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Comparative Genome-Scale Metabolic Modeling of Metallo-Beta-Lactamase-Producing Multidrug-Resistant Klebsiella pneumoniae Clinical Isolates.

Norsigian CJ, Attia H, Szubin R, Yassin AS, Palsson BØ, Aziz RK, Monk JM.

Front Cell Infect Microbiol. 2019 May 24;9:161. doi: 10.3389/fcimb.2019.00161. eCollection 2019.


Laboratory evolution reveals a two-dimensional rate-yield tradeoff in microbial metabolism.

Cheng C, O'Brien EJ, McCloskey D, Utrilla J, Olson C, LaCroix RA, Sandberg TE, Feist AM, Palsson BO, King ZA.

PLoS Comput Biol. 2019 Jun 3;15(6):e1007066. doi: 10.1371/journal.pcbi.1007066. eCollection 2019 Jun.


Primary transcriptome and translatome analysis determines transcriptional and translational regulatory elements encoded in the Streptomyces clavuligerus genome.

Hwang S, Lee N, Jeong Y, Lee Y, Kim W, Cho S, Palsson BO, Cho BK.

Nucleic Acids Res. 2019 May 27. pii: gkz471. doi: 10.1093/nar/gkz471. [Epub ahead of print]


Synthetic Biology Tools for Novel Secondary Metabolite Discovery in Streptomyces.

Lee N, Hwang S, Lee Y, Cho S, Palsson B, Cho BK.

J Microbiol Biotechnol. 2019 May 28;29(5):667-686. doi: 10.4014/jmb.1904.04015. Review.


A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action.

Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ.

Cell. 2019 May 30;177(6):1649-1661.e9. doi: 10.1016/j.cell.2019.04.016. Epub 2019 May 9.


Characterization of CA-MRSA TCH1516 exposed to nafcillin in bacteriological and physiological media.

Poudel S, Tsunemoto H, Meehan M, Szubin R, Olson CA, Lamsa A, Seif Y, Dillon N, Vrbanac A, Sugie J, Dahesh S, Monk JM, Dorrestein PC, Pogliano J, Knight R, Nizet V, Palsson BO, Feist AM.

Sci Data. 2019 Apr 26;6(1):43. doi: 10.1038/s41597-019-0051-4.


BOFdat: Generating biomass objective functions for genome-scale metabolic models from experimental data.

Lachance JC, Lloyd CJ, Monk JM, Yang L, Sastry AV, Seif Y, Palsson BO, Rodrigue S, Feist AM, King ZA, Jacques PÉ.

PLoS Comput Biol. 2019 Apr 22;15(4):e1006971. doi: 10.1371/journal.pcbi.1006971. eCollection 2019 Apr.


Enzyme promiscuity shapes adaptation to novel growth substrates.

Guzmán GI, Sandberg TE, LaCroix RA, Nyerges Á, Papp H, de Raad M, King ZA, Hefner Y, Northen TR, Notebaart RA, Pál C, Palsson BO, Papp B, Feist AM.

Mol Syst Biol. 2019 Apr 8;15(4):e8462. doi: 10.15252/msb.20188462.


Minimal cells, maximal knowledge.

Lachance JC, Rodrigue S, Palsson BO.

Elife. 2019 Mar 12;8. pii: e45379. doi: 10.7554/eLife.45379.


Coupling S-adenosylmethionine-dependent methylation to growth: Design and uses.

Luo H, Hansen ASL, Yang L, Schneider K, Kristensen M, Christensen U, Christensen HB, Du B, Özdemir E, Feist AM, Keasling JD, Jensen MK, Herrgård MJ, Palsson BO.

PLoS Biol. 2019 Mar 11;17(3):e2007050. doi: 10.1371/journal.pbio.2007050. eCollection 2019 Mar.


Adaptive laboratory evolution of a genome-reduced Escherichia coli.

Choe D, Lee JH, Yoo M, Hwang S, Sung BH, Cho S, Palsson B, Kim SC, Cho BK.

Nat Commun. 2019 Feb 25;10(1):935. doi: 10.1038/s41467-019-08888-6.


Creation and analysis of biochemical constraint-based models using the COBRA Toolbox v.3.0.

Heirendt L, Arreckx S, Pfau T, Mendoza SN, Richelle A, Heinken A, Haraldsdóttir HS, Wachowiak J, Keating SM, Vlasov V, Magnusdóttir S, Ng CY, Preciat G, Žagare A, Chan SHJ, Aurich MK, Clancy CM, Modamio J, Sauls JT, Noronha A, Bordbar A, Cousins B, El Assal DC, Valcarcel LV, Apaolaza I, Ghaderi S, Ahookhosh M, Ben Guebila M, Kostromins A, Sompairac N, Le HM, Ma D, Sun Y, Wang L, Yurkovich JT, Oliveira MAP, Vuong PT, El Assal LP, Kuperstein I, Zinovyev A, Hinton HS, Bryant WA, Aragón Artacho FJ, Planes FJ, Stalidzans E, Maass A, Vempala S, Hucka M, Saunders MA, Maranas CD, Lewis NE, Sauter T, Palsson BØ, Thiele I, Fleming RMT.

