Publications

Year of Publication: 2018

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.
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.
Du B, Zielinski DC, Monk JM, Palsson BO.  2018.  Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice. Proceedings of the National Academy of Sciences.
Rowe E, Palsson BO, King ZA.  2018.  Escher-FBA: a web application for interactive flux balance analysis. BMC Systems Biology.
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.
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.
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.
Gao Y, Yurkovich JT, Seo SWoo, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L et al..  2018.  Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.. Nucleic Acids Res.
Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO.  2018.  Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.. PLoS Comput Biol. 14(8):e1006356.
Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Vázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO et al..  2018.  A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0. BMC Biology. 16
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.
Johannsson F, Guðmundsson S, Paglia G, Guðmundsson S, Palsson B, Sigurjónsson OE, Rolfsson O.  2018.  Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution.. Biochem J. 475(13):2225-2240.
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.
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.
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.
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.
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.
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.
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
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.
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
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.
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.
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.
Yurkovich JT, Bordbar A, Sigurjónsson OE, Palsson BO.  2018.  Systems biology as an emerging paradigm in transfusion medicine.. BMC Syst Biol. 12(1):31.
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.
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.
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.
Yurkovich JT, Palsson BO.  2018.  Quantitative -omic data empowers bottom-up systems biology. Current Opinion in Biotechnology. 51:130-136.
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.
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.
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.

Year of Publication: 2017

Nilsson A, Nielsen J, Palsson BO.  2017.  Metabolic Models of Protein Allocation Call for the Kinetome.. Cell Syst. 5(6):538-541.
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.
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.
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.
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.
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.
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.
Yurkovich JT, Yurkovich BJ, Draeger A, Palsson BO, King ZA.  2017.  A Padawan Programmer’s Guide to Developing Software Libraries. Cell Systems.
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.
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.
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.
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).
Notebaart RA, Kintses álint, Feist AM, Papp ázs.  2017.  Underground metabolism: network-level perspective and biotechnological potential. Current Opinion in Biotechnology. 49:108-114.
Nogales J, Gudmundsson S, Duque E., Ramos JLewis, Palsson BO.  2017.  Expanding The Computable Reactome In Pseudomonas putida Reveals Metabolic Cycles Providing Robustness. bioRxiv.
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.
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.
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.
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.
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.
LaCroix RA, Palsson BO, Feist AM.  2017.  A Model for Designing Adaptive Laboratory Evolution Experiments.. Appl Environ Microbiol.
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.
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)
Du B, Zielinski DC, Palsson BO.  2017.  Topological and Kinetic Determinants of the Modal Matrices of Dynamic Models of Metabolism. bioRxiv.
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)
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.

Year of Publication: 2016

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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
Feist AM, Palsson BO.  2016.  What do cells actually want? Genome Biol. 17(1):110.
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.
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.
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, 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.
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.
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.
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.
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.
Yurkovich J.T., Palsson B.O..  2016.  Solving puzzles with missing pieces: The power of systems biology. Proceedings of the IEEE. 104(1)
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.
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.

Year of Publication: 2015

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.
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.
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
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
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.
King ZA, Lloyd CJ, Feist AM, Palsson BO.  2015.  Next-generation genome-scale models for metabolic engineering.. Curr Opin Biotechnol. 35C:23-29.
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.
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.
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.
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.
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.
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.
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.
Rolfsson O, Palsson BO.  2015.  Decoding the jargon of bottom-up metabolic systems biology.. Bioessays.
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.
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.
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
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.

Year of Publication: 2014

Monk J, Nogales J, Palsson BO.  2014.  Optimizing genome-scale network reconstructions.. Nat Biotechnol. 32(5):447-452.
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.
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, Palsson BO.  2014.  Predicting microbial growth.. Science. 344(6191):1448-9.
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.
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.
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.
Geertz-Hansen HMarcus, Blom N, Feist AM, Brunak S, Petersen TNordahl.  2014.  Cofactory: Sequence-based prediction of cofactor specificity of Rossmann folds.. Proteins.
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.
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.
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.
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.
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.
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.
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.
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.
Dräger A, Palsson BØ.  2014.  Improving collaboration by standardization efforts in systems biology.. Front Bioeng Biotechnol. 2:61.
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.
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.
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.
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.
Spahn PN, Lewis NE.  2014.  Systems glycobiology for glycoengineering.. Curr Opin Biotechnol. 30C:218-224.
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.
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.
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)
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.
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.
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.
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.
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.
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

