Author Title [ Year(Asc)]
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.
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.
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.
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.
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.
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.
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.
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.
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
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.
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.
Yurkovich JT, Palsson BO.  2018.  Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology. 51:130-136.
Brunk E, Sahoo S, Zielinski DC, Altunkaya A, Dräger A, Mih N, Gatto F, Nilsson A, Gonzalez GAndres Pre, Aurich MKathrin et al..  2018.  Recon3D enables a three-dimensional view of gene variation in human metabolism.. Nat Biotechnol.
Mih N, Brunk E, Chen K, Catoiu E, Sastry A, Kavvas E, Monk JM, Zhang Z, Palsson BO.  2018.  ssbio: A Python Framework for Structural Systems Biology. Bioinformatics.
Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO.  2018.  The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures. Frontiers in Microbiology. 9
óhannsson F, ðmundsson S, Paglia G, ðmundsson S, Palsson B, ónsson ÓE, Rolfsson O.  2018.  Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution. Biochemical Journal. :BCJ20170921.
Kim D, Seo SWoo, Gao Y, Nam H, Guzman GI, Cho B-K, Palsson BO.  2018.  Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP.. Nucleic Acids Res.
Yurkovich JT, Bordbar A, Sigurjónsson OE, Palsson BO.  2018.  Systems biology as an emerging paradigm in transfusion medicine.. BMC Syst Biol. 12(1):31.
Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC.  2018.  Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.. Biophys J. 114(11):2691-2702.
Kavvas ES, Seif Y, Yurkovich JT, Norsigian C, Poudel S, Greenwald WW, Ghatak S, Palsson BO, Monk JM.  2018.  Updated and standardized genome-scale reconstruction of Mycobacterium tuberculosis H37Rv, iEK1011, simulates flux states indicative of physiological conditions.. BMC Syst Biol. 12(1):25.
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.
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.
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.
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.
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.
Nogales J, Gudmundsson S, Duque E., Ramos JLewis, Palsson BO.  2017.  Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness. bioRxiv.
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.
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.
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.
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.
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)
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.
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.
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.
Nilsson A, Nielsen J, Palsson BO.  2017.  Metabolic Models of Protein Allocation Call for the Kinetome.. Cell Syst. 5(6):538-541.
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.
LaCroix RA, Palsson BO, Feist AM.  2017.  A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol.
Yurkovich JT, Yurkovich BJ, Draeger A, Palsson BO, King ZA.  2017.  A Padawan Programmer’s Guide to Developing Software Libraries. Cell Systems.
Yurkovich JT, Zielinski DC, Yang L, Paglia G, Rolfsson O, Sigurjónsson OE, Broddrick JT, Bordbar A, Wichuk K, Brynjólfsson S et al..  2017.  Quantitative time-course metabolomics in human red blood cells reveal the temperature dependence of human metabolic networks.. J Biol Chem.
Seo SWoo, Gao Y, Kim D, Szubin R, Yang J, Cho B-K, Palsson BO.  2017.  Revealing genome-scale transcriptional regulatory landscape of OmpR highlights its expanded regulatory roles under osmotic stress in Escherichia coli K-12 MG1655.. Sci Rep. 7(1):2181.
Zielinski DC, Jamshidi N, Corbett AJ, Bordbar A, Thomas A, Palsson BO.  2017.  Systems biology analysis of drivers underlying hallmarks of cancer cell metabolism.. Sci Rep. 7:41241.
Chen K, Gao Y, Mih N, Brien EJ ’, Yang L, Palsson BO.  2017.  Thermosensitivity of growth is determined by chaperone-mediated proteome reallocation. Proceedings of the National Academy of Sciences. 377121391183:201705524.
Du B, Zielinski DC, Palsson BO.  2017.  Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism. bioRxiv.
Notebaart RA, Kintses álint, Feist AM, Papp ázs.  2017.  Underground metabolism: network-level perspective and biotechnological potential. Current Opinion in Biotechnology. 49:108-114.
