Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold. - Iddo Friedberg; Tommy Kaplan; Hanah Margalit (ISMB, 2000)

PeCoP: automatic determination of persistently conserved positions in protein families. - Iddo Friedberg; Hanah Margalit (Bioinform., 2002)

The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. - Philip E. Bourne; C. K. J. Allerston; Werner G. Krebs; Wilfred W. Li; Ilya N. Shindyalov; Adam Godzik; Iddo Friedberg; Tong Liu; David L. Wild; Seungwoo Hwang; Zoubin Ghahramani; Li Chen 022; et al. (Pacific Symposium on Biocomputing, 2004)

Fragnostic: walking through protein structure space. - Iddo Friedberg; Adam Godzik (Nucleic Acids Res., 2005)

Automated protein function prediction - the genomic challenge. - Iddo Friedberg (Briefings Bioinform., 2006)

JAFA: a protein function annotation meta-server. - Iddo Friedberg; Tim Harder; Adam Godzik (Nucleic Acids Res., 2006)

Ten Simple Rules for Selecting a Postdoctoral Position. - Philip E. Bourne; Iddo Friedberg (PLoS Comput. Biol., 2006)

Correction: Ten Simple Rules for Selecting a Postdoctoral Position. - Philip E. Bourne; Iddo Friedberg (PLoS Comput. Biol., 2006)

Using an alignment of fragment strings for comparing protein structures. - Iddo Friedberg; Tim Harder; Rachel Kolodny; Einat Sitbon; Zhanwen Li; Adam Godzik (Bioinform., 2007)

The 2006 Automated Function Prediction Meeting. - Ana P. C. Rodrigues; Barry J. Grant; Adam Godzik; Iddo Friedberg (BMC Bioinform., 2007)

Biopython: freely available Python tools for computational molecular biology and bioinformatics. - Peter J. A. Cock; Tiago Rodrigues Antao; Jeffrey T. Chang; Brad A. Chapman; Cymon J. Cox; Andrew Dalke; Iddo Friedberg; Thomas Hamelryck; Frank Kauff; Bartek Wilczynski; Michiel J. L. de Hoon (Bioinform., 2009)

IPRStats: visualization of the functional potential of an InterProScan run. - Ryan J. Kelly; David E. Vincent; Iddo Friedberg (BMC Bioinform., 2010)

A Primer on Metagenomics. - John C. Wooley; Adam Godzik; Iddo Friedberg (PLoS Comput. Biol., 2010)

Biological Database of Images and Genomes: tools for community annotations linking image and genomic information. - Andrew Oberlin; Dominika A. Jurkovic; Mitchell F. Balish; Iddo Friedberg (Database J. Biol. Databases Curation, 2013)

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space. - Alexandra M. Schnoes; David C. Ream; Alexander W. Thorman; Patricia C. Babbitt; Iddo Friedberg (PLoS Comput. Biol., 2013)

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. - Yuxiang Jiang; Wyatt T. Clark; Iddo Friedberg; Predrag Radivojac (Bioinform., 2014)

The automated function prediction SIG looks back at 2013 and prepares for 2014. - Mark N. Wass; Sean D. Mooney; Michal Linial; Predrag Radivojac; Iddo Friedberg (Bioinform., 2014)

An event-driven approach for studying gene block evolution in bacteria. - David C. Ream; Asma R. Bankapur; Iddo Friedberg (Bioinform., 2015)

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. - James T. Morton; Stefan D. Freed; Shaun W. Lee; Iddo Friedberg (BMC Bioinform., 2015)

Ten Simple Rules for a Community Computational Challenge. - Iddo Friedberg; Mark N. Wass; Sean D. Mooney; Predrag Radivojac (PLoS Comput. Biol., 2015)

Highly Bi-Connected Subgraphs for Computational Protein Function Annotation. - Jucheol Moon; Iddo Friedberg; Oliver Eulenstein (COCOON, 2016)

Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics. - Md-Nafiz Hamid; Iddo Friedberg (CoRR, 2018)

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning. - Naihui Zhou; Zachary D. Siegel; Scott Zarecor; Nigel Lee; Darwin A. Campbell; Carson M. Andorf; Dan Nettleton; Carolyn J. Lawrence-Dill; Baskar Ganapathysubramanian; Jonathan W. Kelly; Iddo Friedberg (PLoS Comput. Biol., 2018)

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. - Md-Nafiz Hamid; Iddo Friedberg (Bioinform., 2019)

Tracing the ancestry of operons in bacteria. - Huy N. Nguyen; Ashish Jain; Oliver Eulenstein; Iddo Friedberg (Bioinform., 2019)

Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. - Huy N. Nguyen; Alexey Markin; Iddo Friedberg; Oliver Eulenstein (Bioinform., 2020)

Establishing the reliability of algorithms. - Lara M. Mangravite; Sean D. Mooney; Iddo Friedberg; Justin Guinney (PSB, 2021)

Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). - Jolene Ramsey; Brenley K. McIntosh; Daniel P. Renfro; Suzanne A. Aleksander; Sandra A. LaBonte; Curtis Ross; Adrienne E. Zweifel; Nathan Liles; Shabnam Farrar; Jason J. Gill; Ivan Erill; Sarah Ades; et al. (PLoS Comput. Biol., 2021)

A roadmap for the functional annotation of protein families: a community perspective. - Valérie de Crécy-Lagard; Rocio Amorin de Hegedus; Cecilia N. Arighi; Jill Babor; Alex Bateman; Ian Blaby; Crysten Blaby-Haas; Alan J. Bridge; Stephen K. Burley; Stacey Cleveland; Lucy J. Colwell; Ana Conesa; et al. (Database J. Biol. Databases Curation, 2022)

Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. - Alastair M. Kilpatrick; Farzana Rahman; Audra Anjum; Sayane Shome; K. M. Salim Andalib; Shrabonti Banik; Sanjana F. Chowdhury; Peter Coombe; Yesid Cuesta Astroz; J. Maxwell Douglas; Pradeep Eranti; Aleyna D. Kiran; et al. (Bioinform., 2022)

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)