Year of Publication: 2013
Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee D-H, Qiu Y et al..  2013.  The Genome Organization of Thermotoga maritima Reflects Its Lifestyle.. PLoS Genet. 9(4):e1003485.
McCloskey D, Palsson BØ, Feist AM.  2013.  Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661.
Qiu Y, Nagarajan H, Embree M, Shieu W, Abate E, Juárez K, Cho B-K, Elkins JG, Nevin KP, Barrett CL et al..  2013.  Characterizing the interplay between multiple levels of organization within bacterial sigma factor regulatory networks.. Nat Commun. 4:1755.
Kim Y-M, Schmidt BJ, Kidwai AS, Jones MB, Deatherage Kaiser BL, Brewer HM, Mitchell HD, Palsson BO, McDermott JE, Heffron F et al..  2013.  Salmonella modulates metabolism during growth under conditions that induce expression of virulence genes.. Mol Biosyst.
Thiele I, Swainston N, Fleming RMT, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD et al..  2013.  A community-driven global reconstruction of human metabolism.. Nat Biotechnol.
Fong NL, Lerman JA, Lam I, Palsson BO, Charusanti P.  2013.  Reconciling a Salmonella enterica metabolic model with experimental data confirms that overexpression of the glyoxylate shunt can rescue a lethal ppc deletion mutant.. FEMS Microbiol Lett.
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.. Biotechnol J.
Nakatsuji T, Chiang H-I, Jiang SB, Nagarajan H, Zengler K, Gallo RL.  2013.  The microbiome extends to subepidermal compartments of normal skin.. Nat Commun. 4:1431.
Gong Y, Ebrahim A, Feist AM, Embree M, Zhang T, Lovley D, Zengler K.  2013.  Sulfide-driven microbial electrosynthesis.. Environ Sci Technol. 47(1):568-573.
Hyduke DR, Lewis NE, Palsson BØ.  2013.  Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74.
Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, Brynjólfsson S.  2013.  Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.. Appl Microbiol Biotechnol. 97(6):2395-403.
Rolfsson O, Paglia G, Magnusdóttir M, Palsson BØ, Thiele I.  2013.  Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.. Biochem J. 449(2):427-35.
Ansong C, Deatherage BL, Hyduke D, Schmidt B, McDermott JE, Jones MB, Chauhan S, Charusanti P, Kim Y-M, Nakayasu ES et al..  2013.  Studying Salmonellae and Yersiniae host-pathogen interactions using integrated 'omics and modeling.. Curr Top Microbiol Immunol. 363:21-41.
Year of Publication: 2012
Seo J-H, Hong J S-J, Kim D, Cho B-K, Huang T-W, Tsai S-F, Palsson BO, Charusanti P.  2012.  Multiple-omic data analysis of Klebsiella pneumoniae MGH 78578 reveals its transcriptional architecture and regulatory features.. BMC Genomics. 13(1):679.
Fu W, Magnúsdóttir M, Brynjólfson S, Palsson BO, Paglia G.  2012.  UPLC-UV-MS(E) analysis for quantification and identification of major carotenoid and chlorophyll species in algae.. Anal Bioanal Chem. 404(10):3145-54.
Alain K, Harder J, Widdel F, Zengler K.  2012.  Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate.. Microbiology. 158(Pt 12):2946-57.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO.  2012.  Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.. PLoS One. 7(9):e45635.
Paglia G, Palsson BØ, Sigurjonsson OE.  2012.  Systems biology of stored blood cells: can it help to extend the expiration date? J Proteomics. 76 Spec No.:163-7.
Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J et al..  2012.  Proteomic analysis of Chinese hamster ovary cells.. J Proteome Res. 11(11):5265-76.
Nam H, Lewis NE, Lerman JA, Lee D-H, Chang RL, Kim D, Palsson BO.  2012.  Network context and selection in the evolution to enzyme specificity.. Science. 337(6098):1101-4.
Kim D, Hong J S-J, Qiu Y, Nagarajan H, Seo J-H, Cho B-K, Tsai S-F, Palsson BØ.  2012.  Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling.. PLoS Genet. 8(8):e1002867.
Ho Sui SJ, Lo R, Fernandes AR, Caulfield MDG, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FSL.  2012.  Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.. Int J Antimicrob Agents.
Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BO.  2012.  Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.. J Biotechnol.
Lerman JA, Hyduke DR, Latif H, Portnoy VA, Lewis NE, Orth JD, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Zengler K et al..  2012.  In silico method for modelling metabolism and gene product expression at genome scale. Nat Commun. 3:929.
Bordbar A, Mo ML, Nakayasu ES, Schrimpe-Rutledge AC, Kim Y-M, Metz TO, Jones MB, Frank BC, Smith RD, Peterson SN et al..  2012.  Model-driven multi-omic data analysis elucidates metabolic immunomodulators of macrophage activation.. Mol Syst Biol. 8:558.
Paglia G, Magnúsdóttir M, Thorlacius S, Sigurjónsson OE, Guðmundsson S, Palsson BØ, Thiele I.  2012.  Intracellular metabolite profiling of platelets: evaluation of extraction processes and chromatographic strategies.. J Chromatogr B Analyt Technol Biomed Life Sci. 898:111-20.
Orth JD, Palsson BO.  2012.  Gap-filling analysis of the iJO1366 Escherichia coli metabolic network reconstruction for discovery of metabolic functions.. BMC Syst Biol. 6(1):30.
Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO.  2012.  Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.. PLoS One. 7(3):e33727.
Zengler K, Palsson BO.  2012.  A road map for the development of community systems (CoSy) biology.. Nat Rev Microbiol. 10(5):366-72.
Lewis NE, Nagarajan H, Palsson BO.  2012.  Constraining the metabolic genotype-phenotype relationship using a phylogeny of in silico methods.. Nat Rev Microbiol. 10(4):291-305.
Nogales J, Gudmundsson S, Knight EM, Palsson BO, Thiele I.  2012.  Detailing the optimality of photosynthesis in cyanobacteria through systems biology analysis.. Proc Natl Acad Sci U S A. 109(7):2678-83.
Schellenberger J, Zielinski DC, Choi W, Madireddi S, Portnoy V, Scott DA, Reed JL, Osterman AL, Palsson B.  2012.  Predicting outcomes of steady-state ¹³C isotope tracing experiments using Monte Carlo sampling.. BMC Syst Biol. 6:9.
Ravcheev DA, Li X, Latif H, Zengler K, Leyn SA, Korostelev YD, Kazakov AE, Novichkov PS, Osterman AL, Rodionov DA.  2012.  Transcriptional regulation of central carbon and energy metabolism in bacteria by redox-responsive repressor Rex.. J Bacteriol. 194(5):1145-57.
McDermott JE, Braun P, Bonneau R, Hyduke DR.  2012.  MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH.. Pac Symp Biocomput. 17:283-286.
Paglia G, Hrafnsdóttir S, Magnúsdóttir M, Fleming RMT, Thorlacius S, Palsson BØ, Thiele I.  2012.  Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).. Anal Bioanal Chem. 402(3):1183-98.
Bordbar A, Palsson BO.  2012.  Using the reconstructed genome-scale human metabolic network to study physiology and pathology.. J Intern Med. 271(2):131-41.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ.  2012.  Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71.
Fleming RMT, Maes CM, Saunders MA, Ye Y, Palsson BØ.  2012.  A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.. J Theor Biol. 292:71-7.
Year of Publication: 2011
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.
Lee D-H, Feist AM, Barrett CL, Palsson BØ.  2011.  Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.. PLoS One. 6(10):e26172.
Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO.  2011.  An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.. BMC Syst Biol. 5:163.
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.
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.
Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S et al..  2011.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307.
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.
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.
Ahn S-Y, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ et al..  2011.  Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.. J Biol Chem. 286(36):31522-31.
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.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F.  2011.  Technologies and approaches to elucidate and model the virulence program of salmonella.. Front Microbiol. 2:121.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ.  2011.  The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64.
Applebee KM, Joyce AR, Conrad TM, Pettigrew DW, Palsson BØ.  2011.  Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.. J Biol Chem. 286(26):23150-9.
Portnoy VA, Bezdan D, Zengler K.  2011.  Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.. Curr Opin Biotechnol. 22(4):590-4.
Nam H, Conrad TM, Lewis NE.  2011.  The role of cellular objectives and selective pressures in metabolic pathway evolution.. Curr Opin Biotechnol. 22(4):595-600.
Liao Y-C, Huang T-W, Chen F-C, Charusanti P, Hong JSJ, Chang H-Y, Tsai S-F, Palsson BO, Hsiung CA.  2011.  An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.. J Bacteriol. 193(7):1710-7.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Palsson BØ.  2011.  Adaptive Laboratory Evolution. Microbe.
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.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ.  2011.  Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nature chemical biology. 8(1):65-71.
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.
Barrett CL, Cho B-K, Palsson BO.  2011.  Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis.. Nucleic Acids Res. 39(5):1656-65.
Tremblay P-L, Summers ZM, Glaven RH, Nevin KP, Zengler K, Barrett CL, Qiu Y, Palsson BO, Lovley DR.  2011.  A c-type cytochrome and a transcriptional regulator responsible for enhanced extracellular electron transfer in Geobacter sulfurreducens revealed by adaptive evolution.. Environ Microbiol. 13(1):13-23.
Year of Publication: 2010
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.
Conrad TM, Frazier M, Joyce AR, Cho B-K, Knight EM, Lewis NE, Landick R, Palsson BØ.  2010.  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. 107(47):20500-5.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BØ.  2010.  Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.. PLoS genetics. 6(11):e1001186.
Palsson BØ, Zengler K.  2010.  The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
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.
Orth JD, Palsson BØ.  2010.  Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12.
Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ.  2010.  Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40.
Qiu Y, Cho B-K, Park Y S, Lovley DR, Palsson BØ, Zengler K.  2010.  Structural and operational complexity of the Geobacter sulfurreducens genome.. Genome research. 20(9):1304-11.
Klimes A, Franks AE, Glaven RH, Tran H, Barrett CL, Qiu Y, Zengler K, Lovley DR.  2010.  Production of pilus-like filaments in Geobacter sulfurreducens in the absence of the type IV pilin protein PilA.. FEMS microbiology letters. 310(1):62-8.
Lee D-H, Palsson BØ.  2010.  Adaptive evolution of Escherichia coli K-12 MG1655 during growth on a Nonnative carbon source, L-1,2-propanediol.. Applied and environmental microbiology. 76(13):4158-68.
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.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
Thiele I, Fleming RMT, Bordbar A, Schellenberger J, Palsson BØ.  2010.  Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81.
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.