Yurkovich JT, Yang L, Palsson BO.  2017.  Utilizing biomarkers to forecast quantitative metabolite concentration profiles in human red blood cells. 2017 IEEE Conference on Control Technology and Applications (CCTA).
van Wijk XM, Döhrmann S, Hallström BM, Li S, Voldborg BG, Meng BX, McKee KK, van Kuppevelt TH, Yurchenco PD, Palsson BO et al..  2017.  Whole-Genome Sequencing of Invasion-Resistant Cells Identifies Laminin α2 as a Host Factor for Bacterial Invasion.. MBio. 8(1)
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Mih N, Brunk E, Bordbar A, Palsson BO.  2016.  A Multi-scale Computational Platform to Mechanistically Assess the Effect of Genetic Variation on Drug Responses in Human Erythrocyte Metabolism.. PLoS Comput Biol. 12(7):e1005039.
Gallina AA, Layer M, King ZA, Levering J, Palsson BO, Zengler K, Peers G.  2016.  A Phaeodactylum tricornutum literature database for interactive annotation of content. Algal Research. 18:241-243.
O'Brien EJ, Utrilla J, Palsson BO.  2016.  Quantification and Classification of E. coli Proteome Utilization and Unused Protein Costs across Environments.. PLoS Comput Biol. 12(6):e1004998.
Golabgir A, Gutierrez JM, Hefzi H, Li S, Palsson BO, Herwig C, Lewis NE.  2016.  Quantitative feature extraction from the Chinese hamster ovary bioprocess bibliome using a novel meta-analysis workflow.. Biotechnol Adv.
Ma D, Yang L, Fleming RMT, Thiele I, Palsson BO, Saunders MA.  2016.  Reliable and efficient solution of genome-scale models of Metabolism and macromolecular Expression.. Sci Rep. 7:40863.
Wang M, Carver JJ, Phelan VV, Sanchez LM, Garg N, Peng Y, Nguyen D D, Watrous J, Kapono CA, Luzzatto-Knaan T et al..  2016.  Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking.. Nat Biotechnol. 34(8):828-837.
Yang L, Ma D, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO.  2016.  solveME: fast and reliable solution of nonlinear ME models.. BMC Bioinformatics. 17(1):391.
Yurkovich J.T., Palsson B.O..  2016.  Solving puzzles with missing pieces: The power of systems biology. Proceedings of the IEEE. 104(1)
Kim D, Seo SWoo, Nam H, Guzman GI, Gao Y, Palsson BO.  2016.  Systems assessment of transcriptional regulation on central carbon metabolism by Cra and CRP. bioRxiv.
Brunk E, Mih N, Monk J, Zhang Z, O'Brien EJ, Bliven SE, Chen K, Chang RL, Bourne PE, Palsson BO.  2016.  Systems biology of the structural proteome.. BMC Syst Biol. 10(1):26.
Broddrick JT, Rubin BE, Welkie DG, Du N, Mih N, Diamond S, Lee JJ, Golden SS, Palsson BO.  2016.  Unique attributes of cyanobacterial metabolism revealed by improved genome-scale metabolic modeling and essential gene analysis.. Proc Natl Acad Sci U S A. 113(51):E8344-E8353.
Feist AM, Palsson BO.  2016.  What do cells actually want? Genome Biol. 17(1):110.
Fouts DE, Matthias MA, Adhikarla H, Adler B, Amorim-Santos L, Berg DE, Bulach D, Buschiazzo A, Chang Y-F, Galloway RL et al..  2016.  What Makes a Bacterial Species Pathogenic?:Comparative Genomic Analysis of the Genus Leptospira. PLoS Negl Trop Dis. 10(2):e0004403.
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.
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.
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.
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.
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.
Levering J, Broddrick J, Zengler K.  2015.  Engineering of oleaginous organisms for lipid production.. Curr Opin Biotechnol. 36:32-39.
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.
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.
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.
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.
Rodriguez N, Thomas A, Watanabe L, Vazirabad IY, Kofia V, Gómez HF, Mittag F, Matthes J, Rudolph J, Wrzodek F et al..  2015.  JSBML 1.0: providing a smorgasbord of options to encode systems biology models.. Bioinformatics.
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.
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.
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.
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.
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.
