Publications

Author [ Title(Desc)] Year
A B C D E F G H I J K L M N O P Q R S T U V W X Y Z 
A
Campodonico MA, Vaisman D, Castro JF, Razmilic V, Mercado F, Andrews BA, Feist AM, Asenjo JA.  2016.  Acidithiobacillus ferrooxidans's comprehensive model driven analysis of the electron transfer metabolism and synthetic strain design for biomining applications. Metabolic Engineering Communications. 3
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.. Metab Eng.
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.
Latif H, Sahin M, Tarasova J, Tarasova Y, Portnoy VA, Nogales J, Zengler K.  2015.  Adaptive Evolution of Thermotoga maritima Reveals Plasticity of the ABC Transporter Network.. Appl Environ Microbiol. 81(16):5477-85.
Palsson BØ.  2011.  Adaptive Laboratory Evolution. Microbe.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.. Metab Eng.
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.
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.
Aziz R.K., Monk J.M., Andrews K.A., Nhan J., Khaw V.J., Wong H., Palsson B.O., Charusanti P..  2016.  The aldehyde dehydrogenase, AldA, is essential for L-1,2-propanediol utilization in laboratory-evolved Escherichia coli. Microbiological Research. 194:47-52.
Phaneuf PV, Gosting D, Palsson BO, Feist AM.  2018.  ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.. Nucleic Acids Res.
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.
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.
Hyduke DR, Lewis NE, Palsson BØ.  2013.  Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74.
Chang RL, Xie L, Bourne PE, Palsson BO.  2013.  Antibacterial mechanisms identified through structural systems pharmacology.. BMC Syst Biol. 7(1):102.
Yang JH, Bhargava P, McCloskey D, Mao N, Palsson BO, Collins JJ.  2017.  Antibiotic-Induced Changes to the Host Metabolic Environment Inhibit Drug Efficacy and Alter Immune Function.. Cell Host Microbe.
Oberhardt MA, Palsson BØ, Papin JA.  2009.  Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320.
Cho S, Cho Y-B, Kang TJin, Kim SChang, Palsson B, Cho B-K.  2015.  The architecture of ArgR-DNA complexes at the genome-scale in Escherichia coli.. Nucleic Acids Res.
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.
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.
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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.
Kabimoldayev I, Nguyen ADuc, Yang L, Park S, Lee EYeol, Kim D.  2018.  Basics of genome-scale metabolic modeling and applications on C1-utilization.. FEMS Microbiol Lett.
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.
King ZA, Lu J, Dräger A, Miller P, Federowicz S, Lerman JA, Ebrahim A, Palsson BO, Lewis NE.  2016.  BiGG Models: A platform for integrating, standardizing and sharing genome-scale models.. Nucleic Acids Res.
Rohatgi N, Nielsen TKragh, Bjørn SPetersen, Axelsson I, Paglia G, Voldborg BGunnar, Palsson BO, Rolfsson O.  2014.  Biochemical Characterization of Human Gluconokinase and the Proposed Metabolic Impact of Gluconic Acid as Determined by Constraint Based Metabolic Network Analysis.. PLoS One. 9(6):e98760.
Varma A, Boesch BW, Palsson BØ.  1993.  Biochemical production capabilities of Escherichia coli.. Biotechnology and bioengineering. 42(1):59-73.
Yurkovich JT, Yang L, Palsson BO.  2017.  Biomarkers are used to predict quantitative metabolite concentration profiles in human red blood cells.. PLoS Comput Biol. 13(3):e1005424.
Paglia G, D'Alessandro A, Rolfsson O, Sigurjónsson OE, Bordbar A, Palsson S, Nemkov T, Hansen KC, Gudmundsson S, Palsson BO.  2016.  Biomarkers defining the metabolic age of red blood cells during cold storage.. Blood.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
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.
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.
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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.
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.
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.
Huang T-W, Lam I, Chang H-Y, Tsai S-F, Palsson BO, Charusanti P.  2014.  Capsule deletion via a lamda-Red knockout system perturbs biofilm formation and fimbriae expression in Klebsiella pneumoniae MGH 78578.. BMC Res Notes. 7(1):13.
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.
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.
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.
Zengler K.  2009.  Central role of the cell in microbial ecology.. Microbiology and molecular biology reviews : MMBR. 73(4):712-29.