Nat Protoc. 2019 Mar;14(3):639-702. doi: 10.1038/s41596-018-0098-2.


The y-ome defines the 35% of Escherichia coli genes that lack experimental evidence of function.

Ghatak S, King ZA, Sastry A, Palsson BO.

Nucleic Acids Res. 2019 Mar 18;47(5):2446-2454. doi: 10.1093/nar/gkz030.


Pseudogene repair driven by selection pressure applied in experimental evolution.

Anand A, Olson CA, Yang L, Sastry AV, Catoiu E, Choudhary KS, Phaneuf PV, Sandberg TE, Xu S, Hefner Y, Szubin R, Feist AM, Palsson BO.

Nat Microbiol. 2019 Mar;4(3):386-389. doi: 10.1038/s41564-018-0340-2. Epub 2019 Jan 28.


Acute uncomplicated diverticulitis managed without antibiotics - difficult to introduce a new treatment protocol but few complications.

Azhar N, Kulstad H, Pålsson B, Kurt Schultz J, Lydrup ML, Buchwald P.

Scand J Gastroenterol. 2019 Jan;54(1):64-68. doi: 10.1080/00365521.2018.1552987. Epub 2019 Jan 16.


Cross-compartment metabolic coupling enables flexible photoprotective mechanisms in the diatom Phaeodactylum tricornutum.

Broddrick JT, Du N, Smith SR, Tsuji Y, Jallet D, Ware MA, Peers G, Matsuda Y, Dupont CL, Mitchell BG, Palsson BO, Allen AE.

New Phytol. 2019 May;222(3):1364-1379. doi: 10.1111/nph.15685. Epub 2019 Feb 14.


DynamicME: dynamic simulation and refinement of integrated models of metabolism and protein expression.

Yang L, Ebrahim A, Lloyd CJ, Saunders MA, Palsson BO.

BMC Syst Biol. 2019 Jan 9;13(1):2. doi: 10.1186/s12918-018-0675-6.


A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types.

Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO.

PLoS Comput Biol. 2019 Jan 9;15(1):e1006644. doi: 10.1371/journal.pcbi.1006644. eCollection 2019 Jan.


Dataset on economic analysis of mass production of algae in LED-based photobioreactors.

Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S.

Data Brief. 2018 Dec 7;22:137-139. doi: 10.1016/j.dib.2018.12.010. eCollection 2019 Feb.


Reframing gene essentiality in terms of adaptive flexibility.

Guzmán GI, Olson CA, Hefner Y, Phaneuf PV, Catoiu E, Crepaldi LB, Micas LG, Palsson BO, Feist AM.

BMC Syst Biol. 2018 Dec 17;12(1):143. doi: 10.1186/s12918-018-0653-z.


Gapless, Unambiguous Genome Sequence for Escherichia coli C, a Workhorse of Industrial Biology.

Pekar JE, Phaneuf P, Szubin R, Palsson B, Feist A, Monk JM.

Microbiol Resour Announc. 2018 Oct 4;7(13). pii: e00890-18. doi: 10.1128/MRA.00890-18. eCollection 2018 Oct.


Modeling genome-wide enzyme evolution predicts strong epistasis underlying catalytic turnover rates.

Heckmann D, Zielinski DC, Palsson BO.

Nat Commun. 2018 Dec 10;9(1):5270. doi: 10.1038/s41467-018-07649-1.


Machine learning applied to enzyme turnover numbers reveals protein structural correlates and improves metabolic models.

Heckmann D, Lloyd CJ, Mih N, Ha Y, Zielinski DC, Haiman ZB, Desouki AA, Lercher MJ, Palsson BO.

Nat Commun. 2018 Dec 7;9(1):5252. doi: 10.1038/s41467-018-07652-6.


Estimating Metabolic Equilibrium Constants: Progress and Future Challenges.

Du B, Zielinski DC, Palsson BO.

Trends Biochem Sci. 2018 Dec;43(12):960-969. doi: 10.1016/j.tibs.2018.09.009. Epub 2018 Oct 24. Review.


Sugar-stimulated CO2 sequestration by the green microalga Chlorella vulgaris.

Fu W, Gudmundsson S, Wichuk K, Palsson S, Palsson BO, Salehi-Ashtiani K, Brynjólfsson S.

