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Iddo Friedberg



Publications on Pubmed
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  1. 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]
  2. Ream DC, Bankapur AR, Friedberg I An Event-Driven Approach for Studying Gene Block Evolution in Bacteria Bioinformatics pii:btv128 [OUP]
  3. Friedberg I, Wass M, Mooney SD, Radivojac P Ten Simple Rules for a Community Computational Challenge PLoS Comp Biol 11(4):e1004150 [PLoS]

  4. 2014
  5. 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]
  6. 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]

  7. 2013
  8. 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]
  9. 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 Crécy-Lagard V, Ferguson D, Fomenkov A, Gadda G, Morgan RD, Osterman AL, Rodionov DA, Rodionova IA, Rudd KE, Söll 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, Sjölander K, Salzberg SL, Vitkup D, Letovsky S, Segrè D, Delisi C, Roberts RJ, Steffen M and Kasif S The COMBREX Project: Design, Methodology, and Initial Results PLoS Biology PLoS
  10. 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
  11. 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
  12. 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, Törönen 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, Kaßner R, Seemayer S, Vicedo E, Schaefer C, Achten D, Auer F, Boehm A, Braun T, Hecht M, Heron M, Hönigschmid P, Hopf TA, Kaufmann S, Kiening M, Krompass D, Landerer C, Mahlich Y, Roos M, Björne J, Salakoski T, Wong A, Shatkay H, Gatzmann F, Sommer I, Wass MN, Sternberg MJ, Skunca N, Supek F, Bo?njak M, Panov P, D?eroski 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

  13. 2012
  14. 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.
  15. 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

  16. 2011
  17. 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

  18. 2010
  19. 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
  20. 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
  21. 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
  22. Wooley JC, Godzik A, Friedberg I. A primer on metagenomics. PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. PubMed

  23. 2009
  24. 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
  25. 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

  26. 2007
  27. Rodrigues AP, Grant BJ, Godzik A, Friedberg I. The 2006 automated function prediction meeting. BMC Bioinformatics 2007 May 22;8 S1-4. PubMed
  28. 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
  29. 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.
  30. PubMed PubMed
  31. Friedberg I, Godzik A. Functional differentiation of proteins: implications for structural genomics. Structure 2007 Apr;15(4):405-15. PubMed
  32. 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

  33. 2006
  34. 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
  35. 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
  36. Friedberg I. Automated protein function prediction--the genomic challenge. Brief Bioinform 2006 Sep;7(3):225-42. Epub 2006 May 23. Review.PubMed.
  37. Friedberg I, Jambon M, Godzik A. New avenues in protein function prediction. Protein Sci 2006 Jun;15(6):1527-9.PubMed

  38. 2005
  39. Friedberg I, Godzik A. Connecting the protein structure universe by using sparse recurring fragments. Structure 2005 Aug;13(8):1213-24.PubMed.
  40. Friedberg I, Godzik A. Fragnostic: walking through protein structure space. Nucleic Acids Res 2005 Jul 1;33:W249-51. PubMed

  41. 2004 and earlier
  42. 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.
  43. 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.
  44. Friedberg I, Margalit H. PeCoP: automatic determination of persistently conserved positions in protein families. Bioinformatics 2002 Sep;18(9):1276-7. PubMed.
  45. 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
  46. 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
  47. 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
  48. 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.