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For: Hyduke DR, Lewis NE, Palsson BØ. Analysis of omics data with genome-scale models of metabolism. Mol Biosyst 2013;9:167-74. [PMID: 23247105 PMCID: PMC3594511 DOI: 10.1039/c2mb25453k] [Citation(s) in RCA: 127] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Number Cited by Other Article(s)
1
Mardinoglu A, Palsson BØ. Genome-scale models in human metabologenomics. Nat Rev Genet 2024:10.1038/s41576-024-00768-0. [PMID: 39300314 DOI: 10.1038/s41576-024-00768-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/29/2024] [Indexed: 09/22/2024]
2
Lange E, Kranert L, Krüger J, Benndorf D, Heyer R. Microbiome modeling: a beginner's guide. Front Microbiol 2024;15:1368377. [PMID: 38962127 PMCID: PMC11220171 DOI: 10.3389/fmicb.2024.1368377] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/27/2024] [Indexed: 07/05/2024]  Open
3
Liu Y, Li D, Zhang X, Xia S, Qu Y, Ling X, Li Y, Kong X, Zhang L, Cui CP, Li D. A protein sequence-based deep transfer learning framework for identifying human proteome-wide deubiquitinase-substrate interactions. Nat Commun 2024;15:4519. [PMID: 38806474 PMCID: PMC11133436 DOI: 10.1038/s41467-024-48446-3] [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: 07/17/2023] [Accepted: 04/26/2024] [Indexed: 05/30/2024]  Open
4
Chen Y, Gustafsson J, Yang J, Nielsen J, Kerkhoven EJ. Single-cell omics analysis with genome-scale metabolic modeling. Curr Opin Biotechnol 2024;86:103078. [PMID: 38359604 DOI: 10.1016/j.copbio.2024.103078] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 01/19/2024] [Indexed: 02/17/2024]
5
Eames A, Chandrasekaran S. Leveraging metabolic modeling and machine learning to uncover modulators of quiescence depth. PNAS NEXUS 2024;3:pgae013. [PMID: 38292544 PMCID: PMC10825626 DOI: 10.1093/pnasnexus/pgae013] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Accepted: 12/28/2023] [Indexed: 02/01/2024]
6
Moreno R, Rojo F. What are the signals that control catabolite repression in Pseudomonas? Microb Biotechnol 2024;17:e14407. [PMID: 38227132 PMCID: PMC10832556 DOI: 10.1111/1751-7915.14407] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 12/29/2023] [Accepted: 01/02/2024] [Indexed: 01/17/2024]  Open
7
Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Shams Ud Doha K, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Robasky B, Sharfstein ST, Lewis NE. Inferring secretory and metabolic pathway activity from omic data with secCellFie. Metab Eng 2024;81:273-285. [PMID: 38145748 PMCID: PMC11177574 DOI: 10.1016/j.ymben.2023.12.006] [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: 04/19/2023] [Revised: 11/29/2023] [Accepted: 12/14/2023] [Indexed: 12/27/2023]
8
Mattei G, Gan Z, Ramazzotti M, Palsson BO, Zielinski DC. Differential Expression Analysis Utilizing Condition-Specific Metabolic Pathways. Metabolites 2023;13:1127. [PMID: 37999223 PMCID: PMC10672963 DOI: 10.3390/metabo13111127] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2023] [Revised: 10/19/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023]  Open
9
Alberghina L. The Warburg Effect Explained: Integration of Enhanced Glycolysis with Heterogeneous Mitochondria to Promote Cancer Cell Proliferation. Int J Mol Sci 2023;24:15787. [PMID: 37958775 PMCID: PMC10648413 DOI: 10.3390/ijms242115787] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Revised: 10/19/2023] [Accepted: 10/25/2023] [Indexed: 11/15/2023]  Open
10
Masson HO, Karottki KJLC, Tat J, Hefzi H, Lewis NE. From observational to actionable: rethinking omics in biologics production. Trends Biotechnol 2023;41:1127-1138. [PMID: 37062598 PMCID: PMC10524802 DOI: 10.1016/j.tibtech.2023.03.009] [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: 01/11/2023] [Revised: 03/08/2023] [Accepted: 03/13/2023] [Indexed: 04/18/2023]