Sci Total Environ. 2019 Mar 1;654:275-283. doi: 10.1016/j.scitotenv.2018.11.120. Epub 2018 Nov 9.


Predicting the metabolic capabilities of Synechococcus elongatus PCC 7942 adapted to different light regimes.

Broddrick JT, Welkie DG, Jallet D, Golden SS, Peers G, Palsson BO.

Metab Eng. 2019 Mar;52:42-56. doi: 10.1016/j.ymben.2018.11.001. Epub 2018 Nov 13.


Metagenomics-Based, Strain-Level Analysis of Escherichia coli From a Time-Series of Microbiome Samples From a Crohn's Disease Patient.

Fang X, Monk JM, Nurk S, Akseshina M, Zhu Q, Gemmell C, Gianetto-Hill C, Leung N, Szubin R, Sanders J, Beck PL, Li W, Sandborn WJ, Gray-Owen SD, Knight R, Allen-Vercoe E, Palsson BO, Smarr L.

Front Microbiol. 2018 Oct 30;9:2559. doi: 10.3389/fmicb.2018.02559. eCollection 2018.


Revealing Key Determinants of Clonal Variation in Transgene Expression in Recombinant CHO Cells Using Targeted Genome Editing.

Lee JS, Park JH, Ha TK, Samoudi M, Lewis NE, Palsson BO, Kildegaard HF, Lee GM.

ACS Synth Biol. 2018 Dec 21;7(12):2867-2878. doi: 10.1021/acssynbio.8b00290. Epub 2018 Nov 14.


Identification of growth-coupled production strains considering protein costs and kinetic variability.

Dinh HV, King ZA, Palsson BO, Feist AM.

Metab Eng Commun. 2018 Oct 13;7:e00080. doi: 10.1016/j.mec.2018.e00080. eCollection 2018 Dec.


ALEdb 1.0: a database of mutations from adaptive laboratory evolution experimentation.

Phaneuf PV, Gosting D, Palsson BO, Feist AM.

Nucleic Acids Res. 2019 Jan 8;47(D1):D1164-D1171. doi: 10.1093/nar/gky983.


Machine learning and structural analysis of Mycobacterium tuberculosis pan-genome identifies genetic signatures of antibiotic resistance.

Kavvas ES, Catoiu E, Mih N, Yurkovich JT, Seif Y, Dillon N, Heckmann D, Anand A, Yang L, Nizet V, Monk JM, Palsson BO.

Nat Commun. 2018 Oct 17;9(1):4306. doi: 10.1038/s41467-018-06634-y.


Thermodynamic favorability and pathway yield as evolutionary tradeoffs in biosynthetic pathway choice.

Du B, Zielinski DC, Monk JM, Palsson BO.

Proc Natl Acad Sci U S A. 2018 Oct 30;115(44):11339-11344. doi: 10.1073/pnas.1805367115. Epub 2018 Oct 11.


Characterizing posttranslational modifications in prokaryotic metabolism using a multiscale workflow.

Brunk E, Chang RL, Xia J, Hefzi H, Yurkovich JT, Kim D, Buckmiller E, Wang HH, Cho BK, Yang C, Palsson BO, Church GM, Lewis NE.

Proc Natl Acad Sci U S A. 2018 Oct 23;115(43):11096-11101. doi: 10.1073/pnas.1811971115. Epub 2018 Oct 9.


Escher-FBA: a web application for interactive flux balance analysis.

Rowe E, Palsson BO, King ZA.

BMC Syst Biol. 2018 Sep 26;12(1):84. doi: 10.1186/s12918-018-0607-5.


Evolution of gene knockout strains of E. coli reveal regulatory architectures governed by metabolism.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Nat Commun. 2018 Sep 18;9(1):3796. doi: 10.1038/s41467-018-06219-9.


Genome-scale metabolic reconstructions of multiple Salmonella strains reveal serovar-specific metabolic traits.

Seif Y, Kavvas E, Lachance JC, Yurkovich JT, Nuccio SP, Fang X, Catoiu E, Raffatellu M, Palsson BO, Monk JM.

Nat Commun. 2018 Sep 14;9(1):3771. doi: 10.1038/s41467-018-06112-5.


Systematic discovery of uncharacterized transcription factors in Escherichia coli K-12 MG1655.

Gao Y, Yurkovich JT, Seo SW, Kabimoldayev I, Dräger A, Chen K, Sastry AV, Fang X, Mih N, Yang L, Eichner J, Cho BK, Kim D, Palsson BO.

Nucleic Acids Res. 2018 Nov 16;46(20):10682-10696. doi: 10.1093/nar/gky752.


