College of Veterinary Medicine
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Iddo Friedberg

MS, PhD
Iddo Friedberg

Associate Professor
Vet Microbiology & Preventive Medicine
idoerg@iastate.edu
515-294-5959
2118 Patterson
ISU Directory Link
Iddo Friedberg's Lab

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Research Focus & Interests

I am interested in the large scale analyses of proteins, genomes and metagenomes.

Metagenomics is the study of genomic material extracted directly from the environment. New sequencing technologies have enabled the study of whole populations of genomes taken from microbial communities in the field, as opposed to single species clonal cultures in the lab. Metagenomics offers a way to study how genomes evolve to cope with the microbial biotic and abiotic environments. Our lab helped developed a method to study the correlation between the human gut microbiota and gut gene expression. We are applying this method towards studying infant gut development the effect of gut microbes on human health and wellness.

Bacterial Genome Evolution: Gene blocks are a common occurrence in bacteria: these are genes which lie close together on the chromosome, and may participate in a common cellular or biochemical function. Operons are gene blocks whose member genes are co-transcribed. We have developed a new method to describe the evolution of operons and gene blocks in bacteria. We describe a small set of evolutionary events that can take place in gene block evolution, and count these events to create a new type of molecular clock that tells us how fast or how slow certain gene blocks may have evolved. We hope to learn how new funcitons are acquired by ensembles of genes such as these.

Function Prediction: genomics, proteomics and various other ``-omics'' inundate us with sequence and structure information, but the biological functions of those proteins in many cases still eludes us. Computational prediction of protein and gene function is a rapidly growing research field in bioinformatics [4]. I am the co-organizer of the automated computational protein function prediction meetings: AFP. The AFP meetings bring together researchers to discuss various methods for protein function prediction. My personal interest in function prediction lies in predicting function from protein structure [5]. We have recently started work on predicting gene function based on its genomic context in bacteria, using both genomic and metagenomic data towards that end.

For professional opportunities, and for more information, see my website.

Honors & Awards

Director, the International Society for Computational Biology.

Senior member, the International Society for Computational Biology

Memberships

International Society of Computational Biology

International Society of Biocuration

Selected Publications

2025

 

  • de Crécy-Lagard V, Dias R, Sexson N, Friedberg I , Yuan Y, Swairjo MA Limitations of Current Machine-Learning Models in Predicting Enzymatic Functions for Uncharacterized Proteins (2025) G3 Genes | Genomes | Genetics 15:10 doi
  • Phan A, Joshi P, Kadelka C, Friedberg I A Longitudinal Analysis of Function Annotations of the Human Proteome Reveals Consistently High Biases (2025) Database (OUP) 2025:baaf036 doi
  • Ming Z, Liu F, Moran HR, et al. Lineage labeling with zebrafish hand2 Cre and CreERT2 recombinase CRISPR knock-ins. Developmental Dynamics. 2025; 1-20. doi
  • Chung HC, Friedberg I, Bromberg Y Assembling bacterial puzzles: piecing together functions into microbial pathways NAR Genomics and Bioinformatics 6:3 lqae109 doi

2024

  • Banerjee P, Eulenstein O, Friedberg I Discovering genomic islands in unannotated bacterial genomes using sequence embedding (2024) Bioinformatics Advances 4:1 vbae089 doi
  • Piovesan D, Zago D, Joshi P, De Paolis Kaluza MC, Mehdiabadi M, Ramola R, Monzon AM, Reade W, Friedberg I, Radivojac P, Tosatto SCE CAFA-evaluator: A Python Tool for Benchmarking Ontological Classification Methods (2024) Bioinformatics Advances vbae043, doi
  • The Critical Assessment of Genome Interpretation Consortium. CAGI, the Critical Assessment of Genome Interpretation, establishes progress and prospects for computational genetic variant interpretation methods. (2024) Genome Biol 25, 53 doi

