Iddo Friedberg

Publication Activity (10 Years)

Years Active: 2000-2023
Publications (10 Years): 10

Top Topics

Recurrent Neural Networks

Escherichia Coli

Protein Function

Stochastic Gradient

Top Venues

PLoS Comput. Biol.

Database J. Biol. Databases Curation

Publications

Damiano Piovesan, Davide Zago, Parnal Joshi, M. Clara De Paolis Kaluza, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C. E. Tosatto
CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods. CoRR (2023)
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg
GOThresher: a program to remove annotation biases from protein function annotation datasets. Bioinform. 39 (1) (2023)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia N. Arighi, Jill Babor, Alex Bateman, Ian Blaby, Crysten Blaby-Haas, Alan 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 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
A roadmap for the functional annotation of protein families: a community perspective. Database J. Biol. Databases Curation 2022 (2022) (2022)
Lara Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney
Establishing the reliability of algorithms. PSB (2021)
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
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS Comput. Biol. 17 (10) (2021)
Md-Nafiz Hamid, Iddo Friedberg
Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. Bioinform. 35 (12) (2019)
Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg
Tracing the ancestry of operons in bacteria. Bioinform. 35 (17) (2019)
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
Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning. PLoS Comput. Biol. 14 (7) (2018)
Md-Nafiz Hamid, Iddo Friedberg
Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics. CoRR (2018)
Jucheol Moon, Iddo Friedberg, Oliver Eulenstein
Highly Bi-Connected Subgraphs for Computational Protein Function Annotation. COCOON (2016)
David C. Ream, Asma R. Bankapur, Iddo Friedberg
An event-driven approach for studying gene block evolution in bacteria. Bioinform. 31 (13) (2015)
Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac
Ten Simple Rules for a Community Computational Challenge. PLoS Comput. Biol. 11 (4) (2015)
James T. Morton, Stefan D. Freed, Shaun W. Lee, Iddo Friedberg
A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. BMC Bioinform. 16 (2015)
Yuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac
The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinform. 30 (17) (2014)
Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg
The automated function prediction SIG looks back at 2013 and prepares for 2014. Bioinform. 30 (14) (2014)
Andrew Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg
Biological Database of Images and Genomes: tools for community annotations linking image and genomic information. Database J. Biol. Databases Curation 2013 (2013)
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
Biases in the Experimental Annotations of Protein Function and their Effect on Our Understanding of Protein Function Space CoRR (2013)
Alexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg
Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space. PLoS Comput. Biol. 9 (5) (2013)
Ryan J. Kelly, David E. Vincent, Iddo Friedberg
IPRStats: visualization of the functional potential of an InterProScan run. BMC Bioinform. 11 (S-12) (2010)
John C. Wooley, Adam Godzik, Iddo Friedberg
A Primer on Metagenomics. PLoS Comput. Biol. 6 (2) (2010)
Peter J. A. Cock, Tiago 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
Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinform. 25 (11) (2009)
Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik
Using an alignment of fragment strings for comparing protein structures. Bioinform. 23 (2) (2007)
Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg
The 2006 Automated Function Prediction Meeting. BMC Bioinform. 8 (S-4) (2007)
Philip E. Bourne, Iddo Friedberg
Correction: Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. 2 (12) (2006)
Iddo Friedberg
Automated protein function prediction - the genomic challenge. Briefings Bioinform. 7 (3) (2006)
Philip E. Bourne, Iddo Friedberg
Ten Simple Rules for Selecting a Postdoctoral Position. PLoS Comput. Biol. 2 (11) (2006)
Iddo Friedberg, Tim Harder, Adam Godzik
JAFA: a protein function annotation meta-server. Nucleic Acids Res. 34 (Web-Server-Issue) (2006)
Iddo Friedberg, Adam Godzik
Fragnostic: walking through protein structure space. Nucleic Acids Res. 33 (Web-Server-Issue) (2005)
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
The Status of Structural Genomics Defined Through the Analysis of Current Targets and Structures. Pacific Symposium on Biocomputing (2004)
Iddo Friedberg, Hanah Margalit
PeCoP: automatic determination of persistently conserved positions in protein families. Bioinform. 18 (9) (2002)
Iddo Friedberg, Tommy Kaplan, Hanah Margalit
Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold. ISMB (2000)