The evolution of imitation and mirror neurons in adaptive agents. - Elhanan Borenstein; Eytan Ruppin (Cogn. Syst. Res., 2005)

Evolutionary dynamics of adaptive populations: the effect of phenotypic plasticity, imitation and culture on evolution - Elhanan Borenstein (2006)

An End to Endless Forms: Epistasis, Phenotype Distribution Bias, and Nonuniform Evolution. - Elhanan Borenstein; David C. Krakauer (PLoS Comput. Biol., 2008)

Topological Signatures of Species Interactions in Metabolic Networks. - Elhanan Borenstein; Marcus W. Feldman (J. Comput. Biol., 2009)

Decoupling Environment-Dependent and Independent Genetic Robustness across Bacterial Species. - Shiri Freilich; Anat Kreimer; Elhanan Borenstein; Uri Gophna; Roded Sharan; Eytan Ruppin (PLoS Comput. Biol., 2010)

Computational systems biology and in silico modeling of the human microbiome. - Elhanan Borenstein (Briefings Bioinform., 2012)

NetSeed: a network-based reverse-ecology tool for calculating the metabolic interface of an organism with its environment. - Rogan Carr; Elhanan Borenstein (Bioinform., 2012)

NetCmpt: a network-based tool for calculating the metabolic competition between bacterial species. - Anat Kreimer; Adi Doron-Faigenboim; Elhanan Borenstein; Shiri Freilich (Bioinform., 2012)

Reconstructing the Genomic Content of Microbiome Taxa through Shotgun Metagenomic Deconvolution. - Rogan Carr; Shai S. Shen-Orr; Elhanan Borenstein (PLoS Comput. Biol., 2013)

Emergent Biosynthetic Capacity in Simple Microbial Communities. - Hsuan-Chao Chiu; Roie Levy; Elhanan Borenstein (PLoS Comput. Biol., 2014)

NetCooperate: a network-based tool for inferring host-microbe and microbe-microbe cooperation. - Roie Levy; Rogan Carr; Anat Kreimer; Shiri Freilich; Elhanan Borenstein (BMC Bioinform., 2015)

An algorithm for designing minimal microbial communities with desired metabolic capacities. - Alexander Eng; Elhanan Borenstein (Bioinform., 2016)

Metabolic model-based analysis of the emergence of bacterial cross-feeding via extensive gene loss. - Colin P. McNally; Elhanan Borenstein (BMC Syst. Biol., 2018)

MetaLAFFA: a flexible, end-to-end, distributed computing-compatible metagenomic functional annotation pipeline. - Alexander Eng; Adrian J. Verster; Elhanan Borenstein (BMC Bioinform., 2020)

MIMOSA2: a metabolic network-based tool for inferring mechanism-supported relationships in microbiome-metabolome data. - Cecilia Noecker; Alexander Eng; Efrat Muller; Elhanan Borenstein (Bioinform., 2022)

Integrating phylogenetic and functional data in microbiome studies. - Gavin M. Douglas; Molly G. Hayes; Morgan G. I. Langille; Elhanan Borenstein (Bioinform., 2022)