2023

  • Mahlich Y, Zhu C, Chung H, Velaga PV, De Paolis Kaluza MC, Radivojac P, Friedberg I, Bromberg Y Learning from the unknown: exploring the range of bacterial functionality Nucleic Acids Research, (2023) 51:19, 10162–10175 doi
  • Chung HC, Foxx CL, Hicks JA, Stuber TP, Friedberg I, Dorman KS, Harris B An accurate and interpretable model for antimicrobial resistance in pathogenic Escherichia coli from livestock and companion animal species (2023) PLoS ONE 18:8 e0290473 doi
  • Joshi P, Banerjee S, Hu X, Khade PM, Friedberg I GOThresher: a program to remove annotation biases from protein function annotation datasets Bioinformatics (2023) 39:1 btad048 doi

2022

  • Ramola R, Friedberg I, Radivojac P The field of protein function prediction as viewed by different domain scientists Bioinformatics Advances 2:1 vbac057 (2022) doi
  • de Crecy-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, Deutschbauer A, Dias R, Ding Y, Fang G, Friedberg I, Gerlt J, Goldford J, Gorelik M, Gyori BM, Henry C, Hutinet G, Jaroch M, Karp PD, Kondratova L, Lu Z, Marchler-Bauer A, Martin MJ, McWhite C, Moghe GD, Monaghan P, Morgat A, Mungall CJ, Natale DA, Nelson WC, O’Donoghue S, Orengo C, O’Toole KH, Radivojac P, Reed C, Roberts RJ, Rodionov D, Rodionova IA, Rudolf JD, Saleh L, Sheynkman G, Thibaud-Nissen F, Thomas PD, Uetz P, Vallenet D, Carter EW, Weigele PR, Wood V, Wood-Charlson EM, Xu J A roadmap for the functional annotation of protein families: a community perspective. Database (OUP). 2022 Aug 12;2022. pii: 6663924. doi
  • Wymore Brand M, Proctor AL, Hostetter JM, Zhou N, Friedberg I, Jergens AE, Phillips GJ, Wannemuehler MJ 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. 2022 Apr 5;17(4):e0266005. doi
  • Kilpatrick AM, Rahman F, Anjum A, Shome S, Andalib KMS, Banik S, Chowdhury SF, Coombe P, Astroz YC, Douglas JM, Eranti P, Kiran AD, Kumar S, Lim H, Lorenzi V, Lubiana T, Mahmud S, Puche R, Rybarczyk A, Al Sium SM, Twesigomwe D, Zok T, Orengo CA, Friedberg I, Kelso JF, Welch L Characterizing domain-specific open educational resources by linking ISCB Communities of Special Interest to Wikipedia. Bioinformatics. 2022 Jun 24;38(Suppl 1):i19-i27. doi

2021

  • Ramsey J, McIntosh B, Renfro D, Aleksander SA, LaBonte S, Ross C, Zweifel AE, Liles N, Farrar S, Gill JJ, Erill I, Ades S, Berardini TZ, Bennett JA, Brady S, Britton R, Carbon S, Caruso SM, Clements D, Dalia R, Defelice M, Doyle EL, Friedberg I, Gurney SMR, Hughes L, Johnson A, Kowalski JM, Li D, Lovering RC, Mans TL, McCarthy F, Moore SD, Murphy R, Paustian TD, Perdue S, Peterson CN, Pruss BM, Saha MS, Sheehy RR, Tansey JT, Temple L, Thorman AW, Trevino S, Vollmer AC, Walbot V, Willey J, Siegele DA, Hu JC Crowdsourcing biocuration: The Community Assessment of Community Annotation with Ontologies (CACAO). PLoS Comput Biol. 2021 Oct 28;17(10):e1009463. doi
  • Martinez-Galvez G, Joshi P, Friedberg I, Manduca A, Ekker SC Deploying MMEJ using MENdel in precision gene editing applications for gene therapy and functional genomics. Nucleic Acids Res. 2021 Jan 11;49(1):67-78. doi
  • Mangravite L, Mooney SD, Friedberg I, Guinney J Establishing the reliability of algorithms. Pac Symp Biocomput. 2021;26:341-345.

