• Reference Citation Analysis
  • v
  • v
  • Find an Article
Find an Article PDF (4610646)   Today's Articles (293)   Subscriber (49380)
For: Kastenmüller G, Schenk ME, Gasteiger J, Mewes HW. Uncovering metabolic pathways relevant to phenotypic traits of microbial genomes. Genome Biol 2009;10:R28. [PMID: 19284550 PMCID: PMC2690999 DOI: 10.1186/gb-2009-10-3-r28] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2008] [Revised: 02/12/2009] [Accepted: 03/10/2009] [Indexed: 01/20/2023]  Open
Number Cited by Other Article(s)
1
Siddharth T, Lewis NE. Predicting pathways for old and new metabolites through clustering. J Theor Biol 2024;578:111684. [PMID: 38048983 PMCID: PMC11139542 DOI: 10.1016/j.jtbi.2023.111684] [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: 06/08/2023] [Revised: 11/17/2023] [Accepted: 11/29/2023] [Indexed: 12/06/2023]
2
Karp PD, Paley S, Caspi R, Kothari A, Krummenacker M, Midford PE, Moore LR, Subhraveti P, Gama-Castro S, Tierrafria VH, Lara P, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Sun G, Ahn-Horst TA, Choi H, Covert MW, Collado-Vides J, Paulsen I. The EcoCyc Database (2023). EcoSal Plus 2023;11:eesp00022023. [PMID: 37220074 PMCID: PMC10729931 DOI: 10.1128/ecosalplus.esp-0002-2023] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2023] [Accepted: 04/04/2023] [Indexed: 01/28/2024]
3
Singh DP, Bisen MS, Shukla R, Prabha R, Maurya S, Reddy YS, Singh PM, Rai N, Chaubey T, Chaturvedi KK, Srivastava S, Farooqi MS, Gupta VK, Sarma BK, Rai A, Behera TK. Metabolomics-Driven Mining of Metabolite Resources: Applications and Prospects for Improving Vegetable Crops. Int J Mol Sci 2022;23:ijms232012062. [PMID: 36292920 PMCID: PMC9603451 DOI: 10.3390/ijms232012062] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2022] [Revised: 09/13/2022] [Accepted: 09/23/2022] [Indexed: 11/16/2022]  Open
4
Chen B, Rupani PF, Azman S, Dewil R, Appels L. A redox-based strategy to enhance propionic and butyric acid production during anaerobic fermentation. BIORESOURCE TECHNOLOGY 2022;361:127672. [PMID: 35878771 DOI: 10.1016/j.biortech.2022.127672] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 07/17/2022] [Accepted: 07/18/2022] [Indexed: 06/15/2023]
5
Gasteiger J. Chemistry in Times of Artificial Intelligence. Chemphyschem 2020;21:2233-2242. [PMID: 32808729 PMCID: PMC7702165 DOI: 10.1002/cphc.202000518] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/14/2020] [Indexed: 11/09/2022]
6
Karp PD, Ong WK, Paley S, Billington R, Caspi R, Fulcher C, Kothari A, Krummenacker M, Latendresse M, Midford PE, Subhraveti P, Gama-Castro S, Muñiz-Rascado L, Bonavides-Martinez C, Santos-Zavaleta A, Mackie A, Collado-Vides J, Keseler IM, Paulsen I. The EcoCyc Database. EcoSal Plus 2018;8:10.1128/ecosalplus.ESP-0006-2018. [PMID: 30406744 PMCID: PMC6504970 DOI: 10.1128/ecosalplus.esp-0006-2018] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Indexed: 01/28/2023]
7
Burns JA, Pittis AA, Kim E. Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic. Nat Ecol Evol 2018;2:697-704. [DOI: 10.1038/s41559-018-0477-7] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2017] [Accepted: 01/11/2018] [Indexed: 12/24/2022]
8
Kaur H, Das C, Mande SS. In Silico Analysis of Putrefaction Pathways in Bacteria and Its Implication in Colorectal Cancer. Front Microbiol 2017;8:2166. [PMID: 29163445 PMCID: PMC5682003 DOI: 10.3389/fmicb.2017.02166] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2017] [Accepted: 10/23/2017] [Indexed: 12/15/2022]  Open
9
