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Iddo Friedberg - Publications

Affiliations: 
Miami University (Ohio), Oxford, OH 
Area:
bioinformatics, bacterial genomics, metagenomics, structural bioinformatics, function prediction
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42 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2023 Joshi P, Banerjee S, Hu X, Khade PM, Friedberg I. GOThresher: a program to remove annotation biases from protein function annotation datasets. Bioinformatics (Oxford, England). PMID 36688705 DOI: 10.1093/bioinformatics/btad048  0.368
2022 de Crécy-Lagard V, Amorin de Hegedus R, Arighi C, Babor J, Bateman A, Blaby I, Blaby-Haas C, Bridge AJ, Burley SK, Cleveland S, Colwell LJ, Conesa A, Dallago C, Danchin A, de Waard A, ... ... Friedberg I, et al. A roadmap for the functional annotation of protein families: a community perspective. Database : the Journal of Biological Databases and Curation. 2022. PMID 35961013 DOI: 10.1093/database/baac062  0.353
2019 Zhou N, Jiang Y, Bergquist TR, Lee AJ, Kacsoh BZ, Crocker AW, Lewis KA, Georghiou G, Nguyen HN, Hamid MN, Davis L, Dogan T, Atalay V, Rifaioglu AS, Dalkıran A, ... ... Friedberg I, et al. The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biology. 20: 244. PMID 31744546 DOI: 10.1186/S13059-019-1835-8  0.397
2019 Hu X, Friedberg I. SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. Gigascience. 8. PMID 31648300 DOI: 10.1093/Gigascience/Giz118  0.411
2019 Cao L, Gurevich A, Alexander KL, Naman CB, Leão T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, ... ... Friedberg I, et al. MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Systems. PMID 31629686 DOI: 10.1016/J.Cels.2019.09.004  0.33
2019 Cho KT, Portwood JL, Gardiner JM, Harper LC, Lawrence-Dill CJ, Friedberg I, Andorf CM. MaizeDIG: Maize Database of Images and Genomes. Frontiers in Plant Science. 10: 1050. PMID 31555312 DOI: 10.3389/Fpls.2019.01050  0.655
2019 Kasak L, Bakolitsa C, Hu Z, Yu C, Rine J, Dimster-Denk DF, Pandey G, De Baets G, Bromberg Y, Cao C, Capriotti E, Casadio R, Van Durme J, Giollo M, Karchin R, ... ... Friedberg I, et al. Assessing Computational Predictions of the Phenotypic Effect of Cystathionine-beta-Synthase Variants. Human Mutation. PMID 31301157 DOI: 10.1002/Humu.23868  0.344
2018 Wimalanathan K, Friedberg I, Andorf CM, Lawrence-Dill CJ. Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). Plant Direct. 2: e00052. PMID 31245718 DOI: 10.1002/pld3.52  0.665
2018 Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G. New Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda, Md.). PMID 30463884 DOI: 10.1534/G3.118.200867  0.33
2018 Zhou N, Siegel ZD, Zarecor S, Lee N, Campbell DA, Andorf CM, Nettleton D, Lawrence-Dill CJ, Ganapathysubramanian B, Kelly JW, Friedberg I. Crowdsourcing image analysis for plant phenomics to generate ground truth data for machine learning. Plos Computational Biology. 14: e1006337. PMID 30059508 DOI: 10.1371/Journal.Pcbi.1006337  0.629
2017 Friedberg I, Radivojac P. Community-Wide Evaluation of Computational Function Prediction. Methods in Molecular Biology (Clifton, N.J.). 1446: 133-146. PMID 27812940 DOI: 10.1007/978-1-4939-3743-1_10  0.424
2016 Jiang Y, Oron TR, Clark WT, Bankapur AR, D'Andrea D, Lepore R, Funk CS, Kahanda I, Verspoor KM, Ben-Hur A, Koo da CE, Penfold-Brown D, Shasha D, Youngs N, Bonneau R, ... ... Friedberg I, et al. An expanded evaluation of protein function prediction methods shows an improvement in accuracy. Genome Biology. 17: 184. PMID 27604469 DOI: 10.1186/S13059-016-1037-6  0.381
2015 Morton JT, Freed SD, Lee SW, Friedberg I. A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins. Bmc Bioinformatics. 16: 381. PMID 26558535 DOI: 10.1186/S12859-015-0792-9  0.373
2015 Friedberg I, Wass MN, Mooney SD, Radivojac P. Ten simple rules for a community computational challenge. Plos Computational Biology. 11: e1004150. PMID 25906249 DOI: 10.1371/Journal.Pcbi.1004150  0.401
2015 Ream DC, Bankapur AR, Friedberg I. An event-driven approach for studying gene block evolution in bacteria. Bioinformatics (Oxford, England). 31: 2075-83. PMID 25717195 DOI: 10.1093/Bioinformatics/Btv128  0.304
2014 Jiang Y, Clark WT, Friedberg I, Radivojac P. The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective. Bioinformatics (Oxford, England). 30: i609-16. PMID 25161254 DOI: 10.1093/Bioinformatics/Btu472  0.431
2014 Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I. The automated function prediction SIG looks back at 2013 and prepares for 2014 Bioinformatics. 30: 2091-2092. PMID 24590444 DOI: 10.1093/Bioinformatics/Btu117  0.341
2013 Ream DC, Murakami ST, Schmidt EE, Huang GH, Liang C, Friedberg I, Cheng XW. Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes. Virus Research. 178: 217-25. PMID 24140718 DOI: 10.1016/J.Virusres.2013.10.005  0.344