11
Roell G, Schenk C, Anthony WE, Carr RR, Ponukumati A, Kim J, Akhmatskaya E, Foston M, Dantas G, Moon TS, Tang YJ, García Martín H. A High-Quality Genome-Scale Model for Rhodococcus opacus Metabolism. ACS Synth Biol 2023;12:1632-1644. [PMID: 37186551 PMCID: PMC10278598 DOI: 10.1021/acssynbio.2c00618] [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: 11/16/2022] [Indexed: 05/17/2023]
12
Masson HO, Samoudi M, Robinson CM, Kuo CC, Weiss L, Doha KSU, Campos A, Tejwani V, Dahodwala H, Menard P, Voldborg BG, Sharfstein ST, Lewis NE. Inferring secretory and metabolic pathway activity from omic data with secCellFie. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.05.04.539316. [PMID: 37205389 PMCID: PMC10187314 DOI: 10.1101/2023.05.04.539316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
13
Moreno R, Rojo F. The importance of understanding the regulation of bacterial metabolism. Environ Microbiol 2023;25:54-58. [PMID: 35859345 PMCID: PMC10084369 DOI: 10.1111/1462-2920.16123] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Accepted: 06/30/2022] [Indexed: 01/21/2023]
14
Jamialahmadi O, Salehabadi E, Hashemi-Najafabadi S, Motamedian E, Bagheri F, Mancina RM, Romeo S. Cellular Genome-Scale Metabolic Modeling Identifies New Potential Drug Targets Against Hepatocellular Carcinoma. OMICS : A JOURNAL OF INTEGRATIVE BIOLOGY 2022;26:671-682. [PMID: 36508280 DOI: 10.1089/omi.2022.0122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
15
Simensen V, Seif Y, Almaas E. Phenotypic response of yeast metabolic network to availability of proteinogenic amino acids. Front Mol Biosci 2022;9:963548. [PMID: 36072429 PMCID: PMC9441596 DOI: 10.3389/fmolb.2022.963548] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 07/25/2022] [Indexed: 11/20/2022]  Open
16
Thiele I, Fleming RM. Whole-body metabolic modelling predicts isoleucine dependency of SARS-CoV-2 replication. Comput Struct Biotechnol J 2022;20:4098-4109. [PMID: 35874091 PMCID: PMC9296228 DOI: 10.1016/j.csbj.2022.07.019] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 07/10/2022] [Indexed: 11/21/2022]  Open
17
Rohatgi N, Ghoshdastider U, Baruah P, Kulshrestha T, Skanderup AJ. A pan-cancer metabolic atlas of the tumor microenvironment. Cell Rep 2022;39:110800. [PMID: 35545044 DOI: 10.1016/j.celrep.2022.110800] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Revised: 12/14/2021] [Accepted: 04/20/2022] [Indexed: 11/03/2022]  Open
18
Di Filippo M, Pescini D, Galuzzi BG, Bonanomi M, Gaglio D, Mangano E, Consolandi C, Alberghina L, Vanoni M, Damiani C. INTEGRATE: Model-based multi-omics data integration to characterize multi-level metabolic regulation. PLoS Comput Biol 2022;18:e1009337. [PMID: 35130273 PMCID: PMC8853556 DOI: 10.1371/journal.pcbi.1009337] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Revised: 02/17/2022] [Accepted: 01/13/2022] [Indexed: 12/12/2022]  Open
19
Network Biology and Artificial Intelligence Drive the Understanding of the Multidrug Resistance Phenotype in Cancer. Drug Resist Updat 2022;60:100811. [DOI: 10.1016/j.drup.2022.100811] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 02/07/2023]
20
Zhang HY, Fan ZL, Wang TY. Advances of Glycometabolism Engineering in Chinese Hamster Ovary Cells. Front Bioeng Biotechnol 2021;9:774175. [PMID: 34926421 PMCID: PMC8675083 DOI: 10.3389/fbioe.2021.774175] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2021] [Accepted: 11/16/2021] [Indexed: 12/03/2022]  Open
21