Embree M, Liu JK, Al-Bassam MM, Zengler K.  2015.  Networks of energetic and metabolic interactions define dynamics in microbial communities.. Proc Natl Acad Sci U S A.
King ZA, Lloyd CJ, Feist AM, Palsson BO.  2015.  Next-generation genome-scale models for metabolic engineering.. Curr Opin Biotechnol. 35C:23-29.
Gutierrez JM, Lewis NE.  2015.  Optimizing eukaryotic cell hosts for protein production through systems biotechnology and genome-scale modeling.. Biotechnol J. 10(7):939-49.
Bordbar A., McCloskey D., Zielinski D.C., Sonnenschein N., Jamshidi N., Palsson B.O..  2015.  Personalized Whole-Cell Kinetic Models of Metabolism for Discovery in Genomics and Pharmacodynamics. Cell Systems. 1:283-292.
McCloskey DM, Gangoiti JA, Palsson BO, Feist AM.  2015.  A pH and solvent optimized reverse-phase ion-paring-LC–MS/MS method that leverages multiple scan-types for targeted absolute quantification of intracellular metabolites. Metabolomics. 10.1007/s11306-015-0790-y
Zielinski DC, Filipp FV, Bordbar A, Jensen K, Smith JW, Herrgard MJ, Mo ML, Palsson BO.  2015.  Pharmacogenomic and clinical data link non-pharmacokinetic metabolic dysregulation to drug side effect pathogenesis.. Nat Commun. 6:7101.
Aurich MK, Paglia G, Rolfsson O, Hrafnsdóttir S, Magnúsdóttir M, Stefaniak MM, Palsson BØ, Fleming RMT, Thiele I.  2015.  Prediction of intracellular metabolic states from extracellular metabolomic data.. Metabolomics. 11(3):603-619.
Dräger A, Zielinski DC, Keller R, Rall M, Eichner J, Palsson BO, Zell A.  2015.  SBMLsqueezer 2: context-sensitive creation of kinetic equations in biochemical networks.. BMC Syst Biol. 9(1):68.
Latif H, Szubin R, Tan J, Brunk E, Lechner A, Zengler K, Palsson BO.  2015.  A streamlined ribosome profiling protocol for the characterization of microorganisms.. Biotechniques. 58(6):329-32.
Yang L, Tan J, O'Brien EJ, Monk JM, Kim D, Li HJ, Charusanti P, Ebrahim A, Lloyd CJ, Yurkovich JT et al..  2015.  Systems biology definition of the core proteome of metabolism and expression is consistent with high-throughput data.. Proc Natl Acad Sci U S A.
Aziz R.K., Monk J.M., Lewis R.M., Loh S.I., Mishra A., Nagle A.A., Satyanarayana C., Dhakshinamoorthy S., Luche M., Kitchen D.B. et al..  2015.  Systems biology-guided identification of synthetic lethal gene pairs and its potential use to discover antibiotic combinations. Scientific Reports. doi:10.1038/srep16025
Tan J, Zuniga C, Zengler K.  2015.  Unraveling interactions in microbial communities - from co-cultures to microbiomes.. J Microbiol. 53(5):295-305.
O'Brien EJ, Monk JM, Palsson BO.  2015.  Using Genome-scale Models to Predict Biological Capabilities.. Cell. 161(5):971-987.
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.
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.
Geertz-Hansen HMarcus, Blom N, Feist AM, Brunak S, Petersen TNordahl.  2014.  Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds.. Proteins.
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.
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.
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.
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.
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.
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.
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.
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 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)
Hefzi H., Lewis N.E..  2014.  From random mutagenesis to systems biology in metabolic engineering of mammalian cells. Pharmaceutical Bioprocessing. 2
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)
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.
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.
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.
Dräger A, Palsson BØ.  2014.  Improving collaboration by standardization efforts in systems biology.. Front Bioeng Biotechnol. 2:61.
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.
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.
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.
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.
Kumar A, Harrelson T, Lewis NE, Gallagher EJ, LeRoith D, Shiloach J, Betenbaugh MJ.  2014.  Multi-Tissue Computational Modeling Analyzes Pathophysiology of Type 2 Diabetes in MKR Mice.. PLoS One. 9(7):e102319.
