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Items: 1 to 50 of 86

1.

Community-Wide Evaluation of Computational Function Prediction.

Friedberg I, Radivojac P.

Methods Mol Biol. 2017;1446:133-146.

PMID:
27812940
2.

An expanded evaluation of protein function prediction methods shows an improvement in accuracy.

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, Lin A, Sahraeian SM, Martelli PL, Profiti G, Casadio R, Cao R, Zhong Z, Cheng J, Altenhoff A, Skunca N, Dessimoz C, Dogan T, Hakala K, Kaewphan S, Mehryary F, Salakoski T, Ginter F, Fang H, Smithers B, Oates M, Gough J, Törönen P, Koskinen P, Holm L, Chen CT, Hsu WL, Bryson K, Cozzetto D, Minneci F, Jones DT, Chapman S, Bkc D, Khan IK, Kihara D, Ofer D, Rappoport N, Stern A, Cibrian-Uhalte E, Denny P, Foulger RE, Hieta R, Legge D, Lovering RC, Magrane M, Melidoni AN, Mutowo-Meullenet P, Pichler K, Shypitsyna A, Li B, Zakeri P, ElShal S, Tranchevent LC, Das S, Dawson NL, Lee D, Lees JG, Sillitoe I, Bhat P, Nepusz T, Romero AE, Sasidharan R, Yang H, Paccanaro A, Gillis J, Sedeño-Cortés AE, Pavlidis P, Feng S, Cejuela JM, Goldberg T, Hamp T, Richter L, Salamov A, Gabaldon T, Marcet-Houben M, Supek F, Gong Q, Ning W, Zhou Y, Tian W, Falda M, Fontana P, Lavezzo E, Toppo S, Ferrari C, Giollo M, Piovesan D, Tosatto SC, Del Pozo A, Fernández JM, Maietta P, Valencia A, Tress ML, Benso A, Di Carlo S, Politano G, Savino A, Rehman HU, Re M, Mesiti M, Valentini G, Bargsten JW, van Dijk AD, Gemovic B, Glisic S, Perovic V, Veljkovic V, Veljkovic N, Almeida-E-Silva DC, Vencio RZ, Sharan M, Vogel J, Kansakar L, Zhang S, Vucetic S, Wang Z, Sternberg MJ, Wass MN, Huntley RP, Martin MJ, O'Donovan C, Robinson PN, Moreau Y, Tramontano A, Babbitt PC, Brenner SE, Linial M, Orengo CA, Rost B, Greene CS, Mooney SD, Friedberg I, Radivojac P.

Genome Biol. 2016 Sep 7;17(1):184. doi: 10.1186/s13059-016-1037-6.

3.

Chikungunya Virus in Febrile Humans and Aedes aegypti Mosquitoes, Yucatan, Mexico.

Cigarroa-Toledo N, Blitvich BJ, Cetina-Trejo RC, Talavera-Aguilar LG, Baak-Baak CM, Torres-Chablé OM, Hamid MN, Friedberg I, González-Martinez P, Alonzo-Salomon G, Rosado-Paredes EP, Rivero-Cárdenas N, Reyes-Solis GC, Farfan-Ale JA, Garcia-Rejon JE, Machain-Williams C.

Emerg Infect Dis. 2016 Oct;22(10):1804-7. doi: 10.3201/eid2210.152087. Epub 2016 Oct 15.

4.

A large scale prediction of bacteriocin gene blocks suggests a wide functional spectrum for bacteriocins.

Morton JT, Freed SD, Lee SW, Friedberg I.

BMC Bioinformatics. 2015 Nov 11;16:381. doi: 10.1186/s12859-015-0792-9.

5.

Ten simple rules for a community computational challenge.

Friedberg I, Wass MN, Mooney SD, Radivojac P.

PLoS Comput Biol. 2015 Apr 23;11(4):e1004150. doi: 10.1371/journal.pcbi.1004150. eCollection 2015 Apr. No abstract available.

6.

An event-driven approach for studying gene block evolution in bacteria.

Ream DC, Bankapur AR, Friedberg I.

Bioinformatics. 2015 Jul 1;31(13):2075-83. doi: 10.1093/bioinformatics/btv128. Epub 2015 Feb 25.

7.

The impact of incomplete knowledge on the evaluation of protein function prediction: a structured-output learning perspective.

Jiang Y, Clark WT, Friedberg I, Radivojac P.

Bioinformatics. 2014 Sep 1;30(17):i609-16. doi: 10.1093/bioinformatics/btu472.

8.

The automated function prediction SIG looks back at 2013 and prepares for 2014.

Wass MN, Mooney SD, Linial M, Radivojac P, Friedberg I.