Year of Publication: 2013

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.
Ebrahim A, Lerman JA, Palsson BO, Hyduke DR.  2013.  COBRApy: COnstraints-Based Reconstruction and Analysis for Python.. BMC Syst Biol. 7(1):74.
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.
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.
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.
Latif H, Lerman JA, Portnoy VA, Tarasova Y, Nagarajan H, Schrimpe-Rutledge AC, Smith RD, Adkins JN, Lee D-H, Qiu Y et al..  2013.  The genome organization of Thermotoga maritima reflects its lifestyle.. PLoS Genet. 9(4):e1003485.
McCloskey D, Palsson BØ, Feist AM.  2013.  Basic and applied uses of genome-scale metabolic network reconstructions of Escherichia coli.. Mol Syst Biol. 9:661.
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.
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.
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.
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.
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.
Gonnerman MC, Benedict MN, Feist AM, Metcalf WW, Price ND.  2013.  Genomically and biochemically accurate metabolic reconstruction of Methanosarcina barkeri Fusaro, iMG746.. Biotechnol J.
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.
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.
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.
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.
Hyduke DR, Lewis NE, Palsson BØ.  2013.  Analysis of omics data with genome-scale models of metabolism.. Mol Biosyst. 9(2):167-74.
Fu W, Guðmundsson O, Paglia G, Herjólfsson G, Andrésson OS, Palsson BO, Brynjólfsson S.  2013.  Enhancement of carotenoid biosynthesis in the green microalga Dunaliella salina with light-emitting diodes and adaptive laboratory evolution.. Appl Microbiol Biotechnol. 97(6):2395-403.
Rolfsson O, Paglia G, Magnusdóttir M, Palsson BØ, Thiele I.  2013.  Inferring the metabolism of human orphan metabolites from their metabolic network context affirms human gluconokinase activity.. Biochem J. 449(2):427-35.
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.
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.
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.
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.
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.
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.
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.
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, Xie L, Bourne PE, Palsson BO.  2013.  Antibacterial mechanisms identified through structural systems pharmacology.. BMC Syst Biol. 7(1):102.
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.
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.
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.
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.
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.
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.

Year of Publication: 2012

Paglia G, Palsson BØ, Sigurjonsson OE.  2012.  Systems biology of stored blood cells: can it help to extend the expiration date? J Proteomics. 76 Spec No.:163-7.
Baycin-Hizal D, Tabb DL, Chaerkady R, Chen L, Lewis NE, Nagarajan H, Sarkaria V, Kumar A, Wolozny D, Colao J et al..  2012.  Proteomic analysis of Chinese hamster ovary cells.. J Proteome Res. 11(11):5265-76.
Nam H, Lewis NE, Lerman JA, Lee D-H, Chang RL, Kim D, Palsson BO.  2012.  Network context and selection in the evolution to enzyme specificity.. Science. 337(6098):1101-4.
Kim D, Hong J S-J, Qiu Y, Nagarajan H, Seo J-H, Cho B-K, Tsai S-F, Palsson BØ.  2012.  Comparative Analysis of Regulatory Elements between Escherichia coli and Klebsiella pneumoniae by Genome-Wide Transcription Start Site Profiling.. PLoS Genet. 8(8):e1002867.
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.
Ho Sui SJ, Lo R, Fernandes AR, Caulfield MDG, Lerman JA, Xie L, Bourne PE, Baillie DL, Brinkman FSL.  2012.  Raloxifene attenuates Pseudomonas aeruginosa pyocyanin production and virulence.. Int J Antimicrob Agents.
Fu W, Gudmundsson O, Feist AM, Herjolfsson G, Brynjolfsson S, Palsson BO.  2012.  Maximizing biomass productivity and cell density of Chlorella vulgaris by using light-emitting diode-based photobioreactor.. J Biotechnol.
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.
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.
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.
Charusanti P, Fong NL, Nagarajan H, Pereira AR, Li HJ, Abate EA, Su Y, Gerwick WH, Palsson BO.  2012.  Exploiting adaptive laboratory evolution of Streptomyces clavuligerus for antibiotic discovery and overproduction.. PLoS One. 7(3):e33727.
Zengler K, Palsson BO.  2012.  A road map for the development of community systems (CoSy) biology.. Nat Rev Microbiol. 10(5):366-72.
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.
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.
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.
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.
Alain K, Harder J, Widdel F, Zengler K.  2012.  Anaerobic utilization of toluene by marine alpha- and gammaproteobacteria reducing nitrate.. Microbiology. 158(Pt 12):2946-57.
Thiele I, Fleming RMT, Que R, Bordbar A, Diep D, Palsson BO.  2012.  Multiscale Modeling of Metabolism and Macromolecular Synthesis in E. coli and Its Application to the Evolution of Codon Usage.. PLoS One. 7(9):e45635.
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.
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.
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.
McDermott JE, Braun P, Bonneau R, Hyduke DR.  2012.  MODELING HOST-PATHOGEN INTERACTIONS: COMPUTATIONAL BIOLOGY AND BIOINFORMATICS FOR INFECTIOUS DISEASE RESEARCH.. Pac Symp Biocomput. 17:283-286.
Paglia G, Hrafnsdóttir S, Magnúsdóttir M, Fleming RMT, Thorlacius S, Palsson BØ, Thiele I.  2012.  Monitoring metabolites consumption and secretion in cultured cells using ultra-performance liquid chromatography quadrupole-time of flight mass spectrometry (UPLC-Q-ToF-MS).. Anal Bioanal Chem. 402(3):1183-98.
Fleming RMT, Maes CM, Saunders MA, Ye Y, Palsson BØ.  2012.  A variational principle for computing nonequilibrium fluxes and potentials in genome-scale biochemical networks.. J Theor Biol. 292:71-7.

