jennifer L Reed; Jason A Papin; Iman Famili; Bernhard Ø Palsson
Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.
Biophysical journal 2003;84(2 Pt 1):794-804.
2003: Timothy Allen; Bernhard Ø Palsson
Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.
Journal of theoretical biology 2003;220(1):1-18.
2003: Rafael U Ibarra; P Fu; Bernhard Ø Palsson; Jason R DiTonno; Jeremy S Edwards
Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes.
Journal of molecular microbiology and biotechnology 2003;6(2):101-8.
2003: Jochen Förster; Iman Famili; Bernhard Ø Palsson; Jens Nielsen
Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.
Omics : a journal of integrative biology 2003;7(2):193-202.
2003: Jennifer L Reed; Thuy D Vo; Christophe H Schilling; Bernhard Ø Palsson
An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).
Genome biology 2003;4(9):R54.
2002: Jason A Papin; Nathan Price; Bernhard Ø Palsson
Extreme pathway lengths and reaction participation in genome-scale metabolic networks.
Genome research 2002;12(12):1889-900.
2002: Rafael U Ibarra; Jeremy S Edwards; Bernhard Ø Palsson
Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.
Nature 2002;420(6912):186-9.
2002: Nathan Price; Iman Famili; Daniel A Beard; Bernhard Ø Palsson
Extreme pathways and Kirchhoff's second law.
Biophysical journal 2002;83(5):2879-82.
2002: Markus W Covert; Bernhard Ø Palsson
Transcriptional regulation in constraints-based metabolic models of Escherichia coli.
The Journal of biological chemistry 2002;277(31):28058-64.
2002: Christophe H Schilling; Markus W Covert; Iman Famili; George M Church; Jeremy S Edwards; Bernhard Ø Palsson
Genome-scale metabolic model of Helicobacter pylori 26695.
Journal of bacteriology 2002;184(16):4582-93.
2002: Sharon J Wiback; Bernhard Ø Palsson
Extreme pathway analysis of human red blood cell metabolism.
Biophysical journal 2002;83(2):808-18.
2002: Kenneth J Kauffman; John David Pajerowski; Neema Jamshidi; Bernhard Ø Palsson; Jeremy S Edwards
Description and analysis of metabolic connectivity and dynamics in the human red blood cell.
Biophysical journal 2002;83(2):646-62.
2002: Karl Francis; Bernhard Ø Palsson; Jody Donahue; Stephen Fong; Ewa Carrier
Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.
Experimental hematology 2002;30(5):460-3.
2002: Nathan Price; Jason A Papin; Bernhard Ø Palsson
Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.
Genome research 2002;12(5):760-9.
2002: Gyun Min Lee; Stephen S Fong; Duk Jae Oh; Karl Francis; Bernhard Ø Palsson
Characterization and efficacy of PKH26 as a probe to study the replication history of the human hematopoietic KG1a progenitor cell line.
In vitro cellular & developmental biology. Animal 2002;38(2):90-6.
2002: Jeremy S Edwards; Ramprasad Ramakrishna; Bernhard Ø Palsson
Characterizing the metabolic phenotype: a phenotype phase plane analysis.
Biotechnology and bioengineering 2002;77(1):27-36.
2002: Eugene Kolker; Samuel O Purvine; Alex F Picone; Tim Cherny; Brian Akerley; Robert munson; Bernhard Ø Palsson; Dayle A Daines; Arnold L. Smith
H. influenzae Consortium: integrative study of H. influenzae-human interactions.
Omics : a journal of integrative biology 2002;6(4):341-8.
2001: Markus W Covert; Christophe H Schilling; Bernhard Ø Palsson
Regulation of gene expression in flux balance models of metabolism.
Journal of theoretical biology 2001;213(1):73-88.
2001: Neema Jamshidi; Jeremy S Edwards; T Fahland; G M Church; Bernhard Ø Palsson
Dynamic simulation of the human red blood cell metabolic network.