2013 Anton BP, Chang YC, Brown P, Choi HP, Faller LL, Guleria J, Hu Z, Klitgord N, Levy-Moonshine A, Maksad A, Mazumdar V, McGettrick M, Osmani L, Pokrzywa R, Rachlin J, ... ... Friedberg I, et al. The COMBREX project: design, methodology, and initial results. Plos Biology. 11: e1001638. PMID 24013487 DOI: 10.1371/Journal.Pbio.1001638  0.333
2013 Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I. Biases in the Experimental Annotations of Protein Function and Their Effect on Our Understanding of Protein Function Space Plos Computational Biology. 9. PMID 23737737 DOI: 10.1371/Journal.Pcbi.1003063  0.387
2013 Oberlin AT, Jurkovic DA, Balish MF, Friedberg I. Biological database of images and genomes: tools for community annotations linking image and genomic information. Database : the Journal of Biological Databases and Curation. 2013: bat016. PMID 23550062 DOI: 10.1093/Database/Bat016  0.407
2013 Radivojac P, Clark WT, Oron TR, Schnoes AM, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, ... ... Friedberg I, et al. A large-scale evaluation of computational protein function prediction. Nature Methods. 10: 221-7. PMID 23353650 DOI: 10.1038/Nmeth.2340  0.421
2010 Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Gaudet P, Lewis S, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O, et al. Meeting Report: BioSharing at ISMB 2010. Standards in Genomic Sciences. 3: 254-8. PMID 21304729 DOI: 10.4056/Sigs/1403501  0.304
2010 Kelly RJ, Vincent DE, Friedberg I. IPRStats: Visualization of the functional potential of an InterProScan run Bmc Bioinformatics. 11. PMID 21210980 DOI: 10.1186/1471-2105-11-S12-S13  0.426
2010 Wooley JC, Godzik A, Friedberg I. A primer on metagenomics Plos Computational Biology. 6. PMID 20195499 DOI: 10.1371/Journal.Pcbi.1000667  0.415
2009 Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J. Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009. Standards in Genomic Sciences. 1: 278-82. PMID 21304668 DOI: 10.4056/Sigs.641096  0.311
2009 Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ. Biopython: freely available Python tools for computational molecular biology and bioinformatics. Bioinformatics (Oxford, England). 25: 1422-3. PMID 19304878 DOI: 10.1093/Bioinformatics/Btp163  0.38
2007 Godzik A, Jambon M, Friedberg I. Computational protein function prediction: Are we making progress? Cellular and Molecular Life Sciences. 64: 2505-2511. PMID 17611711 DOI: 10.1007/S00018-007-7211-Y  0.392
2007 Rodrigues APC, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting Bmc Bioinformatics. 8. PMID 17570143 DOI: 10.1186/1471-2105-8-S4-S1  0.405
2007 Friedberg I, Nika K, Tautz L, Saito K, Cerignoli F, Godzik A, Mustelin T. Identification and characterization of DUSP27, a novel dual-specific protein phosphatase Febs Letters. 581: 2527-2533. PMID 17498703 DOI: 10.1016/J.Febslet.2007.04.059  0.316
2007 Friedberg I, Godzik A. Functional Differentiation of Proteins: Implications for Structural Genomics Structure. 15: 405-415. PMID 17437713 DOI: 10.1016/J.Str.2007.02.005  0.384
2007 Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures Bioinformatics. 23: e219-e224. PMID 17237095 DOI: 10.1093/Bioinformatics/Btl310  0.335
2006 Friedberg I, Harder T, Godzik A. JAFA: A protein function annotation meta-server Nucleic Acids Research. 34: W379-W381. PMID 16845030 DOI: 10.1093/Nar/Gkl045  0.427
2006 Friedberg I. Automated protein function prediction - The genomic challenge Briefings in Bioinformatics. 7: 225-242. PMID 16772267 DOI: 10.1093/Bib/Bbl004  0.475
2006 Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction Protein Science. 15: 1527-1529. PMID 16731984 DOI: 10.1110/Ps.062158406  0.453
2005 Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments Structure. 13: 1213-1224. PMID 16084393 DOI: 10.1016/J.Str.2005.05.009  0.334
2005 Friedberg I, Godzik A. Fragnostic: Walking through protein structure space Nucleic Acids Research. 33: W249-W251. PMID 15980462 DOI: 10.1093/Nar/Gki363  0.356
2004 Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics Current Opinion in Structural Biology. 14: 307-312. PMID 15193310 DOI: 10.1016/J.Sbi.2004.04.005  0.371
2004 Alonso A, Sasin J, Bottini N, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T. Protein tyrosine phosphatases in the human genome Cell. 117: 699-711. PMID 15186772 DOI: 10.1016/J.Cell.2004.05.018  0.36
2004 Bourne PE, Allerston CK, Krebs W, Li W, Shindyalov IN, Godzik A, Friedberg I, Liu T, Wild D, Hwang S, Ghahramani Z, Chen L, Westbrook J. The status of structural genomics defined through the analysis of current targets and structures. Pacific Symposium On Biocomputing. Pacific Symposium On Biocomputing. 375-86. PMID 14992518 DOI: 10.1142/9789812704856_0036  0.303
2002 Friedberg I, Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: Roles in preserving protein fold and function Protein Science. 11: 350-360. PMID 11790845 DOI: 10.1110/Ps.18602  0.348
2000 Friedberg I, Kaplan T, Margalit H. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments Protein Science. 9: 2278-2284. PMID 11152139 DOI: 10.1110/Ps.9.11.2278  0.36
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