Palsson BØ, Zengler K.  2010.  The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
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.
Nagarajan H, Embree M, Rotaru A-E, Shrestha PM, Feist AM, Palsson BØ, Lovley DR, Zengler K.  2013.  Characterization and modelling of interspecies electron transfer mechanisms and microbial community dynamics of a syntrophic association.. Nat Commun. 4:2809.
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.
Nagarajan H, Sahin M, Nogales J, Latif H, Lovley DR, Ebrahim A, Zengler K.  2013.  Characterizing acetogenic metabolism using a genome-scale metabolic reconstruction of Clostridium ljungdahlii.. Microb Cell Fact. 12(1):118.
Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho B-K, Yang C et al..  2018.  Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow. Proceedings of the National Academy of Sciences.
Brunk E, George KW, Alonso-Gutierrez J, Thompson M, Baidoo E, Wang G, Petzold CJ, McCloskey D, Monk J, Yang L et al..  2016.  Characterizing Strain Variation in Engineered E. coli Using a Multi-Omics-Based Workflow.. Cell Syst.
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.
Edwards JS, Ramakrishna R, Palsson BØ.  2002.  Characterizing the metabolic phenotype: a phenotype phase plane analysis.. Biotechnology and bioengineering. 77(1):27-36.
Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.  2016.  ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions. bioRxiv.
Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.  2018.  ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.. PLoS One. 13(5):e0197272.
D'Alessandro A, Nemkov T, Yoshida T, Bordbar A, Palsson BO, Hansen KC.  2016.  Citrate metabolism in red blood cells stored in additive solution-3.. Transfusion. 57(2):325-336.
Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO.  2017.  COBRAme: A Computational Framework for Building and Manipulating Models of Metabolism and Gene Expression. bioRxiv.
Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO.  2018.  COBRAme: A computational framework for genome-scale models of metabolism and gene expression.. PLoS Comput Biol. 14(7):e1006302.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.  2013.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python.. BMC Syst Biol. 7(1):74.
Geertz-Hansen HMarcus, Blom N, Feist AM, Brunak S, Petersen TNordahl.  2014.  Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds.. Proteins.
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.
Anton BP, Chang Y-C, Brown P, Choi H-P, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A et al..  2013.  The COMBREX project: design, methodology, and initial results.. PLoS Biol. 11(8):e1001638.
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.
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.
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.
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.
Bosi E, Monk JM, Aziz RK, Fondi M, Nizet V, Palsson BØ.  2016.  Comparative genome-scale modelling of Staphylococcus aureus strains identifies strain-specific metabolic capabilities linked to pathogenicity.. Proc Natl Acad Sci U S A.
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.
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.
Paglia G, Sigurjónsson OE, Rolfsson O, Valgeirsdottir S, Hansen MBagge, Brynjólfsson S, Gudmundsson S, Palsson BO.  2014.  Comprehensive metabolomic study of platelets reveals the expression of discrete metabolic phenotypes during storage.. Transfusion.
Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.  2019.  A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.. PLoS Comput Biol. 15(1):e1006644.
O'Brien EJ, Palsson BO.  2015.  Computing the functional proteome: recent progress and future prospects for genome-scale models.. Curr Opin Biotechnol. 34C:125-134.
Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BØ.  2015.  CONDENSED VERSION--Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.
Mo ML, Palsson BØ, Herrgard MJ.  2009.  Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
Hefzi H, Ang KSiong, Hanscho M, Bordbar A, Ruckerbauer D, Lakshmanan M, Orellana CA, Baycin-Hizal D, Huang Y, Ley D et al..  2016.  A Consensus Genome-scale Reconstruction of Chinese Hamster Ovary Cell Metabolism.. Cell Syst. 3(5):434-443.e8.
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.
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.
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.
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.
Feist AM, Nagarajan H, Rotaru A-E, Tremblay P-L, Zhang T, Nevin KP, Lovley DR, Zengler K.  2014.  Constraint-Based Modeling of Carbon Fixation and the Energetics of Electron Transfer in Geobacter metallireducens.. PLoS Comput Biol. 10(4):e1003575.
Bordbar A, Monk JM, King ZA, Palsson BO.  2014.  Constraint-based models predict metabolic and associated cellular functions.. Nat Rev Genet. 15(2):107-20.