2020

  • Nguyen HN, Markin A, Friedberg I, Eulenstein O Finding orthologous gene blocks in bacteria: the computational hardness of the problem and novel methods to address it. Bioinformatics. 2020 Dec 30;36(Suppl_2):i668-i674. doi
  • Nett RS, Nguyen H, Nagel R, Marcassa A, Charles TC, Friedberg I, Peters RJ Unraveling a Tangled Skein: Evolutionary Analysis of the Bacterial Gibberellin Biosynthetic Operon. mSphere. 2020 Jun 3;5(3). pii: 5/3/e00292-20. doi
  • Fields FR, Freed SD, Carothers KE, Hamid MN, Hammers DE, Ross JN, Kalwajtys VR, Gonzalez AJ, Hildreth AD, Friedberg I, Lee SW Novel antimicrobial peptide discovery using machine learning and biophysical selection of minimal bacteriocin domains. Drug Dev Res. 2020 Feb;81(1):43-51. doi

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, Dalkiran A, Cetin Atalay R, Zhang C, Hurto RL, Freddolino PL, Zhang Y, Bhat P, Supek F, Fernandez JM, Gemovic B, Perovic VR, Davidovic RS, Sumonja N, Veljkovic N, Asgari E, Mofrad MRK, Profiti G, Savojardo C, Martelli PL, Casadio R, Boecker F, Schoof H, Kahanda I, Thurlby N, McHardy AC, Renaux A, Saidi R, Gough J, Freitas AA, Antczak M, Fabris F, Wass MN, Hou J, Cheng J, Wang Z, Romero AE, Paccanaro A, Yang H, Goldberg T, Zhao C, Holm L, Toronen P, Medlar AJ, Zosa E, Borukhov I, Novikov I, Wilkins A, Lichtarge O, Chi PH, Tseng WC, Linial M, Rose PW, Dessimoz C, Vidulin V, Dzeroski S, Sillitoe I, Das S, Lees JG, Jones DT, Wan C, Cozzetto D, Fa R, Torres M, Warwick Vesztrocy A, Rodriguez JM, Tress ML, Frasca M, Notaro M, Grossi G, Petrini A, Re M, Valentini G, Mesiti M, Roche DB, Reeb J, Ritchie DW, Aridhi S, Alborzi SZ, Devignes MD, Koo DCE, Bonneau R, Gligorijevic V, Barot M, Fang H, Toppo S, Lavezzo E, Falda M, Berselli M, Tosatto SCE, Carraro M, Piovesan D, Ur Rehman H, Mao Q, Zhang S, Vucetic S, Black GS, Jo D, Suh E, Dayton JB, Larsen DJ, Omdahl AR, McGuffin LJ, Brackenridge DA, Babbitt PC, Yunes JM, Fontana P, Zhang F, Zhu S, You R, Zhang Z, Dai S, Yao S, Tian W, Cao R, Chandler C, Amezola M, Johnson D, Chang JM, Liao WH, Liu YW, Pascarelli S, Frank Y, Hoehndorf R, Kulmanov M, Boudellioua I, Politano G, Di Carlo S, Benso A, Hakala K, Ginter F, Mehryary F, Kaewphan S, Bjorne J, Moen H, Tolvanen MEE, Salakoski T, Kihara D, Jain A, Smuc T, Altenhoff A, Ben-Hur A, Rost B, Brenner SE, Orengo CA, Jeffery CJ, Bosco G, Hogan DA, Martin MJ, O’Donovan C, Mooney SD, Greene CS, Radivojac P, Friedberg I The CAFA challenge reports improved protein function prediction and new functional annotations for hundreds of genes through experimental screens. Genome Biol. 2019 Nov 19;20(1):244. doi
  • Wierson WA, Simone BW, WareJoncas Z, Mann C, Welker JM, Kar B, Emch MJ, Friedberg I, Gendron WAC, Barry MA, Clark KJ, Dobbs DL, McGrail MA, Ekker SC, Essner JJ Expanding the CRISPR Toolbox with ErCas12a in Zebrafish and Human Cells. CRISPR J. 2019 Dec;2(6):417-433. doi
  • Nguyen HN, Jain A, Eulenstein O, Friedberg I Tracing the ancestry of operons in bacteria. Bioinformatics. 2019 Sep 1;35(17):2998-3004. doi
