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Author Details

Iddo Friedberg
Iowa State University
1997
66
25
Gloria M Sheynkman (CM4AI)
PMIDPaper TitleJournal TitlePublished Year
36688705GOThresher: a program to remove annotation biases from protein function annotation datasets.Bioinformatics2023
37616210An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species.PLoS One2023
37739408Learning from the unknown: exploring the range of bacterial functionality.Nucleic Acids Res2023
35961013A roadmap for the functional annotation of protein families: a community perspective.Database (Oxford)2022
35381031Vertical 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 One2022
35758800Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia.Bioinformatics2022
36699361The field of protein function prediction as viewed by different domain scientists.Bioinform Adv2022
33305328Deploying MMEJ using MENdel in precision gene editing applications for gene therapy and functional genomics.Nucleic Acids Res2021
33691031Establishing the reliability of algorithms.Pac Symp Biocomput2021
34710081Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO).PLoS Comput Biol2021
31483516Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains.Drug Dev Res2020
33381825Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it.Bioinformatics2020
32493722Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon.mSphere2020
30689726Tracing the ancestry of operons in bacteria.Bioinformatics2019
31744546The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens.Genome Biol2019
31742435Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells.CRISPR J2019
31648300SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier.Gigascience2019
31301157Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants.Hum Mutat2019
31555312MaizeDIG: Maize Database of Images and Genomes.Front Plant Sci2019
31629686MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities.Cell Syst2019
30463884New <i>Drosophila</i> Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods.G3 (Bethesda)2019
30418485Identifying antimicrobial peptides using word embedding with deep recurrent neural networks.Bioinformatics2019
31245718Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER).Plant Direct2018
30059508Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning.PLoS Comput Biol2018
27812940Community-Wide Evaluation of Computational Function Prediction.Methods Mol Biol2017
27347760Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico.Emerg Infect Dis2016
27604469An expanded evaluation of protein function prediction methods shows an improvement in accuracy.Genome Biol2016
25717195An event-driven approach for studying gene block evolution in bacteria.Bioinformatics2015
26558535A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins.BMC Bioinformatics2015
25906249Ten simple rules for a community computational challenge.PLoS Comput Biol2015
24590444The automated function prediction SIG looks back at 2013 and prepares for 2014.Bioinformatics2014
25161254The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.Bioinformatics2014
23353650A large-scale evaluation of computational protein function prediction.Nat Methods2013
24140718Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes.Virus Res2013
24013487The COMBREX project: design, methodology, and initial results.PLoS Biol2013
23737737Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.PLoS Comput Biol2013
23550062Biological database of images and genomes: tools for community annotations linking image and genomic information.Database (Oxford)2013
22585924Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides.Adv Nutr2012
22546241A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.Genome Biol2012
21390078Protist diversity in a permanently ice-covered Antarctic lake during the polar night transition.ISME J2011
20195499A primer on metagenomics.PLoS Comput Biol2010
21304729Meeting Report: BioSharing at ISMB 2010.Stand Genomic Sci2010
21304724Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010.Stand Genomic Sci2010
21210980IPRStats: visualization of the functional potential of an InterProScan run.BMC Bioinformatics2010
19304878Biopython: freely available Python tools for computational molecular biology and bioinformatics.Bioinformatics2009
21304668Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009.Stand Genomic Sci2009
17237095Using an alignment of fragment strings for comparing protein structures.Bioinformatics2007
17570143The 2006 automated function prediction meeting.BMC Bioinformatics2007
17611711Computational protein function prediction: are we making progress?Cell Mol Life Sci2007
17437713Functional differentiation of proteins: implications for structural genomics.Structure2007
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Collaborators

University of California Riverside
Co-authored papers 13
Indiana University
Co-authored papers 12
University of Washington
Co-authored papers 8
University of California berkeley
Co-authored papers 5
University College London, Institute of Structural and Molecular Biology
Co-authored papers 5
University of Kent
Co-authored papers 5
The First Affiliated Hospital of Soochow University
Co-authored papers 4
University of California
Co-authored papers 4
Indiana University
Co-authored papers 4
University of California san francisco
Co-authored papers 4
Institute of Life Sciences, The Hebrew University of Jerusalem
Co-authored papers 4
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 4
European Bioinformatics Institute (EMBL-EBI)
Co-authored papers 4
The MITRE Corporation
Co-authored papers 3
University of Bristol
Co-authored papers 3
University of Padova
Co-authored papers 3
European Bioinformatics Institute
Co-authored papers 3
Colorado State University
Co-authored papers 3
Co-authored papers 3
Department of Pharmacy and Biotechnology, University of Bologna
Co-authored papers 3
Purdue University
Co-authored papers 3
University College London
Co-authored papers 3
BioMarin Pharmaceutical Inc.
Co-authored papers 3
European Bioinformatics Institute
Co-authored papers 3
USDA-ARS, Corn Insects and Crop Genetics Research Unit
Co-authored papers 3
Technical University of Munich (TUM)
Co-authored papers 3
Baylor College of Medicine
Co-authored papers 3
Biodiversity Institute, University of Oxford
Co-authored papers 3
Imperial College London
Co-authored papers 3
Royal Holloway University of London
Co-authored papers 3