Thomas A, Rahmanian S, Bordbar A, Palsson BØ, Jamshidi N.  2014.  Network reconstruction of platelet metabolism identifies metabolic signature for aspirin resistance.. Sci Rep. 4:3925.
King ZA, Feist AM.  2014.  Optimal cofactor swapping can increase the theoretical yield for chemical production in Escherichia coli and Saccharomyces cerevisiae.. Metab Eng. 24C:117-128.
Monk J, Nogales J, Palsson BO.  2014.  Optimizing genome-scale network reconstructions.. Nat Biotechnol. 32(5):447-452.
Monk J, Palsson BO.  2014.  Predicting microbial growth.. Science. 344(6191):1448-9.
Liu JK, Brien EJO, Lerman JA, Zengler K, Palsson BO, Feist AM.  2014.  Reconstruction and modeling protein translocation and compartmentalization in Escherichia coli at the genome-scale.. BMC Syst Biol. 8(1):110.
Chen P, Torralba M, Tan J, Embree M, Zengler K, Stärkel P, van Pijkeren J-P, DePew J, Loomba R, Ho SB et al..  2014.  Supplementation of Saturated Long-chain Fatty Acids Maintains Intestinal Eubiosis and Reduces Ethanol-induced Liver Injury in Mice.. Gastroenterology.
Nam H, Campodonico M, Bordbar A, Hyduke DR, Kim S, Zielinski DC, Palsson BO.  2014.  A Systems Approach to Predict Oncometabolites via Context-Specific Genome-Scale Metabolic Networks.. PLoS Comput Biol. 10(9):e1003837.
Spahn PN, Lewis NE.  2014.  Systems glycobiology for glycoengineering.. Curr Opin Biotechnol. 30C:218-224.
Lewis CA, Parker SJ, Fiske BP, McCloskey D, Gui DY, Green CR, Vokes NI, Feist AM, Heiden MGVander, Metallo CM.  2014.  Tracing Compartmentalized NADPH Metabolism in the Cytosol and Mitochondria of Mammalian Cells.. Mol Cell.
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.
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.
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.
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.
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.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.  2013.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python.. BMC Syst Biol. 7(1):74.
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, 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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Wu W, Jamshidi N, Eraly SA, Liu HC, Bush KT, Palsson BO, Nigam SK.  2013.  Multispecific Drug Transporter Oat3 (Slc22a8) Regulates Multiple Metabolic Pathways.. Drug Metab Dispos.
King ZA, Feist AM.  2013.  Optimizing Cofactor Specificity of Oxidoreductase Enzymes for the Generation of Microbial Production Strains—OptSwap. Industrial Biotechnology. 9(4):236-246.
Büchel F, Saliger S, Dräger A, Hoffmann S, Wrzodek C, Zell A, Kahle PJ.  2013.  Parkinson's disease: dopaminergic nerve cell model is consistent with experimental finding of increased extracellular transport of α-synuclein.. BMC Neurosci. 14:136.
Büchel F, Rodriguez N, Swainston N, Wrzodek C, Czauderna T, Keller R, Mittag F, Schubert M, Glont M, Golebiewski M et al..  2013.  Path2Models: large-scale generation of computational models from biochemical pathway maps.. BMC Syst Biol. 7:116.
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. 342(1):62-9.
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.
Chaouiya C, Bérenguier D, Keating SM, Naldi A, van Iersel MP, Rodriguez N, Dräger A, Büchel F, Cokelaer T, Kowal B et al..  2013.  SBML qualitative models: a model representation format and infrastructure to foster interactions between qualitative modelling formalisms and tools.. BMC Syst Biol. 7:135.
Embree M, Nagarajan H, Movahedi N, Chitsaz H, Zengler K.  2013.  Single-cell genome and metatranscriptome sequencing reveal metabolic interactions of an alkane-degrading methanogenic community.. ISME J.
Chang RL, Andrews K, Kim D, Li Z, Godzik A, Palsson BO.  2013.  Structural systems biology evaluation of metabolic thermotolerance in Escherichia coli.. Science. 340(6137):1220-3.
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.
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.