Bioinformatics. 2014 Jul 15;30(14):2091-2. doi: 10.1093/bioinformatics/btu117. Epub 2014 Mar 3. No abstract available.

9.

Comparative analysis of error-prone replication mononucleotide repeats across baculovirus genomes.

Ream DC, Murakami ST, Schmidt EE, Huang GH, Liang C, Friedberg I, Cheng XW.

Virus Res. 2013 Dec 26;178(2):217-25. doi: 10.1016/j.virusres.2013.10.005. Epub 2013 Oct 17.

10.

The COMBREX project: design, methodology, and initial results.

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, Kasif S.

PLoS Biol. 2013;11(8):e1001638. doi: 10.1371/journal.pbio.1001638. Epub 2013 Aug 27. No abstract available.

11.

Biases in the experimental annotations of protein function and their effect on our understanding of protein function space.

Schnoes AM, Ream DC, Thorman AW, Babbitt PC, Friedberg I.

PLoS Comput Biol. 2013;9(5):e1003063. doi: 10.1371/journal.pcbi.1003063. Epub 2013 May 30.

12.

Biological database of images and genomes: tools for community annotations linking image and genomic information.

Oberlin AT, Jurkovic DA, Balish MF, Friedberg I.

Database (Oxford). 2013 Apr 2;2013:bat016. doi: 10.1093/database/bat016. Print 2013.

13.

A large-scale evaluation of computational protein function prediction.

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, Škunca N, Supek F, Bošnjak M, Panov P, Džeroski S, Šmuc T, Kourmpetis YA, van Dijk AD, ter 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.

Nat Methods. 2013 Mar;10(3):221-7. doi: 10.1038/nmeth.2340. Epub 2013 Jan 27.

14.

G503 is obligatory for coupling of regulatory domains in NCX proteins.

Giladi M, Friedberg I, Fang X, Hiller R, Wang YX, Khananshvili D.

Biochemistry. 2012 Sep 18;51(37):7313-20. doi: 10.1021/bi300739z. Epub 2012 Sep 4.

PMID:
22924554
15.

Host-microbe interactions in the neonatal intestine: role of human milk oligosaccharides.

Donovan SM, Wang M, Li M, Friedberg I, Schwartz SL, Chapkin RS.

Adv Nutr. 2012 May 1;3(3):450S-5S. doi: 10.3945/an.112.001859. Review.

16.

A metagenomic study of diet-dependent interaction between gut microbiota and host in infants reveals differences in immune response.

Schwartz S, Friedberg I, Ivanov IV, Davidson LA, Goldsby JS, Dahl DB, Herman D, Wang M, Donovan SM, Chapkin RS.

Genome Biol. 2012 Apr 30;13(4):r32. doi: 10.1186/gb-2012-13-4-r32.

17.

Protist diversity in a permanently ice-covered Antarctic lake during the polar night transition.

Bielewicz S, Bell E, Kong W, Friedberg I, Priscu JC, Morgan-Kiss RM.

ISME J. 2011 Sep;5(9):1559-64. doi: 10.1038/ismej.2011.23. Epub 2011 Mar 10.

18.

Meeting Report: BioSharing at ISMB 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, Bramlett B, Gregurick S, Lapp H, Orchard S, Rocca-Serra P, Ruttenberg A, Shah N, Taylor C, Thessen A.

Stand Genomic Sci. 2010 Dec 4;3(3):254-8. doi: 10.4056/sigs/1403501.

19.

Meeting Report: Metagenomics, Metadata and MetaAnalysis (M3) at ISMB 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.

Stand Genomic Sci. 2010 Dec 4;3(3):232-4. doi: 10.4056/sigs.1383476.

20.

IPRStats: visualization of the functional potential of an InterProScan run.

Kelly RJ, Vincent DE, Friedberg I.

BMC Bioinformatics. 2010 Dec 21;11 Suppl 12:S13. doi: 10.1186/1471-2105-11-S12-S13.

21.

A primer on metagenomics.

Wooley JC, Godzik A, Friedberg I.

PLoS Comput Biol. 2010 Feb 26;6(2):e1000667. doi: 10.1371/journal.pcbi.1000667. Review.

22.

Biopython: freely available Python tools for computational molecular biology and bioinformatics.

Cock PJ, Antao T, Chang JT, Chapman BA, Cox CJ, Dalke A, Friedberg I, Hamelryck T, Kauff F, Wilczynski B, de Hoon MJ.

Bioinformatics. 2009 Jun 1;25(11):1422-3. doi: 10.1093/bioinformatics/btp163. Epub 2009 Mar 20.

23.

Meeting Report: "Metagenomics, Metadata and Meta-analysis" (M3) Special Interest Group at ISMB 2009.

