Iddo Friedberg

According to our database, Iddo Friedberg authored at least 32 papers between 2000 and 2023.

Collaborative distances:

• Dijkstra number of four.
• Erdős number of three.

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., January, 2023

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

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, 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

Bioinform., 2022

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, 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

Database J. Biol. Databases Curation, 2022

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, 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

PLoS Comput. Biol., 2021

Establishing the reliability of algorithms.

Lara M. Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney

Proceedings of the Biocomputing 2021: Proceedings of the Pacific Symposium, 2021

2020

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

2019

Tracing the ancestry of operons in bacteria.

Huy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg

Bioinform., 2019

Identifying antimicrobial peptides using word embedding with deep recurrent neural networks.

Md-Nafiz Hamid, Iddo Friedberg

Bioinform., 2019

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

Reliable uncertainty estimate for antibiotic resistance classification with Stochastic Gradient Langevin Dynamics.

Md-Nafiz Hamid, Iddo Friedberg

CoRR, 2018

2016

Highly Bi-Connected Subgraphs for Computational Protein Function Annotation.

Jucheol Moon, Iddo Friedberg, Oliver Eulenstein

Proceedings of the Computing and Combinatorics - 22nd International Conference, 2016

2015

Ten Simple Rules for a Community Computational Challenge.

Iddo Friedberg, Mark N. Wass, Sean D. Mooney, Predrag Radivojac

PLoS Comput. Biol., 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

An event-driven approach for studying gene block evolution in bacteria.

David C. Ream, Asma R. Bankapur, Iddo Friedberg

Bioinform., 2015

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

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

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

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

2010

A Primer on Metagenomics.

John C. Wooley, Adam Godzik, Iddo Friedberg

PLoS Comput. Biol., 2010

IPRStats: visualization of the functional potential of an InterProScan run.

Ryan J. Kelly, David E. Vincent, Iddo Friedberg

BMC Bioinform., 2010

2009

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

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

Bioinform., 2009

2007

The 2006 Automated Function Prediction Meeting.

Ana P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg

BMC Bioinform., 2007

Using an alignment of fragment strings for comparing protein structures.

Iddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik

Bioinform., 2007

2006

Correction: Ten Simple Rules for Selecting a Postdoctoral Position.

Philip E. Bourne, Iddo Friedberg

PLoS Comput. Biol., 2006

Ten Simple Rules for Selecting a Postdoctoral Position.

Philip E. Bourne, Iddo Friedberg

PLoS Comput. Biol., 2006

JAFA: a protein function annotation meta-server.

Iddo Friedberg, Tim Harder, Adam Godzik

Nucleic Acids Res., 2006

Automated protein function prediction - the genomic challenge.

Iddo Friedberg

Briefings Bioinform., 2006

2005

Fragnostic: walking through protein structure space.

Iddo Friedberg, Adam Godzik

Nucleic Acids Res., 2005

2004

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, John D. Westbrook

Proceedings of the Biocomputing 2004, 2004

2002

PeCoP: automatic determination of persistently conserved positions in protein families.

Iddo Friedberg, Hanah Margalit

Bioinform., 2002

2000

Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common Fold.

Iddo Friedberg, Tommy Kaplan, Hanah Margalit

Proceedings of the Eighth International Conference on Intelligent Systems for Molecular Biology, 2000