Iddo Friedberg

ORCID

Publication Activity (10 Years)

Years Active: 2016-2024
Publications (10 Years): 25

Top Venues

Bioinformatics advances

bioRxiv : the preprint server for biology

NAR genomics and bioinformatics

Genome biology

Iowa State University

Hebrew University Faculty of Medicine (PHD)

This page only lists publications with an associated author ORCID identifier.

Affiliation History

Iowa State University Jun 01 2015

United States

Associate Professor :: Veterinary Microbiology and Preventive Medicine

Miami University

United States

Assistant Professor :: Microbiology

University of California San Diego Jun 01 2007 - Aug 01 2009

United States

Scientist

Sanford-Burnham Medical Research Institute

United States

Postdoctoral Associate

Education History

Hebrew University Faculty of Medicine

Israel

PHD :: Computational Biology

Hebrew University of Jerusalem

Israel

MSC :: Biological Chemistry

Hebrew University of Jerusalem Faculty of Science

Israel

BSC :: Biology

Publications

Damiano Piovesan, Davide Zago, Parnal Joshi, M Clara De Paolis Kaluza, Mahta Mehdiabadi, Rashika Ramola, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C E Tosatto
CAFA-evaluator: a Python tool for benchmarking ontological classification methods. Bioinformatics advances 4 (1) (2024)
Priyanka Banerjee, Oliver Eulenstein, Iddo Friedberg
Discovering genomic islands in unannotated bacterial genomes using sequence embedding. Bioinformatics advances 4 (1) (2024)
Joseph Zinski, Henri C Chung, Parnal Joshi, Finn Warrick, Brian D Berg, Greg Glova, Maura McGrail, Darius Balciunas, Iddo Friedberg, Mary C Mullins
EpicTope: narrating protein sequence features to identify non-disruptive epitope tagging sites. bioRxiv : the preprint server for biology (2024)
Damiano Piovesan, Davide Zago, Parnal Joshi, M Clara De Paolis Kaluza, Mahta Mehdiabadi, Rashika Ramola, Alexander Miguel Monzon, Walter Reade, Iddo Friedberg, Predrag Radivojac, Silvio C E Tosatto
CAFA-evaluator: a Python tool for benchmarking ontological classification methods. Bioinformatics advances 4 (1) (2024)
Henri C Chung, Iddo Friedberg, Yana Bromberg
Assembling bacterial puzzles: piecing together functions into microbial pathways. NAR genomics and bioinformatics 6 (3) (2024)
Henri C Chung, Iddo Friedberg, Yana Bromberg
Assembling bacterial puzzles: piecing together functions into microbial pathways. NAR genomics and bioinformatics 6 (3) (2024)
Valérie de Crécy-Lagard, Raquel Dias, Iddo Friedberg, Yifeng Yuan, Manal A Swairjo
Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins. bioRxiv : the preprint server for biology (2024)
Joseph Zinski, Henri C Chung, Parnal Joshi, Finn Warrick, Brian D Berg, Greg Glova, Maura McGrail, Darius Balciunas, Iddo Friedberg, Mary C Mullins
EpicTope: narrating protein sequence features to identify non-disruptive epitope tagging sites. bioRxiv : the preprint server for biology (2024)
Priyanka Banerjee, Oliver Eulenstein, Iddo Friedberg
Discovering genomic islands in unannotated bacterial genomes using sequence embedding. Bioinformatics advances 4 (1) (2024)
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M Khade, Iddo Friedberg
GOThresher: a program to remove annotation biases from protein function annotation datasets. Bioinformatics (Oxford, England) 39 (1) (2023)