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.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
Nagarajan H, Butler JE, Klimes A, Qiu Y, Zengler K, Ward J, Young ND, Methé BA, Palsson BØ, Lovley DR et al..  2010.  De Novo assembly of the complete genome of an enhanced electricity-producing variant of Geobacter sulfurreducens using only short reads.. PloS one. 5(6):e10922.
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.
Schellenberger J, Park JO, Conrad TM, Palsson BØ.  2010.  BiGG: a Biochemical Genetic and Genomic knowledgebase of large scale metabolic reconstructions.. BMC bioinformatics. 11:213.
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.
Thiele I, Palsson BØ.  2010.  A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.
Year of Publication: 2009
Palsson BØ.  2009.  Metabolic systems biology.. FEBS letters. 583(24):3900-4.
Zengler K.  2009.  Central role of the cell in microbial ecology.. Microbiology and molecular biology reviews : MMBR. 73(4):712-29.
Cho B-K, Zengler K, Qiu Y, Park Y S, Knight EM, Barrett CL, Gao Y, Palsson BØ.  2009.  The transcription unit architecture of the Escherichia coli genome.. Nature biotechnology. 27(11):1043-9.
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.
Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
Cho B-K, Palsson BØ.  2009.  Can the protein occupancy landscape show the topologically isolated chromosomal domains in the E. coli genome?: An exciting prospect. Molecular cell. 35(3):255-6.
Manichaikul A, Ghamsari L, Hom EFY, Lin C, Murray RR, Chang RL, Balaji S, Hao T, Shen Y, Chavali AK et al..  2009.  Metabolic network analysis integrated with transcript verification for sequenced genomes.. Nature methods. 6(8):589-92.
Cho B-K, Palsson BØ.  2009.  Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6.
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.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
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.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BØ.  2009.  Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
Oberhardt MA, Palsson BØ, Papin JA.  2009.  Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320.
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.
Barrett CL, Herrgard MJ, Palsson BØ.  2009.  Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation.. BMC systems biology. 3:30.
Conrad TM, Joyce AR, Applebee KM, Barrett CL, Xie B, Gao Y, Palsson BØ.  2009.  Whole-genome resequencing of Escherichia coli K-12 MG1655 undergoing short-term laboratory evolution in lactate minimal media reveals flexible selection of adaptive mutations.. Genome biology. 10(10):R118.
Sigurdsson MI, Jamshidi N, Jonsson JJ, Palsson BØ.  2009.  Genome-scale network analysis of imprinted human metabolic genes.. Epigenetics : official journal of the DNA Methylation Society. 4(1):43-6.
Mo ML, Palsson BØ.  2009.  Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
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.
Mo ML, Palsson BØ, Herrgard MJ.  2009.  Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
Year of Publication: 2008
Cho B-K, Barrett CL, Knight EM, Park Y S, Palsson BØ.  2008.  Genome-scale reconstruction of the Lrp regulatory network in Escherichia coli.. Proceedings of the National Academy of Sciences of the United States of America. 105(49):19462-7.
Portnoy VA, Herrgard MJ, Palsson BØ.  2008.  Aerobic fermentation of D-glucose by an evolved cytochrome oxidase-deficient Escherichia coli strain.. Applied and environmental microbiology. 74(24):7561-9.
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.
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.
Shlomi T, Cabili MN, Herrgard MJ, Palsson BØ, Ruppin E.  2008.  Network-based prediction of human tissue-specific metabolism.. Nature biotechnology. 26(9):1003-10.
Applebee KM, Herrgard MJ, Palsson BØ.  2008.  Impact of individual mutations on increased fitness in adaptively evolved strains of Escherichia coli.. Journal of bacteriology. 190(14):5087-94.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
Cho B-K, Knight EM, Barrett CL, Palsson BØ.  2008.  Genome-wide analysis of Fis binding in Escherichia coli indicates a causative role for A-/AT-tracts.. Genome research. 18(6):900-10.
Becker SA, Palsson BØ.  2008.  Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
Joyce AR, Palsson BØ.  2008.  Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57.
Cho B-K, Knight EM, Palsson BØ.  2008.  Genomewide identification of protein binding locations using chromatin immunoprecipitation coupled with microarray.. Methods in molecular biology (Clifton, N.J.). 439:131-45.
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.
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.
Year of Publication: 2007
Shlomi T, Herrgard MJ, Portnoy VA, Naim E, Palsson BØ, Sharan R, Ruppin E.  2007.  Systematic condition-dependent annotation of metabolic genes.. Genome research. 17(11):1626-33.
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.
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.
Mo ML, Jamshidi N, Palsson BØ.  2007.  A genome-scale, constraint-based approach to systems biology of human metabolism.. Molecular bioSystems. 3(9):598-603.
Cho B-K, Charusanti P, Herrgard MJ, Palsson BØ.  2007.  Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4.
Hua Q, Joyce AR, Palsson BØ, Fong S.  2007.  Metabolic characterization of Escherichia coli strains adapted to growth on lactate.. Applied and environmental microbiology. 73(14):4639-47.
Anderson MJ, DeLabarre B, Raghunathan A, Palsson BØ, Brunger AT, Quake SR.  2007.  Crystal structure of a hyperactive Escherichia coli glycerol kinase mutant Gly230 --> Asp obtained using microfluidic crystallization devices.. Biochemistry. 46(19):5722-31.
Vo TD, Paul Lee WN, Palsson BØ.  2007.  Systems analysis of energy metabolism elucidates the affected respiratory chain complex in Leigh's syndrome.. Molecular genetics and metabolism. 91(1):15-22.
