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For: Rahman SA, Schomburg D. Observing local and global properties of metabolic pathways: ‘load points’ and ‘choke points’ in the metabolic networks. Bioinformatics 2006;22:1767-74. [PMID: 16682421 DOI: 10.1093/bioinformatics/btl181] [Citation(s) in RCA: 80] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Ashraf H, Dikarlo P, Masia A, Zarbo IR, Solla P, Ijaz UZ, Sechi LA. Network analysis of gut microbial communities reveal key genera for a multiple sclerosis cohort with Mycobacterium avium subspecies paratuberculosis infection. Gut Pathog 2024;16:37. [PMID: 38987816 PMCID: PMC11238521 DOI: 10.1186/s13099-024-00627-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/14/2024] [Accepted: 06/28/2024] [Indexed: 07/12/2024]  Open
2
Nehvi IB, Quadir N, Khubaib M, Sheikh JA, Shariq M, Mohareer K, Banerjee S, Rahman SA, Ehtesham NZ, Hasnain SE. ArgD of Mycobacterium tuberculosis is a functional N-acetylornithine aminotransferase with moonlighting function as an effective immune modulator. Int J Med Microbiol 2022;312:151544. [DOI: 10.1016/j.ijmm.2021.151544] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 12/02/2021] [Accepted: 12/05/2021] [Indexed: 12/18/2022]  Open
3
Aromolaran O, Aromolaran D, Isewon I, Oyelade J. Machine learning approach to gene essentiality prediction: a review. Brief Bioinform 2021;22:6219158. [PMID: 33842944 DOI: 10.1093/bib/bbab128] [Citation(s) in RCA: 56] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 03/04/2021] [Accepted: 03/17/2021] [Indexed: 12/17/2022]  Open
4
Dusad V, Thiel D, Barahona M, Keun HC, Oyarzún DA. Opportunities at the Interface of Network Science and Metabolic Modeling. Front Bioeng Biotechnol 2021;8:591049. [PMID: 33569373 PMCID: PMC7868444 DOI: 10.3389/fbioe.2020.591049] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2020] [Accepted: 12/22/2020] [Indexed: 12/17/2022]  Open
5
Curran DM, Grote A, Nursimulu N, Geber A, Voronin D, Jones DR, Ghedin E, Parkinson J. Modeling the metabolic interplay between a parasitic worm and its bacterial endosymbiont allows the identification of novel drug targets. eLife 2020;9:e51850. [PMID: 32779567 PMCID: PMC7419141 DOI: 10.7554/elife.51850] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 07/14/2020] [Indexed: 12/17/2022]  Open
6
Oyelade J, Isewon I, Aromolaran O, Uwoghiren E, Dokunmu T, Rotimi S, Aworunse O, Obembe O, Adebiyi E. Computational Identification of Metabolic Pathways of Plasmodium falciparum using the k-Shortest Path Algorithm. Int J Genomics 2019;2019:1750291. [PMID: 31662957 PMCID: PMC6791207 DOI: 10.1155/2019/1750291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 11/28/2018] [Accepted: 07/29/2019] [Indexed: 02/02/2023]  Open
7
Garg A, Kumari B, Singhal N, Kumar M. Using molecular-mimicry-inducing pathways of pathogens as novel drug targets. Drug Discov Today 2019;24:1943-1952. [DOI: 10.1016/j.drudis.2018.10.010] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2018] [Revised: 09/04/2018] [Accepted: 10/16/2018] [Indexed: 01/27/2023]
8
Meshram RJ, Goundge MB, Kolte BS, Gacche RN. An in silico approach in identification of drug targets in Leishmania: A subtractive genomic and metabolic simulation analysis. Parasitol Int 2018;69:59-70. [PMID: 30503238 DOI: 10.1016/j.parint.2018.11.006] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/17/2018] [Accepted: 11/28/2018] [Indexed: 12/26/2022]
9
In Silico Knockout Screening of Plasmodium falciparum Reactions and Prediction of Novel Essential Reactions by Analysing the Metabolic Network. BIOMED RESEARCH INTERNATIONAL 2018;2018:8985718. [PMID: 29789805 PMCID: PMC5896307 DOI: 10.1155/2018/8985718] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/03/2017] [Revised: 02/04/2018] [Accepted: 02/19/2018] [Indexed: 01/18/2023]
10
Muller EE, Faust K, Widder S, Herold M, Martínez Arbas S, Wilmes P. Using metabolic networks to resolve ecological properties of microbiomes. ACTA ACUST UNITED AC 2018. [DOI: 10.1016/j.coisb.2017.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
11
Thilaga M, Ramasamy V, Nadarajan R, Nandagopal D. Shortest path based network analysis to characterize cognitive load states of human brain using EEG based functional brain networks. J Integr Neurosci 2018. [DOI: 10.3233/jin-170049] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]  Open
