CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. - Damiano Piovesan; Davide Zago; Parnal Joshi; M. Clara De Paolis Kaluza; Alexander Miguel Monzon; Walter Reade; Iddo Friedberg; Predrag Radivojac; Silvio C. E. Tosatto (CoRR, 2023)

GOThresher: a program to remove annotation biases from protein function annotation datasets. - Parnal Joshi; Sagnik Banerjee; Xiao Hu; Pranav M. Khade; Iddo Friedberg (Bioinform., 2023)

A longitudinal analysis of function annotations of the human proteome reveals consistently high biases. - An Phan; Parnal Joshi; Claus Kadelka; Iddo Friedberg (Database J. Biol. Databases Curation, 2025)