Duarte NC, Becker SA, Jamshidi N, Thiele I, Mo ML, Vo TD, Srivas R, Palsson BØ.  2007.  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. 104(6):1777-82.
Yeung M, Thiele I, Palsson BØ.  2007.  Estimation of the number of extreme pathways for metabolic networks.. BMC bioinformatics. 8(1):363.
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.
Herring CD, Palsson BØ.  2007.  An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.. BMC genomics. 8:274.
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.
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.
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.
Year of Publication: 2006
Herring CD, Raghunathan A, Honisch C, Patel T, Applebee KM, Joyce AR, Albert TJ, Blattner FR, van den Boom D, Cantor CR et al..  2006.  Comparative genome sequencing of Escherichia coli allows observation of bacterial evolution on a laboratory timescale.. Nature genetics. 38(12):1406-12.
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.
Vo TD, Palsson BØ.  2006.  Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.. Biotechnology and bioengineering. 95(5):972-83.
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.
Reed JL, Patel TR, Chen KH, Joyce AR, Applebee KM, Herring CD, Bui OT, Knight EM, Fong S, Palsson BØ.  2006.  Systems approach to refining genome annotation.. Proceedings of the National Academy of Sciences of the United States of America. 103(46):17480-4.
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.
Gianchandani EP, Papin JA, Price ND, Joyce AR, Palsson BØ.  2006.  Matrix formalism to describe functional states of transcriptional regulatory systems.. PLoS computational biology. 2(8):e101.
Cho B-K, Knight EM, Palsson BØ.  2006.  Transcriptional regulation of the fad regulon genes of Escherichia coli by ArcA.. Microbiology (Reading, England). 152(Pt 8):2207-19.
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.
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.
Barrett CL, Palsson BØ.  2006.  Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.. PLoS computational biology. 2(5):e52.
Herrgard MJ, Lee B-S, Portnoy VA, Palsson BØ.  2006.  Integrated analysis of regulatory and metabolic networks reveals novel regulatory mechanisms in Saccharomyces cerevisiae.. Genome research. 16(5):627-35.
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.
Joyce AR, Palsson BØ.  2006.  The model organism as a system: integrating 'omics' data sets.. Nature reviews. Molecular cell biology. 7(3):198-210.
Jamshidi N, Palsson BØ.  2006.  Systems biology of the human red blood cell.. Blood cells, molecules & diseases. 36(2):239-47.
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.
Reed JL, Famili I, Thiele I, Palsson BØ.  2006.  Towards multidimensional genome annotation.. Nature reviews. Genetics. 7(2):130-41.
Barrett CL, Price ND, Palsson BØ.  2006.  Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition.. BMC bioinformatics. 7:132.
Clark IB, Hanania EG, Stevens J, Gallina M, Fieck A, Brandes R, Palsson BØ, Koller MR.  2006.  Optoinjection for efficient targeted delivery of a broad range of compounds and macromolecules into diverse cell types.. Journal of biomedical optics. 11(1):014034.
Becker SA, Price ND, Palsson BØ.  2006.  Metabolite coupling in genome-scale metabolic networks.. BMC bioinformatics. 7:111.
Jamshidi N, Palsson BØ.  2006.  Systems biology of SNPs.. Molecular systems biology. 2:38.
Cho B-K, Knight EM, Palsson BØ.  2006.  PCR-based tandem epitope tagging system for Escherichia coli genome engineering.. BioTechniques. 40(1):67-72.
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.
Allen TE, Price ND, Joyce AR, Palsson BØ.  2006.  Long-range periodic patterns in microbial genomes indicate significant multi-scale chromosomal organization.. PLoS computational biology. 2(1):e2.
Year of Publication: 2005
Barrett CL, Herring CD, Reed JL, Palsson BØ.  2005.  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. 102(52):19103-8.
Fong S, Joyce AR, Palsson BØ.  2005.  Parallel adaptive evolution cultures of Escherichia coli lead to convergent growth phenotypes with different gene expression states.. Genome research. 15(10):1365-72.
Hanania EG, Fieck A, Stevens J, Bodzin LJ, Palsson BØ, Koller MR.  2005.  Automated in situ measurement of cell-specific antibody secretion and laser-mediated purification for rapid cloning of highly-secreting producers.. Biotechnology and bioengineering. 91(7):872-6.
Herring CD, Raffaelle M, Allen TE, Kanin EI, Landick R, Ansari AZ, Palsson BØ.  2005.  Immobilization of Escherichia coli RNA polymerase and location of binding sites by use of chromatin immunoprecipitation and microarrays.. Journal of bacteriology. 187(17):6166-74.
Fong S, Joyce AR, Palsson BØ.  2005.  The econometrics of evolution.. Nature chemical biology. 1(4):191-2.
Fong S, Burgard AP, Herring CD, Knight EM, Blattner FR, Maranas CD, Palsson BØ.  2005.  In silico design and adaptive evolution of Escherichia coli for production of lactic acid.. Biotechnology and bioengineering. 91(5):643-8.
Thiele I, Vo TD, Price ND, Palsson BØ.  2005.  Expanded metabolic reconstruction of Helicobacter pylori (iIT341 GSM/GPR): an in silico genome-scale characterization of single- and double-deletion mutants.. Journal of bacteriology. 187(16):5818-30.
Bell SL, Palsson BØ.  2005.  Expa: a program for calculating extreme pathways in biochemical reaction networks.. Bioinformatics (Oxford, England). 21(8):1739-40.
