RepTar: a database of predicted cellular targets of host and viral miRNAs. - Naama Elefant; Amnon Berger; Harel Shein; Matan Hofree; Hanah Margalit; Yael Altuvia (Nucleic Acids Res., 2011)

Analysis of genomic variants via gene networks. - Matan Hofree (2014)

Identifying Mutation Specific Cancer Pathways Using a Structurally Resolved Protein Interaction Network. - Billur Engin; Matan Hofree; Hannah Carter (Pacific Symposium on Biocomputing, 2015)

Erratum: Identifying mutation specific cancer pathways using a structurally resolved protein interaction network. - Billur Engin; Matan Hofree; Hannah Carter (PSB, 2018)