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For: Suthers PF, Zomorrodi A, Maranas CD. Genome-scale gene/reaction essentiality and synthetic lethality analysis. Mol Syst Biol 2009;5:301. [PMID: 19690570 DOI: 10.1038/msb.2009.56] [Citation(s) in RCA: 120] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2008] [Accepted: 07/08/2009] [Indexed: 01/18/2023]  Open
Number Cited by Other Article(s)
1
Guil F, García R, García JM. Adding metabolic tasks to human GEM models to improve the study of gene targets and their associated toxicities. Sci Rep 2024;14:17265. [PMID: 39068208 PMCID: PMC11283532 DOI: 10.1038/s41598-024-68073-8] [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: 04/23/2024] [Accepted: 07/19/2024] [Indexed: 07/30/2024]  Open
2
Mirzaei S, Tefagh M. GEM-based computational modeling for exploring metabolic interactions in a microbial community. PLoS Comput Biol 2024;20:e1012233. [PMID: 38900842 PMCID: PMC11218945 DOI: 10.1371/journal.pcbi.1012233] [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: 11/16/2023] [Revised: 07/02/2024] [Accepted: 06/03/2024] [Indexed: 06/22/2024]  Open
3
Mahout M, Carlson RP, Simon L, Peres S. Logic programming-based Minimal Cut Sets reveal consortium-level therapeutic targets for chronic wound infections. NPJ Syst Biol Appl 2024;10:34. [PMID: 38565568 PMCID: PMC10987626 DOI: 10.1038/s41540-024-00360-6] [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: 07/29/2023] [Accepted: 03/13/2024] [Indexed: 04/04/2024]  Open
4
Hassani L, Moosavi MR, Setoodeh P, Zare H. FastKnock: an efficient next-generation approach to identify all knockout strategies for strain optimization. Microb Cell Fact 2024;23:37. [PMID: 38287320 PMCID: PMC10823710 DOI: 10.1186/s12934-023-02277-x] [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: 06/30/2023] [Accepted: 12/15/2023] [Indexed: 01/31/2024]  Open
5
Angarita-Rodríguez A, González-Giraldo Y, Rubio-Mesa JJ, Aristizábal AF, Pinzón A, González J. Control Theory and Systems Biology: Potential Applications in Neurodegeneration and Search for Therapeutic Targets. Int J Mol Sci 2023;25:365. [PMID: 38203536 PMCID: PMC10778851 DOI: 10.3390/ijms25010365] [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: 10/21/2023] [Revised: 12/01/2023] [Accepted: 12/19/2023] [Indexed: 01/12/2024]  Open
6
Somers J, Fenner M, Kong G, Thirumalaisamy D, Yashar WM, Thapa K, Kinali M, Nikolova O, Babur Ö, Demir E. A framework for considering prior information in network-based approaches to omics data analysis. Proteomics 2023;23:e2200402. [PMID: 37986684 DOI: 10.1002/pmic.202200402] [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: 07/19/2023] [Revised: 09/20/2023] [Accepted: 09/21/2023] [Indexed: 11/22/2023]
7
Sen P, Orešič M. Integrating Omics Data in Genome-Scale Metabolic Modeling: A Methodological Perspective for Precision Medicine. Metabolites 2023;13:855. [PMID: 37512562 PMCID: PMC10383060 DOI: 10.3390/metabo13070855] [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: 06/15/2023] [Revised: 07/11/2023] [Accepted: 07/17/2023] [Indexed: 07/30/2023]  Open
8
Hassani L, Moosavi MR, Setoodeh P, Zare H. FastKnock: An efficient next-generation approach to identify all knockout strategies for strain optimization. RESEARCH SQUARE 2023:rs.3.rs-3126389. [PMID: 37503204 PMCID: PMC10371132 DOI: 10.21203/rs.3.rs-3126389/v1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 07/29/2023]
9
Zhu SB, Jiang QH, Chen ZG, Zhou X, Jin YT, Deng Z, Guo FB. Mslar: Microbial synthetic lethal and rescue database. PLoS Comput Biol 2023;19:e1011218. [PMID: 37289843 DOI: 10.1371/journal.pcbi.1011218] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2022] [Accepted: 05/26/2023] [Indexed: 06/10/2023]  Open
10
Dehghan Manshadi M, Setoodeh P, Zare H. Rapid-SL identifies synthetic lethal sets with an arbitrary cardinality. Sci Rep 2022;12:14022. [PMID: 35982201 PMCID: PMC9388495 DOI: 10.1038/s41598-022-18177-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2022] [Accepted: 08/05/2022] [Indexed: 11/09/2022]  Open
11
Guo HX, Zhu SB, Deng Z, Guo FB. EcoliGD: An Online Tool for Designing Escherichia coli Genome. ACS Synth Biol 2022;11:2267-2274. [PMID: 35770895 DOI: 10.1021/acssynbio.2c00165] [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: 11/30/2022]
