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Multidimensional annotation of the Escherichia coli K-12 genome.
Karp PD, Keseler IM, Shearer A, Latendresse M, Krummenacker M, Paley SM, Paulsen I, Collado-Vides J, Gama-Castro S, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spínola MI, Bonavides-Martinez C, Ingraham J. Karp PD, et al. Among authors: ingraham j. Nucleic Acids Res. 2007;35(22):7577-90. doi: 10.1093/nar/gkm740. Epub 2007 Oct 16. Nucleic Acids Res. 2007. PMID: 17940092 Free PMC article.
EcoCyc: a comprehensive database resource for Escherichia coli.
Keseler IM, Collado-Vides J, Gama-Castro S, Ingraham J, Paley S, Paulsen IT, Peralta-Gil M, Karp PD. Keseler IM, et al. Among authors: ingraham j. Nucleic Acids Res. 2005 Jan 1;33(Database issue):D334-7. doi: 10.1093/nar/gki108. Nucleic Acids Res. 2005. PMID: 15608210 Free PMC article.
MetaCyc: a multiorganism database of metabolic pathways and enzymes.
Caspi R, Foerster H, Fulcher CA, Hopkinson R, Ingraham J, Kaipa P, Krummenacker M, Paley S, Pick J, Rhee SY, Tissier C, Zhang P, Karp PD. Caspi R, et al. Among authors: ingraham j. Nucleic Acids Res. 2006 Jan 1;34(Database issue):D511-6. doi: 10.1093/nar/gkj128. Nucleic Acids Res. 2006. PMID: 16381923 Free PMC article.
What limits genomics, proteomics, transcriptomics?
Schaechter M, Ingraham JL. Schaechter M, et al. Among authors: ingraham jl. Int Microbiol. 2002 Jun;5(2):51-2. doi: 10.1007/s10123-002-0065-0. Int Microbiol. 2002. PMID: 12180780 Free article. No abstract available.
Illuminating protein space with a programmable generative model.
Ingraham JB, Baranov M, Costello Z, Barber KW, Wang W, Ismail A, Frappier V, Lord DM, Ng-Thow-Hing C, Van Vlack ER, Tie S, Xue V, Cowles SC, Leung A, Rodrigues JV, Morales-Perez CL, Ayoub AM, Green R, Puentes K, Oplinger F, Panwar NV, Obermeyer F, Root AR, Beam AL, Poelwijk FJ, Grigoryan G. Ingraham JB, et al. Nature. 2023 Nov;623(7989):1070-1078. doi: 10.1038/s41586-023-06728-8. Epub 2023 Nov 15. Nature. 2023. PMID: 37968394 Free PMC article.
Simultaneous enhancement of multiple functional properties using evolution-informed protein design.
Fram B, Truebridge I, Su Y, Riesselman AJ, Ingraham JB, Passera A, Napier E, Thadani NN, Lim S, Roberts K, Kaur G, Stiffler M, Marks DS, Bahl CD, Khan AR, Sander C, Gauthier NP. Fram B, et al. Among authors: ingraham jb. bioRxiv [Preprint]. 2023 May 9:2023.05.09.539914. doi: 10.1101/2023.05.09.539914. bioRxiv. 2023. Update in: Nat Commun. 2024 Jun 20;15(1):5141. doi: 10.1038/s41467-024-49119-x. PMID: 37214973 Free PMC article. Updated. Preprint.
134 results