S.D. Burz, S. Čaušević, et al. (incl. A.R. Pacheco). From microbiome composition to functional engineering, one step at a time. Microbiology and Molecular Biology Reviews (2023). [View]
M. Schäfer*, A.R. Pacheco*, R. Künzler, M. Bortfeld-Miller, C.M. Field, E. Vayena, V. Hatzimanikatis, and J.A. Vorholt. Metabolic interaction models recapitulate leaf microbiota ecology. Science 380, eadf5121 (2023). [View] *Contributed equally
A.R. Pacheco and J.A. Vorholt. Resolving metabolic interaction mechanisms in plant microbiomes. Current Opinion in Microbiology 74, 102317 (2023). [View]
A.R. Pacheco*, C. Pauvert*, D. Kishore, and D. Segrè. Toward FAIR representations of microbial interactions. mSystems e00659-22 (2022). [View] *Contributed equally
N. Ankrah, D.B. Bernstein, M. Biggs, M. Carey, M. Engevik, B. García-Jiménez, M. Lakshmanan, A.R. Pacheco, S. Sulheim, and G. Medlock. Enhancing microbiome research through trustworthy genome-scale metabolic modeling. mSystems 6,6 (2021). [View]
I. Dukovski, D. Bajić, J.M. Chacón, M. Quintin, J.C.C. Vila, S. Sulheim, A.R. Pacheco, D.B. Bernstein, W.J. Riehl, K.S. Korolev, A. Sanchez, W.R. Harcombe, and D. Segrè. A metabolic modeling platform for the computation of microbial ecosystems in time and space (COMETS). Nature Protocols 16, 5020-5082 (2021). [View]
D.C. Moyer, A.R. Pacheco, D.B. Bernstein, and D. Segrè. Stoichiometric Modeling of Artificial String Chemistries Reveals Constraints on Metabolic Network Structure. Journal of Molecular Evolution 89, 472-483 (2021). [View]
A.R. Pacheco and D. Segrè. An evolutionary algorithm for designing microbial communities via environmental modification. J. R. Soc. Interface 18, 20210348 (2021). [View]
A.R. Pacheco, M.L. Osborne, and D. Segrè. Non-additive microbial community responses to environmental complexity. Nature Communications 12, 2365 (2021). [View]
A.R. Pacheco and D. Segrè. A multidimensional perspective on microbial interactions. FEMS Microbiology Letters 366, 1–11 (2019). [View]
A.R. Pacheco, M. Moel, and D. Segrè. Costless metabolic secretions as drivers of interspecies interactions in microbial ecosystems. Nature Communications 10, 103 (2019). [View]
B.M. Maoz, A. Herland, E.A. FitzGerald, T. Grevesse, C. Vidoulez, A.R. Pacheco, S.P. Sheehy, T.E. Park, S. Dauth, R. Mannix, N. Budnik, K. Shores, A. Cho, J.C. Nawroth, D. Segrè, B. Budnik, D.E. Ingber, and K.K. Parker. Endothelial-neuronal cell metabolic coupling across the blood-brain barrier revealed using linked human organs-on-chips. Nature Biotechnology 36, 865–874 (2018). [View]
J. Beal, T. Haddock-Angelli, M. Gershater, K. de Mora, M. Lizarazo, J. Hollenhorst, R. Rettberg, iGEM Interlab Study Contributors (incl. A.R. Pacheco). Reproducibility of Fluorescent Expression from Engineered Biological Constructs in E. coli. PLOS ONE 11, e0150182 (2016). [View]
T. Haddock, D. Densmore, E. Appleton, S. Carr, S. Iverson, A.R. Pacheco, et al. The Modular Cloning Assembly: Standardized Assembly of Bacterial Transcriptional Units Using Type IIS Restriction Enzymes BsaI and BpiI. The BioBricks Foundation RFC 94 (2015). [View]
A.R. Pacheco. Environmental modulation of microbial ecosystems. (2021). [View]