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.
Liu HC, Jamshidi N, Chen Y, Eraly SA, Cho SYee, Bhatnagar V, Wu W, Bush KT, Abagyan R, Palsson BO et al..  2016.  Construction and Evaluation of an Organic Anion Transporter 1 (OAT1)-Centered Metabolic Network.. J Biol Chem.
Becker SA, Palsson BØ.  2008.  Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
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.
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.
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.
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.
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.
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.
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Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S.  2018.  Dataset on economic analysis of mass production of algae in LED-based photobioreactors.. Data Brief. 22:137-139.
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.
Seo SWoo, Kim D, Latif H, O'Brien EJ, Szubin R, Palsson BO.  2014.  Deciphering Fur transcriptional regulatory network highlights its complex role beyond iron metabolism in Escherichia coli.. Nat Commun. 5:4910.
Cho B-K, Federowicz S, Park Y-S, Zengler K, Palsson BØ.  2011.  Deciphering the transcriptional regulatory logic of amino acid metabolism.. Nat Chem Biol. 8(1):65-71.
Seo SWoo, Kim D, O'Brien EJ, Szubin R, Palsson BO.  2015.  Decoding genome-wide GadEWX-transcriptional regulatory networks reveals multifaceted cellular responses to acid stress in Escherichia coli.. Nat Commun. 6:7970.
Rolfsson O, Palsson BO.  2015.  Decoding the jargon of bottom-up metabolic systems biology.. Bioessays.
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.
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.
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.
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.
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.
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.
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.
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.
Federowicz S, Kim D, Ebrahim A, Lerman J, Nagarajan H, Cho B-K, Zengler K, Palsson B.  2014.  Determining the control circuitry of redox metabolism at the genome-scale.. PLoS Genet. 10(4):e1004264.
Palsson S, Hickling TP, Bradshaw-Pierce EL, Zager M, Jooss K, Brien PJO, Spilker ME, Palsson BO, Vicini P.  2013.  The development of a fully-integrated immune response model (FIRM) simulator of the immune response through integration of multiple subset models.. BMC Syst Biol. 7(1):95.
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.
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.
LaCroix RA, Sandberg TE, O'Brien EJ, Utrilla J, Ebrahim A, Guzman GI, Szubin R, Palsson BO, Feist AM.  2014.  Discovery of key mutations enabling rapid growth of Escherichia coli K-12 MG1655 on glucose minimal media using adaptive laboratory evolution.. Appl Environ Microbiol.
Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.  2017.  Dissecting the genetic and metabolic mechanisms of adaptation to the knockout of a major metabolic enzyme in Escherichia coli.. Proc Natl Acad Sci U S A.
Ebrahim A, Almaas E, Bauer E, Bordbar A, Burgard AP, Chang RL, Dräger A, Famili I, Feist AM, Fleming RMt et al..  2015.  Do genome-scale models need exact solvers or clearer standards? Mol Syst Biol. 11(10):831.
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.
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.
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.
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Fong S, Joyce AR, Palsson BØ.  2005.  The econometrics of evolution.. Nature chemical biology. 1(4):191-2.
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.
Fu W, Paglia G, Magnúsdóttir M, Steinarsdóttir EA, Gudmundsson S, Palsson BO, Andrésson OS, Brynjólfsson S.  2014.  Effects of abiotic stressors on lutein production in the green microalga Dunaliella salina.. Microb Cell Fact. 13(1):3.
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.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Bordbar A, Yurkovich JT, Paglia G, Rolfsson O, Sigurjónsson OE, Palsson BO.  2017.  Elucidating dynamic metabolic physiology through network integration of quantitative time-course metabolomics.. Sci Rep. 7:46249.
Levering J, Broddrick J, Zengler K.  2015.  Engineering of oleaginous organisms for lipid production.. Curr Opin Biotechnol. 36:32-39.
Nielsen J, Fussenegger M, Keasling J, Lee S Y, Liao JC, Prather K, Palsson B.  2014.  Engineering synergy in biotechnology.. Nat Chem Biol. 10(5):319-22.
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.
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.