12
Halder V, McDonnell B, Uthayakumar D, Usher J, Shapiro RS. Genetic interaction analysis in microbial pathogens: unravelling networks of pathogenesis, antimicrobial susceptibility and host interactions. FEMS Microbiol Rev 2021;45:fuaa055. [PMID: 33145589 DOI: 10.1093/femsre/fuaa055] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2020] [Accepted: 10/16/2020] [Indexed: 12/13/2022]  Open
13
Towards the routine use of in silico screenings for drug discovery using metabolic modelling. Biochem Soc Trans 2021;48:955-969. [PMID: 32369553 PMCID: PMC7329353 DOI: 10.1042/bst20190867] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 04/01/2020] [Accepted: 04/06/2020] [Indexed: 12/12/2022]
14
Sambamoorthy G, Raman K. MinReact: a systematic approach for identifying minimal metabolic networks. Bioinformatics 2020;36:4309-4315. [PMID: 32407533 DOI: 10.1093/bioinformatics/btaa497] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Revised: 04/22/2020] [Accepted: 05/07/2020] [Indexed: 12/12/2022]  Open
15
Bu QT, Li YP, Xie H, Wang J, Li ZY, Chen XA, Mao XM, Li YQ. Comprehensive dissection of dispensable genomic regions in Streptomyces based on comparative analysis approach. Microb Cell Fact 2020;19:99. [PMID: 32375781 PMCID: PMC7204314 DOI: 10.1186/s12934-020-01359-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2020] [Accepted: 04/29/2020] [Indexed: 02/05/2023]  Open
16
Liu Y, Wu M, Liu C, Li XL, Zheng J. SL2MF: Predicting Synthetic Lethality in Human Cancers via Logistic Matrix Factorization. IEEE/ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS 2020;17:748-757. [PMID: 30969932 DOI: 10.1109/tcbb.2019.2909908] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
17
Sastoque A, Triana S, Ehemann K, Suarez L, Restrepo S, Wösten H, de Cock H, Fernández-Niño M, González Barrios AF, Celis Ramírez AM. New Therapeutic Candidates for the Treatment of Malassezia pachydermatis -Associated Infections. Sci Rep 2020;10:4860. [PMID: 32184419 PMCID: PMC7078309 DOI: 10.1038/s41598-020-61729-1] [Citation(s) in RCA: 4] [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: 12/18/2019] [Accepted: 02/24/2020] [Indexed: 11/26/2022]  Open
18
Li GH, Dai S, Han F, Li W, Huang J, Xiao W. FastMM: an efficient toolbox for personalized constraint-based metabolic modeling. BMC Bioinformatics 2020;21:67. [PMID: 32085724 PMCID: PMC7035665 DOI: 10.1186/s12859-020-3410-4] [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: 03/12/2019] [Accepted: 02/12/2020] [Indexed: 11/24/2022]  Open
19
An integrated computational and experimental study to investigate Staphylococcus aureus metabolism. NPJ Syst Biol Appl 2020;6:3. [PMID: 32001720 PMCID: PMC6992624 DOI: 10.1038/s41540-019-0122-3] [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: 05/14/2019] [Accepted: 12/19/2019] [Indexed: 12/11/2022]  Open
20
Rawls K, Dougherty BV, Papin J. Metabolic Network Reconstructions to Predict Drug Targets and Off-Target Effects. Methods Mol Biol 2020;2088:315-330. [PMID: 31893380 DOI: 10.1007/978-1-0716-0159-4_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
21
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: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023]  Open
22
Sambamoorthy G, Raman K. Understanding the evolution of functional redundancy in metabolic networks. Bioinformatics 2019;34:i981-i987. [PMID: 30423058 PMCID: PMC6129275 DOI: 10.1093/bioinformatics/bty604] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]  Open
23
Modeling the Interplay between Photosynthesis, CO2 Fixation, and the Quinone Pool in a Purple Non-Sulfur Bacterium. Sci Rep 2019;9:12638. [PMID: 31477760 PMCID: PMC6718658 DOI: 10.1038/s41598-019-49079-z] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 08/19/2019] [Indexed: 11/17/2022]  Open
24
Vijayakumar S, Conway M, Lió P, Angione C. Seeing the wood for the trees: a forest of methods for optimization and omic-network integration in metabolic modelling. Brief Bioinform 2019;19:1218-1235. [PMID: 28575143 DOI: 10.1093/bib/bbx053] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2017] [Indexed: 11/13/2022]  Open
25