Thiele I, Price ND, Vo TD, Palsson BØ.  2005.  Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet.. The Journal of biological chemistry. 280(12):11683-95.
Famili I, Mahadevan R, Palsson BØ.  2005.  k-Cone analysis: determining all candidate values for kinetic parameters on a network scale.. Biophysical journal. 88(3):1616-25.
Papin JA, Hunter T, Palsson BØ, Subramaniam S.  2005.  Reconstruction of cellular signalling networks and analysis of their properties.. Nature reviews. Molecular cell biology. 6(2):99-111.
Mahadevan R, Palsson BØ.  2005.  Properties of metabolic networks: structure versus function.. Biophysical journal. 88(1):L07-9.
Herrgard MJ, Palsson BØ.  2005.  Untangling the web of functional and physical interactions in yeast.. Journal of biology. 4(2):5.
Becker SA, Palsson BØ.  2005.  Genome-scale reconstruction of the metabolic network in Staphylococcus aureus N315: an initial draft to the two-dimensional annotation.. BMC microbiology. 5:8.
Year of Publication: 2004
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.
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.
Westerhoff HV, Palsson BØ.  2004.  The evolution of molecular biology into systems biology.. Nature biotechnology. 22(10):1249-52.
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.
Fong S, Palsson BØ.  2004.  Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.. Nature genetics. 36(10):1056-8.
Koller MR, Hanania EG, Stevens J, Eisfeld TM, Sasaki GC, Fieck A, Palsson BØ.  2004.  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. 61(2):153-61.
Vo TD, Greenberg HJ, Palsson BØ.  2004.  Reconstruction and functional characterization of the human mitochondrial metabolic network based on proteomic and biochemical data.. The Journal of biological chemistry. 279(38):39532-40.
Duarte NC, Palsson BØ, Fu P.  2004.  Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.. BMC genomics. 5:63.
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.
Papin JA, Stelling J, Price ND, Klamt S, Schuster S, Palsson BØ.  2004.  Comparison of network-based pathway analysis methods.. Trends in biotechnology. 22(8):400-5.
Papin JA, Palsson BØ.  2004.  The JAK-STAT signaling network in the human B-cell: an extreme signaling pathway analysis.. Biophysical journal. 87(1):37-46.
Duarte NC, Herrgard MJ, Palsson BØ.  2004.  Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model.. Genome research. 14(7):1298-309.
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, Palsson BØ.  2004.  Flagellar biosynthesis in silico: building quantitative models of regulatory networks.. Cell. 117(6):689-90.
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, 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.
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.
Herrgard MJ, Covert MW, Palsson BØ.  2004.  Reconstruction of microbial transcriptional regulatory networks.. Current opinion in biotechnology. 15(1):70-7.
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.
Year of Publication: 2003
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.
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.
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.
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.
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.
Herrgard MJ, Covert MW, Palsson BØ.  2003.  Reconciling gene expression data with known genome-scale regulatory network structures.. Genome research. 13(11):2423-34.
Wiback SJ, Mahadevan R, Palsson BØ.  2003.  Reconstructing metabolic flux vectors from extreme pathways: defining the alpha-spectrum.. Journal of theoretical biology. 224(3):313-24.
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.
Kolker E, Purvine S, Galperin MY, Stolyar S, Goodlett DR, Nesvizhskii AI, Keller A, Xie T, Eng JK, Yi E et al..  2003.  Initial proteome analysis of model microorganism Haemophilus influenzae strain Rd KW20.. Journal of bacteriology. 185(15):4593-602.
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.
Förster J, Famili I, Palsson BØ, Nielsen J.  2003.  Large-scale evaluation of in silico gene deletions in Saccharomyces cerevisiae.. Omics : a journal of integrative biology. 7(2):193-202.
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.
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, Palsson BØ.  2003.  Thirteen years of building constraint-based in silico models of Escherichia coli.. Journal of bacteriology. 185(9):2692-9.
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, Palsson BØ.  2003.  Constraints-based models: regulation of gene expression reduces the steady-state solution space.. Journal of theoretical biology. 221(3):309-25.
Raghunathan A, Palsson BØ.  2003.  Scalable method to determine mutations that occur during adaptive evolution of Escherichia coli.. Biotechnology letters. 25(5):435-41.
Förster J, Famili I, Fu P, Palsson BØ, Nielsen J.  2003.  Genome-scale reconstruction of the Saccharomyces cerevisiae metabolic network.. Genome research. 13(2):244-53.
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.
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.
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, Palsson BØ.  2003.  Sequence-based analysis of metabolic demands for protein synthesis in prokaryotes.. Journal of theoretical biology. 220(1):1-18.
Year of Publication: 2002
Papin JA, Price ND, Palsson BØ.  2002.  Extreme pathway lengths and reaction participation in genome-scale metabolic networks.. Genome research. 12(12):1889-900.
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.
Jamshidi N, Wiback SJ, Palsson BØ.  2002.  In silico model-driven assessment of the effects of single nucleotide polymorphisms (SNPs) on human red blood cell metabolism.. Genome research. 12(11):1687-92.
Price ND, Famili I, Beard DA, Palsson BØ.  2002.  Extreme pathways and Kirchhoff's second law.. Biophysical journal. 83(5):2879-82.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BØ.  2002.  Genome-scale metabolic model of Helicobacter pylori 26695.. Journal of bacteriology. 184(16):4582-93.