Bioinformatics (Oxford, England) 2001;17(3):286-7.
2001: Markus W Covert; Christophe H Schilling; Iman Famili; Jeremy S Edwards; Igor Goryanin; E Selkov; Bernhard Ø Palsson
Metabolic modeling of microbial strains in silico.
Trends in biochemical sciences 2001;26(3):179-86.
2001: Ramprasad Ramakrishna; Jeremy S Edwards; A McCulloch; Bernhard Ø Palsson
Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.
American journal of physiology. Regulatory, integrative and comparative physiology 2001;280(3):R695-704.
2001: Jeremy S Edwards; Rafael U Ibarra; Bernhard Ø Palsson
In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.
Nature biotechnology 2001;19(2):125-30.
2000: Jeremy S Edwards; Bernhard Ø Palsson
Robustness analysis of the Escherichia coli metabolic network.
Biotechnology progress 2000;16(6):927-39.
2000: Bernhard Ø Palsson
The challenges of in silico biology.
Nature biotechnology 2000;18(11):1147-50.
2000: DJ Oh; AR Martinez; GM Lee; Karl Francis; Bernhard Ø Palsson
Intercellular adhesion can be visualized using fluorescently labeled fibrosarcoma HT1080 cells cocultured with hematopoietic cell lines or CD34(+) enriched human mobilized peripheral blood cells.
Cytometry 2000;40(2):119-25.
2000: DJ Oh; AR Martinez; GM Lee; Karl Francis; Bernhard Ø Palsson
Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium.
Cytometry 2000;40(2):109-18.
2000: J S Edwards; Bernhard Ø Palsson
The Escherichia coli MG1655 in silico metabolic genotype: its definition, characteristics, and capabilities.
Proceedings of the National Academy of Sciences of the United States of America 2000;97(10):5528-33.
2000: Christophe H Schilling; Bernhard Ø Palsson
Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.
Journal of theoretical biology 2000;203(3):249-83.
2000: Christophe H Schilling; D Letscher; Bernhard Ø Palsson
Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.
Journal of theoretical biology 2000;203(3):229-48.
2000: Christophe H Schilling; Jeremy S Edwards; D Letscher; Bernhard Ø Palsson
Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.
Biotechnology and bioengineering 2000;71(4):286-306.
2000: J S Edwards; Bernhard Ø Palsson
Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.
BMC bioinformatics 2000;1():1.
1999: W Holloway; AR Martinez; DJ Oh; Karl Francis; Ramprasad Ramakrishna; Bernhard Ø Palsson
Key adhesion molecules are present on long podia extended by hematopoietic cells.
Cytometry 1999;37(3):171-7.
1999: DJ Oh; GM Lee; Karl Francis; Bernhard Ø Palsson
Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line.
Cytometry 1999;36(4):312-8.
1999: Jeremy S Edwards; Bernhard Ø Palsson
Systems properties of the Haemophilus influenzae Rd metabolic genotype.
The Journal of biological chemistry 1999;274(25):17410-6.
1999: Christophe H Schilling; S Schuster; Bernhard Ø Palsson; R Heinrich
Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.
Biotechnology progress 1999;15(3):296-303.
1999: Christophe H Schilling; Jeremy S Edwards; Bernhard Ø Palsson
Toward metabolic phenomics: analysis of genomic data using flux balances.
Biotechnology progress 1999;15(3):288-95.
1999: Bernhard Ø Palsson; S Thorgeirsson
Genetic databases. Decoding developments in Iceland.
Nature biotechnology 1999;17(5):407.
1998: Karl Francis; Ramprasad Ramakrishna; W Holloway; Bernhard Ø Palsson
Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells.
Blood 1998;92(10):3616-23.
1998: R K Mandalam; Bernhard Ø Palsson
Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures.
Biotechnology and bioengineering 1998;59(5):605-11.
1998: ST Andreadis; A Oveta Fuller; Bernhard Ø Palsson
Cell cycle dependence of retroviral transduction: An issue of overlapping time scales.