Growth Adaptation of gnd and sdhCB Escherichia coli Deletion Strains Diverges From a Similar Initial Perturbation of the Transcriptome.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Front Microbiol. 2018 Aug 7;9:1793. doi: 10.3389/fmicb.2018.01793. eCollection 2018.


A unified resource for transcriptional regulation in Escherichia coli K-12 incorporating high-throughput-generated binding data into RegulonDB version 10.0.

Santos-Zavaleta A, Sánchez-Pérez M, Salgado H, Velázquez-Ramírez DA, Gama-Castro S, Tierrafría VH, Busby SJW, Aquino P, Fang X, Palsson BO, Galagan JE, Collado-Vides J.

BMC Biol. 2018 Aug 16;16(1):91. doi: 10.1186/s12915-018-0555-y.


Network-level allosteric effects are elucidated by detailing how ligand-binding events modulate utilization of catalytic potentials.

Yurkovich JT, Alcantar MA, Haiman ZB, Palsson BO.

PLoS Comput Biol. 2018 Aug 7;14(8):e1006356. doi: 10.1371/journal.pcbi.1006356. eCollection 2018 Aug.


Multiple Optimal Phenotypes Overcome Redox and Glycolytic Intermediate Metabolite Imbalances in Escherichia coli pgi Knockout Evolutions.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Appl Environ Microbiol. 2018 Sep 17;84(19). pii: e00823-18. doi: 10.1128/AEM.00823-18. Print 2018 Oct 1.


COBRAme: A computational framework for genome-scale models of metabolism and gene expression.

Lloyd CJ, Ebrahim A, Yang L, King ZA, Catoiu E, O'Brien EJ, Liu JK, Palsson BO.

PLoS Comput Biol. 2018 Jul 5;14(7):e1006302. doi: 10.1371/journal.pcbi.1006302. eCollection 2018 Jul.


Systems analysis of metabolism in platelet concentrates during storage in platelet additive solution.

Jóhannsson F, Guðmundsson S, Paglia G, Guðmundsson S, Palsson B, Sigurjónsson ÓE, Rolfsson Ó.

Biochem J. 2018 Jul 17;475(13):2225-2240. doi: 10.1042/BCJ20170921.


Adaptive laboratory evolution resolves energy depletion to maintain high aromatic metabolite phenotypes in Escherichia coli strains lacking the Phosphotransferase System.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Metab Eng. 2018 Jul;48:233-242. doi: 10.1016/j.ymben.2018.06.005. Epub 2018 Jun 15.


Escherichia coli B2 strains prevalent in inflammatory bowel disease patients have distinct metabolic capabilities that enable colonization of intestinal mucosa.

Fang X, Monk JM, Mih N, Du B, Sastry AV, Kavvas E, Seif Y, Smarr L, Palsson BO.

BMC Syst Biol. 2018 Jun 11;12(1):66. doi: 10.1186/s12918-018-0587-5.


The Staphylococcus aureus Two-Component System AgrAC Displays Four Distinct Genomic Arrangements That Delineate Genomic Virulence Factor Signatures.

Choudhary KS, Mih N, Monk J, Kavvas E, Yurkovich JT, Sakoulas G, Palsson BO.

Front Microbiol. 2018 May 25;9:1082. doi: 10.3389/fmicb.2018.01082. eCollection 2018.


Temperature-Dependent Estimation of Gibbs Energies Using an Updated Group-Contribution Method.

Du B, Zhang Z, Grubner S, Yurkovich JT, Palsson BO, Zielinski DC.

Biophys J. 2018 Jun 5;114(11):2691-2702. doi: 10.1016/j.bpj.2018.04.030.


Adaptation to the coupling of glycolysis to toxic methylglyoxal production in tpiA deletion strains of Escherichia coli requires synchronized and counterintuitive genetic changes.

McCloskey D, Xu S, Sandberg TE, Brunk E, Hefner Y, Szubin R, Feist AM, Palsson BO.

Metab Eng. 2018 Jul;48:82-93. doi: 10.1016/j.ymben.2018.05.012. Epub 2018 May 26.


ChIP-exo interrogation of Crp, DNA, and RNAP holoenzyme interactions.

Latif H, Federowicz S, Ebrahim A, Tarasova J, Szubin R, Utrilla J, Zengler K, Palsson BO.

PLoS One. 2018 May 17;13(5):e0197272. doi: 10.1371/journal.pone.0197272. eCollection 2018.


iCN718, an Updated and Improved Genome-Scale Metabolic Network Reconstruction of Acinetobacter baumannii AYE.

Norsigian CJ, Kavvas E, Seif Y, Palsson BO, Monk JM.

Front Genet. 2018 Apr 10;9:121. doi: 10.3389/fgene.2018.00121. eCollection 2018.

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