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Publications

2018

Wimalanathan K, Friedberg I, Andorf CM, Lawrence‐Dill CJ. Maize GO Annotation—Methods, Evaluation, and Review (maize‐GAMER). Plant Direct. 2018;2:1–15. [Plant Direct]

Zachary D Siegel, Naihui Zhou, Scott Zarecor, Nigel Lee, Darwin A Campbell, Carson M Andorf, Dan Nettleton, Carolyn J Lawrence-Dill, Baskar Ganapathysubramanian, Iddo Friedberg, Jonathan W Kelly Crowdsourcing Image Analysis for Plant Phenomics to Generate Ground Truth Data for Machine Learning  bioRxiv 265918 [bioRxiv Preprint]

Md Nafiz Hamid, Iddo Friedberg Identifying Antimicrobial Peptides using Word Embedding with Deep Recurrent Neural Networks bioRxiv 255505 [bioRxiv Preprint]

2017

Friedberg I., Radivojac P.  Community-Wide Evaluation of Computational Function Prediction. In: Dessimoz C., Škunca N. (eds) The Gene Ontology Handbook. Methods in Molecular Biology, vol 1446. Humana Press, New York, NY [Springer]

Huy Ngoc Nguyen, Ashish Jain, Oliver Eulenstein, Iddo Friedberg . (2017) Ancestral Reconstruction of Gene Blocks using an Event-Based Method bioRxiv 212886 [bioRxiv Preprint]

Hosein Mohimani, Alexey Gurevich, Kelsey L Alexander, C. Benjamin Naman, Tiago Leao, Evgenia Glukhov, Nathan A Moss, Tal Luzzatto Knaan, Fernando Vargas, Louis-Felix Nothias, Nitin K Singh, John G Sanders, Rodolfo A S Benitez, Luke R Thompson, Md Nafiz Hamid, James T Morton, Alla Mikheenko, Alexander Shlemov, Anton Korobeynikov, Iddo Friedberg, Rob Knight, Kasthuri Venkateswaran, William Gerwick, Lena Gerwick, Peter C Dorrestein, Pavel A Pevzner MetaRiPPquest: A Peptidogenomics Approach for the Discovery of Ribosomally Synthesized and Post-translationally Modified Peptides bioRxiv 227504 [bioRxiv Preprint]

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, Alonzo-Salomon 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 Emerging Infectious Diseases [PubMed]

Moon J, Friedberg I and Eulenstein O Highly Bi-Connected Subgraphs for computational protein function annotation The 22nd International Computing and Combinatorics Conference [COCOON]

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 Genome Biology 17:184 [Genome Biology]

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 [BMC]

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 Virus Research 178(2):217-25 [PubMed]

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, Swaminathan R, Allen B, Housman G, Monahan C, Rochussen K, Tao K, Bhagwat AS, Brenner SE, Columbus L, de Crecy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Soll D, Spain J, Xu SY, Bateman A, Blumenthal RM, Bollinger JM, Chang WS, Ferrer M, Friedberg I, Galperin MY, Gobeill J, Haft D, Hunt J, Karp P, Klimke W, Krebs C, Macelis D, Madupu R, Martin MJ, Miller JH, O'Donovan C, Palsson B, Ruch P, Setterdahl A, Sutton G, Tate J, Yakunin A, Tchigvintsev D, Plata G, Hu J, Greiner R, Horn D, Sjolander K, Salzberg SL, Vitkup D, Letovsky S, Segre D, Delisi C, Roberts RJ, Steffen M and Kasif S The COMBREX Project: Design, Methodology, and Initial Results PLoS Biology [PLoS]

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, Wittkop T, Sokolov A, Graim K, Funk C, Verspoor K, Ben-Hur A, Pandey G, Yunes JM, Talwalkar AS, Repo S, Souza ML, Piovesan D, Casadio R, Wang Z, Cheng J, Fang H, Gough J, Koskinen P, Toronen P, Nokso-Koivisto J, Holm L, Cozzetto D, Buchan DW, Bryson K, Jones DT, Limaye B, Inamdar H, Datta A, Manjari SK, Joshi R, Chitale M, Kihara D, Lisewski AM, Erdin S, Venner E, Lichtarge O, Rentzsch R, Yang H, Romero AE, Bhat P, Paccanaro A, Hamp T, Kasner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Honigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Bjorne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bosnjak M, Panov P, Dzeroski S, Smuc T, Kourmpetis YA, van Dijk AD, Braak CJ, Zhou Y, Gong Q, Dong X, Tian W, Falda M, Fontana P, Lavezzo E, Di Camillo B, Toppo S, Lan L, Djuric N, Guo Y, Vucetic S, 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. [PubMed]