12
Khan S, Somvanshi P, Bhardwaj T, Mandal RK, Dar SA, Wahid M, Jawed A, Lohani M, Khan M, Areeshi MY, Haque S. Aspartate‐β‐semialdeyhyde dehydrogenase as a potential therapeutic target of Mycobacterium tuberculosis H37Rv: Evidence from in silico elementary mode analysis of biological network model. J Cell Biochem 2017;119:2832-2842. [DOI: 10.1002/jcb.26458] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Accepted: 10/24/2017] [Indexed: 02/06/2023]
13
Abd Algfoor Z, Shahrizal Sunar M, Abdullah A, Kolivand H. Identification of metabolic pathways using pathfinding approaches: a systematic review. Brief Funct Genomics 2017;16:87-98. [PMID: 26969656 DOI: 10.1093/bfgp/elw002] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
14
Quinn RA, Whiteson K, Lim YW, Zhao J, Conrad D, LiPuma JJ, Rohwer F, Widder S. Ecological networking of cystic fibrosis lung infections. NPJ Biofilms Microbiomes 2016;2:4. [PMID: 28649398 PMCID: PMC5460249 DOI: 10.1038/s41522-016-0002-1] [Citation(s) in RCA: 67] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2016] [Revised: 07/13/2016] [Accepted: 07/27/2016] [Indexed: 11/22/2022]  Open
15
Kaltdorf M, Srivastava M, Gupta SK, Liang C, Binder J, Dietl AM, Meir Z, Haas H, Osherov N, Krappmann S, Dandekar T. Systematic Identification of Anti-Fungal Drug Targets by a Metabolic Network Approach. Front Mol Biosci 2016;3:22. [PMID: 27379244 PMCID: PMC4911368 DOI: 10.3389/fmolb.2016.00022] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 05/24/2016] [Indexed: 11/13/2022]  Open
16
Frainay C, Jourdan F. Computational methods to identify metabolic sub-networks based on metabolomic profiles. Brief Bioinform 2016;18:43-56. [PMID: 26822099 DOI: 10.1093/bib/bbv115] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2015] [Revised: 12/16/2015] [Indexed: 11/13/2022]  Open
17
Ekins S, Madrid PB, Sarker M, Li SG, Mittal N, Kumar P, Wang X, Stratton TP, Zimmerman M, Talcott C, Bourbon P, Travers M, Yadav M, Freundlich JS. Combining Metabolite-Based Pharmacophores with Bayesian Machine Learning Models for Mycobacterium tuberculosis Drug Discovery. PLoS One 2015;10:e0141076. [PMID: 26517557 PMCID: PMC4627656 DOI: 10.1371/journal.pone.0141076] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2015] [Accepted: 10/05/2015] [Indexed: 12/15/2022]  Open
18
Roume H, Heintz-Buschart A, Muller EEL, May P, Satagopam VP, Laczny CC, Narayanasamy S, Lebrun LA, Hoopmann MR, Schupp JM, Gillece JD, Hicks ND, Engelthaler DM, Sauter T, Keim PS, Moritz RL, Wilmes P. Comparative integrated omics: identification of key functionalities in microbial community-wide metabolic networks. NPJ Biofilms Microbiomes 2015;1:15007. [PMID: 28721231 PMCID: PMC5515219 DOI: 10.1038/npjbiofilms.2015.7] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2015] [Revised: 04/24/2015] [Accepted: 05/06/2015] [Indexed: 11/08/2022]  Open
19
Narang P, Khan S, Hemrom AJ, Lynn AM. MetaNET--a web-accessible interactive platform for biological metabolic network analysis. BMC SYSTEMS BIOLOGY 2014;8:130. [PMID: 25779921 PMCID: PMC4267457 DOI: 10.1186/s12918-014-0130-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 11/12/2014] [Indexed: 11/10/2022]
20
Rezola A, Pey J, Tobalina L, Rubio A, Beasley JE, Planes FJ. Advances in network-based metabolic pathway analysis and gene expression data integration. Brief Bioinform 2014;16:265-79. [DOI: 10.1093/bib/bbu009] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
21
Barupal DK, Lee SJ, Karoly ED, Adhya S. Inactivation of metabolic genes causes short- and long-range dys-regulation in Escherichia coli metabolic network. PLoS One 2013;8:e78360. [PMID: 24363806 PMCID: PMC3868466 DOI: 10.1371/journal.pone.0078360] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 09/19/2013] [Indexed: 01/01/2023]  Open
22
Plaimas K, Wang Y, Rotimi SO, Olasehinde G, Fatumo S, Lanzer M, Adebiyi E, König R. Computational and experimental analysis identified 6-diazo-5-oxonorleucine as a potential agent for treating infection by Plasmodium falciparum. INFECTION, GENETICS AND EVOLUTION : JOURNAL OF MOLECULAR EPIDEMIOLOGY AND EVOLUTIONARY GENETICS IN INFECTIOUS DISEASES 2013;20:389-95. [PMID: 24121016 DOI: 10.1016/j.meegid.2013.09.019] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/12/2013] [Revised: 09/17/2013] [Accepted: 09/18/2013] [Indexed: 10/26/2022]