Hwang K-S, Kim H U, Charusanti P, Palsson BØ, Lee S Y.  2013.  Systems biology and biotechnology of Streptomyces species for the production of secondary metabolites.. Biotechnol Adv. 32(2):255-268.
Keller R, Dörr A, Tabira A, Funahashi A, Ziller MJ, Adams R, Rodriguez N, Le Novère N, Hiroi N, Planatscher H et al..  2013.  The systems biology simulation core algorithm.. BMC Syst Biol. 7:55.
Eichner J, Topf F, Dräger A, Wrzodek C, Wanke D, Zell A.  2013.  TFpredict and SABINE: sequence-based prediction of structural and functional characteristics of transcription factors.. PLoS One. 8(12):e82238.
Rodionov DA, Rodionova IA, Li X, Ravcheev DA, Tarasova Y, Portnoy VA, Zengler K, Osterman AL.  2013.  Transcriptional regulation of the carbohydrate utilization network in Thermotoga maritima.. Front Microbiol. 4:244.
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.
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.
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.
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.
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.
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.
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.
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.
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, 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.
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.
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.
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.
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.
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.
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.
Zengler K, Palsson BO.  2012.  A road map for the development of community systems (CoSy) biology.. Nat Rev Microbiol. 10(5):366-72.
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.
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.
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.
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.
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.
Palsson BØ.  2011.  Adaptive Laboratory Evolution. Microbe.
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.
Thiele I, Hyduke DR, Steeb B, Fankam G, Allen DK, Bazzani S, Charusanti P, Chen F-C, Fleming RMT, Hsiung CA et al..  2011.  A community effort towards a knowledge-base and mathematical model of the human pathogen Salmonella Typhimurium LT2.. BMC Syst Biol. 5:8.
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.  2011.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535.
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.
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.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
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.
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.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S et al..  2011.  The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41.
Rolfsson O, Palsson BØ, Thiele I.  2011.  The human metabolic reconstruction Recon 1 directs hypotheses of novel human metabolic functions.. BMC Syst Biol. 5:155.
Bordbar A, Jamshidi N, Palsson BO.  2011.  iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.. BMC Syst Biol. 5:110.
Mahadevan R, Palsson BØ, Lovley DR.  2011.  In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50.
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.
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.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
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.
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.
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.
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.
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.
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.
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.
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.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
Palsson BØ, Zengler K.  2010.  The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
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.
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.
Sigurdsson MI, Jamshidi N, Steingrimsson E, Thiele I, Palsson BØ.  2010.  A detailed genome-wide reconstruction of mouse metabolism based on human Recon 1.. BMC systems biology. 4:140.
Chang RL, Xie L, Xie L, Bourne PE, Palsson BØ.  2010.  Drug off-target effects predicted using structural analysis in the context of a metabolic network model.. PLoS computational biology. 6(9):e1000938.
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.
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.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N.  2010.  Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
Lewis NE, Schramm G, Bordbar A, Schellenberger J, Andersen MP, Cheng JK, Patel N, Yee A, Lewis RA, Eils R et al..  2010.  Large-scale in silico modeling of metabolic interactions between cell types in the human brain.. Nature biotechnology. 28(12):1279-85.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.  2010.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
Lewis NE, Hixson KK, Conrad TM, Lerman JA, Charusanti P, Polpitiya AD, Adkins JN, Schramm G, Purvine SO, Lopez-Ferrer D et al..  2010.  Omic data from evolved E. coli are consistent with computed optimal growth from genome-scale models.. Molecular systems biology. 6:390.
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.
Thiele I, Palsson BØ.  2010.  A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.
Thiele I, Palsson BØ.  2010.  Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
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.
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.
Orth JD, Palsson BØ.  2010.  Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12.
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.
Oberhardt MA, Palsson BØ, Papin JA.  2009.  Applications of genome-scale metabolic reconstructions.. Molecular systems biology. 5:320.
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.
Zengler K.  2009.  Central role of the cell in microbial ecology.. Microbiology and molecular biology reviews : MMBR. 73(4):712-29.
Mo ML, Palsson BØ, Herrgard MJ.  2009.  Connecting extracellular metabolomic measurements to intracellular flux states in yeast.. BMC systems biology. 3:37.