Wiback SJ, Palsson BØ.  2002.  Extreme pathway analysis of human red blood cell metabolism.. Biophysical journal. 83(2):808-18.
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.
Covert MW, Palsson BØ.  2002.  Transcriptional regulation in constraints-based metabolic models of Escherichia coli.. The Journal of biological chemistry. 277(31):28058-64.
Francis K, Palsson BØ, Donahue J, Fong S, Carrier E.  2002.  Murine Sca-1(+)/Lin(-) cells and human KG1a cells exhibit multiple pseudopod morphologies during migration.. Experimental hematology. 30(5):460-3.
Price ND, Papin JA, Palsson BØ.  2002.  Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis.. Genome research. 12(5):760-9.
Edwards JS, Covert MW, Palsson BØ.  2002.  Metabolic modelling of microbes: the flux-balance approach.. Environmental microbiology. 4(3):133-40.
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.
Lee G M, Fong S, Oh D J, Francis K, Palsson BØ.  2002.  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. 38(2):90-6.
Kolker E, Purvine S, Picone A, Cherny T, Akerley BJ, Munson RS, Palsson BØ, Daines DA, Smith AL.  2002.  H. influenzae Consortium: integrative study of H. influenzae-human interactions.. Omics : a journal of integrative biology. 6(4):341-8.
Edwards JS, Ramakrishna R, Palsson BØ.  2002.  Characterizing the metabolic phenotype: a phenotype phase plane analysis.. Biotechnology and bioengineering. 77(1):27-36.
Year of Publication: 2001
Covert MW, Schilling CH, Palsson BØ.  2001.  Regulation of gene expression in flux balance models of metabolism.. Journal of theoretical biology. 213(1):73-88.
Jamshidi N, Edwards JS, Fahland T, Church GM, Palsson BØ.  2001.  Dynamic simulation of the human red blood cell metabolic network.. Bioinformatics (Oxford, England). 17(3):286-7.
Covert MW, Schilling CH, Famili I, Edwards JS, Goryanin II, Selkov E, Palsson BØ.  2001.  Metabolic modeling of microbial strains in silico.. Trends in biochemical sciences. 26(3):179-86.
Ramakrishna R, Edwards JS, McCulloch A, Palsson BØ.  2001.  Flux-balance analysis of mitochondrial energy metabolism: consequences of systemic stoichiometric constraints.. American journal of physiology. Regulatory, integrative and comparative physiology. 280(3):R695-704.
Edwards JS, Ibarra RU, Palsson BØ.  2001.  In silico predictions of Escherichia coli metabolic capabilities are consistent with experimental data.. Nature biotechnology. 19(2):125-30.
Year of Publication: 2000
Edwards JS, Palsson BØ.  2000.  Robustness analysis of the Escherichia coli metabolic network.. Biotechnology progress. 16(6):927-39.
Edwards JS, Palsson BØ.  2000.  Multiple steady states in kinetic models of red cell metabolism.. Journal of theoretical biology. 207(1):125-7.
Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BØ.  2000.  Extension of osmolality-induced podia is observed from fluorescently labeled hematopoietic cell lines in hyperosmotic medium.. Cytometry. 40(2):109-18.
Oh DJ, Martinez AR, Lee GM, Francis K, Palsson BØ.  2000.  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. 40(2):119-25.
Edwards JS, Palsson BØ.  2000.  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. 97(10):5528-33.
Schilling CH, Palsson BØ.  2000.  Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.. Journal of theoretical biology. 203(3):249-83.
Schilling CH, Letscher D, Palsson BØ.  2000.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.. Journal of theoretical biology. 203(3):229-48.
Schilling CH, Edwards JS, Letscher D, Palsson BØ.  2000.  Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.. Biotechnology and bioengineering. 71(4):286-306.
Lee GM, Fong S, Francis K, Oh DJ, Palsson BØ.  2000.  In situ labeling of adherent cells with PKH26.. In vitro cellular & developmental biology. Animal. 36(1):4-6.
Edwards JS, Palsson BØ.  2000.  Metabolic flux balance analysis and the in silico analysis of Escherichia coli K-12 gene deletions.. BMC bioinformatics. 1:1.
Year of Publication: 1999
Holloway W, Martinez AR, Oh DJ, Francis K, Ramakrishna R, Palsson BØ.  1999.  Key adhesion molecules are present on long podia extended by hematopoietic cells.. Cytometry. 37(3):171-7.
Huang S, Law P, Francis K, Palsson BØ, Ho AD.  1999.  Symmetry of initial cell divisions among primitive hematopoietic progenitors is independent of ontogenic age and regulatory molecules.. Blood. 94(8):2595-604.
Oh DJ, Lee GM, Francis K, Palsson BØ.  1999.  Phototoxicity of the fluorescent membrane dyes PKH2 and PKH26 on the human hematopoietic KG1a progenitor cell line.. Cytometry. 36(4):312-8.
Edwards JS, Palsson BØ.  1999.  Systems properties of the Haemophilus influenzae Rd metabolic genotype.. The Journal of biological chemistry. 274(25):17410-6.
Schilling CH, Edwards JS, Palsson BØ.  1999.  Toward metabolic phenomics: analysis of genomic data using flux balances.. Biotechnology progress. 15(3):288-95.
Schilling CH, Schuster S, Palsson BØ, Heinrich R.  1999.  Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.. Biotechnology progress. 15(3):296-303.
