Mesobiotic Emergence: molecular and Ensemble Complexity in Early Evolution. - Barak Shenhav; Daniel Segrè; Doron Lancet (Adv. Complex Syst., 2003)

Environments that Induce Synthetic Microbial Ecosystems. - Niels Klitgord; Daniel Segrè (PLoS Comput. Biol., 2010)

Signatures of Arithmetic Simplicity in Metabolic Network Architecture. - William J. Riehl; Paul L. Krapivsky; Sidney Redner; Daniel Segrè (PLoS Comput. Biol., 2010)

A system-level approach for deciphering the transcriptional response to prion infection. - Mattia Zampieri; Giuseppe Legname; Daniel Segrè; Claudio Altafini (Bioinform., 2011)

COMBREX: a project to accelerate the functional annotation of prokaryotic genomes. - Richard J. Roberts; Yi-Chien Chang; Zhenjun Hu; John Rachlin; Brian P. Anton; Revonda M. Pokrzywa; Han-Pil Choi; Lina L. Faller; Jyotsna Guleria; Genevieve Housman; Niels Klitgord; Varun Mazumdar; et al. (Nucleic Acids Res., 2011)

Comparative multi-goal tradeoffs in systems engineering of microbial metabolism. - David Byrne; Alexandra Dumitriu; Daniel Segrè (BMC Syst. Biol., 2012)

Temporal Expression-based Analysis of Metabolism. - Sara B. Collins; Ed Reznik; Daniel Segrè (PLoS Comput. Biol., 2012)

Flux Imbalance Analysis and the Sensitivity of Cellular Growth to Changes in Metabolite Pools. - Ed Reznik; Pankaj Mehta; Daniel Segrè (PLoS Comput. Biol., 2013)

Learning cellular objectives from fluxes by inverse optimization. - Qi Zhao; Arion Stettner; Ed Reznik; Daniel Segrè; Ioannis Ch. Paschalidis (CDC, 2015)

Optimal allocation of metabolic functions among organisms in a microbial ecosystem. - Qi Zhao; Daniel Segrè; Ioannis Ch. Paschalidis (CDC, 2016)

Visualization of Metabolic Interaction Networks in Microbial Communities Using VisANT 5.0. - Brian Granger; Yi-Chien Chang; Yan Wang; Charles DeLisi; Daniel Segrè; Zhenjun Hu (PLoS Comput. Biol., 2016)