Why imaging data alone is not enough: AI-based integration of imaging, omics, and clinical data. Eur J Nucl Med Mol Imaging 2019;46:2722-2730. [PMID: 31203421 DOI: 10.1007/s00259-019-04382-9] [Citation(s) in RCA: 49] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Accepted: 05/28/2019] [Indexed: 12/13/2022]
26
Santos-Merino M, Singh AK, Ducat DC. New Applications of Synthetic Biology Tools for Cyanobacterial Metabolic Engineering. Front Bioeng Biotechnol 2019;7:33. [PMID: 30873404 PMCID: PMC6400836 DOI: 10.3389/fbioe.2019.00033] [Citation(s) in RCA: 114] [Impact Index Per Article: 22.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Accepted: 02/05/2019] [Indexed: 01/25/2023]  Open
27
Wang PH, Correia K, Ho HC, Venayak N, Nemr K, Flick R, Mahadevan R, Edwards EA. An interspecies malate-pyruvate shuttle reconciles redox imbalance in an anaerobic microbial community. ISME JOURNAL 2019;13:1042-1055. [PMID: 30607026 DOI: 10.1038/s41396-018-0333-4] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Revised: 11/26/2018] [Accepted: 11/29/2018] [Indexed: 11/09/2022]
28
Castillo S, Patil KR, Jouhten P. Yeast Genome-Scale Metabolic Models for Simulating Genotype-Phenotype Relations. PROGRESS IN MOLECULAR AND SUBCELLULAR BIOLOGY 2019;58:111-133. [PMID: 30911891 DOI: 10.1007/978-3-030-13035-0_5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
29
Klobucar K, Brown ED. Use of genetic and chemical synthetic lethality as probes of complexity in bacterial cell systems. FEMS Microbiol Rev 2018;42:4563584. [PMID: 29069427 DOI: 10.1093/femsre/fux054] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2017] [Accepted: 10/23/2017] [Indexed: 12/22/2022]  Open
30
Zhang C, Bidkhori G, Benfeitas R, Lee S, Arif M, Uhlén M, Mardinoglu A. ESS: A Tool for Genome-Scale Quantification of Essentiality Score for Reaction/Genes in Constraint-Based Modeling. Front Physiol 2018;9:1355. [PMID: 30323767 PMCID: PMC6173058 DOI: 10.3389/fphys.2018.01355] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2018] [Accepted: 09/07/2018] [Indexed: 11/17/2022]  Open
31
Xu N, Ye C, Liu L. Genome-scale biological models for industrial microbial systems. Appl Microbiol Biotechnol 2018;102:3439-3451. [PMID: 29497793 DOI: 10.1007/s00253-018-8803-1] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2017] [Revised: 01/19/2018] [Accepted: 01/21/2018] [Indexed: 01/08/2023]
32
Wang L, Maranas CD. MinGenome: An In Silico Top-Down Approach for the Synthesis of Minimized Genomes. ACS Synth Biol 2018;7:462-473. [PMID: 29254336 DOI: 10.1021/acssynbio.7b00296] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
33
Massucci FA, Sagués F, Serrano MÁ. Metabolic plasticity in synthetic lethal mutants: Viability at higher cost. PLoS Comput Biol 2018;14:e1005949. [PMID: 29381693 PMCID: PMC5806928 DOI: 10.1371/journal.pcbi.1005949] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2017] [Revised: 02/09/2018] [Accepted: 12/29/2017] [Indexed: 12/15/2022]  Open
34
Control of primary metabolism by a virulence regulatory network promotes robustness in a plant pathogen. Nat Commun 2018;9:418. [PMID: 29379078 PMCID: PMC5788922 DOI: 10.1038/s41467-017-02660-4] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2017] [Accepted: 12/17/2017] [Indexed: 11/09/2022]  Open
35
Sen P, Kemppainen E, Orešič M. Perspectives on Systems Modeling of Human Peripheral Blood Mononuclear Cells. Front Mol Biosci 2018;4:96. [PMID: 29376056 PMCID: PMC5767226 DOI: 10.3389/fmolb.2017.00096] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2017] [Accepted: 12/21/2017] [Indexed: 12/12/2022]  Open
36
Computational Prediction of Synthetic Lethals in Genome-Scale Metabolic Models Using Fast-SL. Methods Mol Biol 2018;1716:315-336. [PMID: 29222760 DOI: 10.1007/978-1-4939-7528-0_14] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
37
Sakharkar MK, Rajamanickam K, Chandra R, Khan HA, Alhomida AS, Yang J. Identification of novel drug targets in bovine respiratory disease: an essential step in applying biotechnologic techniques to develop more effective therapeutic treatments. Drug Des Devel Ther 2018;12:1135-1146. [PMID: 29765203 PMCID: PMC5944452 DOI: 10.2147/dddt.s163476] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]  Open
38
