Publications

Author Title [ Year(Asc)]
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2011
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA et al..  2011.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC Syst Biol. 5:8.
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.  2011.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S et al..  2011.  The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41.
Rolfsson O, Palsson BØ, Thiele I.  2011.  The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.. BMC Syst Biol. 5:155.
Bordbar A, Jamshidi N, Palsson BO.  2011.  iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.. BMC Syst Biol. 5:110.
Mahadevan R, Palsson BØ, Lovley DR.  2011.  In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50.
Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K et al..  2011.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518.
Bordbar A, Feist AM, Usaite-Black R, Woodcock J, Palsson BO, Famili I.  2011.  A multi-tissue type genome-scale metabolic network for analysis of whole-body systems physiology.. BMC Syst Biol. 5:180.
2010
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.  2010.  A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology. 4:140.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ.  2010.  Drug off-target effects predicted using structural analysis in the context of a metabolic network model.. PLoS computational biology. 6(9):e1000938.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N.  2010.  Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R et al..  2010.  Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.  2010.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D et al..  2010.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390.
Thiele I, Palsson BØ.  2010.  Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
Hyduke DR, Palsson BØ.  2010.  Towards genome-scale signalling network reconstructions.. Nature reviews. Genetics. 11(4):297-307.
Orth JD, Thiele I, Palsson BØ.  2010.  What is flux balance analysis? Nature biotechnology. 28(3):245-8.
2009
Mo ML, Palsson BØ, Herrgard MJ.  2009.  Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
Raghunathan A, Reed JL, Shin S, Palsson BØ, Daefler S.  2009.  Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.. BMC systems biology. 3:38.
Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
Gianchandani EP, Joyce AR, Palsson BØ, Papin JA.  2009.  Functional states of the genome-scale Escherichia coli transcriptional regulatory system.. PLoS computational biology. 5(6):e1000403.
Lewis NE, Cho B-K, Knight EM, Palsson BØ.  2009.  Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44.
Thiele I, Jamshidi N, Fleming RMT, Palsson BØ.  2009.  Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312.
Li F, Thiele I, Jamshidi N, Palsson BØ.  2009.  Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292.
Zhang Y, Thiele I, Weekes D, Li Z, Jaroszewski L, Ginalski K, Deacon AM, Wooley J, Lesley SA, Wilson IA et al..  2009.  Three-dimensional structural view of the central metabolic network of Thermotoga maritima.. Science (New York, N.Y.). 325(5947):1544-9.
Mo ML, Palsson BØ.  2009.  Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
Jamshidi N, Palsson BØ.  2009.  Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology. 3:44.
2008
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M et al..  2008.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.. Nature biotechnology. 26(10):1155-60.
Becker SA, Palsson BØ.  2008.  Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
Jamshidi N, Palsson BØ.  2008.  Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171.
Nogales J, Palsson BØ, Thiele I.  2008.  A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.. BMC systems biology. 2:79.
Lee J, Yun H, Feist AM, Palsson BØ, Lee S Y.  2008.  Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.. Applied microbiology and biotechnology. 80(5):849-62.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
Joyce AR, Palsson BØ.  2008.  Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57.
Becker SA, Palsson BØ.  2008.  Three factors underlying incorrect in silico predictions of essential metabolic genes.. BMC systems biology. 2:14.
Jamshidi N, Palsson BØ.  2008.  Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology. 4(9):e1000177.
2007
Vo TD, Palsson BØ.  2007.  Building the power house: recent advances in mitochondrial studies through proteomics and systems biology.. American journal of physiology. Cell physiology. 292(1):C164-77.
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.  2007.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.. Molecular systems biology. 3:121.
Oh Y-K, Palsson BØ, Park SM, Schilling CH, Mahadevan R.  2007.  Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.. The Journal of biological chemistry. 282(39):28791-9.
Jamshidi N, Vo TD, Palsson BØ.  2007.  In silico analysis of SNPs and other high-throughput data.. Methods in molecular biology (Clifton, N.J.). 366:267-85.
Jamshidi N, Palsson BØ.  2007.  Investigating the metabolic capabilities of Mycobacterium tuberculosis H37Rv using the in silico strain iNJ661 and proposing alternative drug targets.. BMC systems biology. 1:26.
Resendis-Antonio O, Reed JL, Encarnación S, Collado-Vides J, Palsson BØ.  2007.  Metabolic reconstruction and modeling of nitrogen fixation in Rhizobium etli.. PLoS computational biology. 3(10):1887-95.
Becker SA, Feist AM, Mo ML, Hannum G, Palsson BØ, Herrgard MJ.  2007.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox.. Nature protocols. 2(3):727-38.
Joyce AR, Palsson BØ.  2007.  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. 64:265,267-309.
2006
Price ND, Thiele I, Palsson BØ.  2006.  Candidate states of Helicobacter pylori's genome-scale metabolic network upon application of "loop law" thermodynamic constraints.. Biophysical journal. 90(11):3919-28.