Parnal Joshi, Sagnik Banerjee, Xiao Hu, Pranav M Khade, Iddo Friedberg
GOThresher: a program to remove annotation biases from protein function annotation datasets. Bioinformatics (Oxford, England) 39 (1) (2023)
Henri C Chung, Christine L Foxx, Jessica A Hicks, Tod P Stuber, Iddo Friedberg, Karin S Dorman, Beth Harris
An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species. PloS one 18 (8) (2023)
Yannick Mahlich, Chengsheng Zhu, Henri Chung, Pavan K Velaga, M Clara De Paolis Kaluza, Predrag Radivojac, Iddo Friedberg, Yana Bromberg
Learning from the unknown: exploring the range of bacterial functionality. Nucleic acids research (2023)
Rashika Ramola, Iddo Friedberg, Predrag Radivojac
The field of protein function prediction as viewed by different domain scientists. Bioinformatics advances 2 (1) (2022)
Rashika Ramola, Iddo Friedberg, Predrag Radivojac
The field of protein function prediction as viewed by different domain scientists. Bioinformatics advances 2 (1) (2022)
Meghan Wymore Brand, Alexandra L Proctor, Jesse M Hostetter, Naihui Zhou, Iddo Friedberg, Albert E Jergens, Gregory J Phillips, Michael J Wannemuehler
Vertical transmission of attaching and invasive E. coli from the dam to neonatal mice predisposes to more severe colitis following exposure to a colitic insult later in life. PloS one 17 (4) (2022)
Valérie de Crécy-Lagard, Rocio Amorin de Hegedus, Cecilia Noemi Arighi, Jill Babor, Alex Bateman, Ian K 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 Henry, Geoffrey Hutinet, Marshall Jaroch, Peter D Karp, Liudmyla Kondratova, Zhiyong Lu, Aron Marchler-Bauer, Maria-Jesus Martin, Claire McWhite, Gaurav D Moghe, Paul Monaghan, Anne Morgat, Christopher John Mungall, Darren A Natale, William C Nelson, Seán O'Donoghue, Christine Orengo, Katherine H O'Toole, Predrag Radivojac, Colbie Reed, Richard J Roberts, Dmitri Rodionov, Irina A Rodionova, Jeffrey D Rudolf, Lana Saleh, Gloria M Sheynkman, Francoise Thibaud-Nissen, Paul D Thomas, Peter Uetz, David Vallenet, Erica Watson Carter, Peter R Weigele, Valerie Wood, Elisha M Wood-Charlson, Jin Xu
A roadmap for the functional annotation of protein families: a community perspective. Database : the journal of biological databases and curation 2022 (2022)
Jolene Ramsey, Brenley McIntosh, Daniel Renfro, Suzanne A Aleksander, Sandra LaBonte, Curtis Ross, Adrienne E Zweifel, Nathan Liles, Shabnam Farrar, Jason J Gill, Ivan Erill, Sarah E Ades, Tanya Z Berardini, Jennifer A Bennett, Siobhan Brady, Robert A Britton, Seth J Carbon, Steven M Caruso, Dave Clements, Ritu Dalia, Meredith Defelice, Erin L Doyle, Iddo Friedberg, Susan M R Gurney, Lee E Hughes, Allison A Johnson, Jason M Kowalski, Donghui Li, Ruth C Lovering, Tamara L Mans, Fiona McCarthy, Sean D Moore, Rebecca L 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 M Willey, Deborah A Siegele, James C Hu
Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS computational biology 17 (10) (2021)
Ryan S Nett, Huy Nguyen, Raimund Nagel, Ariana Marcassa, Trevor C Charles, Iddo Friedberg, Reuben J Peters
Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon. mSphere 5 (3) (2020)