Ravi S, Gunawan R. ΔFBA-Predicting metabolic flux alterations using genome-scale metabolic models and differential transcriptomic data. PLoS Comput Biol 2021;17:e1009589. [PMID: 34758020 PMCID: PMC8608322 DOI: 10.1371/journal.pcbi.1009589] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2021] [Revised: 11/22/2021] [Accepted: 10/25/2021] [Indexed: 12/04/2022]  Open
22
Rodenburg SYA, Seidl MF, de Ridder D, Govers F. Uncovering the Role of Metabolism in Oomycete-Host Interactions Using Genome-Scale Metabolic Models. Front Microbiol 2021;12:748178. [PMID: 34707596 PMCID: PMC8543037 DOI: 10.3389/fmicb.2021.748178] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Accepted: 09/10/2021] [Indexed: 12/17/2022]  Open
23
Medeiros Filho F, do Nascimento APB, Costa MDOCE, Merigueti TC, de Menezes MA, Nicolás MF, Dos Santos MT, Carvalho-Assef APD, da Silva FAB. A Systematic Strategy to Find Potential Therapeutic Targets for Pseudomonas aeruginosa Using Integrated Computational Models. Front Mol Biosci 2021;8:728129. [PMID: 34616771 PMCID: PMC8488468 DOI: 10.3389/fmolb.2021.728129] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2021] [Accepted: 08/31/2021] [Indexed: 12/26/2022]  Open
24
Khaleghi MK, Savizi ISP, Lewis NE, Shojaosadati SA. Synergisms of machine learning and constraint-based modeling of metabolism for analysis and optimization of fermentation parameters. Biotechnol J 2021;16:e2100212. [PMID: 34390201 DOI: 10.1002/biot.202100212] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2021] [Revised: 08/10/2021] [Accepted: 08/11/2021] [Indexed: 11/06/2022]
25
Bryan L, Clynes M, Meleady P. The emerging role of cellular post-translational modifications in modulating growth and productivity of recombinant Chinese hamster ovary cells. Biotechnol Adv 2021;49:107757. [PMID: 33895332 DOI: 10.1016/j.biotechadv.2021.107757] [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: 12/16/2020] [Revised: 04/19/2021] [Accepted: 04/19/2021] [Indexed: 02/06/2023]
26
Weglarz-Tomczak E, Mondeel TDGA, Piebes DGE, Westerhoff HV. Simultaneous Integration of Gene Expression and Nutrient Availability for Studying the Metabolism of Hepatocellular Carcinoma Cell Lines. Biomolecules 2021;11:biom11040490. [PMID: 33805227 PMCID: PMC8064315 DOI: 10.3390/biom11040490] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 03/07/2021] [Accepted: 03/19/2021] [Indexed: 01/08/2023]  Open
27
Gupta A, Kumar A, Anand R, Bairagi N, Chatterjee S. Genome scale metabolic model driven strategy to delineate host response to Mycobacterium tuberculosis infection. Mol Omics 2021;17:296-306. [PMID: 33595587 DOI: 10.1039/d0mo00138d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
28
Weglarz-Tomczak E, Rijlaarsdam DJ, Tomczak JM, Brul S. GEM-Based Metabolic Profiling for Human Bone Osteosarcoma under Different Glucose and Glutamine Availability. Int J Mol Sci 2021;22:1470. [PMID: 33540580 PMCID: PMC7867237 DOI: 10.3390/ijms22031470] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2020] [Revised: 01/24/2021] [Accepted: 01/27/2021] [Indexed: 12/31/2022]  Open
29
Machicao J, Craighero F, Maspero D, Angaroni F, Damiani C, Graudenzi A, Antoniotti M, Bruno OM. On the Use of Topological Features of Metabolic Networks for the Classification of Cancer Samples. Curr Genomics 2021;22:88-97. [PMID: 34220296 PMCID: PMC8188584 DOI: 10.2174/1389202922666210301084151] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2020] [Revised: 12/16/2020] [Accepted: 12/18/2020] [Indexed: 11/30/2022]  Open
30