King ZA, Dräger A, Ebrahim A, Sonnenschein N, Lewis NE, Palsson BO.  2015.  Escher: A Web Application for Building, Sharing, and Embedding Data-Rich Visualizations of Biological Pathways.. PLoS Comput Biol. 11(8):e1004321.
Rowe E, Palsson BO, King ZA.  2018.  Escher-FBA: a web application for interactive flux balance analysis. BMC Systems Biology.
Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.  2018.  Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.. BMC Syst Biol. 12(1):66.
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.
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.
Du B, Zielinski DC, Palsson BO.  2018.  Estimating Metabolic Equilibrium Constants: Progress and Future Challenges. Trends in Biochemical Sciences.
Yeung M, Thiele I, Palsson BØ.  2007.  Estimation of the number of extreme pathways for metabolic networks.. BMC bioinformatics. 8(1):363.
Herring CD, Palsson BØ.  2007.  An evaluation of Comparative Genome Sequencing (CGS) by comparing two previously-sequenced bacterial genomes.. BMC genomics. 8:274.
Du B, Zielinski DC, Kavvas ES, Dräger A, Tan J, Zhang Z, Ruggiero KE, Arzumanyan GA, Palsson BO.  2016.  Evaluation of rate law approximations in bottom-up kinetic models of metabolism.. BMC Syst Biol. 10(1):40.
Sandberg TE, Long CP, Gonzalez JE, Feist AM, Antoniewicz MR, Palsson BO.  2016.  Evolution of E. coli on [U-13C]Glucose Reveals a Negligible Isotopic Influence on Metabolism and Physiology.. PLoS One. 11(3):e0151130.
Sandberg TE, Pedersen M, LaCroix RA, Ebrahim A, Bonde M, Herrgard MJ, Palsson BO, Sommer M, Feist AM.  2014.  Evolution of Escherichia coli to 42 °C and Subsequent Genetic Engineering Reveals Adaptive Mechanisms and Novel Mutations.. Mol Biol Evol.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.. Nat Commun. 9(1):3796.
Westerhoff HV, Palsson BØ.  2004.  The evolution of molecular biology into systems biology.. Nature biotechnology. 22(10):1249-52.
Bell SL, Palsson BØ.  2005.  Expa: a program for calculating extreme pathways in biochemical reaction networks.. Bioinformatics (Oxford, England). 21(8):1739-40.
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.
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.
Nogales J, Gudmundsson S, Duque E., Ramos JLewis, Palsson BO.  2017.  Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness. bioRxiv.
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.
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.
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.
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.
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.
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.
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.
Price ND, Famili I, Beard DA, Palsson BØ.  2002.  Extreme pathways and Kirchhoff's second law.. Biophysical journal. 83(5):2879-82.
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Long CP, Gonzalez JE, Feist AM, Palsson BO, Antoniewicz MR.  2017.  Fast growth phenotype of E. coli K-12 from adaptive laboratory evolution does not require intracellular flux rewiring.. Metab Eng.
McCloskey DM, Utrilla J, Naviaux RK, Palsson BO, Feist AM.  2014.  Fast Swinnex filtration (FSF): a fast and robust sampling and extraction method suitable for metabolomics analysis of cultures grown in complex media. Metabolomics. 10(10.1007/s11306-014-0686-2)
Herrgard MJ, Palsson BØ.  2004.  Flagellar biosynthesis in silico: building quantitative models of regulatory networks.. Cell. 117(6):689-90.
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.
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.
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.
Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
Jamshidi N, Palsson BØ.  2008.  Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171.
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.
Hefzi H., Lewis N.E..  2014.  From random mutagenesis to systems biology in metabolic engineering of mammalian cells. Pharmaceutical Bioprocessing. 2
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.
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.
Abdel-Haleem AM, Hefzi H, Mineta K, Gao X, Gojobori T, Palsson BO, Lewis NE, Jamshidi N.  2018.  Functional interrogation of Plasmodium genus metabolism identifies species- and stage-specific differences in nutrient essentiality and drug targeting.. PLoS Comput Biol. 14(1):e1005895.
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.
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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.
Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM.  2018.  Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology. Microbiology Resource Announcements. 7
Latif H, Li HJ, Charusanti P, Palsson BØ, Aziz RK.  2014.  A Gapless, Unambiguous Genome Sequence of the Enterohemorrhagic Escherichia coli O157:H7 Strain EDL933.. Genome Announc. 2(4)
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.