  • 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, Katsonis P, Leonardi E, Lichtarge O, Martelli PL, Masica D, Mooney SD, Olatubosun A, Radivojac P, Rousseau F, Pal LR, Savojardo C, Schymkowitz J, Thusberg J, Tosatto SCE, Vihinen M, Valiaho J, Repo S, Moult J, Brenner SE, Friedberg I Assessing computational predictions of the phenotypic effect of cystathionine-beta-synthase variants. Hum Mutat. 2019 Sep;40(9):1530-1545. doi
  • Kacsoh BZ, Barton S, Jiang Y, Zhou N, Mooney SD, Friedberg I, Radivojac P, Greene CS, Bosco G New Drosophila Long-Term Memory Genes Revealed by Assessing Computational Function Prediction Methods. G3 (Bethesda). 2019 Jan 9;9(1):251-267. doi
  • Hu X, Friedberg I SwiftOrtho: A fast, memory-efficient, multiple genome orthology classifier. Gigascience. 2019 Oct 1;8(10). pii: 5606727. doi
  • Hamid MN, Friedberg I Identifying antimicrobial peptides using word embedding with deep recurrent neural networks. Bioinformatics. 2019 Jun 1;35(12):2009-2016. doi
  • Cho KT, Portwood JL 2nd, Gardiner JM, Harper LC, Lawrence-Dill CJ, Friedberg I, Andorf CM MaizeDIG: Maize Database of Images and Genomes. Front Plant Sci. 2019 Aug 28;10:1050. doi
  • Cao L, Gurevich A, Alexander KL, Naman CB, Leao T, Glukhov E, Luzzatto-Knaan T, Vargas F, Quinn R, Bouslimani A, Nothias LF, Singh NK, Sanders JG, Benitez RAS, Thompson LR, Hamid MN, Morton JT, Mikheenko A, Shlemov A, Korobeynikov A, Friedberg I, Knight R, Venkateswaran K, Gerwick WH, Gerwick L, Dorrestein PC, Pevzner PA, Mohimani H MetaMiner: A Scalable Peptidogenomics Approach for Discovery of Ribosomal Peptide Natural Products with Blind Modifications from Microbial Communities. Cell Syst. 2019 Dec 18;9(6):600-608.e4. doiFull publication list on PubMed, Google Scholar

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 Comput Biol. 2018 Jul 30;14(7):e1006337. doi
  • Wimalanathan K, Friedberg I, Andorf CM, Lawrence-Dill CJ Maize GO Annotation-Methods, Evaluation, and Review (maize-GAMER). Plant Direct. 2018 Apr 11;2(4):e00052. doi

2017

  • Mohimani, Hosein, Gurevich, Alexey, Alexander, Kelsey L, Naman, C. Benjamin, Leao, Tiago, Glukhov, Evgenia, Moss, Nathan A, Luzzatto Knaan, Tal, Vargas, Fernando, Nothias, Louis Felix, Singh, Nitin K, Sanders, John G, Benitez, Rodolfo A S, Thompson, Luke R, Hamid, Md Nafiz, Morton, James T, Mikheenko, Alla, Shlemov, Alexander, Korobeynikov, Anton, Friedberg Iddo, Knight, Rob, Venkateswaran, Kasthuri, Gerwick, William, Gerwick, Lena, Dorrestein, Peter C and Pevzner, Pavel A (2017) MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post translationally Modified Peptides (2017) Biorxiv 227504 Link
  • Huy Ngoc Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg Tracing the Ancestry of Operons in Bacteria (2017) Biorxiv 212886 Link
  • Kokulapalan Wimalanathan, Iddo Friedberg, Carson M. Andorf, Carolyn J. Lawrence Dill Maize GO Annotation Methods, Evaluation, and Review (maize GAMER) (2017) Biorxiv 222836