Patra P, Das M, Kundu P, Ghosh A. Recent advances in systems and synthetic biology approaches for developing novel cell-factories in non-conventional yeasts. Biotechnol Adv 2021;47:107695. [PMID: 33465474 DOI: 10.1016/j.biotechadv.2021.107695] [Citation(s) in RCA: 70] [Impact Index Per Article: 23.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2020] [Revised: 12/14/2020] [Accepted: 01/09/2021] [Indexed: 12/14/2022]
31
Dahal S, Zhao J, Yang L. Genome-scale Modeling of Metabolism and Macromolecular Expression and Their Applications. BIOTECHNOL BIOPROC E 2021. [DOI: 10.1007/s12257-020-0061-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
32
García-Jiménez B, Torres-Bacete J, Nogales J. Metabolic modelling approaches for describing and engineering microbial communities. Comput Struct Biotechnol J 2020;19:226-246. [PMID: 33425254 PMCID: PMC7773532 DOI: 10.1016/j.csbj.2020.12.003] [Citation(s) in RCA: 40] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Revised: 12/02/2020] [Accepted: 12/05/2020] [Indexed: 12/17/2022]  Open
33
Systematically gap-filling the genome-scale metabolic model of CHO cells. Biotechnol Lett 2020;43:73-87. [PMID: 33040240 DOI: 10.1007/s10529-020-03021-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 10/03/2020] [Indexed: 10/23/2022]
34
Wang X, Rai N, Merchel Piovesan Pereira B, Eetemadi A, Tagkopoulos I. Accelerated knowledge discovery from omics data by optimal experimental design. Nat Commun 2020;11:5026. [PMID: 33024104 PMCID: PMC7538421 DOI: 10.1038/s41467-020-18785-y] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2019] [Accepted: 08/27/2020] [Indexed: 12/15/2022]  Open
35
González J, Pinzón A, Angarita-Rodríguez A, Aristizabal AF, Barreto GE, Martín-Jiménez C. Advances in Astrocyte Computational Models: From Metabolic Reconstructions to Multi-omic Approaches. Front Neuroinform 2020;14:35. [PMID: 32848690 PMCID: PMC7426703 DOI: 10.3389/fninf.2020.00035] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2020] [Accepted: 07/14/2020] [Indexed: 12/12/2022]  Open
36
Ghoshdastidar D, Gutzeit M, Carpentier A, von Luxburg U. Two-sample hypothesis testing for inhomogeneous random graphs. Ann Stat 2020. [DOI: 10.1214/19-aos1884] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
37
Revealing 29 sets of independently modulated genes in Staphylococcus aureus, their regulators, and role in key physiological response. Proc Natl Acad Sci U S A 2020;117:17228-17239. [PMID: 32616573 PMCID: PMC7382225 DOI: 10.1073/pnas.2008413117] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
38
StanDep: Capturing transcriptomic variability improves context-specific metabolic models. PLoS Comput Biol 2020;16:e1007764. [PMID: 32396573 PMCID: PMC7244210 DOI: 10.1371/journal.pcbi.1007764] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Revised: 05/22/2020] [Accepted: 03/02/2020] [Indexed: 12/26/2022]  Open
39
Integration of Time-Series Transcriptomic Data with Genome-Scale CHO Metabolic Models for mAb Engineering. Processes (Basel) 2020. [DOI: 10.3390/pr8030331] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
40
Bekiaris PS, Klamt S. Automatic construction of metabolic models with enzyme constraints. BMC Bioinformatics 2020;21:19. [PMID: 31937255 PMCID: PMC6961255 DOI: 10.1186/s12859-019-3329-9] [Citation(s) in RCA: 48] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Accepted: 12/17/2019] [Indexed: 11/11/2022]  Open
41
Metabolic Modeling of Streptococcus mutans Reveals Complex Nutrient Requirements of an Oral Pathogen. mSystems 2019;4:4/5/e00529-19. [PMID: 31662430 PMCID: PMC6819733 DOI: 10.1128/msystems.00529-19] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
42