Mahadevan R, Bond DR, Butler JE, Esteve-Nuñez A, Coppi MV, Palsson BØ, Schilling CH, Lovley DR.  2006.  Characterization of metabolism in the Fe(III)-reducing organism Geobacter sulfurreducens by constraint-based modeling.. Applied and environmental microbiology. 72(2):1558-68.
Joyce AR, Reed JL, White A, Edwards R, Osterman AL, Baba T, Mori H, Lesely SA, Palsson BØ, Agarwalla S.  2006.  Experimental and computational assessment of conditionally essential genes in Escherichia coli.. Journal of bacteriology. 188(23):8259-71.
Herrgard MJ, Fong S, Palsson BØ.  2006.  Identification of genome-scale metabolic network models using experimentally measured flux profiles.. PLoS computational biology. 2(7):e72.
Fong S, Nanchen A, Palsson BØ, Sauer U.  2006.  Latent pathway activation and increased pathway capacity enable Escherichia coli adaptation to loss of key metabolic enzymes.. The Journal of biological chemistry. 281(12):8024-33.
Hua Q, Joyce AR, Fong S, Palsson BØ.  2006.  Metabolic analysis of adaptive evolution for in silico-designed lactate-producing strains.. Biotechnology and bioengineering. 95(5):992-1002.
Becker SA, Price ND, Palsson BØ.  2006.  Metabolite coupling in genome-scale metabolic networks.. BMC bioinformatics. 7:111.
Joyce AR, Palsson BØ.  2006.  The model organism as a system: integrating 'omics' data sets.. Nature reviews. Molecular cell biology. 7(3):198-210.
Feist AM, Scholten JCM, Palsson BØ, Brockman FJ, Ideker T.  2006.  Modeling methanogenesis with a genome-scale metabolic reconstruction of Methanosarcina barkeri.. Molecular systems biology. 2:2006.0004.
Barrett CL, Kim T Y, Kim H U, Palsson BØ, Lee S Y.  2006.  Systems biology as a foundation for genome-scale synthetic biology.. Current opinion in biotechnology. 17(5):488-92.
Jamshidi N, Palsson BØ.  2006.  Systems biology of the human red blood cell.. Blood cells, molecules & diseases. 36(2):239-47.
2004
Westerhoff HV, Palsson BØ.  2004.  The evolution of molecular biology into systems biology.. Nature biotechnology. 22(10):1249-52.
Herrgard MJ, Palsson BØ.  2004.  Flagellar biosynthesis in silico: building quantitative models of regulatory networks.. Cell. 117(6):689-90.
Reed JL, Palsson BØ.  2004.  Genome-scale in silico models of E. coli have multiple equivalent phenotypic states: assessment of correlated reaction subsets that comprise network states.. Genome research. 14(9):1797-805.
Price ND, Reed JL, Palsson BØ.  2004.  Genome-scale models of microbial cells: evaluating the consequences of constraints.. Nature reviews. Microbiology. 2(11):886-97.
Papin JA, Reed JL, Palsson BØ.  2004.  Hierarchical thinking in network biology: the unbiased modularization of biochemical networks.. Trends in biochemical sciences. 29(12):641-7.
Honisch C, Raghunathan A, Cantor CR, Palsson BØ, van den Boom D.  2004.  High-throughput mutation detection underlying adaptive evolution of Escherichia coli-K12.. Genome research. 14(12):2495-502.
Palsson BØ.  2004.  In silico biotechnology. Era of reconstruction and interrogation.. Current opinion in biotechnology. 15(1):50-1.
Raghunathan A, Price ND, Galperin MY, Makarova KS, Purvine S, Picone AF, Cherny T, Xie T, Reilly TJ, Munson R et al..  2004.  In Silico Metabolic Model and Protein Expression of Haemophilus influenzae Strain Rd KW20 in Rich Medium.. Omics : a journal of integrative biology. 8(1):25-41.
Duarte NC, Palsson BØ, Fu P.  2004.  Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.. BMC genomics. 5:63.
Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BØ.  2004.  Integrating high-throughput and computational data elucidates bacterial networks.. Nature. 429(6987):92-6.
Wiback SJ, Famili I, Greenberg HJ, Palsson BØ.  2004.  Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space.. Journal of theoretical biology. 228(4):437-47.
Herrgard MJ, Covert MW, Palsson BØ.  2004.  Reconstruction of microbial transcriptional regulatory networks.. Current opinion in biotechnology. 15(1):70-7.
Papin JA, Palsson BØ.  2004.  Topological analysis of mass-balanced signaling networks: a framework to obtain network properties including crosstalk.. Journal of theoretical biology. 227(2):283-97.
Price ND, Schellenberger J, Palsson BØ.  2004.  Uniform sampling of steady-state flux spaces: means to design experiments and to interpret enzymopathies.. Biophysical journal. 87(4):2172-86.
Wiback SJ, Mahadevan R, Palsson BØ.  2004.  Using metabolic flux data to further constrain the metabolic solution space and predict internal flux patterns: the Escherichia coli spectrum.. Biotechnology and bioengineering. 86(3):317-31.