2016

  • Cigarroa-Toledo N, Blitvich BJ, Cetina-Trejo RC, Talavera-Aguilar LG, Baak-Baak CM, Torres-Chable OM, Hamid MN, Friedberg I, Gonzalez-Martinez P, AlonzoSalomon G, Rosado-Paredes EP, Rivero-Cardenas N, Reyes-Solis GC, Farfan-Ale JA, Garcia-Rejon JE, Machain-Williams C Isolation of Chikungunya virus from febrile patients and Aedes aegypti in Yucatan, Mexico (2016) Emerging Infectious Diseases Oct 15;22(10)
  • Moon J, Friedberg I and Eulenstein O Highly Bi-Connected Subgraphs for computational protein function annotation The 22nd International Computing and Combinatorics Conference (COCOON) (2016)
  • Jiang Y, Ronnen-Oron T, Clark WT, Bankapur, AR, D'Andrea D,...,Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I and Radivojac P An expanded evaluation of protein function prediction methods shows an improvement in accuracy (2016) Genome Biology (in press)

2015

  • Morton JT, Freed SD, Lee SW, and Friedberg I A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins BMC Bioinformatics 16:381

Pope WH, Bowman CA, Russell DA et al. Whole genome comparison of a large collection of mycobacteriophages reveals a continuum of phage genetic diversity. Elife 4:e06416 [Elife]

Ream DC, Bankapur AR, Friedberg I An Event-Driven Approach for Studying Gene Block Evolution in Bacteria Bioinformatics pii:btv128 [OUP]

Friedberg I, Wass M, Mooney SD, Radivojac P Ten Simple Rules for a Community Computational Challenge PLoS Comp Biol 11(4):e1004150 [PLoS]

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 30(17):i609-16 [PubMed]

Wass M, Mooney S, Linial M, Radivojac P, Friedberg I The Automated Function Prediction SIG Looks Back at 2013 and Prepares for 2014.Bioinformatics [PubMed]

2013

Ream DC, Murakami ST, Schmidt EE, Huang GH, Liang C, Friedberg I and Cheng XW Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes (2013) Virus Research 178(2):217-25 [PubMed]

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 PLoS

Oberlin AT, Jurkovic DA, Balish MF, Friedberg I Biological Database of Images and Genomes: tools for community annotations linking image and genomic information (2013) Database OUP

Radivojac P, Clark WT, Oron TR, Schnoes AM, ..., Bairoch A, Linial M, Babbitt PC, Brenner SE, Orengo C, Rost B, Mooney SD, Friedberg I. A large-scale evaluation of computational protein function prediction methods Nature Methods NPG

2012

Donovan SM, Wang M, Li M, Friedberg I, Schwartz SL, Chapkin RS. Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides. Adv Nutr. 2012 May 1;3(3):450S-5S. doi: 10.3945/an.112.001859.

Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin RS. A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response. Genome Biol. 2012 Apr 30;13(4):r32. 

2011

Bielewicz S, Bell E, Kong W, Friedberg I, Priscu JC, Morgan-Kiss RM. Protist diversity in a permanently ice-covered Antarctic lake during the polar night transition. ISME J. 2011 Sep;5(9):1559-64. Mar 10.

2010

Kelly RJ, Vincent DE, Friedberg I. IPRStats: visualization of the functional potential of an InterProScan run. BMC Bioinformatics. 2010 Dec 21;11 Suppl 1.S13.

Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667.