Biotechnology and bioengineering 1998;58(2-3):272-81.
1998: Jeremy S Edwards; Bernhard Ø Palsson
How will bioinformatics influence metabolic engineering?
Biotechnology and bioengineering 1998;58(2-3):162-9.
1998: Christophe H Schilling; Bernhard Ø Palsson
The underlying pathway structure of biochemical reaction networks.
Proceedings of the National Academy of Sciences of the United States of America 1998;95(8):4193-8.
1997: K Francis; Bernhard Ø Palsson
Effective intercellular communication distances are determined by the relative time constants for cyto/chemokine secretion and diffusion.
Proceedings of the National Academy of Sciences of the United States of America 1997;94(23):12258-62.
1997: ST Andreadis; David Brott; A Oveta Fuller; Bernhard Ø Palsson
Moloney murine leukemia virus-derived retroviral vectors decay intracellularly with a half-life in the range of 5.5 to 7.5 hours.
Journal of virology 1997;71(10):7541-8.
1997: ST Andreadis; Bernhard Ø Palsson
Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors.
Human gene therapy 1997;8(3):285-91.
1997: Bernhard Ø Palsson; S Andreadis
The physico-chemical factors that govern retrovirus-mediated gene transfer.
Experimental hematology 1997;25(2):94-102.
1997: Bernhard Ø Palsson
What lies beyond bioinformatics?
Nature biotechnology 1997;15(1):3-4.
1996: Manfred R Koller; M Oxender; D A Brott; Bernhard Ø Palsson
flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion.
Journal of hematotherapy 1996;5(5):449-59.
1996: S T Andreadis; Bernhard Ø Palsson
Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses.
Journal of theoretical biology 1996;182(1):1-20.
1996: A S Chuck; Michael F Clarke; Bernhard Ø Palsson
Retroviral infection is limited by Brownian motion.
Human gene therapy 1996;7(13):1527-34.
1996: A S Chuck; Bernhard Ø Palsson
Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.
Human gene therapy 1996;7(6):743-50.
1996: C E Rogers; M S Bradley; Bernhard Ø Palsson; Manfred R Koller
Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.
Experimental hematology 1996;24(5):597-604.
1995: P G Eipers; John C Krauss; Bernhard Ø Palsson; Stephen G Emerson; Robert F Todd III; Michael F Clarke
Retroviral-mediated gene transfer in human bone marrow cells growth in continuous perfusion culture vessels.
Blood 1995;86(10):3754-62.
1995: Manfred R Koller; M S Bradley; Bernhard Ø Palsson
Growth factor consumption and production in perfusion cultures of human bone marrow correlate with specific cell production.
Experimental hematology 1995;23(12):1275-83.
1995: Manfred R Koller; M A Palsson; I Manchel; Bernhard Ø Palsson
Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects.
Blood 1995;86(5):1784-93.
1995: Manfred R Koller; I Manchel; B S Newsom; M A Palsson; Bernhard Ø Palsson
Bioreactor expansion of human bone marrow: comparison of unprocessed, density-separated, and CD34-enriched cells.
Journal of hematotherapy 1995;4(3):159-69.
1993: Manfred R Koller; Stephen G Emerson; Bernhard Ø Palsson
Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures.
Blood 1993;82(2):378-84.
1993: Bernhard Ø Palsson; I D Lee
Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients.
Journal of theoretical biology 1993;161(3):299-315.
1993: Bernhard Ø Palsson; S H Paek; Richard M Schwartz; M Palsson; G M Lee; Samuel Michael Silver; Stephen G Emerson
Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system.
Bio/technology (Nature Publishing Company) 1993;11(3):368-72.
1992: I D Lee; Bernhard Ø Palsson
A Macintosh software package for simulation of human red blood cell metabolism.
Computer methods and programs in biomedicine 1992;38(4):195-226.
1992: Jay D Keasling; Bernhard Ø Palsson; S Cooper
Replication of prophage P1 is cell-cycle specific.