23
Oberhardt MA, Yizhak K, Ruppin E. Metabolically re-modeling the drug pipeline. Curr Opin Pharmacol 2013;13:778-85. [DOI: 10.1016/j.coph.2013.05.006] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 05/04/2013] [Accepted: 05/06/2013] [Indexed: 02/07/2023]
24
Taylor CM, Wang Q, Rosa BA, Huang SCC, Powell K, Schedl T, Pearce EJ, Abubucker S, Mitreva M. Discovery of anthelmintic drug targets and drugs using chokepoints in nematode metabolic pathways. PLoS Pathog 2013;9:e1003505. [PMID: 23935495 PMCID: PMC3731235 DOI: 10.1371/journal.ppat.1003505] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/03/2013] [Indexed: 12/19/2022]  Open
25
Yadav MK, Pandey SK, Swati D. DRUG TARGET PRIORITIZATION IN PLASMODIUM FALCIPARUM THROUGH METABOLIC NETWORK ANALYSIS, AND INHIBITOR DESIGNING USING VIRTUAL SCREENING AND DOCKING APPROACH. J Bioinform Comput Biol 2013;11:1350003. [DOI: 10.1142/s0219720013500030] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
26
Chung BKS, Dick T, Lee DY. In silico analyses for the discovery of tuberculosis drug targets. J Antimicrob Chemother 2013;68:2701-9. [DOI: 10.1093/jac/dkt273] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
27
Jadhav A, Ezhilarasan V, Prakash Sharma O, Pan A. Clostridium-DT(DB): a comprehensive database for potential drug targets of Clostridium difficile. Comput Biol Med 2013;43:362-7. [PMID: 23415847 DOI: 10.1016/j.compbiomed.2013.01.009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2011] [Revised: 01/15/2013] [Accepted: 01/20/2013] [Indexed: 01/05/2023]
28
Sarker M, Talcott C, Galande AK. In silico systems biology approaches for the identification of antimicrobial targets. Methods Mol Biol 2013;993:13-30. [PMID: 23568461 DOI: 10.1007/978-1-62703-342-8_2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
29
Choorapoikayil S, Schoepe J, Buchinger S, Schomburg D. Analysis of in vivo Function of Predicted Isoenzymes—A Metabolomic Approach. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2012;16:668-80. [DOI: 10.1089/omi.2012.0055] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
30
Chandra N, Padiadpu J. Network approaches to drug discovery. Expert Opin Drug Discov 2012;8:7-20. [PMID: 23140510 DOI: 10.1517/17460441.2013.741119] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
31
Dandekar T, Fieselmann A, Majeed S, Ahmed Z. Software applications toward quantitative metabolic flux analysis and modeling. Brief Bioinform 2012;15:91-107. [PMID: 23142828 DOI: 10.1093/bib/bbs065] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]  Open
32
Sharma A, Pan A. Identification of potential drug targets in Yersinia pestis using metabolic pathway analysis: MurE ligase as a case study. Eur J Med Chem 2012;57:185-95. [DOI: 10.1016/j.ejmech.2012.09.018] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2012] [Revised: 09/07/2012] [Accepted: 09/11/2012] [Indexed: 01/14/2023]
33
Ontological Analysis and Pathway Modelling in Drug Discovery. Pharmaceut Med 2012. [DOI: 10.1007/bf03256689] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
34
Klein C, Marino A, Sagot MF, Vieira Milreu P, Brilli M. Structural and dynamical analysis of biological networks. Brief Funct Genomics 2012;11:420-33. [PMID: 22908211 DOI: 10.1093/bfgp/els030] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
35
Chanumolu SK, Rout C, Chauhan RS. UniDrug-target: a computational tool to identify unique drug targets in pathogenic bacteria. PLoS One 2012;7:e32833. [PMID: 22431985 PMCID: PMC3303792 DOI: 10.1371/journal.pone.0032833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2011] [Accepted: 01/31/2012] [Indexed: 11/30/2022]  Open
36
Kim HU, Sohn SB, Lee SY. Metabolic network modeling and simulation for drug targeting and discovery. Biotechnol J 2011;7:330-42. [DOI: 10.1002/biot.201100159] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2011] [Revised: 09/09/2011] [Accepted: 10/08/2011] [Indexed: 11/08/2022]
37
ČUPERLOVIĆ-CULF MIROSLAVA. THE IMPORTANCE OF INHIBITORS FOR THE SIMULATION OF METABOLIC PROCESSES: IN SILICOZn2+ INHIBITION OF m-ACONITASE FROM ANALYSIS OF GLYCOLYSIS AND KREBS CYCLE KINETIC MODELS. J Bioinform Comput Biol 2011. [DOI: 10.1142/s0219720010004872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
