Iddo Friedberg - researchr alias

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Viewing Publication 1 - 28 from 28

2023

GOThresher: a program to remove annotation biases from protein function annotation datasetsParnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M. Khade, Iddo Friedberg. bioinformatics, 39(1), January 2023. [doi]

2022

A roadmap for the functional annotation of protein families: a community perspectiveValérie 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 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. biodb, 2022(2022), 2022. [doi]

2021

Establishing the reliability of algorithmsLara Mangravite, Sean D. Mooney, Iddo Friedberg, Justin Guinney. psb 2020: [doi]

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. ploscb, 17(10), 2021. [doi]

2019

Identifying antimicrobial peptides using word embedding with deep recurrent neural networksMd-Nafiz Hamid, Iddo Friedberg. bioinformatics, 35(12):2009-2016, 2019. [doi]

Tracing the ancestry of operons in bacteriaHuy N. Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg. bioinformatics, 35(17):2998-3004, 2019. [doi]

2018

Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learningNaihui 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. ploscb, 14(7), 2018. [doi]

2016

Highly Bi-Connected Subgraphs for Computational Protein Function AnnotationJucheol Moon, Iddo Friedberg, Oliver Eulenstein. cocoon 2016: 573-584 [doi]

2015

2014

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspectiveYuxiang Jiang, Wyatt T. Clark, Iddo Friedberg, Predrag Radivojac. bioinformatics, 30(17):609-616, 2014. [doi]

The automated function prediction SIG looks back at 2013 and prepares for 2014Mark N. Wass, Sean D. Mooney, Michal Linial, Predrag Radivojac, Iddo Friedberg. bioinformatics, 30(14):2091-2092, 2014. [doi]

2013

Biological Database of Images and Genomes: tools for community annotations linking image and genomic informationAndrew Oberlin, Dominika A. Jurkovic, Mitchell F. Balish, Iddo Friedberg. biodb, 2013, 2013. [doi]

Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function SpaceAlexandra M. Schnoes, David C. Ream, Alexander W. Thorman, Patricia C. Babbitt, Iddo Friedberg. ploscb, 9(5), 2013. [doi]

2010

IPRStats: visualization of the functional potential of an InterProScan runRyan J. Kelly, David E. Vincent, Iddo Friedberg. bmcbi, 11(S-12), 2010. [doi]

A Primer on MetagenomicsJohn C. Wooley, Adam Godzik, Iddo Friedberg. ploscb, 6(2), 2010. [doi]

2009

Biopython: freely available Python tools for computational molecular biology and bioinformaticsPeter 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. bioinformatics, 25(11):1422-1423, 2009. [doi]

2007

Using an alignment of fragment strings for comparing protein structuresIddo Friedberg, Tim Harder, Rachel Kolodny, Einat Sitbon, Zhanwen Li, Adam Godzik. bioinformatics, 23(2):219-224, 2007. [doi]

The 2006 Automated Function Prediction MeetingAna P. C. Rodrigues, Barry J. Grant, Adam Godzik, Iddo Friedberg. bmcbi, 8(S-4), 2007. [doi]

2006

Ten Simple Rules for Selecting a Postdoctoral PositionPhilip E. Bourne, Iddo Friedberg. ploscb, 2(11), 2006. [doi]

Correction: Ten Simple Rules for Selecting a Postdoctoral PositionPhilip E. Bourne, Iddo Friedberg. ploscb, 2(12), 2006. [doi]

Automated protein function prediction - the genomic challengeIddo Friedberg. bib, 7(3):225-242, 2006. [doi]

JAFA: a protein function annotation meta-serverIddo Friedberg, Tim Harder, Adam Godzik. nar, 34(Web-Server-Issue):379-381, 2006. [doi]

2005

Fragnostic: walking through protein structure spaceIddo Friedberg, Adam Godzik. nar, 33(Web-Server-Issue):249-251, 2005. [doi]

2004

The Status of Structural Genomics Defined Through the Analysis of Current Targets and StructuresPhilip 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. psb 2004: 375-386 [doi]

2002

PeCoP: automatic determination of persistently conserved positions in protein familiesIddo Friedberg, Hanah Margalit. bioinformatics, 18(9):1276-1277, 2002.

2000

Glimmers in the Midnight Zone: Characterization of Aligned Identical Residues in Sequence-Dissimilar Proteins Sharing a Common FoldIddo Friedberg, Tommy Kaplan, Hanah Margalit. ismb 2000: 162-170

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Publications by 'Iddo Friedberg'

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2023

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