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Items: 1 to 50 of 579

1.

Structure of Galactarate Dehydratase, a New Fold in an Enolase Involved in Bacterial Fitness after Antibiotic Treatment.

Rosas-Lemus M, Minasov G, Shuvalova L, Wawrzak Z, Kiryukhina O, Mih N, Jaroszewski L, Palsson B, Godzik A, Satchell KJF.

Protein Sci. 2019 Dec 6. doi: 10.1002/pro.3796. [Epub ahead of print]

PMID:
31811683
2.

Genome-scale model of metabolism and gene expression provides a multi-scale description of acid stress responses in Escherichia coli.

Du B, Yang L, Lloyd CJ, Fang X, Palsson BO.

PLoS Comput Biol. 2019 Dec 6;15(12):e1007525. doi: 10.1371/journal.pcbi.1007525. eCollection 2019 Dec.

3.

The Escherichia coli transcriptome mostly consists of independently regulated modules.

Sastry AV, Gao Y, Szubin R, Hefner Y, Xu S, Kim D, Choudhary KS, Yang L, King ZA, Palsson BO.

Nat Commun. 2019 Dec 4;10(1):5536. doi: 10.1038/s41467-019-13483-w.

4.

Expanding the uses of genome-scale models with protein structures.

Mih N, Palsson BO.

Mol Syst Biol. 2019 Nov;15(11):e8601. doi: 10.15252/msb.20188601.

5.

Adaptive evolution reveals a tradeoff between growth rate and oxidative stress during naphthoquinone-based aerobic respiration.

Anand A, Chen K, Yang L, Sastry AV, Olson CA, Poudel S, Seif Y, Hefner Y, Phaneuf PV, Xu S, Szubin R, Feist AM, Palsson BO.

Proc Natl Acad Sci U S A. 2019 Nov 25. pii: 201909987. doi: 10.1073/pnas.1909987116. [Epub ahead of print]

6.

BiGG Models 2020: multi-strain genome-scale models and expansion across the phylogenetic tree.

Norsigian CJ, Pusarla N, McConn JL, Yurkovich JT, Dräger A, Palsson BO, King Z.

Nucleic Acids Res. 2019 Nov 7. pii: gkz1054. doi: 10.1093/nar/gkz1054. [Epub ahead of print]

PMID:
31696234
7.

High-quality genome-scale metabolic modelling of Pseudomonas putida highlights its broad metabolic capabilities.

Nogales J, Mueller J, Gudmundsson S, Canalejo FJ, Duque E, Monk J, Feist AM, Ramos JL, Niu W, Palsson BO.

Environ Microbiol. 2019 Oct 27. doi: 10.1111/1462-2920.14843. [Epub ahead of print]

PMID:
31657101
8.

OxyR is a convergent target for mutations acquired during adaptation to oxidative stress-prone metabolic states.

Anand A, Chen K, Catoiu E, Sastry AV, Olson CA, Sandberg TE, Seif Y, Xu S, Szubin R, Yang L, Feist AM, Palsson BO.

Mol Biol Evol. 2019 Oct 25. pii: msz251. doi: 10.1093/molbev/msz251. [Epub ahead of print]

PMID:
31651953
9.

Adaptive laboratory evolution of Escherichia coli under acid stress.

Du B, Olson CA, Sastry AV, Fang X, Phaneuf PV, Chen K, Wu M, Szubin R, Xu S, Gao Y, Hefner Y, Feist AM, Palsson BO.

Microbiology. 2019 Oct 18. doi: 10.1099/mic.0.000867. [Epub ahead of print]

PMID:
31625833
10.

Evolution and regulation of nitrogen flux through compartmentalized metabolic networks in a marine diatom.

Smith SR, Dupont CL, McCarthy JK, Broddrick JT, Oborník M, Horák A, Füssy Z, Cihlář J, Kleessen S, Zheng H, McCrow JP, Hixson KK, Araújo WL, Nunes-Nesi A, Fernie A, Nikoloski Z, Palsson BO, Allen AE.