Naihui Zhou, Yuxiang Jiang, Timothy R Bergquist, Alexandra J Lee, Balint Z Kacsoh, Alex W Crocker, Kimberley A Lewis, George Georghiou, Huy N Nguyen, Md Nafiz Hamid, Larry Davis, Tunca Dogan, Volkan Atalay, Ahmet S Rifaioglu, Alperen Dalkıran, Rengul Cetin Atalay, Chengxin Zhang, Rebecca L Hurto, Peter L Freddolino, Yang Zhang, Prajwal Bhat, Fran Supek, José M Fernández, Branislava Gemovic, Vladimir R Perovic, Radoslav S Davidović, Neven Sumonja, Nevena Veljkovic, Ehsaneddin Asgari, Mohammad R K Mofrad, Giuseppe Profiti, Castrense Savojardo, Pier Luigi Martelli, Rita Casadio, Florian Boecker, Heiko Schoof, Indika Kahanda, Natalie Thurlby, Alice C McHardy, Alexandre Renaux, Rabie Saidi, Julian Gough, Alex A Freitas, Magdalena Antczak, Fabio Fabris, Mark N Wass, Jie Hou, Jianlin Cheng, Zheng Wang, Alfonso E Romero, Alberto Paccanaro, Haixuan Yang, Tatyana Goldberg, Chenguang Zhao, Liisa Holm, Petri Törönen, Alan J Medlar, Elaine Zosa, Itamar Borukhov, Ilya Novikov, Angela Wilkins, Olivier Lichtarge, Po-Han Chi, Wei-Cheng Tseng, Michal Linial, Peter W Rose, Christophe Dessimoz, Vedrana Vidulin, Saso Dzeroski, Ian Sillitoe, Sayoni Das, Jonathan Gill Lees, David T Jones, Cen Wan, Domenico Cozzetto, Rui Fa, Mateo Torres, Alex Warwick Vesztrocy, Jose Manuel Rodriguez, Michael L Tress, Marco Frasca, Marco Notaro, Giuliano Grossi, Alessandro Petrini, Matteo Re, Giorgio Valentini, Marco Mesiti, Daniel B Roche, Jonas Reeb, David W Ritchie, Sabeur Aridhi, Seyed Ziaeddin Alborzi, Marie-Dominique Devignes, Da Chen Emily Koo, Richard Bonneau, Vladimir Gligorijević, Meet Barot, Hai Fang, Stefano Toppo, Enrico Lavezzo, Marco Falda, Michele Berselli, Silvio C E Tosatto, Marco Carraro, Damiano Piovesan, Hafeez Ur Rehman, Qizhong Mao, Shanshan Zhang, Slobodan Vucetic, Gage S Black, Dane Jo, Erica Suh, Jonathan B Dayton, Dallas J Larsen, Ashton R Omdahl, Liam J McGuffin, Danielle A Brackenridge, Patricia C Babbitt, Jeffrey M Yunes, Paolo Fontana, Feng Zhang, Shanfeng Zhu, Ronghui You, Zihan Zhang, Suyang Dai, Shuwei Yao, Weidong Tian, Renzhi Cao, Caleb Chandler, Miguel Amezola, Devon Johnson, Jia-Ming Chang, Wen-Hung Liao, Yi-Wei Liu, Stefano Pascarelli, Yotam Frank, Robert Hoehndorf, Maxat Kulmanov, Imane Boudellioua, Gianfranco Politano, Stefano Di Carlo, Alfredo Benso, Kai Hakala, Filip Ginter, Farrokh Mehryary, Suwisa Kaewphan, Jari Björne, Hans Moen, Martti E E Tolvanen, Tapio Salakoski, Daisuke Kihara, Aashish Jain, Tomislav Šmuc, Adrian Altenhoff, Asa Ben-Hur, Burkhard Rost, Steven E Brenner, Christine A Orengo, Constance J Jeffery, Giovanni Bosco, Deborah A Hogan, Maria J Martin, Claire O'Donovan, Sean D Mooney, Casey S Greene, Predrag Radivojac, Iddo Friedberg
The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome biology 20 (1) (2019)
Balint Z Kacsoh, Stephen Barton, Yuxiang Jiang, Naihui Zhou, Sean D Mooney, Iddo Friedberg, Predrag Radivojac, Casey S Greene, Giovanni Bosco
New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda, Md.) 9 (1) (2019)
Francisco R Fields, Stefan D Freed, Katelyn E Carothers, Md Nafiz Hamid, Daniel E Hammers, Jessica N Ross, Veronica R Kalwajtys, Alejandro J Gonzalez, Andrew D Hildreth, Iddo Friedberg, Shaun W Lee
Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains. Drug development research 81 (1) (2019)