Year of Publication: 1998
Francis K, Ramakrishna R, Holloway W, Palsson BØ.  1998.  Two new pseudopod morphologies displayed by the human hematopoietic KG1a progenitor cell line and by primary human CD34(+) cells.. Blood. 92(10):3616-23.
Koller MR, Palsson MA, Manchel I, Maher RJ, Palsson BØ.  1998.  Tissue culture surface characteristics influence the expansion of human bone marrow cells.. Biomaterials. 19(21):1963-72.
Mandalam RK, Palsson BØ.  1998.  Elemental balancing of biomass and medium composition enhances growth capacity in high-density Chlorella vulgaris cultures.. Biotechnology and bioengineering. 59(5):605-11.
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.
Edwards JS, Palsson BØ.  1998.  How will bioinformatics influence metabolic engineering? Biotechnology and bioengineering. 58(2-3):162-9.
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.
Year of Publication: 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.
Andreadis ST, Brott DA, Fuller AO, Palsson BØ.  1997.  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. 71(10):7541-8.
Andreadis ST, Palsson BØ.  1997.  Coupled effects of polybrene and calf serum on the efficiency of retroviral transduction and the stability of retroviral vectors.. Human gene therapy. 8(3):285-91.
Palsson BØ.  1997.  What lies beyond bioinformatics? Nature biotechnology. 15(1):3-4.
Koller MR, Manchel I, Palsson BØ.  1997.  Importance of parenchymal:stromal cell ratio for the ex vivo reconstitution of human hematopoiesis.. Stem cells (Dayton, Ohio). 15(4):305-13.
Year of Publication: 1996
Koller MR, Manchel I, Brott DA, Brott DA.  1996.  Donor-to-donor variability in the expansion potential of human bone marrow cells is reduced by accessory cells but not by soluble growth factors.. Experimental hematology. 24(13):1484-93.
Koller MR, Oxender M, Brott DA, Palsson BØ.  1996.  flt-3 ligand is more potent than c-kit ligand for the synergistic stimulation of ex vivo hematopoietic cell expansion.. Journal of hematotherapy. 5(5):449-59.
Peng CA, Koller MR, Palsson BØ.  1996.  Unilineage model of hematopoiesis predicts self-renewal of stem and progenitor cells based on ex vivo growth data.. Biotechnology and bioengineering. 52(1):24-33.
Andreadis ST, Palsson BØ.  1996.  Kinetics of retrovirus mediated gene transfer: the importance of intracellular half-life of retroviruses.. Journal of theoretical biology. 182(1):1-20.
Chuck AS, Clarke MF, Palsson BØ.  1996.  Retroviral infection is limited by Brownian motion.. Human gene therapy. 7(13):1527-34.
Chuck AS, Palsson BØ.  1996.  Membrane adsorption characteristics determine the kinetics of flow-through transductions.. Biotechnology and bioengineering. 51(3):260-70.
Koller MR, Manchel I, Palsson MA, Maher RJ, Palsson BØ.  1996.  Different measures of human hematopoietic cell culture performance are optimized under vastly different conditions.. Biotechnology and bioengineering. 50(5):505-13.
Peng CA, Palsson BØ.  1996.  Cell growth and differentiation on feeder layers is predicted to be influenced by bioreactor geometry.. Biotechnology and bioengineering. 50(5):479-92.
Peng CA, Palsson BØ.  1996.  Determination of specific oxygen uptake rates in human hematopoietic cultures and implications for bioreactor design.. Annals of biomedical engineering. 24(3):373-81.
Chuck AS, Palsson BØ.  1996.  Consistent and high rates of gene transfer can be obtained using flow-through transduction over a wide range of retroviral titers.. Human gene therapy. 7(6):743-50.
Rogers CE, Bradley MS, Palsson BØ, Koller MR.  1996.  Flow cytometric analysis of human bone marrow perfusion cultures: erythroid development and relationship with burst-forming units-erythroid.. Experimental hematology. 24(5):597-604.
Year of Publication: 1995
Eipers PG, Krauss JC, Palsson BØ, Emerson SG, Todd RF, Clarke MF.  1995.  Retroviral-mediated gene transfer in human bone marrow cells growth in continuous perfusion culture vessels.. Blood. 86(10):3754-62.
Koller MR, Bradley MS, Palsson BØ.  1995.  Growth factor consumption and production in perfusion cultures of human bone marrow correlate with specific cell production.. Experimental hematology. 23(12):1275-83.
Koller MR, Palsson MA, Manchel I, Palsson BØ.  1995.  Long-term culture-initiating cell expansion is dependent on frequent medium exchange combined with stromal and other accessory cell effects.. Blood. 86(5):1784-93.
Koller MR, Manchel I, Newsom BS, Palsson MA, Palsson BØ.  1995.  Bioreactor expansion of human bone marrow: comparison of unprocessed, density-separated, and CD34-enriched cells.. Journal of hematotherapy. 4(3):159-69.
Emerson SG, Palsson BØ, Clarke MF, Silver SM, Adams PT, Koller MR, Van Zant G, Rummel S, Armstrong RD, Maluta J.  1995.  In vitro expansion of hematopoietic cells for clinical application.. Cancer treatment and research. 76:215-23.
Varma A, Palsson BØ.  1995.  Parametric sensitivity of stoichiometric flux balance models applied to wild-type Escherichia coli metabolism.. Biotechnology and bioengineering. 45(1):69-79.
