Iddo Friedberg

34 papers A 1Misc 3Journal 30
YearRankTypeTitle / Venue / Authors
2025 J jnl
A longitudinal analysis of function annotations of the human proteome reveals consistently high biases.
Database J. Biol. Databases Curation
An Phan, Parnal Joshi, Claus Kadelka, Iddo Friedberg
2023 J jnl
CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods.
CoRR
Damiano Piovesan, Davide Zago, Parnal Joshi, M. Clara De Paolis Kaluza, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C. E. Tosatto
2023 J jnl
GOThresher: a program to remove annotation biases from protein function annotation datasets.
Bioinform.
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
2022 J jnl
A roadmap for the functional annotation of protein families: a community perspective.
Database J. Biol. Databases Curation
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, Christian Dallago, Antoine Danchin, Anita de Waard, Adam Deutschbauer, Raquel Dias, Yousong Ding, Gang Fang, Iddo Friedberg, John Gerlt, Joshua Goldford, Mark Gorelik, Benjamin M. Gyori, Christopher S. Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D. Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria Jesus Martin, Claire D. McWhite, Gaurav D. Moghe, Paul Monaghan, Anne Morgat, Christopher J. Mungall, Darren A. Natale, William C. Nelson, Seán I. O'Donoghue, Christine A. Orengo, Katherine H. O'Toole, Predrag Radivojac, Colbie Reed, Richard J. Roberts, Dmitri Rodionov, Irina A. Rodionova, Jeffrey DePons, Lana Saleh, Gloria M. Sheynkman, Françoise Thibaud-Nissen, Paul D. Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter Weigele, Valerie Wood, Elisha M. Wood-Charlson, Jin Xu
2022 J jnl
Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.
Bioinform.
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, Sachendra Kumar, Hyeri Lim, Valentina Lorenzi, Tiago Lubiana, Sakib Mahmud, Rafael Puche, Agnieszka Rybarczyk, Syed Muktadir Al Sium, David Twesigomwe, Tomasz Zok, Christine A. Orengo, Iddo Friedberg, Janet Kelso, Lonnie R. Welch
2021 J jnl
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).
PLoS Comput. Biol.
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, Tanya Z. Berardini, Jennifer A. Bennett, Siobhan M. Brady, Robert Britton, Seth Carbon, Steven M. Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L. Doyle, Iddo Friedberg, Susan M. R. Gurney, Lee Hughes, Allison Johnson, Jason M. Kowalski, Donghui Li, Ruth C. Lovering, Tamara L. Mans, Fiona McCarthy, Sean D. Moore, Rebecca Murphy, Timothy D. Paustian, Sarah Perdue, Celeste N. Peterson, Birgit M. Prüß, Margaret S. Saha, Robert R. Sheehy, John T. Tansey, Louise Temple, Alexander William Thorman, Saul Trevino, Amy Cheng Vollmer, Virginia Walbot, Joanne Willey, Deborah A. Siegele, James C. Hu
2021 Misc conf
Establishing the reliability of algorithms.
PSB
Lara M. Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney
2020 J jnl
Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.
Bioinform.
Huy N. Nguyen, Alexey Markin, Iddo Friedberg, Oliver Eulenstein
2019 J jnl
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks.
Bioinform.
Md-Nafiz Hamid, Iddo Friedberg
2019 J jnl
Tracing the ancestry of operons in bacteria.
Bioinform.
Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg
2018 J jnl
Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.
PLoS Comput. Biol.
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
2018 J jnl
Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics.
CoRR
Md-Nafiz Hamid, Iddo Friedberg
2016 Misc conf
Highly Bi-Connected Subgraphs for Computational Protein Function Annotation.
COCOON
Jucheol Moon, Iddo Friedberg, Oliver Eulenstein
2015 J jnl
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins.
BMC Bioinform.
James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg
2015 J jnl
An event-driven approach for studying gene block evolution in bacteria.
Bioinform.
David C. Ream, Asma R. Bankapur, Iddo Friedberg
2015 J jnl
Ten Simple Rules for a Community Computational Challenge.
PLoS Comput. Biol.
Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
2014 J jnl
The automated function prediction SIG looks back at 2013 and prepares for 2014.
Bioinform.
Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg
2014 J jnl
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.
Bioinform.
Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac
2013 J jnl
Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space.
PLoS Comput. Biol.
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
2013 J jnl
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space
CoRR
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
2013 J jnl
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information.
Database J. Biol. Databases Curation
Andrew Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg
2010 J jnl
A Primer on Metagenomics.
PLoS Comput. Biol.
John C. Wooley, Adam Godzik, Iddo Friedberg
2010 J jnl
IPRStats: visualization of the functional potential of an InterProScan run.
BMC Bioinform.
Ryan J. Kelly, David E. Vincent, Iddo Friedberg
2009 J jnl
Biopython: freely available Python tools for computational molecular biology and bioinformatics.
Bioinform.
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
2007 J jnl
The 2006 Automated Function Prediction Meeting.
BMC Bioinform.
Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg
2007 J jnl
Using an alignment of fragment strings for comparing protein structures.
Bioinform.
Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik
2006 J jnl
Automated protein function prediction - the genomic challenge.
Briefings Bioinform.
Iddo Friedberg
2006 J jnl
Correction: Ten Simple Rules for Selecting a Postdoctoral Position.
PLoS Comput. Biol.
Philip E. Bourne, Iddo Friedberg
2006 J jnl
JAFA: a protein function annotation meta-server.
Nucleic Acids Res.
Iddo Friedberg, Tim Harder, Adam Godzik
2006 J jnl
Ten Simple Rules for Selecting a Postdoctoral Position.
PLoS Comput. Biol.
Philip E. Bourne, Iddo Friedberg
2005 J jnl
Fragnostic: walking through protein structure space.
Nucleic Acids Res.
Iddo Friedberg, Adam Godzik
2004 Misc conf
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures.
Pacific Symposium on Biocomputing
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, John D. Westbrook
2002 J jnl
PeCoP: automatic determination of persistently conserved positions in protein families.
Bioinform.
Iddo Friedberg, Hanah Margalit
2000 A conf
Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold.
ISMB
Iddo Friedberg, Tommy Kaplan, Hanah Margalit