38
Stelzer M, Sun J, Kamphans T, Fekete SP, Zeng AP. An extended bioreaction database that significantly improves reconstruction and analysis of genome-scale metabolic networks. Integr Biol (Camb) 2011;3:1071-86. [DOI: 10.1039/c1ib00008j] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
39
Kranz AL, Eils R, König R. Enhancers regulate progression of development in mammalian cells. Nucleic Acids Res 2011;39:8689-702. [PMID: 21785139 PMCID: PMC3203619 DOI: 10.1093/nar/gkr602] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]  Open
40
Comparing metabolic network models based on genomic and automatically inferred enzyme information from Plasmodium and its human host to define drug targets in silico. INFECTION GENETICS AND EVOLUTION 2011;11:708-15. [DOI: 10.1016/j.meegid.2011.04.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
41
Pey J, Prada J, Beasley JE, Planes FJ. Path finding methods accounting for stoichiometry in metabolic networks. Genome Biol 2011;12:R49. [PMID: 21619601 PMCID: PMC3219972 DOI: 10.1186/gb-2011-12-5-r49] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2011] [Revised: 05/14/2011] [Accepted: 05/27/2011] [Indexed: 01/30/2023]  Open
42
Baths V, Roy U, Singh T. Disruption of cell wall fatty acid biosynthesis in Mycobacterium tuberculosis using a graph theoretic approach. Theor Biol Med Model 2011;8:5. [PMID: 21453530 PMCID: PMC3087688 DOI: 10.1186/1742-4682-8-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2011] [Accepted: 03/31/2011] [Indexed: 12/01/2022]  Open
43
Lee DY, Chung BKS, Yusufi FN, Selvarasu S. In silico genome-scale modeling and analysis for identifying anti-tubercular drug targets. Drug Dev Res 2010. [DOI: 10.1002/ddr.20408] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
44
Koschützki D, Junker BH, Schwender J, Schreiber F. Structural analysis of metabolic networks based on flux centrality. J Theor Biol 2010;265:261-9. [PMID: 20471988 DOI: 10.1016/j.jtbi.2010.05.009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2009] [Revised: 05/07/2010] [Accepted: 05/07/2010] [Indexed: 11/19/2022]
45
Graph methods for the investigation of metabolic networks in parasitology. Parasitology 2010;137:1393-407. [PMID: 20444302 DOI: 10.1017/s0031182010000363] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
46
Plaimas K, Eils R, König R. Identifying essential genes in bacterial metabolic networks with machine learning methods. BMC SYSTEMS BIOLOGY 2010;4:56. [PMID: 20438628 PMCID: PMC2874528 DOI: 10.1186/1752-0509-4-56] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/17/2009] [Accepted: 05/03/2010] [Indexed: 01/05/2023]
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Zhao J, Jiang P, Zhang W. Molecular networks for the study of TCM pharmacology. Brief Bioinform 2009;11:417-30. [PMID: 20038567 DOI: 10.1093/bib/bbp063] [Citation(s) in RCA: 163] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]  Open
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Karp PD, Paley SM, Krummenacker M, Latendresse M, Dale JM, Lee TJ, Kaipa P, Gilham F, Spaulding A, Popescu L, Altman T, Paulsen I, Keseler IM, Caspi R. Pathway Tools version 13.0: integrated software for pathway/genome informatics and systems biology. Brief Bioinform 2009;11:40-79. [PMID: 19955237 DOI: 10.1093/bib/bbp043] [Citation(s) in RCA: 331] [Impact Index Per Article: 20.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]  Open
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Emmert-Streib F, Dehmer M. Predicting cell cycle regulated genes by causal interactions. PLoS One 2009;4:e6633. [PMID: 19688096 PMCID: PMC2723924 DOI: 10.1371/journal.pone.0006633] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2009] [Accepted: 04/23/2009] [Indexed: 11/28/2022]  Open
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Emmert-Streib F, Dehmer M. Hierarchical coordination of periodic genes in the cell cycle of Saccharomyces cerevisiae. BMC SYSTEMS BIOLOGY 2009;3:76. [PMID: 19619302 PMCID: PMC2721836 DOI: 10.1186/1752-0509-3-76] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/12/2009] [Accepted: 07/20/2009] [Indexed: 11/25/2022]
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