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For: McCloskey D, Xu J, Schrübbers L, Christensen HB, Herrgård MJ. RapidRIP quantifies the intracellular metabolome of 7 industrial strains of E. coli. Metab Eng 2018;47:383-392. [PMID: 29702276 DOI: 10.1016/j.ymben.2018.04.009] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/27/2018] [Accepted: 04/12/2018] [Indexed: 11/20/2022]
Number Cited by Other Article(s)
1
Li B, Srivastava S, Shaikh M, Mereddy G, Garcia MR, Shah A, Ofori-Anyinam N, Chu T, Cheney N, Yang JH. Bioenergetic stress potentiates antimicrobial resistance and persistence. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.12.603336. [PMID: 39026737 PMCID: PMC11257553 DOI: 10.1101/2024.07.12.603336] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/20/2024]
2
Kujawinski EB, Braakman R, Longnecker K, Becker JW, Chisholm SW, Dooley K, Kido Soule MC, Swarr GJ, Halloran K. Metabolite diversity among representatives of divergent Prochlorococcus ecotypes. mSystems 2023;8:e0126122. [PMID: 37815355 PMCID: PMC10654061 DOI: 10.1128/msystems.01261-22] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 08/31/2023] [Indexed: 10/11/2023]  Open
3
Cosetta CM, Niccum B, Kamkari N, Dente M, Podniesinski M, Wolfe BE. Bacterial-fungal interactions promote parallel evolution of global transcriptional regulators in a widespread Staphylococcus species. THE ISME JOURNAL 2023;17:1504-1516. [PMID: 37524910 PMCID: PMC10432416 DOI: 10.1038/s41396-023-01462-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2023] [Revised: 06/06/2023] [Accepted: 06/15/2023] [Indexed: 08/02/2023]
4
de Leeuw M, Matos MRA, Nielsen LK. Omics data for sampling thermodynamically feasible kinetic models. Metab Eng 2023;78:41-47. [PMID: 37209863 DOI: 10.1016/j.ymben.2023.05.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 05/03/2023] [Accepted: 05/07/2023] [Indexed: 05/22/2023]
5
Donati S, Mattanovich M, Hjort P, Jacobsen SAB, Blomquist SD, Mangaard D, Gurdo N, Pastor FP, Maury J, Hanke R, Herrgård MJ, Wulff T, Jakočiūnas T, Nielsen LK, McCloskey D. An automated workflow for multi-omics screening of microbial model organisms. NPJ Syst Biol Appl 2023;9:14. [PMID: 37208327 DOI: 10.1038/s41540-023-00277-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Accepted: 04/19/2023] [Indexed: 05/21/2023]  Open
6
Li S, Zhang Z, Liu FL, Yuan BF, Liu TG, Feng YQ. Comprehensive Profiling of Phosphomonoester Metabolites in Saccharomyces cerevisiae by the Chemical Isotope Labeling-LC-MS Method. J Proteome Res 2023;22:114-122. [PMID: 36484485 DOI: 10.1021/acs.jproteome.2c00507] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
7
Calero P, Gurdo N, Nikel PI. Role of the CrcB transporter of Pseudomonas putida in the multi-level stress response elicited by mineral fluoride. Environ Microbiol 2022;24:5082-5104. [PMID: 35726888 PMCID: PMC9796867 DOI: 10.1111/1462-2920.16110] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 06/16/2022] [Accepted: 06/19/2022] [Indexed: 01/07/2023]
8
Joffré E, Xiao X, Correia MSP, Nookaew I, Sasse S, Globisch D, Zhu B, Sjöling Å. Analysis of Growth Phases of Enterotoxigenic Escherichia coli Reveals a Distinct Transition Phase before Entry into Early Stationary Phase with Shifts in Tryptophan, Fucose, and Putrescine Metabolism and Degradation of Neurotransmitter Precursors. Microbiol Spectr 2022;10:e0175521. [PMID: 35876501 PMCID: PMC9431495 DOI: 10.1128/spectrum.01755-21] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Accepted: 03/03/2022] [Indexed: 11/20/2022]  Open
9
Fernández-Cabezón L, Rosich I Bosch B, Kozaeva E, Gurdo N, Nikel PI. Dynamic flux regulation for high-titer anthranilate production by plasmid-free, conditionally-auxotrophic strains of Pseudomonas putida. Metab Eng 2022;73:11-25. [PMID: 35659519 DOI: 10.1016/j.ymben.2022.05.008] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2022] [Revised: 05/05/2022] [Accepted: 05/29/2022] [Indexed: 10/18/2022]
10
Wong N, Jantama K. Engineering Escherichia coli for a high yield of 1,3-propanediol near the theoretical maximum through chromosomal integration and gene deletion. Appl Microbiol Biotechnol 2022;106:2937-2951. [PMID: 35416488 DOI: 10.1007/s00253-022-11898-y] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2021] [Revised: 03/15/2022] [Accepted: 03/26/2022] [Indexed: 11/02/2022]