Journal of bacteriology 1992;174(13):4457-62.
1992: Jay D Keasling; Bernhard Ø Palsson; S Cooper
Replication of mini-F plasmids during the bacterial division cycle.
Research in microbiology 1992;143(6):541-8.
1992: J M Savinell; Bernhard Ø Palsson
Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.
Journal of theoretical biology 1992;155(2):215-42.
1992: J M Savinell; Bernhard Ø Palsson
Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods.
Journal of theoretical biology 1992;155(2):201-14.
1992: J M Savinell; Bernhard Ø Palsson
Network analysis of intermediary metabolism using linear optimization. II. Interpretation of hybridoma cell metabolism.
Journal of theoretical biology 1992;154(4):455-73.
1992: J M Savinell; Bernhard Ø Palsson
Network analysis of intermediary metabolism using linear optimization. I. Development of mathematical formalism.
Journal of theoretical biology 1992;154(4):421-54.
1992: Jay D Keasling; Bernhard Ø Palsson; S Cooper
Replication of the R6K plasmid during the Escherichia coli cell cycle.
Journal of bacteriology 1992;174(3):1060-2.
1992: A Varma; F Y el-Awar; Bernhard Ø Palsson; Stephen G Emerson; Michael F Clarke
Can Dexter cultures support stem cell proliferation?
Experimental hematology 1992;20(1):87-91.
1992: Richard M Schwartz; J Caldwell; Michael F Clarke; S G Emerson; Bernhard Ø Palsson
The influence of extra-cellular matrix and stroma remodeling on the productivity of long-term human bone marrow cultures.
Cytotechnology 1992;10(3):217-24.
1991: Richard M Schwartz; Stephen G Emerson; Michael F Clarke; Bernhard Ø Palsson
In vitro myelopoiesis stimulated by rapid medium exchange and supplementation with hematopoietic growth factors.
Blood 1991;78(12):3155-61.
1991: S S Ozturk; Bernhard Ø Palsson
Growth, metabolic, and antibody production kinetics of hybridoma cell culture: 2. Effects of serum concentration, dissolved oxygen concentration, and medium pH in a batch reactor.
Biotechnology progress 1991;7(6):481-94.
1991: S S Ozturk; Bernhard Ø Palsson
Growth, metabolic, and antibody production kinetics of hybridoma cell culture: 1. Analysis of data from controlled batch reactors.
Biotechnology progress 1991;7(6):471-80.
1991: Richard M Schwartz; Bernhard Ø Palsson; Stephen G Emerson
Rapid medium perfusion rate significantly increases the productivity and longevity of human bone marrow cultures.
Proceedings of the National Academy of Sciences of the United States of America 1991;88(15):6760-4.
1991: J Caldwell; Bernhard Ø Palsson; B Locey; S G Emerson
Culture perfusion schedules influence the metabolic activity and granulocyte-macrophage colony-stimulating factor production rates of human bone marrow stromal cells.
Journal of cellular physiology 1991;147(2):344-53.
1991: Jay D Keasling; Bernhard Ø Palsson; S Cooper
Cell-cycle-specific F plasmid replication: regulation by cell size control of initiation.
Journal of bacteriology 1991;173(8):2673-80.
1991: S S Ozturk; Bernhard Ø Palsson
Examination of serum and bovine serum albumin as shear protective agents in agitated cultures of hybridoma cells.
Journal of biotechnology 1991;18(1-2):13-28.
1991: S G Emerson; Bernhard Ø Palsson; Michael F Clarke
The construction of high efficiency human bone marrow tissue ex vivo.
Journal of cellular biochemistry 1991;45(3):268-72.
1991: G M Lee; A Varma; Bernhard Ø Palsson
Application of population balance model to the loss of hybridoma antibody productivity.
Biotechnology progress 1991;7(1):72-5.