From Genomes to Phenotypes: Traitar, the Microbial Trait Analyzer. mSystems 2016;1:mSystems00101-16. [PMID: 28066816 PMCID: PMC5192078 DOI: 10.1128/msystems.00101-16] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Accepted: 11/12/2016] [Indexed: 01/17/2023]  Open
10
Brbić M, Piškorec M, Vidulin V, Kriško A, Šmuc T, Supek F. The landscape of microbial phenotypic traits and associated genes. Nucleic Acids Res 2016;44:10074-10090. [PMID: 27915291 PMCID: PMC5137458 DOI: 10.1093/nar/gkw964] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2016] [Revised: 09/21/2016] [Accepted: 10/11/2016] [Indexed: 12/31/2022]  Open
11
Gasteiger J. Explorations into Chemical Reactions and Biochemical Pathways. Mol Inform 2016;35:588-592. [DOI: 10.1002/minf.201600038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Accepted: 04/25/2016] [Indexed: 11/07/2022]
12
Tamames J, Sánchez PD, Nikel PI, Pedrós-Alió C. Quantifying the Relative Importance of Phylogeny and Environmental Preferences As Drivers of Gene Content in Prokaryotic Microorganisms. Front Microbiol 2016;7:433. [PMID: 27065987 PMCID: PMC4814473 DOI: 10.3389/fmicb.2016.00433] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2015] [Accepted: 03/17/2016] [Indexed: 01/15/2023]  Open
13
Chemoinformatics: Achievements and Challenges, a Personal View. Molecules 2016;21:151. [PMID: 26828468 PMCID: PMC6273366 DOI: 10.3390/molecules21020151] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2015] [Revised: 01/14/2016] [Accepted: 01/20/2016] [Indexed: 11/16/2022]  Open
14
Burns JA, Paasch A, Narechania A, Kim E. Comparative Genomics of a Bacterivorous Green Alga Reveals Evolutionary Causalities and Consequences of Phago-Mixotrophic Mode of Nutrition. Genome Biol Evol 2015. [PMID: 26224703 PMCID: PMC5741210 DOI: 10.1093/gbe/evv144] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]  Open
15
Karp PD, Weaver D, Paley S, Fulcher C, Kubo A, Kothari A, Krummenacker M, Subhraveti P, Weerasinghe D, Gama-Castro S, Huerta AM, Muñiz-Rascado L, Bonavides-Martinez C, Weiss V, Peralta-Gil M, Santos-Zavaleta A, Schröder I, Mackie A, Gunsalus R, Collado-Vides J, Keseler IM, Paulsen I. The EcoCyc Database. EcoSal Plus 2014;6:10.1128/ecosalplus.ESP-0009-2013. [PMID: 26442933 PMCID: PMC4243172 DOI: 10.1128/ecosalplus.esp-0009-2013] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2014] [Indexed: 11/20/2022]
16
Gasteiger J. Some solved and unsolved problems of chemoinformatics. SAR AND QSAR IN ENVIRONMENTAL RESEARCH 2014;25:443-455. [PMID: 24716817 DOI: 10.1080/1062936x.2014.898688] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
17
Metatranscriptomics of the human oral microbiome during health and disease. mBio 2014;5:e01012-14. [PMID: 24692635 PMCID: PMC3977359 DOI: 10.1128/mbio.01012-14] [Citation(s) in RCA: 239] [Impact Index Per Article: 23.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]  Open
18
Combining chemoinformatics with bioinformatics: in silico prediction of bacterial flavor-forming pathways by a chemical systems biology approach "reverse pathway engineering". PLoS One 2014;9:e84769. [PMID: 24416282 PMCID: PMC3885609 DOI: 10.1371/journal.pone.0084769] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2013] [Accepted: 11/18/2013] [Indexed: 12/05/2022]  Open
19
Boon E, Meehan CJ, Whidden C, Wong DHJ, Langille MGI, Beiko RG. Interactions in the microbiome: communities of organisms and communities of genes. FEMS Microbiol Rev 2014;38:90-118. [PMID: 23909933 PMCID: PMC4298764 DOI: 10.1111/1574-6976.12035] [Citation(s) in RCA: 119] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2013] [Revised: 07/02/2013] [Accepted: 07/10/2013] [Indexed: 12/17/2022]  Open
