Bernstein DB, Akkas B, Price MN and Arkin AP. Evaluating E. coli genome-scale metabolic model accuracy with high-throughput mutant fitness data.Mol Syst Biol. 2023, 19(12): e11566. PMID: 37888487.
Jo C, Bernstein DB, Vaisman N, Frydman HM and Segrè D. Construction and Modeling of a Coculture Microplate for Real-Time Measurement of Microbial Interactions.mSystems. 2023, 8(2): e0001721. PMID: 36802169.
2021
Ankrah NYD, Bernstein DB, Biggs M, Carey M, Engevik M, García-Jiménez B, Lakshmanan M, Pacheco AR, Sulheim S and Medlock GL. Enhancing Microbiome Research through Genome-Scale Metabolic Modeling.mSystems. 2021, 6(6): e0059921. PMID: 34904863.
Dukovski I, Bajić D, Chacón JM, Quintin M, Vila JCC, Sulheim S, Pacheco AR, Bernstein DB, Riehl WJ, Korolev KS, Sanchez A, Harcombe WR and Segrè D. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS).Nat Protoc. 2021, 16(11): 5030-5082. PMID: 34635859.
Bernstein DB, Sulheim S, Almaas E and Segrè D. Addressing uncertainty in genome-scale metabolic model reconstruction and analysis.Genome Biol. 2021, 22(1): 64. PMID: 33602294.
2019
Bernstein DB, Dewhirst FE and Segrè D. Metabolic network percolation quantifies biosynthetic capabilities across the human oral microbiome.Elife. 2019. PMID: 31194675.