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. [PubMed]

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. [PubMed]

2010

Field D, Sansone S, Delong EF, Sterk P, Friedberg I, Kottmann R, Hirschman L, Garrity G, Cochrane G, Wooley J, Meyer F, Hunter S, White O. Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 2010. Stand Genomic Sci. 2010 Dec 4;3(3):232-4. [PubMed]

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. [PubMed]

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

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. 2009 Jun 1;25(11):1422-3. Epub 2009 Mar 20. [PubMed]

Field D, Friedberg I, Sterk P, Kottmann R, Glockner 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. Stand Genomic Sci. 2009 Dec 29;1(3):278-82. [PubMed]

2007 

Rodrigues AP, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics 2007 May 22;8 S1-4. [PubMed]

Godzik A, Jambon M, Friedberg I. Computational protein function prediction: are we making progress? Cell Mol Life Sci 2007 Oct;64(19-20):2505-11. Review. [PubMed

Friedberg Ilan, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg Iddo, Godzik A, Mustelin T. Identification and characterization of DUSP27, a novel dual-specific protein phosphatase. FEBS Lett 2007 May 29;581(13):2527-33. Epub 2007 Apr 30. [PubMed

Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure 2007 Apr;15(4):405-15. [PubMed]

Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A. Using an alignment of fragment strings for comparing protein structures. Bioinformatics 2007 Jan 15;23(2):e219-24. [PubMed]

2006

Bourne PE, Friedberg I. Ten simple rules for selecting a postdoctoral position. PLoS Comput Biol 2006 Nov 24;2(11):e121. 2006 Dec;2(12):e181. [PubMed]

Friedberg I, Harder T, Godzik A. JAFA: a protein function annotation meta-server. Nucleic Acids Res 2006 Jul 1;34(Web Server issue):W379-81. [PubMed]

Friedberg I. Automated protein function prediction--the genomic challenge. Brief Bioinform 2006 Sep;7(3):225-42. Epub 2006 May 23. Review. [PubMed]

Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci 2006 Jun;15(6):1527-9. [PubMed]

2005

Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments. Structure 2005 Aug;13(8):1213-24. [PubMed]

Friedberg I, Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res 2005 Jul 1;33:W249-51. [PubMed]

2004 and earlier

Friedberg I, Jaroszewski L, Ye Y, Godzik A. The interplay of fold recognition and experimental structure determination in structural genomics. Curr Opin Struct Biol 2004 Jun;14(3):307-12. [PubMed]

Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T. Protein tyrosine phosphatases in the human genome. Cell 2004 Jun 11;117(6):699-711. [PubMed]

Friedberg I, Margalit H. PeCoP: automatic determination of persistently conserved positions in protein families. Bioinformatics 2002 Sep;18(9):1276-7. [PubMed]

Friedberg I, Margalit H. Persistently conserved positions in structurally similar, sequence dissimilar proteins: roles in preserving protein fold and function. Protein Sci 2002 Feb;11(2):350-60. [PubMed]

Friedberg I, Kaplan T, Margalit H. Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments. Protein Sci 2000 Nov;9(11):2278-84. [PubMed]

Friedberg I, Kaplan T, Margalit H. Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold. Proc Int Conf Intell Syst Mol Biol (Now Bioinformatics) 2000;8:162-70. [PubMed]

Cherradi N, Rossier MF, Vallotton MB, Timberg R, Friedberg I, Orly J, Wang XJ, Stocco DM, Capponi AM. Submitochondrial distribution of three key steroidogenic proteins (steroidogenic acute regulatory protein and cytochrome p450scc and 3beta-hydroxysteroid dehydrogenase isomerase enzymes) upon stimulation by intracellular calcium in adrenal glomerulosa cells. J Biol Chem 1997 Mar 21;272(12):7899-907. [PubMed]