1991: J Caldwell; B Locey; Michael F Clarke; S G Emerson; Bernhard Ø Palsson
Influence of medium exchange schedules on metabolic, growth, and GM-CSF secretion rates of genetically engineered NIH-3T3 cells.
Biotechnology progress 1991;7(1):1-8.
1990: S S Ozturk; Bernhard Ø Palsson
Effect of initial cell density on hybridoma growth, metabolism, and monoclonal antibody production.
Journal of biotechnology 1990;16(3-4):259-78.
1990: S S Ozturk; Bernhard Ø Palsson
Effects of dissolved oxygen on hybridoma cell growth, metabolism, and antibody production kinetics in continuous culture.
Biotechnology progress 1990;6(6):437-46.
1990: S S Ozturk; Jennifer B Dressman; Bernhard Ø Palsson
On the use of the quasi-equilibrium assumption for drug dissolution.
Pharmaceutical research 1990;7(4):425-9.
1990: S S Ozturk; Bernhard Ø Palsson
Loss of antibody productivity during long-term cultivation of a hybridoma cell line in low serum and serum-free media.
Hybridoma 1990;9(2):167-75.
1990: S S Ozturk; Bernhard Ø Palsson
Chemical decomposition of glutamine in cell culture media: effect of media type, pH, and serum concentration.
Biotechnology progress 1990;6(2):121-8.
1990: A Joshi; Bernhard Ø Palsson
Metabolic dynamics in the human red cell. Part IV--Data prediction and some model computations.
Journal of theoretical biology 1990;142(1):69-85.
1990: A Joshi; Bernhard Ø Palsson
Metabolic dynamics in the human red cell. Part III--Metabolic reaction rates.
Journal of theoretical biology 1990;142(1):41-68.
1990: Bernhard Ø Palsson; Jay D Keasling; Stephen G Emerson
The regulatory mechanisms of human immunodeficiency virus replication predict multiple expression rates.
Proceedings of the National Academy of Sciences of the United States of America 1990;87(2):772-6.
1990: I D Lee; Bernhard Ø Palsson
A comprehensive model of human erythrocyte metabolism: extensions to include pH effects.
Biomedica biochimica acta 1990;49(8-9):771-89.
1989: A Joshi; Bernhard Ø Palsson
Metabolic dynamics in the human red cell. Part II--Interactions with the environment.
Journal of theoretical biology 1989;141(4):529-45.
1989: A Joshi; Bernhard Ø Palsson
Metabolic dynamics in the human red cell. Part I--A comprehensive kinetic model.
Journal of theoretical biology 1989;141(4):515-28.
1989: Jay D Keasling; Bernhard Ø Palsson
ColE1 plasmid replication: a simple kinetic description from a structured model.
Journal of theoretical biology 1989;141(4):447-61.
1989: G M Lee; J M Savinell; Bernhard Ø Palsson
Serum can act as a shear protecting agent in agitated hybridoma cell cultures.
Hybridoma 1989;8(6):639-45.
1989: G M Lee; T K Huard; Bernhard Ø Palsson
Effect of serum concentration on hybridoma cell growth and monoclonal antibody production at various initial cell densities.
Hybridoma 1989;8(3):369-75.
1989: Jay D Keasling; Bernhard Ø Palsson
On the kinetics of plasmid replication.
Journal of theoretical biology 1989;136(4):487-92.
1988: S S Ozturk; Bernhard Ø Palsson; B Donohoe; Jennifer B Dressman
Kinetics of release from enteric-coated tablets.
Pharmaceutical research 1988;5(9):550-65.
1988: S S Ozturk; Bernhard Ø Palsson; Jennifer B Dressman
Dissolution of ionizable drugs in buffered and unbuffered solutions.
Pharmaceutical research 1988;5(5):272-82.
1988: Bernhard Ø Palsson; T M Groshans
Mathematical modelling of dynamics and control in metabolic networks: VI. Dynamic bifurcations in single biochemical control loops.
Journal of theoretical biology 1988;131(1):43-53.