EcoCyc Publications

If you use EcoCyc in your research, we ask that you cite the following publication:

[EcoCyc25] Karp, P.D., Paley, S., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Moore, L.R., Subhraveti, P., Gama-Castro, S., Tierrafria, V., Paloma, L., Muñiz-Rascado, L., Bonavides-Martinez, C., Santos-Zavaleta, A., Mackie, A., Sun, G., Ahn-Horst, T.A., Choi, H., Covert, M.W., Collado-Vides, J. and Paulsen, I., The EcoCyc database (2025)
EcoSal Plus doi:10.1128/ecosalplus.ESP-0019-2024

[EcoCyc24] Moore, L.R., Caspi, R., Boyd, D., Berkem, M., Mackie, A., Paley, S., Karp, P.D. Revisiting the y-ome of Escherichia coli
Nucleic Acids Research doi::10.1093/nar/gkae857 (2024)

See Also

[EcoCyc21] Keseler, I.M., Gama-Castro, S., Mackie, A., Billington, R., Billington, R., Caspi, R., Kothari, A., Krummenacker, M., Midford, P., Muñiz-Rascado, L., Ong, W., Paley, S., Santos-Zavaleta, A., Subhraveti, P., Tierrafria, V., Wolfe, A., Collado-Vides, J., Paulsen, I., and Karp, P.D.,
The EcoCyc database in 2021
Front Microbiol 2021; 12: 711077.

[EcoCyc17] Keseler, I.M., Mackie, A., Santos-Zavaleta, A., Billington, R., Bonavides-Martinez, C., Caspi, R., Fulcher, C., Gama-Castro, S., Kothari, A., Krummenacker, M., Latendresse, M., Muñiz-Rascado, L., Ong, Q., Paley, S., Peralta-Gil, M., Subhraveti, P., Velazquez-Ramirez, D.A., Weaver, D., Collado-Vides, J., Paulsen, I., and Karp, P.D.,
The EcoCyc database: reflecting new knowledge about Escherichia coli K-12
Nucleic Acids Research 45:D543-550 2017.

[EcoCyc14] Weaver, D.S., Keseler, I.M., Mackie, A., I.T. Paulsen, and Karp, P.D.,
A genome-scale metabolic flux model of Escherichia coli K12 derived from the EcoCyc database
BMC Systems Biology 2014, 8:79.

[EcoCyc14] Keseler, I.M., Skrzypek, M., Weerasinghe, D., Chen, A.Y., Fulcher, C., Li, G.W., Lemmer, K.C., Mladinich, K.M., Chow,E.D., Sherlock, G.,and Karp, P.D.,
Curation accuracy of model organism databases
Oxford Journals 10.1093/database/bau058

[EcoCyc14] P.D. Karp, D. Weaver, S. Paley, C. Fulcher, A. Kubo, A. Kothari, M. Krummenacker, P. Subhraveti, D. Weerasinghe, S.Gama-Castro, A.M. Huerta, L., Muniz-Rascado, C.Bonavides-Martinez, V.Weiss, M.Peralta-Gil, A. Santos-Zavaleta, I. Schroder, A. Mackie, R. Gunsalus, J. Collado-Vides, I.M.Keseler, and I. Paulsen.
The EcoCyc Database
EcoSal Plus doi:10.1128/ecosalplus.ESP-0009-2013

[EcoCyc14] Mackie, A., Paley, S., Keseler, I.M., Shearer, A., Paulsen, I.T., and Karp, P.D.,
Addition of Escherichia coli K-12 growth observation and gene essentiality data to the EcoCyc database.
J Bacteriol. 196(5):982-8

[EcoCyc13] A. Mackie., I.M.Keseler., L.Nolan., P.D.Karp., and I.T.Paulsen.,
Dead end metabolites--defining the known unknowns of the E. coli metabolic network.
PLoS One. 8(9):e75210. doi: 10.1371/journal.pone.0075210. eCollection 2013.

