MetaCyc

MetaCyc is a database of nonredundant, experimentally elucidated metabolic pathways. MetaCyc contains more than 2097 pathways from more than 2460 different organisms and is curated from the scientific experimental literature. MetaCyc contains pathways involved in both primary and secondary metabolism, as well as associated compounds, enzymes, and genes The goal of MetaCyc is to catalog the universe of metabolism by storing a representative sample of each experimentally elucidated pathway. MetaCyc is used in a variety of scientific applications, such as providing a reference data set for computationally predicting the metabolic pathways of organisms from their sequenced genomes, supporting metabolic engineering, helping to compare biochemical networks, and serving as an encyclopedia of metabolism.


References in zbMATH (referenced in 28 articles )

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  1. Rubert, Diego P.; Araujo, Eloi; Stefanes, Marco A.; Stoye, Jens; Martinez, Fábio V.: Searching and inferring colorful topological motifs in vertex-colored graphs (2020)
  2. Frioux, Clémence; Schaub, Torsten; Schellhorn, Sebastian; Siegel, Anne; Wanko, Philipp: Hybrid metabolic network completion (2018)
  3. Erciyes, K.: Distributed and sequential algorithms for bioinformatics (2015)
  4. Pinter, Ron Y.; Zehavi, Meirav: Algorithms for topology-free and alignment network queries (2014)
  5. Samal, Satya Swarup; Errami, Hassan; Weber, Andreas: PoCaB: a software infrastructure to explore algebraic methods for bio-chemical reaction networks (2012)
  6. Desai, Dhwani K.; Nandi, Soumyadeep; Srivastava, Prashant K.; Lynn, Andrew M.: ModEnzA: accurate identification of metabolic enzymes using function specific profile HMMs with optimised discrimination threshold and modified emission probabilities (2011)
  7. Latendresse, Mario; Karp, Peter D.: Web-based metabolic network visualization with a zooming user interface (2011) ioport
  8. Stingo, Francesco C.; Chen, Yian A.; Tadesse, Mahlet G.; Vannucci, Marina: Incorporating biological information into linear models: a Bayesian approach to the selection of pathways and genes (2011)
  9. Baldan, Paolo; Cocco, Nicoletta; Marin, Andrea; Simeoni, Marta: Petri nets for modelling metabolic pathways: a survey (2010)
  10. Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne M.; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander Glennon; Zhang, Peifen; Karp, Peter D.: The metacyc database of metabolic pathways and enzymes and the biocyc collection of pathway/genome databases (2010) ioport
  11. Chen, Chuming; McGarvey, Peter B.; Huang, Hongzhan; Wu, Cathy H.: Protein bioinformatics infrastructure for the integration and analysis of multiple high-throughput “omics” data (2010) ioport
  12. Hawari, Aliah Hazmah; Mohamed-Hussein, Zeti-Azura: Simulation of a Petri net-based model of the terpenoid biosynthesis pathway (2010) ioport
  13. Likić, Vladimir A.; McConville, Malcolm J.; Lithgow, Trevor; Bacic, Antony: Systems biology: the next frontier for bioinformatics (2010)
  14. Chou, I-Chun; Voit, Eberhard O.: Recent developments in parameter estimation and structure identification of biochemical and genomic systems (2009)
  15. Dogrusöz, Ugur; Cetintas, Ahmet; Demir, Emek; Babur, Ozgun: Algorithms for effective querying of compound graph-based pathway databases (2009) ioport
  16. Draper, John; Enot, David P.; Parker, David; Beckmann, Manfred; Snowdon, Stuart; Lin, Wanchang; Zubair, Hassan: Metabolite signal identification in accurate mass metabolomics data with mzeddb, an interactive \textitm/zannotation tool utilising predicted ionisation behaviour ’rules’ (2009) ioport
  17. Félix, Liliana; Rosselló, Francesc; Valiente, Gabriel: Efficient reconstruction of metabolic pathways by bidirectional chemical search (2009)
  18. Heath, Allison P.; Kavraki, Lydia E.: Computational challenges in systems biology (2009)
  19. Picard, Franck; Miele, Vincent; Daudin, Jean-Jacques; Cottret, Ludovic; Robin, Stéphane: Deciphering the connectivity structure of biological networks using mixnet (2009) ioport
  20. Tran, Nam; Baral, Chitta: Hypothesizing about signaling networks (2009)

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