2003
Price ND, Reed JL, Papin JA, Famili I, Palsson BØ.  2003.  Analysis of metabolic capabilities using singular value decomposition of extreme pathway matrices.. Biophysical journal. 84(2 Pt 1):794-804.
Covert MW, Palsson BØ.  2003.  Constraints-based models: regulation of gene expression reduces the steady-state solution space.. Journal of theoretical biology. 221(3):309-25.
Famili I, Palsson BØ.  2003.  The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools.. Biophysical journal. 85(1):16-26.
Fong S, Marciniak JY, Palsson BØ.  2003.  Description and interpretation of adaptive evolution of Escherichia coli K-12 MG1655 by using a genome-scale in silico metabolic model.. Journal of bacteriology. 185(21):6400-8.
Palsson BØ, Price ND, Papin JA.  2003.  Development of network-based pathway definitions: the need to analyze real metabolic networks.. Trends in biotechnology. 21(5):195-8.
Reed JL, Vo TD, Schilling CH, Palsson BØ.  2003.  An expanded genome-scale model of Escherichia coli K-12 (iJR904 GSM/GPR).. Genome biology. 4(9):R54.
Allen TE, Herrgard MJ, Liu M, Qiu Y, Glasner JD, Blattner FR, Palsson BØ.  2003.  Genome-scale analysis of the uses of the Escherichia coli genome: model-driven analysis of heterogeneous data sets.. Journal of bacteriology. 185(21):6392-9.
Price ND, Papin JA, Schilling CH, Palsson BØ.  2003.  Genome-scale microbial in silico models: the constraints-based approach.. Trends in biotechnology. 21(4):162-9.
Covert MW, Famili I, Palsson BØ.  2003.  Identifying constraints that govern cell behavior: a key to converting conceptual to computational models in biology? Biotechnology and bioengineering. 84(7):763-72.
Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BØ.  2003.  Metabolic pathways in the post-genome era.. Trends in biochemical sciences. 28(5):250-8.
Price ND, Reed JL, Papin JA, Wiback SJ, Palsson BØ.  2003.  Network-based analysis of metabolic regulation in the human red blood cell.. Journal of theoretical biology. 225(2):185-94.
Ibarra RU, Fu P, Palsson BØ, DiTonno JR, Edwards JS.  2003.  Quantitative analysis of Escherichia coli metabolic phenotypes within the context of phenotypic phase planes.. Journal of molecular microbiology and biotechnology. 6(2):101-8.
Famili I, Forster J, Nielsen J, Palsson BØ.  2003.  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. 100(23):13134-9.
Allen TE, Palsson BØ.  2003.  Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.. Journal of theoretical biology. 220(1):1-18.
Famili I, Palsson BØ.  2003.  Systemic metabolic reactions are obtained by singular value decomposition of genome-scale stoichiometric matrices.. Journal of theoretical biology. 224(1):87-96.
Reed JL, Palsson BØ.  2003.  Thirteen years of building constraint-based in silico models of Escherichia coli.. Journal of bacteriology. 185(9):2692-9.
2002
Edwards JS, Ramakrishna R, Palsson BØ.  2002.  Characterizing the metabolic phenotype: a phenotype phase plane analysis.. Biotechnology and bioengineering. 77(1):27-36.
Kauffman KJ, Pajerowski J D, Jamshidi N, Palsson BØ, Edwards JS.  2002.  Description and analysis of metabolic connectivity and dynamics in the human red blood cell.. Biophysical journal. 83(2):646-62.
Ibarra RU, Edwards JS, Palsson BØ.  2002.  Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth.. Nature. 420(6912):186-9.
Wiback SJ, Palsson BØ.  2002.  Extreme pathway analysis of human red blood cell metabolism.. Biophysical journal. 83(2):808-18.
Papin JA, Price ND, Palsson BØ.  2002.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks.. Genome research. 12(12):1889-900.
Papin JA, Price ND, Edwards JS, Palsson BØ.  2002.  The genome-scale metabolic extreme pathway structure in Haemophilus influenzae shows significant network redundancy.. Journal of theoretical biology. 215(1):67-82.
Edwards JS, Covert MW, Palsson BØ.  2002.  Metabolic modelling of microbes: the flux-balance approach.. Environmental microbiology. 4(3):133-40.
Covert MW, Palsson BØ.  2002.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli.. The Journal of biological chemistry. 277(31):28058-64.
1998
Andreadis ST, Fuller AO, Palsson BØ.  1998.  Cell cycle dependence of retroviral transduction: An issue of overlapping time scales.. Biotechnology and bioengineering. 58(2-3):272-81.
Schilling CH, Palsson BØ.  1998.  The underlying pathway structure of biochemical reaction networks.. Proceedings of the National Academy of Sciences of the United States of America. 95(8):4193-8.
1997
Francis K, Palsson BØ.  1997.  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. 94(23):12258-62.

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