[EcoCyc13] Keseler, I.M., Mackie, A., Peralta-Gil, M., Santos-Zavaleta, A., Gama-Castro, S., Bonavides-Martinez, C., Fulcher, C., Huerta, A.M., Kothari, A., Krummenacker, M., Latendresse, M., Muniz-Rascado, L., Ong, Q., Paley, S., Schroder, I., Shearer, A., Subhraveti, P., Travers, M., Weerasinghe, D., Weiss, V., Collado-Vides, J., Gunsalus, R.P., Paulsen, I., and Karp, P.D.,
EcoCyc: fusing model organism databases with systems biology
Nucleic Acids Research 41:D605-612 2013.

[EcoCyc11] Keseler, I.M., Collado-Vides, J., Santos-Zavaleta, A., Peralta-Gil, M., Gama-Castro, S., Muniz-Rascado, L., Bonavides-Martinez, C., Paley, S., Krummenacker, M., Altman, T., Kaipa, P., Spaulding, A., Pacheco, J., Latendresse, M., Fulcher, C., Sarker, M., Shearer, A.G., Mackie, A., Paulsen, I., Gunsalus, R.P., and Karp, P.D.,
EcoCyc: a comprehensive database of Escherichia coli biology
Nucleic Acids Research 39:D583-590 2011.

[EcoCyc09] Keseler, I.M., Bonavides-Martinez, C., Collado-Vides, J., Gama-Castro, S., Gunsalus, R.P., Johnson, D.A., Krummenacker, M., Nolan, L.M., Paley, S., Paulsen, I.T., Peralta-Gil, M., Santos-Zavaleta, A., Shearer, A.G., and Karp, P.D.,
EcoCyc: A comprehensive view of Escherichia coli biology
Nucleic Acids Research 37:D464-D470 2009.

[EcoCyc07] Karp, P.D., Keseler, I.M., Shearer, A., Latendresse, M., Krummenacker, M., Paley, S.M., Paulsen, I., Collado-Vides, J., Gama-Castro, S., Peralta-Gil, M., Santos-Zavaleta, A., Penaloza-Spinola, M.I., Bonavides-Martinez, C., and Ingraham, J.,
Multidimensional annotation of the Escherichia coli K-12 genome
Nucleic Acids Research 35:7577-90 2007.

[Ecoli06] Salgado H., Santos-Zavaleta A., Gama-Castro S., Peralta-Gil M., Penaloza-Spinola M.I., Martinez-Antonio A., Karp P.D., and Collado-Vides J.,
The comprehensive updated regulatory network of Escherichia coli K-12
BMC Bioinformatics 7:5 2006.

[Ecoli05] Riley M., Abe T., Arnaud M.B., Berlyn M.K.B., Blattner F.R., Chaudhuri R.R., Glasner J.D., Horiuchi T., Keseler I.M., Kosuge T., Mori H., Perna N.T., Plunkett III G., Rudd K.E., Serres M.H., Thomas G.H., Thomson N.R., Wishart D., and Wanner B.L.,
Escherichia coli K-12: a cooperatively developed annotation snapshot - 2005
Nucleic Acids Research 34:1-9 2006.

[EcoCyc05] I.M. Keseler, J. Collado-Vides, S. Gama-Castro, J. Ingraham, S. Paley, I.T. Paulsen, M. Peralta-Gil and P.D. Karp.
EcoCyc: A comprehensive database resource for Escherichia coli
Nucleic Acids Research 33:D334-7 2005.

[EcoCyc02] Karp, P.D., Riley, M., Saier, M., Paulsen, I.T., Collado-Vides, J., Paley, S.M., Pellegrini-Toole, A., Bonavides, C., and Gama-Castro, S.,
The EcoCyc Database
Nucleic Acids Research 30:56-58 2002.

[EcoCyc99] Karp, P.D., and Riley, M.,
EcoCyc: The Resource and the Lessons Learned [PDF]
Kluwer Academic Publishers, pp47-62 1999.

See also: The BioCyc Publications Page