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For: Cottret L, Jourdan F. 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: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Number Cited by Other Article(s)
1
Salzer L, Novoa-Del-Toro EM, Frainay C, Kissoyan KAB, Jourdan F, Dierking K, Witting M. APEX: an Annotation Propagation Workflow through Multiple Experimental Networks to Improve the Annotation of New Metabolite Classes in Caenorhabditis elegans. Anal Chem 2023;95:17550-17558. [PMID: 37984857 DOI: 10.1021/acs.analchem.3c02797] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2023]
2
Baron C, Cherkaoui S, Therrien-Laperriere S, Ilboudo Y, Poujol R, Mehanna P, Garrett ME, Telen MJ, Ashley-Koch AE, Bartolucci P, Rioux JD, Lettre G, Des Rosiers C, Ruiz M, Hussin JG. Gene-metabolite annotation with shortest reactional distance enhances metabolite genome-wide association studies results. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.03.22.533869. [PMID: 36993181 PMCID: PMC10055409 DOI: 10.1101/2023.03.22.533869] [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] [Indexed: 06/19/2023]
3
Amara A, Frainay C, Jourdan F, Naake T, Neumann S, Novoa-del-Toro EM, Salek RM, Salzer L, Scharfenberg S, Witting M. Networks and Graphs Discovery in Metabolomics Data Analysis and Interpretation. Front Mol Biosci 2022;9:841373. [PMID: 35350714 PMCID: PMC8957799 DOI: 10.3389/fmolb.2022.841373] [Citation(s) in RCA: 24] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2021] [Accepted: 02/18/2022] [Indexed: 01/19/2023]  Open
4
Serral F, Pardo AM, Sosa E, Palomino MM, Nicolás MF, Turjanski AG, Ramos PIP, Fernández Do Porto D. Pathway Driven Target Selection in Klebsiella pneumoniae: Insights Into Carbapenem Exposure. Front Cell Infect Microbiol 2022;12:773405. [PMID: 35174104 PMCID: PMC8841789 DOI: 10.3389/fcimb.2022.773405] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2021] [Accepted: 01/07/2022] [Indexed: 12/13/2022]  Open
5
Serral F, Castello FA, Sosa EJ, Pardo AM, Palumbo MC, Modenutti C, Palomino MM, Lazarowski A, Auzmendi J, Ramos PIP, Nicolás MF, Turjanski AG, Martí MA, Fernández Do Porto D. From Genome to Drugs: New Approaches in Antimicrobial Discovery. Front Pharmacol 2021;12:647060. [PMID: 34177572 PMCID: PMC8219968 DOI: 10.3389/fphar.2021.647060] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/28/2020] [Accepted: 05/17/2021] [Indexed: 01/31/2023]  Open
6
Ramos PIP, Arge LWP, Lima NCB, Fukutani KF, de Queiroz ATL. Leveraging User-Friendly Network Approaches to Extract Knowledge From High-Throughput Omics Datasets. Front Genet 2019;10:1120. [PMID: 31798629 PMCID: PMC6863976 DOI: 10.3389/fgene.2019.01120] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2019] [Accepted: 10/16/2019] [Indexed: 11/13/2022]  Open
7
Megalios A, Daly R, Burgess K. MetaboCraft: building a Minecraft plugin for metabolomics. Bioinformatics 2019;34:2693-2694. [PMID: 29608638 PMCID: PMC6061834 DOI: 10.1093/bioinformatics/bty102] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/04/2017] [Accepted: 03/27/2018] [Indexed: 12/02/2022]  Open
8
Treur J. Modelling and analysis of the dynamics of adaptive temporal-causal network models for evolving social interactions. COMPUTATIONAL SOCIAL NETWORKS 2017;4:4. [PMID: 29266142 PMCID: PMC5732605 DOI: 10.1186/s40649-017-0039-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/16/2017] [Accepted: 05/31/2017] [Indexed: 11/19/2022]
9
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: 42] [Impact Index Per Article: 5.3] [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
10
Shameer S, Logan-Klumpler FJ, Vinson F, Cottret L, Merlet B, Achcar F, Boshart M, Berriman M, Breitling R, Bringaud F, Bütikofer P, Cattanach AM, Bannerman-Chukualim B, Creek DJ, Crouch K, de Koning HP, Denise H, Ebikeme C, Fairlamb AH, Ferguson MAJ, Ginger ML, Hertz-Fowler C, Kerkhoven EJ, Mäser P, Michels PAM, Nayak A, Nes DW, Nolan DP, Olsen C, Silva-Franco F, Smith TK, Taylor MC, Tielens AGM, Urbaniak MD, van Hellemond JJ, Vincent IM, Wilkinson SR, Wyllie S, Opperdoes FR, Barrett MP, Jourdan F. TrypanoCyc: a community-led biochemical pathways database for Trypanosoma brucei. Nucleic Acids Res 2014;43:D637-44. [PMID: 25300491 PMCID: PMC4384016 DOI: 10.1093/nar/gku944] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
11
Klein CC, Cottret L, Kielbassa J, Charles H, Gautier C, Ribeiro de Vasconcelos AT, Lacroix V, Sagot MF. Exploration of the core metabolism of symbiotic bacteria. BMC Genomics 2012;13:438. [PMID: 22938206 PMCID: PMC3543179 DOI: 10.1186/1471-2164-13-438] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2012] [Accepted: 08/18/2012] [Indexed: 12/01/2022]  Open
12
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: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
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