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Strucko T, Zirngibl K, Pereira F, Kafkia E, Mohamed ET, Rettel M, Stein F, Feist AM, Jouhten P, Patil KRaosaheb et al..  2018.  Laboratory evolution reveals regulatory and metabolic trade-offs of glycerol utilization in Saccharomyces cerevisiae.. Metab Eng. 47:73-82.
Spahn PN, Lewis NE.  2014.  Systems glycobiology for glycoengineering.. Curr Opin Biotechnol. 30C:218-224.
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.
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.
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.
Shlomi T, Herrgard MJ, Portnoy VA, Naim E, Palsson BØ, Sharan R, Ruppin E.  2007.  Systematic condition-dependent annotation of metabolic genes.. Genome research. 17(11):1626-33.
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.
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.
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.
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.
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.
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.
Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.  2019.  A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.. PLoS Comput Biol. 15(1):e1006644.
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.
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.
Schilling CH, Covert MW, Famili I, Church GM, Edwards JS, Palsson BØ.  2002.  Genome-scale metabolic model of Helicobacter pylori 26695.. Journal of bacteriology. 184(16):4582-93.
Schilling CH, Edwards JS, Palsson BØ.  1999.  Toward metabolic phenomics: analysis of genomic data using flux balances.. Biotechnology progress. 15(3):288-95.
Schilling CH, Schuster S, Palsson BØ, Heinrich R.  1999.  Metabolic pathway analysis: basic concepts and scientific applications in the post-genomic era.. Biotechnology progress. 15(3):296-303.
Schilling CH, Edwards JS, Letscher D, Palsson BØ.  2000.  Combining pathway analysis with flux balance analysis for the comprehensive study of metabolic systems.. Biotechnology and bioengineering. 71(4):286-306.
Schilling CH, Letscher D, Palsson BØ.  2000.  Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective.. Journal of theoretical biology. 203(3):229-48.
Schilling CH, Palsson BØ.  2000.  Assessment of the metabolic capabilities of Haemophilus influenzae Rd through a genome-scale pathway analysis.. Journal of theoretical biology. 203(3):249-83.
Schilling CH, Palsson BØ.  1998.  The underlying pathway structure of biochemical reaction networks.. Proceedings of the National Academy of Sciences of the United States of America. 95(8):4193-8.
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.
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.
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.
Schellenberger J, Palsson BØ.  2009.  Use of randomized sampling for analysis of metabolic networks.. The Journal of biological chemistry. 284(9):5457-61.
Schellenberger J, Lewis NE, Palsson BØ.  2011.  Elimination of thermodynamically infeasible loops in steady-state metabolic models.. Biophys J. 100(3):544-53.
Savinell JM, Palsson BØ.  1992.  Optimal selection of metabolic fluxes for in vivo measurement. I. Development of mathematical methods.. Journal of theoretical biology. 155(2):201-14.
Savinell JM, Palsson BØ.  1992.  Optimal selection of metabolic fluxes for in vivo measurement. II. Application to Escherichia coli and hybridoma cell metabolism.. Journal of theoretical biology. 155(2):215-42.
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.
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
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.
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.
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.



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