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Iddo Friedberg



Publications on Pubmed
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  1. 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]
  2. Moon J, Friedberg I and Eulenstein O Highly Bi-Connected Subgraphs for computational protein function annotation The 22nd International Computing and Combinatorics Conference (COCOON) (accepted)
  3. Friedberg I and Radivojac P Community-Wide Evaluation of Computational Function Prediction (Book chapter, accepted) [arXiv]
  4. 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 Biology17:184 [Genome Biology]

  5. 2015
  6. 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]
  7. 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]
  8. Ream DC, Bankapur AR, Friedberg I An Event-Driven Approach for Studying Gene Block Evolution in Bacteria Bioinformatics pii:btv128 [OUP]
  9. Friedberg I, Wass M, Mooney SD, Radivojac P Ten Simple Rules for a Community Computational Challenge PLoS Comp Biol 11(4):e1004150 [PLoS]

  10. 2014
  11. 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]
  12. 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]

  13. 2013
  14. 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]
  15. 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
  16. 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
  17. 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
  18. 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, T�r�nen 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, H�nigschmid 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, Bo?njak 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

  19. 2012
  20. 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.
  21. 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

  22. 2011
  23. 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

  24. 2010
  25. 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, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A. Meeting Report: BioSharing at ISMB 2010. Stand Genomic Sci. 2010 Dec 4;3(3):254-8.PubMed
  26. 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
  27. 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
  28. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. PubMed

  29. 2009
  30. 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
  31. Field D, Friedberg I, Sterk P, Kottmann R, Gl??ckner 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

  32. 2007
  33. Rodrigues AP, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics 2007 May 22;8 S1-4. PubMed
  34. 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 PubMed
  35. 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.
  36. PubMed PubMed
  37. Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure 2007 Apr;15(4):405-15. PubMed
  38. 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

  39. 2006
  40. 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
  41. 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 PubMed
  42. Friedberg I. Automated protein function prediction--the genomic challenge. Brief Bioinform 2006 Sep;7(3):225-42. Epub 2006 May 23. Review.PubMed.
  43. Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci 2006 Jun;15(6):1527-9.PubMed

  44. 2005
  45. Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments. Structure 2005 Aug;13(8):1213-24.PubMed.
  46. Friedberg I, Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res 2005 Jul 1;33:W249-51. PubMed

  47. 2004 and earlier
  48. 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.
  49. 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.
  50. Friedberg I, Margalit H. PeCoP: automatic determination of persistently conserved positions in protein families. Bioinformatics 2002 Sep;18(9):1276-7. PubMed.
  51. 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
  52. 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
  53. 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
  54. 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.