20
Konietzny SGA, Pope PB, Weimann A, McHardy AC. Inference of phenotype-defining functional modules of protein families for microbial plant biomass degraders. BIOTECHNOLOGY FOR BIOFUELS 2014;7:124. [PMID: 25342967 PMCID: PMC4189754 DOI: 10.1186/s13068-014-0124-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2014] [Accepted: 08/05/2014] [Indexed: 05/14/2023]
21
Psomopoulos FE, Mitkas PA, Ouzounis CA. Detection of genomic idiosyncrasies using fuzzy phylogenetic profiles. PLoS One 2013;8:e52854. [PMID: 23341912 PMCID: PMC3544837 DOI: 10.1371/journal.pone.0052854] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2012] [Accepted: 11/22/2012] [Indexed: 11/18/2022]  Open
22
In-silico identification of phenotype-biased functional modules. Proteome Sci 2012;10 Suppl 1:S2. [PMID: 22759578 PMCID: PMC3380726 DOI: 10.1186/1477-5956-10-s1-s2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
23
Schmidt MC, Rocha AM, Padmanabhan K, Shpanskaya Y, Banfield J, Scott K, Mihelcic JR, Samatova NF. NIBBS-search for fast and accurate prediction of phenotype-biased metabolic systems. PLoS Comput Biol 2012;8:e1002490. [PMID: 22589706 PMCID: PMC3349732 DOI: 10.1371/journal.pcbi.1002490] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 03/08/2012] [Indexed: 02/07/2023]  Open
24
Use of comparative genomics approaches to characterize interspecies differences in response to environmental chemicals: challenges, opportunities, and research needs. Toxicol Appl Pharmacol 2011;271:372-85. [PMID: 22142766 DOI: 10.1016/j.taap.2011.11.011] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Revised: 11/11/2011] [Accepted: 11/16/2011] [Indexed: 01/12/2023]
25
Whitmore SE, Lamont RJ. The pathogenic persona of community-associated oral streptococci. Mol Microbiol 2011;81:305-14. [PMID: 21635580 DOI: 10.1111/j.1365-2958.2011.07707.x] [Citation(s) in RCA: 74] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
26
Lingner T, Mühlhausen S, Gabaldón T, Notredame C, Meinicke P. Predicting phenotypic traits of prokaryotes from protein domain frequencies. BMC Bioinformatics 2010;11:481. [PMID: 20868492 PMCID: PMC2955703 DOI: 10.1186/1471-2105-11-481] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2010] [Accepted: 09/24/2010] [Indexed: 12/03/2022]  Open
27
MacDonald NJ, Beiko RG. Efficient learning of microbial genotype-phenotype association rules. ACTA ACUST UNITED AC 2010;26:1834-40. [PMID: 20529891 DOI: 10.1093/bioinformatics/btq305] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
28
Kuboniwa M, Lamont RJ. Subgingival biofilm formation. Periodontol 2000 2010;52:38-52. [PMID: 20017794 DOI: 10.1111/j.1600-0757.2009.00311.x] [Citation(s) in RCA: 114] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
29
Heinemann M, Sauer U. Systems biology of microbial metabolism. Curr Opin Microbiol 2010;13:337-43. [PMID: 20219420 DOI: 10.1016/j.mib.2010.02.005] [Citation(s) in RCA: 89] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2010] [Accepted: 02/13/2010] [Indexed: 12/20/2022]
30
Dale JM, Popescu L, Karp PD. Machine learning methods for metabolic pathway prediction. BMC Bioinformatics 2010;11:15. [PMID: 20064214 PMCID: PMC3146072 DOI: 10.1186/1471-2105-11-15] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2009] [Accepted: 01/08/2010] [Indexed: 12/29/2022]  Open
PrevPage 1 of 1 1Next
© 2004-2024 Baishideng Publishing Group Inc. All rights reserved. 7041 Koll Center Parkway, Suite 160, Pleasanton, CA 94566, USA