Nat Commun. 2019 Oct 7;10(1):4552. doi: 10.1038/s41467-019-12407-y.

11.

The Transcription Unit Architecture of Streptomyces lividans TK24.

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

Front Microbiol. 2019 Sep 6;10:2074. doi: 10.3389/fmicb.2019.02074. eCollection 2019.

12.

Inactivation of a Mismatch-Repair System Diversifies Genotypic Landscape of Escherichia coli During Adaptive Laboratory Evolution.

Kang M, Kim K, Choe D, Cho S, Kim SC, Palsson B, Cho BK.

Front Microbiol. 2019 Aug 16;10:1845. doi: 10.3389/fmicb.2019.01845. eCollection 2019.

13.

Strain-Specific Metabolic Requirements Revealed by a Defined Minimal Medium for Systems Analyses of Staphylococcus aureus.

Machado H, Weng LL, Dillon N, Seif Y, Holland M, Pekar JE, Monk JM, Nizet V, Palsson BO, Feist AM.

Appl Environ Microbiol. 2019 Oct 16;85(21). pii: e01773-19. doi: 10.1128/AEM.01773-19. Print 2019 Nov 1.

PMID:
31471305
14.

Systems Biology and Pangenome of Salmonella O-Antigens.

Seif Y, Monk JM, Machado H, Kavvas E, Palsson BO.

MBio. 2019 Aug 27;10(4). pii: e01247-19. doi: 10.1128/mBio.01247-19.

15.

The emergence of adaptive laboratory evolution as an efficient tool for biological discovery and industrial biotechnology.

Sandberg TE, Salazar MJ, Weng LL, Palsson BO, Feist AM.

Metab Eng. 2019 Dec;56:1-16. doi: 10.1016/j.ymben.2019.08.004. Epub 2019 Aug 8. Review.

PMID:
31401242
16.

Metabolic Systems Analysis of Shock-Induced Endotheliopathy (SHINE) in Trauma: A New Research Paradigm.

Henriksen HH, McGarrity S, SigurÐardóttir RS, Nemkov T, D'Alessandro A, Palsson BO, Stensballe J, Wade CE, Rolfsson Ó, Johansson PI.

Ann Surg. 2019 Jun 26. doi: 10.1097/SLA.0000000000003307. [Epub ahead of print]

PMID:
31274658
17.

Cellular responses to reactive oxygen species are predicted from molecular mechanisms.

Yang L, Mih N, Anand A, Park JH, Tan J, Yurkovich JT, Monk JM, Lloyd CJ, Sandberg TE, Seo SW, Kim D, Sastry AV, Phaneuf P, Gao Y, Broddrick JT, Chen K, Heckmann D, Szubin R, Hefner Y, Feist AM, Palsson BO.

Proc Natl Acad Sci U S A. 2019 Jul 9;116(28):14368-14373. doi: 10.1073/pnas.1905039116. Epub 2019 Jul 3.

PMID:
31270234
18.

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.

19.

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.

20.

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 Jul 9;47(12):6114-6129. doi: 10.1093/nar/gkz471.

21.

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.

22.

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.

PMID:
31080069
23.

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.

24.

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.

25.

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.

26.

Minimal cells, maximal knowledge.

Lachance JC, Rodrigue S, Palsson BO.

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

27.

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.

28.

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.

29.

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.

PMID:
30787451
30.

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.

31.

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.

PMID:
30692668
32.

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.

PMID:
30650309
33.

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.

34.

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.

35.

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.

36.

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.

37.

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.

38.

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.

39.

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.

40.

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.

41.

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.

PMID:
30472988
42.

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.

PMID:
30445327
43.

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.

PMID:
30439494
44.

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.

45.

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.

PMID:
30388888
46.

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.

47.

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.

48.

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.

49.

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.

50.

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.

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