Mohamed ET, Wang S, Lennen RM, Herrgard MJ, Simmons BA, Singer SW, Feist AM.  2017.  Generation of a platform strain for ionic liquid tolerance using adaptive laboratory evolution.. Microb Cell Fact. 16(1):204.
Campodonico MA, Andrews BA, Asenjo JA, Palsson BO, Feist AM.  2014.  Generation of an atlas for commodity chemical production in Escherichia coli and a novel pathway prediction algorithm, GEM-Path.. Metab Eng. 25C:140-158.
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.
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.
Choe D, Szubin R, Dahesh S, Cho S, Nizet V, Palsson B, Cho B-K.  2018.  Genome-scale analysis of Methicillin-resistant Staphylococcus aureus USA300 reveals a tradeoff between pathogenesis and drug resistance.. Sci Rep. 8(1):2215.
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.
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.
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, 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.
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.
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.
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.
Monk JM, Charusanti P, Aziz RK, Lerman JA, Premyodhin N, Orth JD, Feist AM, Palsson BØ.  2013.  Genome-scale metabolic reconstructions of multiple Escherichia coli strains highlight strain-specific adaptations to nutritional environments.. Proc Natl Acad Sci U S A.
Seif Y, Kavvas E, Lachance J-C, Yurkovich JT, Nuccio S-P, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM.  2018.  Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.. Nat Commun. 9(1):3771.
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.
Levering J, Broddrick J, Dupont CL, Peers G, Beeri K, Mayers J, Gallina AA, Allen AE, Palsson BO, Zengler K.  2016.  Genome-Scale Model Reveals Metabolic Basis of Biomass Partitioning in a Model Diatom.. PLoS One. 11(5):e0155038.
O'Brien EJ, Lerman JA, Chang RL, Hyduke DR, Palsson BØ.  2013.  Genome-scale models of metabolism and gene expression extend and refine growth phenotype prediction.. Mol Syst Biol. 9:693.
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.
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.
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.
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.
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.
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.
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.
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.
Cho B-K, Kim D, Knight EM, Zengler K, Palsson BO.  2014.  Genome-scale reconstruction of the sigma factor network in Escherichia coli: topology and functional states.. BMC Biol. 12(1):4.
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.
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.
Seo SWoo, Kim D, Szubin R, Palsson BO.  2015.  Genome-wide Reconstruction of OxyR and SoxRS Transcriptional Regulatory Networks under Oxidative Stress in Escherichia coli K-12 MG1655.. Cell Rep.
Lewis NE, Liu X, Li Y, Nagarajan H, Yerganian G, O'Brien E, Bordbar A, Roth AM, Rosenbloom J, Bian C et al..  2013.  Genomic landscapes of Chinese hamster ovary cell lines as revealed by the Cricetulus griseus draft genome.. Nat Biotechnol.
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.
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.. Biotechnol J.
Schmidt BJ, Ebrahim A, Metz TO, Adkins JN, Palsson BØ, Hyduke DR.  2013.  GIM3E: condition-specific models of cellular metabolism developed from metabolomics and expression data.. Bioinformatics.
Cheng K-K, Lee B-S, Masuda T, Ito T, Ikeda K, Hirayama A, Deng L, Dong J, Shimizu K, Soga T et al..  2014.  Global metabolic network reorganization by adaptive mutations allows fast growth of Escherichia coli on glycerol.. Nat Commun. 5:3233.
Utrilla J, O'Brien EJ, Chen K, McCloskey D, Cheung J, Wang H, Armenta-Medina D, Feist AM, Palsson BO.  2016.  Global Rebalancing of Cellular Resources by Pleiotropic Point Mutations Illustrates a Multi-scale Mechanism of Adaptive Evolution.. Cell Syst. 2(4):260-71.
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.
Fang X, Sastry A, Mih N, Kim D, Tan J, Yurkovich JT, Lloyd CJ, Gao Y, Yang L, Palsson BO.  2017.  Global transcriptional regulatory network for Escherichia coli robustly connects gene expression to transcription factor activities.. Proc Natl Acad Sci U S A.
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.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome. Frontiers in Microbiology.
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.