11
Reiter A, Asgari J, Wiechert W, Oldiges M. Metabolic Footprinting of Microbial Systems Based on Comprehensive In Silico Predictions of MS/MS Relevant Data. Metabolites 2022;12:257. [PMID: 35323700 PMCID: PMC8949988 DOI: 10.3390/metabo12030257] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Revised: 03/08/2022] [Accepted: 03/12/2022] [Indexed: 12/12/2022]  Open
12
Abram KJ, McCloskey D. A Comprehensive Evaluation of Metabolomics Data Preprocessing Methods for Deep Learning. Metabolites 2022;12:202. [PMID: 35323644 PMCID: PMC8948616 DOI: 10.3390/metabo12030202] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Revised: 02/15/2022] [Accepted: 02/17/2022] [Indexed: 12/04/2022]  Open
13
Mapping enzyme catalysis with metabolic biosensing. Nat Commun 2021;12:6803. [PMID: 34815408 PMCID: PMC8611028 DOI: 10.1038/s41467-021-27185-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2021] [Accepted: 11/05/2021] [Indexed: 11/15/2022]  Open
14
Lauritsen I, Frendorf PO, Capucci S, Heyde SAH, Blomquist SD, Wendel S, Fischer EC, Sekowska A, Danchin A, Nørholm MHH. Temporal evolution of master regulator Crp identifies pyrimidines as catabolite modulator factors. Nat Commun 2021;12:5880. [PMID: 34620864 PMCID: PMC8497467 DOI: 10.1038/s41467-021-26098-x] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 09/07/2021] [Indexed: 12/19/2022]  Open
15
Wang L, Upadhyay V, Maranas CD. dGPredictor: Automated fragmentation method for metabolic reaction free energy prediction and de novo pathway design. PLoS Comput Biol 2021;17:e1009448. [PMID: 34570771 PMCID: PMC8496854 DOI: 10.1371/journal.pcbi.1009448] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2021] [Revised: 10/07/2021] [Accepted: 09/13/2021] [Indexed: 11/19/2022]  Open
16
An ion-pair free LC-MS/MS method for quantitative metabolite profiling of microbial bioproduction systems. Talanta 2021;222:121625. [DOI: 10.1016/j.talanta.2020.121625] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2020] [Revised: 08/31/2020] [Accepted: 09/02/2020] [Indexed: 11/23/2022]
17
Kutuzova S, Colaianni P, Röst H, Sachsenberg T, Alka O, Kohlbacher O, Burla B, Torta F, Schrübbers L, Kristensen M, Nielsen L, Herrgård MJ, McCloskey D. SmartPeak Automates Targeted and Quantitative Metabolomics Data Processing. Anal Chem 2020;92:15968-15974. [PMID: 33269929 DOI: 10.1021/acs.analchem.0c03421] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
18
Volkova S, Matos MRA, Mattanovich M, Marín de Mas I. Metabolic Modelling as a Framework for Metabolomics Data Integration and Analysis. Metabolites 2020;10:E303. [PMID: 32722118 PMCID: PMC7465778 DOI: 10.3390/metabo10080303] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 07/08/2020] [Accepted: 07/22/2020] [Indexed: 01/05/2023]  Open
19
Leavell MD, Singh AH, Kaufmann-Malaga BB. High-throughput screening for improved microbial cell factories, perspective and promise. Curr Opin Biotechnol 2020;62:22-28. [DOI: 10.1016/j.copbio.2019.07.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2019] [Revised: 07/24/2019] [Accepted: 07/27/2019] [Indexed: 01/11/2023]
20
Vavricka CJ, Hasunuma T, Kondo A. Dynamic Metabolomics for Engineering Biology: Accelerating Learning Cycles for Bioproduction. Trends Biotechnol 2020;38:68-82. [DOI: 10.1016/j.tibtech.2019.07.009] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 12/15/2022]
21
Kopp J, Slouka C, Spadiut O, Herwig C. The Rocky Road From Fed-Batch to Continuous Processing With E. coli. Front Bioeng Biotechnol 2019;7:328. [PMID: 31824931 PMCID: PMC6880763 DOI: 10.3389/fbioe.2019.00328] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2019] [Accepted: 10/28/2019] [Indexed: 12/21/2022]  Open
22
Yang JH, Wright SN, Hamblin M, McCloskey D, Alcantar MA, Schrübbers L, Lopatkin AJ, Satish S, Nili A, Palsson BO, Walker GC, Collins JJ. A White-Box Machine Learning Approach for Revealing Antibiotic Mechanisms of Action. Cell 2019;177:1649-1661.e9. [PMID: 31080069 PMCID: PMC6545570 DOI: 10.1016/j.cell.2019.04.016] [Citation(s) in RCA: 188] [Impact Index Per Article: 31.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2018] [Revised: 03/19/2019] [Accepted: 04/08/2019] [Indexed: 12/13/2022]
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