The MONGOOSE Rational Arithmetic Toolbox. Methods Mol Biol 2017. [PMID: 29222749 DOI: 10.1007/978-1-4939-7528-0_3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
39
Coupling Fluxes, Enzymes, and Regulation in Genome-Scale Metabolic Models. METHODS IN MOLECULAR BIOLOGY (CLIFTON, N.J.) 2017;1716:337-351. [PMID: 29222761 DOI: 10.1007/978-1-4939-7528-0_15] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
40
Joshi CJ, Peebles CA, Prasad A. Modeling and analysis of flux distribution and bioproduct formation in Synechocystis sp. PCC 6803 using a new genome-scale metabolic reconstruction. ALGAL RES 2017. [DOI: 10.1016/j.algal.2017.09.013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
41
Gottstein W, Olivier BG, Bruggeman FJ, Teusink B. Constraint-based stoichiometric modelling from single organisms to microbial communities. J R Soc Interface 2017;13:rsif.2016.0627. [PMID: 28334697 PMCID: PMC5134014 DOI: 10.1098/rsif.2016.0627] [Citation(s) in RCA: 61] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2016] [Accepted: 10/17/2016] [Indexed: 12/13/2022]  Open
42
Apaolaza I, San José-Eneriz E, Tobalina L, Miranda E, Garate L, Agirre X, Prósper F, Planes FJ. An in-silico approach to predict and exploit synthetic lethality in cancer metabolism. Nat Commun 2017;8:459. [PMID: 28878380 PMCID: PMC5587678 DOI: 10.1038/s41467-017-00555-y] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2016] [Accepted: 07/07/2017] [Indexed: 02/02/2023]  Open
43
Characterizing Gene and Protein Crosstalks in Subjects at Risk of Developing Alzheimer’s Disease: A New Computational Approach. Processes (Basel) 2017. [DOI: 10.3390/pr5030047] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]  Open
44
Tiruveedula GSS, Wangikar PP. Gene essentiality, conservation index and co-evolution of genes in cyanobacteria. PLoS One 2017;12:e0178565. [PMID: 28594867 PMCID: PMC5464585 DOI: 10.1371/journal.pone.0178565] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2017] [Accepted: 05/15/2017] [Indexed: 11/18/2022]  Open
45
Labena AA, Ye YN, Dong C, Zhang FZ, Guo FB. SSER: Species specific essential reactions database. BMC SYSTEMS BIOLOGY 2017;11:50. [PMID: 28420402 PMCID: PMC5395902 DOI: 10.1186/s12918-017-0426-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/23/2016] [Accepted: 04/13/2017] [Indexed: 01/05/2023]
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Cohen O, Oberhardt M, Yizhak K, Ruppin E. Essential Genes Embody Increased Mutational Robustness to Compensate for the Lack of Backup Genetic Redundancy. PLoS One 2016;11:e0168444. [PMID: 27997585 PMCID: PMC5173180 DOI: 10.1371/journal.pone.0168444] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2016] [Accepted: 12/01/2016] [Indexed: 11/23/2022]  Open
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The Genome-Wide Interaction Network of Nutrient Stress Genes in Escherichia coli. mBio 2016;7:mBio.01714-16. [PMID: 27879333 PMCID: PMC5120140 DOI: 10.1128/mbio.01714-16] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]  Open
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Machado D, Herrgård MJ, Rocha I. Stoichiometric Representation of Gene-Protein-Reaction Associations Leverages Constraint-Based Analysis from Reaction to Gene-Level Phenotype Prediction. PLoS Comput Biol 2016;12:e1005140. [PMID: 27711110 PMCID: PMC5053500 DOI: 10.1371/journal.pcbi.1005140] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 09/13/2016] [Indexed: 12/05/2022]  Open
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Hendry JI, Prasannan CB, Joshi A, Dasgupta S, Wangikar PP. Metabolic model of Synechococcus sp. PCC 7002: Prediction of flux distribution and network modification for enhanced biofuel production. BIORESOURCE TECHNOLOGY 2016;213:190-197. [PMID: 27036328 DOI: 10.1016/j.biortech.2016.02.128] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/02/2016] [Revised: 02/25/2016] [Accepted: 02/26/2016] [Indexed: 05/18/2023]
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Jackson RA, Chen ES. Synthetic lethal approaches for assessing combinatorial efficacy of chemotherapeutic drugs. Pharmacol Ther 2016;162:69-85. [DOI: 10.1016/j.pharmthera.2016.01.014] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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