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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.
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.
Lee CG, Palsson BØ.  1994.  High-density algal photobioreactors using light-emitting diodes.. Biotechnology and bioengineering. 44(10):1161-7.
Cho S, Choe D, Lee E, Kim SChang, Palsson B, Cho B-K.  2018.  High-Level dCas9 Expression Induces Abnormal Cell Morphology in Escherichia coli.. ACS Synth Biol. 7(4):1085-1094.
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.
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.
Pronk JT, Lee S Y, Lievense J, Pierce J, Palsson B, Uhlen M, Nielsen J.  2015.  How to set up collaborations between academia and industrial biotech companies.. Nat Biotechnol. 33(3):237-40.
Edwards JS, Palsson BØ.  1998.  How will bioinformatics influence metabolic engineering? Biotechnology and bioengineering. 58(2-3):162-9.
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.
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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.
Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM.  2018.  iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE. Frontiers in Genetics. 9
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.
Dinh HV, King ZA, Palsson BO, Feist AM.  2018.  Identification of growth-coupled production strains considering protein costs and kinetic variability. Metabolic Engineering Communications. 7:e00080.
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.
Bordbar A, Johansson PI, Paglia G, Harrison SJ, Wichuk K, Magnúsdóttir M, Valgeirsdottir S, Gybel-Brask M, Ostrowski SR, Palsson S et al..  2016.  Identified metabolic signature for assessing red blood cell unit quality is associated with endothelial damage markers and clinical outcomes.. Transfusion.
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.
Monk JM, Lloyd CJ, Brunk E, Mih N, Sastry A, King Z, Takeuchi R, Nomura W, Zhang Z, Mori H et al..  2017.  iML1515, a knowledgebase that computes Escherichia coli traits.. Nat Biotechnol. 35(10):904-908.
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.
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.
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.
Dräger A, Palsson BØ.  2014.  Improving collaboration by standardization efforts in systems biology.. Front Bioeng Biotechnol. 2:61.
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.
Palsson BØ.  2004.  In silico biotechnology. Era of reconstruction and interrogation.. Current opinion in biotechnology. 15(1):50-1.
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.
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.
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.
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.
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.
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.
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.
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.
Mundhada H, Seoane JM, Schneider K, Koza A, Christensen HB, Klein T, Phaneuf PV, Herrgard M, Feist AM, Nielsen AT.  2016.  Increased production of L-serine in Escherichia coli through Adaptive Laboratory Evolution.. Metab Eng. 39:141-150.
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.
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.
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.
Duarte NC, Palsson BØ, Fu P.  2004.  Integrated analysis of metabolic phenotypes in Saccharomyces cerevisiae.. BMC genomics. 5:63.
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.
Levering J, Dupont CL, Allen AE, Palsson BO, Zengler K.  2017.  Integrated Regulatory and Metabolic Networks of the Marine Diatom Phaeodactylum tricornutum Predict the Response to Rising CO2 Levels.. mSystems. 2(1)
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.
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.
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.
M Islam A, Zengler K, Edwards EA, Mahadevan R, Stephanopoulos G.  2015.  Investigating Moorella thermoacetica metabolism with a genome-scale constraint-based metabolic model.. Integr Biol (Camb). 7(8):869-82.
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.
Paglia G, Williams JP, Menikarachchi L, J Thompson W, Tyldesley-Worster R, Halldórsson S, Rolfsson O, Moseley A, Grant D, Langridge J et al..  2014.  Ion mobility derived collision cross sections to support metabolomics applications.. Anal Chem. 86(8):3985-93.
Paglia G, Angel P, Williams JP, Richardson K, Olivos HJ, J Thompson W, Menikarachchi L, Lai S, Walsh C, Moseley A et al..  2014.  Ion Mobility-Derived Collision Cross Section As an Additional Measure for Lipid Fingerprinting and Identification.. Anal Chem.
Vo TD, Palsson BØ.  2006.  Isotopomer analysis of myocardial substrate metabolism: a systems biology approach.. Biotechnology and bioengineering. 95(5):972-83.
Barrett CL, Palsson BØ.  2006.  Iterative reconstruction of transcriptional regulatory networks: an algorithmic approach.. PLoS computational biology. 2(5):e52.