Year of Publication: 2011

Schellenberger J, Que R, Fleming RMT, Thiele I, Orth JD, Feist AM, Zielinski DC, Bordbar A, Lewis NE, Rahmanian S et al..  2011.  Quantitative prediction of cellular metabolism with constraint-based models: the COBRA Toolbox v2.0.. Nat Protoc. 6(9):1290-307.
Chang RL, Ghamsari L, Manichaikul A, Hom EFY, Balaji S, Fu W, Shen Y, Hao T, Palsson BØ, Salehi-Ashtiani K et al..  2011.  Metabolic network reconstruction of Chlamydomonas offers insight into light-driven algal metabolism.. Mol Syst Biol. 7:518.
Xu X, Nagarajan H, Lewis NE, Pan S, Cai Z, Liu X, Chen W, Xie M, Wang W, Hammond S et al..  2011.  The genomic sequence of the Chinese hamster ovary (CHO)-K1 cell line.. Nat Biotechnol. 29(8):735-41.
Conrad TM, Lewis NE, Palsson BØ.  2011.  Microbial laboratory evolution in the era of genome-scale science.. Mol Syst Biol. 7:509.
Ahn S-Y, Jamshidi N, Mo ML, Wu W, Eraly SA, Dnyanmote A, Bush KT, Gallegos TF, Sweet DH, Palsson BØ et al..  2011.  Linkage of organic anion transporter-1 to metabolic pathways through integrated "omics"-driven network and functional analysis.. J Biol Chem. 286(36):31522-31.
Bordbar A, Jamshidi N, Palsson BO.  2011.  iAB-RBC-283: A proteomically derived knowledge-base of erythrocyte metabolism that can be used to simulate its physiological and patho-physiological states.. BMC Syst Biol. 5:110.
McDermott JE, Yoon H, Nakayasu ES, Metz TO, Hyduke DR, Kidwai AS, Palsson BO, Adkins JN, Heffron F.  2011.  Technologies and approaches to elucidate and model the virulence program of salmonella.. Front Microbiol. 2:121.
Cho B-K, Federowicz SA, Embree M, Park Y-S, Kim D, Palsson BØ.  2011.  The PurR regulon in Escherichia coli K-12 MG1655.. Nucleic Acids Res. 39(15):6456-64.
Applebee KM, Joyce AR, Conrad TM, Pettigrew DW, Palsson BØ.  2011.  Functional and metabolic effects of adaptive glycerol kinase (GLPK) mutants in Escherichia coli.. J Biol Chem. 286(26):23150-9.
Portnoy VA, Bezdan D, Zengler K.  2011.  Adaptive laboratory evolution--harnessing the power of biology for metabolic engineering.. Curr Opin Biotechnol. 22(4):590-4.
Nam H, Conrad TM, Lewis NE.  2011.  The role of cellular objectives and selective pressures in metabolic pathway evolution.. Curr Opin Biotechnol. 22(4):595-600.
Liao Y-C, Huang T-W, Chen F-C, Charusanti P, Hong JSJ, Chang H-Y, Tsai S-F, Palsson BO, Hsiung CA.  2011.  An experimentally validated genome-scale metabolic reconstruction of Klebsiella pneumoniae MGH 78578, iYL1228.. J Bacteriol. 193(7):1710-7.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Palsson BØ.  2011.  Adaptive Laboratory Evolution. Microbe.
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.
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.
Lee D-H, Feist AM, Barrett CL, Palsson BØ.  2011.  Cumulative number of cell divisions as a meaningful timescale for adaptive laboratory evolution of Escherichia coli.. PLoS One. 6(10):e26172.
Charusanti P, Chauhan S, McAteer K, Lerman JA, Hyduke DR, Motin VL, Ansong C, Adkins JN, Palsson BO.  2011.  An experimentally-supported genome-scale metabolic network reconstruction for Yersinia pestis CO92.. BMC Syst Biol. 5:163.
Orth JD, Conrad TM, Na J, Lerman JA, Nam H, Feist AM, Palsson BØ.  2011.  A comprehensive genome-scale reconstruction of Escherichia coli metabolism--2011.. Mol Syst Biol. 7:535.
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.
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.
Mahadevan R, Palsson BØ, Lovley DR.  2011.  In situ to in silico and back: elucidating the physiology and ecology of Geobacter spp. using genome-scale modelling.. Nat Rev Microbiol. 9(1):39-50.
Barrett CL, Cho B-K, Palsson BO.  2011.  Sensitive and accurate identification of protein-DNA binding events in ChIP-chip assays using higher order derivative analysis.. Nucleic Acids Res. 39(5):1656-65.
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.