Zampieri G, Vijayakumar S, Yaneske E, Angione C. Machine and deep learning meet genome-scale metabolic modeling. PLoS Comput Biol 2019;15:e1007084. [PMID: 31295267 PMCID: PMC6622478 DOI: 10.1371/journal.pcbi.1007084] [Citation(s) in RCA: 150] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
43
Richelle A, Joshi C, Lewis NE. Assessing key decisions for transcriptomic data integration in biochemical networks. PLoS Comput Biol 2019;15:e1007185. [PMID: 31323017 PMCID: PMC6668847 DOI: 10.1371/journal.pcbi.1007185] [Citation(s) in RCA: 38] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2018] [Revised: 07/31/2019] [Accepted: 06/14/2019] [Indexed: 12/21/2022]  Open
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Orellana-Saez M, Pacheco N, Costa JI, Mendez KN, Miossec MJ, Meneses C, Castro-Nallar E, Marcoleta AE, Poblete-Castro I. In-Depth Genomic and Phenotypic Characterization of the Antarctic Psychrotolerant Strain Pseudomonas sp. MPC6 Reveals Unique Metabolic Features, Plasticity, and Biotechnological Potential. Front Microbiol 2019;10:1154. [PMID: 31178851 PMCID: PMC6543543 DOI: 10.3389/fmicb.2019.01154] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2019] [Accepted: 05/07/2019] [Indexed: 12/12/2022]  Open
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Identifying and targeting cancer-specific metabolism with network-based drug target prediction. EBioMedicine 2019;43:98-106. [PMID: 31126892 PMCID: PMC6558238 DOI: 10.1016/j.ebiom.2019.04.046] [Citation(s) in RCA: 51] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2018] [Revised: 04/24/2019] [Accepted: 04/24/2019] [Indexed: 12/12/2022]  Open
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Jamialahmadi O, Hashemi-Najafabadi S, Motamedian E, Romeo S, Bagheri F. A benchmark-driven approach to reconstruct metabolic networks for studying cancer metabolism. PLoS Comput Biol 2019;15:e1006936. [PMID: 31009458 PMCID: PMC6497301 DOI: 10.1371/journal.pcbi.1006936] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2018] [Revised: 05/02/2019] [Accepted: 03/11/2019] [Indexed: 02/07/2023]  Open
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Seif Y, Monk JM, Mih N, Tsunemoto H, Poudel S, Zuniga C, Broddrick J, Zengler K, Palsson BO. A computational knowledge-base elucidates the response of Staphylococcus aureus to different media types. PLoS Comput Biol 2019;15:e1006644. [PMID: 30625152 PMCID: PMC6326480 DOI: 10.1371/journal.pcbi.1006644] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2018] [Accepted: 11/14/2018] [Indexed: 12/15/2022]  Open
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Kawata K, Yugi K, Hatano A, Kokaji T, Tomizawa Y, Fujii M, Uda S, Kubota H, Matsumoto M, Nakayama KI, Kuroda S. Reconstruction of global regulatory network from signaling to cellular functions using phosphoproteomic data. Genes Cells 2018;24:82-93. [PMID: 30417516 DOI: 10.1111/gtc.12655] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 11/04/2018] [Accepted: 11/05/2018] [Indexed: 12/21/2022]
49
Integrating -omics data into genome-scale metabolic network models: principles and challenges. Essays Biochem 2018;62:563-574. [PMID: 30315095 DOI: 10.1042/ebc20180011] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Revised: 08/30/2018] [Accepted: 08/31/2018] [Indexed: 12/13/2022]
50
Brandl J, Aguilar-Pontes MV, Schäpe P, Noerregaard A, Arvas M, Ram AFJ, Meyer V, Tsang A, de Vries RP, Andersen MR. A community-driven reconstruction of the Aspergillus niger metabolic network. Fungal Biol Biotechnol 2018;5:16. [PMID: 30275963 PMCID: PMC6158834 DOI: 10.1186/s40694-018-0060-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2018] [Accepted: 09/17/2018] [Indexed: 11/17/2022]  Open
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