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Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KRaosaheb et al..  2018.  Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.. Metab Eng. 47:73-82.
Sandberg TE, Lloyd CJ, Palsson BO, Feist AM.  2017.  Laboratory Evolution to Alternating Substrate Environments Yields Distinct Phenotypic and Genetic Adaptive Strategies.. Appl Environ Microbiol.
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.
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.
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.
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.
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.
King ZA, O'Brien EJ, Feist AM, Palsson BO.  2016.  Literature mining supports a next-generation modeling approach to predict cellular byproduct secretion.. Metab Eng.
Patil SA, Gildemyn S, Pant D, Zengler K, Logan BE, Rabaey K.  2015.  A logical data representation framework for electricity-driven bioproduction processes.. Biotechnol Adv. 33(6 Pt 1):736-44.
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.
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.
Merritt SE, Palsson BØ.  1993.  Loss of antibody productivity is highly reproducible in multiple hybridoma subclones.. Biotechnology and bioengineering. 42(2):247-50.
M
Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V et al..  2018.  Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance. Nature Communications.
Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AAmer, Lercher MJ, Palsson BO.  2018.  Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models. Nature Communications. 9
Sastry A, Monk J, Tegel H, Uhlen M, Palsson BO, Rockberg J, Brunk E.  2017.  Machine Learning in Computational Biology to Accelerate High-Throughput Protein Expression.. Bioinformatics.
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.
Rolfsson O, Johannsson F, Magnúsdóttir M, Paglia G, Sigurjónsson OE, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S, Palsson B.  2017.  Mannose and fructose metabolism in red blood cells during cold storage in SAGM.. Transfusion.
Spahn PN, Hansen AH, Hansen HG, Arnsdorf J, Kildegaard HF, Lewis NE.  2015.  A Markov chain model for N-linked protein glycosylation - towards a low-parameter tool for model-driven glycoengineering.. Metab Eng.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
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.
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.
Chuck AS, Palsson BØ.  1996.  Membrane adsorption characteristics determine the kinetics of flow-through transductions.. Biotechnology and bioengineering. 51(3):260-70.
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.
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.
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.
Paglia G, Sigurjónsson OE, Bordbar A, Rolfsson O, Magnúsdóttir M, Palsson S, Wichuk K, Gudmundsson S, Palsson BO.  2016.  Metabolic fate of adenine in red blood cells during storage in SAGM solution.. Transfusion.
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.
Fong S, Palsson BØ.  2004.  Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes.. Nature genetics. 36(10):1056-8.
Olavarria K, De Ingeniis J, Zielinski DC, Fuentealba M, Muñoz R, McCloskey D, Feist AM, Cabrera R.  2014.  The Metabolic Impact of a NADH-producing Glucose-6-phosphate Dehydrogenase in Escherichia coli.. Microbiology.
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.
Edwards JS, Covert MW, Palsson BØ.  2002.  Metabolic modelling of microbes: the flux-balance approach.. Environmental microbiology. 4(3):133-40.
Nilsson A, Nielsen J, Palsson BO.  2017.  Metabolic Models of Protein Allocation Call for the Kinetome.. Cell Syst. 5(6):538-541.
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.
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.
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.
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.
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.
Palsson BØ.  2009.  Metabolic systems biology.. FEBS letters. 583(24):3900-4.
Becker SA, Price ND, Palsson BØ.  2006.  Metabolite coupling in genome-scale metabolic networks.. BMC bioinformatics. 7:111.
Paglia G, Sigurjónsson OE, Rolfsson O, Hansen MBagge, Brynjólfsson S, Gudmundsson S, Palsson BO.  2014.  Metabolomic analysis of platelets during storage: a comparison between apheresis- and buffy coat-derived platelet concentrates.. Transfusion.
Rolfsson Ó, Sigurjonsson ÓE, Magnusdottir M, Johannsson F, Paglia G, Guðmundsson S, Bordbar A, Palsson S, Brynjólfsson S, Guðmundsson S et al..  2017.  Metabolomics comparison of red cells stored in four additive solutions reveals differences in citrate anticoagulant permeability and metabolism.. Vox Sang.
Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J et al..  2018.  Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient. Frontiers in Microbiology.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
Cho B-K, Charusanti P, Herrgard MJ, Palsson BØ.  2007.  Microbial regulatory and metabolic networks.. Current opinion in biotechnology. 18(4):360-4.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
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.