Raghunathan A, Reed JL, Shin S, Palsson BØ, Daefler S.  2009.  Constraint-based analysis of metabolic capacity of Salmonella typhimurium during host-pathogen interaction.. BMC systems biology. 3:38.
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.
Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
Gianchandani EP, Joyce AR, Palsson BØ, Papin JA.  2009.  Functional states of the genome-scale Escherichia coli transcriptional regulatory system.. PLoS computational biology. 5(6):e1000403.
Lewis NE, Cho B-K, Knight EM, Palsson BØ.  2009.  Gene expression profiling and the use of genome-scale in silico models of Escherichia coli for analysis: providing context for content.. Journal of bacteriology. 191(11):3437-44.
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.
Thiele I, Jamshidi N, Fleming RMT, Palsson BØ.  2009.  Genome-scale reconstruction of Escherichia coli's transcriptional and translational machinery: a knowledge base, its mathematical formulation, and its functional characterization.. PLoS computational biology. 5(3):e1000312.
Li F, Thiele I, Jamshidi N, Palsson BØ.  2009.  Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292.
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.
Palsson BØ.  2009.  Metabolic systems biology.. FEBS letters. 583(24):3900-4.
Cho B-K, Palsson BØ.  2009.  Probing the basis for genotype-phenotype relationships.. Nature methods. 6(8):565-6.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BØ.  2009.  Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
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.
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.
Mo ML, Palsson BØ.  2009.  Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
Jamshidi N, Palsson BØ.  2009.  Using in silico models to simulate dual perturbation experiments: procedure development and interpretation of outcomes.. BMC systems biology. 3:44.
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.
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.
Herrgard MJ, Swainston N, Dobson P, Dunn WB, Arga YK, Arvas M, Blüthgen N, Borger S, Costenoble R, Heinemann M et al..  2008.  A consensus yeast metabolic network reconstruction obtained from a community approach to systems biology.. Nature biotechnology. 26(10):1155-60.
Becker SA, Palsson BØ.  2008.  Context-specific metabolic networks are consistent with experiments.. PLoS computational biology. 4(5):e1000082.
Jamshidi N, Palsson BØ.  2008.  Formulating genome-scale kinetic models in the post-genome era.. Molecular systems biology. 4:171.
Nogales J, Palsson BØ, Thiele I.  2008.  A genome-scale metabolic reconstruction of Pseudomonas putida KT2440: iJN746 as a cell factory.. BMC systems biology. 2:79.
Lee J, Yun H, Feist AM, Palsson BØ, Lee S Y.  2008.  Genome-scale reconstruction and in silico analysis of the Clostridium acetobutylicum ATCC 824 metabolic network.. Applied microbiology and biotechnology. 80(5):849-62.
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.
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.
Feist AM, Palsson BØ.  2008.  The growing scope of applications of genome-scale metabolic reconstructions using Escherichia coli.. Nature biotechnology. 26(6):659-67.
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.
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.
Joyce AR, Palsson BØ.  2008.  Predicting gene essentiality using genome-scale in silico models.. Methods in molecular biology (Clifton, N.J.). 416:433-57.
Becker SA, Palsson BØ.  2008.  Three factors underlying incorrect in silico predictions of essential metabolic genes.. BMC systems biology. 2:14.
Jamshidi N, Palsson BØ.  2008.  Top-down analysis of temporal hierarchy in biochemical reaction networks.. PLoS computational biology. 4(9):e1000177.
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.
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.
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.
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.
Feist AM, Henry CS, Reed JL, Krummenacker M, Joyce AR, Karp PD, Broadbelt LJ, Hatzimanikatis V, Palsson BØ.  2007.  A genome-scale metabolic reconstruction for Escherichia coli K-12 MG1655 that accounts for 1260 ORFs and thermodynamic information.. Molecular systems biology. 3:121.
Oh Y-K, Palsson BØ, Park SM, Schilling CH, Mahadevan R.  2007.  Genome-scale reconstruction of metabolic network in Bacillus subtilis based on high-throughput phenotyping and gene essentiality data.. The Journal of biological chemistry. 282(39):28791-9.
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.
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,