Year of Publication: 1994
Lee CG, Palsson BØ.  1994.  High-density algal photobioreactors using light-emitting diodes.. Biotechnology and bioengineering. 44(10):1161-7.
Varma A, Palsson BØ.  1994.  Stoichiometric flux balance models quantitatively predict growth and metabolic by-product secretion in wild-type Escherichia coli W3110.. Applied and environmental microbiology. 60(10):3724-31.
Oh DJ, Koller MR, Palsson BØ.  1994.  Frequent harvesting from perfused bone marrow cultures results in increased overall cell and progenitor expansion.. Biotechnology and bioengineering. 44(5):609-16.
Levee MG, Lee GM, Paek SH, Palsson BØ.  1994.  Microencapsulated human bone marrow cultures: a potential culture system for the clonal outgrowth of hematopoietic progenitor cells.. Biotechnology and bioengineering. 43(8):734-9.
Hubbell JA, Palsson BØ, Papoutsakis ET.  1994.  Preface: Tissue engineering and cell therapies: II.. Biotechnology and bioengineering. 43(8):683.
Hubbell JA, Palsson BØ, Papoutsakis ET.  1994.  Preface. Tissue engineering and cell therapies.. Biotechnology and bioengineering. 43(7):541.
Varma A, Palsson BØ.  1994.  Predictions for oxygen supply control to enhance population stability of engineered production strains.. Biotechnology and bioengineering. 43(4):275-85.
Lee GM, Kim SJ, Palsson BØ.  1994.  Enhanced specific antibody productivity of calcium alginate-entrapped hybridoma is cell line-specific.. Cytotechnology. 16(1):1-15.
Lee GM, Palsson BØ.  1994.  Monoclonal antibody production using free-suspended and entrapped hybridoma cells.. Biotechnology & genetic engineering reviews. 12:509-33.
Year of Publication: 1993
Varma A, Palsson BØ.  1993.  Metabolic capabilities of Escherichia coli: I. synthesis of biosynthetic precursors and cofactors.. Journal of theoretical biology. 165(4):477-502.
Palsson BØ, Shen BQ, Meyerhoff ME, Trojanowicz M.  1993.  Simultaneous determination of ammonia nitrogen and L-glutamine in bioreactor media using flow injection.. The Analyst. 118(11):1361-5.
Lee GM, Palsson BØ.  1993.  Stability of antibody productivity is improved when hybridoma cells are entrapped in calcium alginate beads.. Biotechnology and bioengineering. 42(9):1131-5.
Koller MR, Palsson BØ.  1993.  Review: tissue engineering: reconstitution of human hematopoiesis ex vivo.. Biotechnology and bioengineering. 42(8):909-30.
Varma A, Boesch BW, Palsson BØ.  1993.  Stoichiometric interpretation of Escherichia coli glucose catabolism under various oxygenation rates.. Applied and environmental microbiology. 59(8):2465-73.
Koller MR, Emerson SG, Palsson BØ.  1993.  Large-scale expansion of human stem and progenitor cells from bone marrow mononuclear cells in continuous perfusion cultures.. Blood. 82(2):378-84.
Merritt SE, Palsson BØ.  1993.  Loss of antibody productivity is highly reproducible in multiple hybridoma subclones.. Biotechnology and bioengineering. 42(2):247-50.
Varma A, Boesch BW, Palsson BØ.  1993.  Biochemical production capabilities of Escherichia coli.. Biotechnology and bioengineering. 42(1):59-73.
Meyerhoff ME, Trojanowicz M, Palsson BØ.  1993.  Simultaneous enzymatic/electrochemical determination of glucose and L-glutamine in hybridoma media by flow-injection analysis.. Biotechnology and bioengineering. 41(10):964-9.
Palsson BØ, Lee ID.  1993.  Model complexity has a significant effect on the numerical value and interpretation of metabolic sensitivity coefficients.. Journal of theoretical biology. 161(3):299-315.
Palsson BØ, Paek SH, Schwartz RM, Palsson MA, Lee GM, Silver S, Emerson SG.  1993.  Expansion of human bone marrow progenitor cells in a high cell density continuous perfusion system.. Bio/technology (Nature Publishing Company). 11(3):368-72.
Lee GM, Chuck AS, Palsson BØ.  1993.  Cell Culture conditions determine the enhancement of specific monoclonal antibody productivity of calcium alginate-entrapped S3H5/gamma2bA2 hybridoma cells.. Biotechnology and bioengineering. 41(3):330-40.
Year of Publication: 1992
Lee ID, Palsson BØ.  1992.  A Macintosh software package for simulation of human red blood cell metabolism.. Computer methods and programs in biomedicine. 38(4):195-226.
Keasling JD, Palsson BØ, Cooper S.  1992.  Replication of prophage P1 is cell-cycle specific.. Journal of bacteriology. 174(13):4457-62.
Keasling JD, Palsson BØ, Cooper S.  1992.  Replication of mini-F plasmids during the bacterial division cycle.. Research in microbiology. 143(6):541-8.
Savinell JM, Palsson BØ.  1992.  Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.. Journal of theoretical biology. 155(2):215-42.
Savinell JM, Palsson BØ.  1992.  Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods.. Journal of theoretical biology. 155(2):201-14.
Javanmardian M, Palsson BØ.  1992.  Continuous photoautotrophic cultures of the eukaryotic alga Chlorella vulgaris can exhibit stable oscillatory dynamics.. Biotechnology and bioengineering. 39(5):487-97.