Year of Publication: 2010

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.
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.
Bordbar A, Lewis NE, Schellenberger J, Palsson BØ, Jamshidi N.  2010.  Insight into human alveolar macrophage and M. tuberculosis interactions via metabolic reconstructions.. Molecular systems biology. 6:422.
Orth JD, Palsson BØ.  2010.  Systematizing the generation of missing metabolic knowledge.. Biotechnology and bioengineering. 107(3):403-12.
Portnoy VA, Scott DA, Lewis NE, Tarasova Y, Osterman AL, Palsson BØ.  2010.  Deletion of genes encoding cytochrome oxidases and quinol monooxygenase blocks the aerobic-anaerobic shift in Escherichia coli K-12 MG1655.. Applied and environmental microbiology. 76(19):6529-40.
Conrad TM, Frazier M, Joyce AR, Cho B-K, Knight EM, Lewis NE, Landick R, Palsson BØ.  2010.  RNA polymerase mutants found through adaptive evolution reprogram Escherichia coli for optimal growth in minimal media.. Proceedings of the National Academy of Sciences of the United States of America. 107(47):20500-5.
Lerman JA, Palsson BØ.  2010.  Microbiology. Topping off a multiscale balancing act.. Science (New York, N.Y.). 330(6007):1058-9.
Charusanti P, Conrad TM, Knight EM, Venkataraman K, Fong NL, Xie B, Gao Y, Palsson BØ.  2010.  Genetic basis of growth adaptation of Escherichia coli after deletion of pgi, a major metabolic gene.. PLoS genetics. 6(11):e1001186.
Palsson BØ, Zengler K.  2010.  The challenges of integrating multi-omic data sets.. Nature chemical biology. 6(11):787-9.
Thiele I, Fleming RMT, Bordbar A, Schellenberger J, Palsson BØ.  2010.  Functional characterization of alternate optimal solutions of Escherichia coli's transcriptional and translational machinery.. Biophysical journal. 98(10):2072-81.
Feist AM, Zielinski DC, Orth JD, Schellenberger J, Herrgard MJ, Palsson BØ.  2010.  Model-driven evaluation of the production potential for growth-coupled products of Escherichia coli.. Metabolic engineering. 12(3):173-86.
Orth JD, Thiele I, Palsson BØ.  2010.  What is flux balance analysis? Nature biotechnology. 28(3):245-8.
Feist AM, Palsson BØ.  2010.  The biomass objective function.. Current opinion in microbiology. 13(3):344-9.
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.
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.
Jamshidi N, Palsson BØ.  2010.  Mass action stoichiometric simulation models: incorporating kinetics and regulation into stoichiometric models.. Biophysical journal. 98(2):175-85.
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.
Thiele I, Palsson BØ.  2010.  Reconstruction annotation jamborees: a community approach to systems biology.. Molecular systems biology. 6:361.
Hyduke DR, Palsson BØ.  2010.  Towards genome-scale signalling network reconstructions.. Nature reviews. Genetics. 11(4):297-307.
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.
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.
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.
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.
Thiele I, Palsson BØ.  2010.  A protocol for generating a high-quality genome-scale metabolic reconstruction.. Nature protocols. 5(1):93-121.

Year of Publication: 2009

Jamshidi N, Palsson BØ.  2009.  Flux-concentration duality in dynamic nonequilibrium biological networks.. Biophysical journal. 97(5):L11-3.
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.
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.
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.
Mo ML, Palsson BØ.  2009.  Understanding human metabolic physiology: a genome-to-systems approach.. Trends in biotechnology. 27(1):37-44.
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.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
Li F, Thiele I, Jamshidi N, Palsson BØ.  2009.  Identification of potential pathway mediation targets in Toll-like receptor signaling.. PLoS computational biology. 5(2):e1000292.
Feist AM, Herrgard MJ, Thiele I, Reed JL, Palsson BØ.  2009.  Reconstruction of biochemical networks in microorganisms.. Nature reviews. Microbiology. 7(2):129-43.
Palsson BØ.  2009.  Metabolic systems biology.. FEBS letters. 583(24):3900-4.