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.
McCloskey D, Young JD, Xu S, Palsson BO, Feist AM.  2015.  MID Max: LC-MS/MS Method for Measuring the Precursor and Product Mass Isotopomer Distributions of Metabolic Intermediates and Cofactors for Metabolic Flux Analysis Applications.. Anal Chem.
Bordbar A, Nagarajan H, Lewis NE, Latif H, Ebrahim A, Federowicz S, Schellenberger J, Palsson BO.  2014.  Minimal metabolic pathway structure is consistent with associated biomolecular interactions.. Mol Syst Biol. 10(7):737.
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.
LaCroix RA, Palsson BO, Feist AM.  2017.  A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol.
Joyce AR, Palsson BØ.  2006.  The model organism as a system: integrating 'omics' data sets.. Nature reviews. Molecular cell biology. 7(3):198-210.
Aziz RK, Khaw VL, Monk JM, Brunk E, Lewis R, Loh SI, Mishra A, Nagle AA, Satyanarayana C, Dhakshinamoorthy S et al..  2015.  Model-driven discovery of synergistic inhibitors against E. coli and S. enterica serovar Typhimurium targeting a novel synthetic lethal pair, aldA and prpC.. Front Microbiol. 6:958.
Guzman GI, Utrilla J, Nurk S, Brunk E, Monk JM, Ebrahim A, Palsson BO, Feist AM.  2015.  Model-driven discovery of underground metabolic functions in Escherichia coli.. Proc Natl Acad Sci U S A.
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.
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.
McCloskey D, Gangoiti JA, King ZA, Naviaux RK, Barshop BA, Palsson BO, Feist AM.  2013.  A model-driven quantitative metabolomics analysis of aerobic and anaerobic metabolism in E. coli K-12 MG1655 that is biochemically and thermodynamically consistent.. Biotechnol Bioeng.
Heckmann D, Zielinski DC, Palsson BO.  2018.  Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates. Nature Communications. 9
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.
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.
McCloskey D, Young JD, Xu S, Palsson BØ, Feist AM.  2016.  A modeling method for increased precision and scope of directly measurable fluxes at a genome-scale.. Anal Chem.
Yang L, Yurkovich JT, King ZA, Palsson BO.  2018.  Modeling the multi-scale mechanisms of macromolecular resource allocation. Current Opinion in Microbiology. 45:8-15.
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.
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.
Lee GM, Palsson BØ.  1994.  Monoclonal antibody production using free-suspended and entrapped hybridoma cells.. Biotechnology & genetic engineering reviews. 12:509-33.
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.
Nguyen D D, Wu C-H, Moree WJ, Lamsa A, Medema MH, Zhao X, Gavilan RG, Aparicio M, Atencio L, Jackson C et al..  2013.  MS/MS networking guided analysis of molecule and gene cluster families.. Proc Natl Acad Sci U S A. 110(28):E2611-20.
Pacini T, Fu W, Gudmundsson S, A Chiaravalle E, Brynjolfson S, Palsson BO, Astarita G, Paglia G.  2015.  Multidimensional Analytical Approach Based on UHPLC-UV-Ion Mobility-MS for the Screening of Natural Pigments.. Anal Chem. 87(5):2593-9.
Ebrahim A, Brunk E, Tan J, O'Brien EJ, Kim D, Szubin R, Lerman JA, Lechner A, Sastry A, Bordbar A et al..  2016.  Multi-omic data integration enables discovery of hidden biological regularities.. Nat Commun. 7:13091.
Monk JM, Koza A, Campodonico MA, Machado D, Seoane JMiguel, Palsson BO, Herrgard MJ, Feist AM.  2016.  Multi-omics Quantification of Species Variation of Escherichia coli Links Molecular Features with Strain Phenotypes.. Cell Syst.
McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.  2018.  Multiple optimal phenotypes overcome redox and glycolytic intermediate metabolite imbalances in knockout evolutions.. Appl Environ Microbiol.
Edwards JS, Palsson BØ.  2000.  Multiple steady states in kinetic models of red cell metabolism.. Journal of theoretical biology. 207(1):125-7.
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.