Laura Kasak, Constantina Bakolitsa, Zhiqiang Hu, Changhua Yu, Jasper Rine, Dago F Dimster-Denk, Gaurav Pandey, Greet De Baets, Yana Bromberg, Chen Cao, Emidio Capriotti, Rita Casadio, Joost Van Durme, Manuel Giollo, Rachel Karchin, Panagiostis Katsonis, Emanuela Leonardi, Olivier Lichtarge, Pier Luigi Martelli, David Masica, Sean D Mooney, Ayodeji Olatubosun, Predrag Radivojac, Frederic Rousseau, Lipika R Pal, Castrense Savojardo, Joost Schymkowitz, Janita Thusberg, Silvio C E Tosatto, Mauno Vihinen, Jouni Väliaho, Susanna Repo, John Moult, Steven E Brenner, Iddo Friedberg
Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Human mutation 40 (9) (2019)
Naihui Zhou, Zachary D Siegel, Scott Zarecor, Nigel Lee, Darwin A Campbell, Carson M Andorf, Daniel S 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 computational biology 14 (7) (2018)
Yuxiang Jiang, Tal Ronnen Oron, Wyatt T Clark, Asma R Bankapur, Daniel D'Andrea, Rosalba Lepore, Christopher S Funk, Indika Kahanda, Karin M Verspoor, Asa Ben-Hur, Da Chen Emily Koo, Duncan Penfold-Brown, Dennis Shasha, Noah Youngs, Richard Bonneau, Alexandra Lin, Sayed M E Sahraeian, Pier Luigi Martelli, Giuseppe Profiti, Rita Casadio, Renzhi Cao, Zhaolong Zhong, Jianlin Cheng, Adrian Altenhoff, Nives Skunca, Christophe Dessimoz, Tunca Dogan, Kai Hakala, Suwisa Kaewphan, Farrokh Mehryary, Tapio Salakoski, Filip Ginter, Hai Fang, Ben Smithers, Matt Oates, Julian Gough, Petri Törönen, Patrik Koskinen, Liisa Holm, Ching-Tai Chen, Wen-Lian Hsu, Kevin Bryson, Domenico Cozzetto, Federico Minneci, David T Jones, Samuel Chapman, Dukka Bkc, Ishita K Khan, Daisuke Kihara, Dan Ofer, Nadav Rappoport, Amos Stern, Elena Cibrian-Uhalte, Paul Denny, Rebecca E Foulger, Reija Hieta, Duncan Legge, Ruth C Lovering, Michele Magrane, Anna N Melidoni, Prudence Mutowo-Meullenet, Klemens Pichler, Aleksandra Shypitsyna, Biao Li, Pooya Zakeri, Sarah ElShal, Léon-Charles Tranchevent, Sayoni Das, Natalie L Dawson, David Lee, Jonathan G Lees, Ian Sillitoe, Prajwal Bhat, Tamás Nepusz, Alfonso E Romero, Rajkumar Sasidharan, Haixuan Yang, Alberto Paccanaro, Jesse Gillis, Adriana E Sedeño-Cortés, Paul Pavlidis, Shou Feng, Juan M Cejuela, Tatyana Goldberg, Tobias Hamp, Lothar Richter, Asaf Salamov, Toni Gabaldon, Marina Marcet-Houben, Fran Supek, Qingtian Gong, Wei Ning, Yuanpeng Zhou, Weidong Tian, Marco Falda, Paolo Fontana, Enrico Lavezzo, Stefano Toppo, Carlo Ferrari, Manuel Giollo, Damiano Piovesan, Silvio C E Tosatto, Angela Del Pozo, José M Fernández, Paolo Maietta, Alfonso Valencia, Michael L Tress, Alfredo Benso, Stefano Di Carlo, Gianfranco Politano, Alessandro Savino, Hafeez Ur Rehman, Matteo Re, Marco Mesiti, Giorgio Valentini, Joachim W Bargsten, Aalt D J van Dijk, Branislava Gemovic, Sanja Glisic, Vladmir Perovic, Veljko Veljkovic, Nevena Veljkovic, Danillo C Almeida-E-Silva, Ricardo Z N Vencio, Malvika Sharan, Jörg Vogel, Lakesh Kansakar, Shanshan Zhang, Slobodan Vucetic, Zheng Wang, Michael J E Sternberg, Mark N Wass, Rachael P Huntley, Maria J Martin, Claire O'Donovan, Peter N Robinson, Yves Moreau, Anna Tramontano, Patricia C Babbitt, Steven E Brenner, Michal Linial, Christine A Orengo, Burkhard Rost, Casey S Greene, Sean D Mooney, Iddo Friedberg, Predrag Radivojac
An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome biology 17 (1) (2016)

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Publication Activity (10 Years)

Top Topics

Top Venues

Iddo Friedberg