Field D, Friedberg I, Sterk P, Kottmann R, Glöckner FO, Hirschman L, Garrity GM, Cochrane G, Wooley J, Gilbert J.

Stand Genomic Sci. 2009 Dec 29;1(3):278-82. doi: 10.4056/sigs.641096.

24.

The 2006 automated function prediction meeting.

Rodrigues AP, Grant BJ, Godzik A, Friedberg I.

BMC Bioinformatics. 2007 May 22;8 Suppl 4:S1-4. No abstract available.

25.

Computational protein function prediction: are we making progress?

Godzik A, Jambon M, Friedberg I.

Cell Mol Life Sci. 2007 Oct;64(19-20):2505-11. Review.

PMID:
17611711
26.

Identification and characterization of DUSP27, a novel dual-specific protein phosphatase.

Friedberg I, Nika K, Tautz L, Saito K, Cerignoli F, Friedberg I, Godzik A, Mustelin T.

FEBS Lett. 2007 May 29;581(13):2527-33. Epub 2007 Apr 30.

27.

Functional differentiation of proteins: implications for structural genomics.

Friedberg I, Godzik A.

Structure. 2007 Apr;15(4):405-15.

28.

Using an alignment of fragment strings for comparing protein structures.

Friedberg I, Harder T, Kolodny R, Sitbon E, Li Z, Godzik A.

Bioinformatics. 2007 Jan 15;23(2):e219-24.

PMID:
17237095
29.

Ten simple rules for selecting a postdoctoral position.

Bourne PE, Friedberg I.

PLoS Comput Biol. 2006 Nov 24;2(11):e121. No abstract available. Erratum in: PLoS Comput Biol. 2006 Dec;2(12):e181.

30.

Proteolytic processing by matrix metalloproteinases and phosphorylation by protein kinase CK2 of fetuin-A, the major globulin of fetal calf serum.

Kübler D, Gosenca D, Wind M, Heid H, Friedberg I, Jahnen-Dechent W, Lehmann WD.

Biochimie. 2007 Mar;89(3):410-8. Epub 2006 Nov 10.

PMID:
17110014
31.

JAFA: a protein function annotation meta-server.

Friedberg I, Harder T, Godzik A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81.

32.

Automated protein function prediction--the genomic challenge.

Friedberg I.

Brief Bioinform. 2006 Sep;7(3):225-42. Epub 2006 May 23. Review.

PMID:
16772267
33.

New avenues in protein function prediction.

Friedberg I, Jambon M, Godzik A.

Protein Sci. 2006 Jun;15(6):1527-9. No abstract available.

34.

Connecting the protein structure universe by using sparse recurring fragments.

Friedberg I, Godzik A.

Structure. 2005 Aug;13(8):1213-24.

35.

Fragnostic: walking through protein structure space.

Friedberg I, Godzik A.

Nucleic Acids Res. 2005 Jul 1;33(Web Server issue):W249-51.

36.

The interplay of fold recognition and experimental structure determination in structural genomics.

Friedberg I, Jaroszewski L, Ye Y, Godzik A.

Curr Opin Struct Biol. 2004 Jun;14(3):307-12. Review.

PMID:
15193310
37.

Protein tyrosine phosphatases in the human genome.

Alonso A, Sasin J, Bottini N, Friedberg I, Friedberg I, Osterman A, Godzik A, Hunter T, Dixon J, Mustelin T.

Cell. 2004 Jun 11;117(6):699-711. Review.

38.

The status of structural genomics defined through the analysis of current targets and structures.

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.

Pac Symp Biocomput. 2004:375-86.

39.
40.

PeCoP: automatic determination of persistently conserved positions in protein families.

Friedberg I, Margalit H.

Bioinformatics. 2002 Sep;18(9):1276-7.

PMID:
12217925
42.

Evaluation of PSI-BLAST alignment accuracy in comparison to structural alignments.

Friedberg I, Kaplan T, Margalit H.

Protein Sci. 2000 Nov;9(11):2278-84.

43.

Glimmers in the midnight zone: characterization of aligned identical residues in sequence-dissimilar proteins sharing a common fold.

Friedberg I, Kaplan T, Margalit H.

Proc Int Conf Intell Syst Mol Biol. 2000;8:162-70.

PMID:
10977077
44.

Recombinant in vitro tools to predict drug metabolism and safety.

Friedberg I I.

Pharm Sci Technolo Today. 2000 Mar;3(3):99-105.

PMID:
10707045
45.

Secondary dimerization between members of the epidermal growth factor receptor family.

Gamett DC, Pearson G, Cerione RA, Friedberg I.

J Biol Chem. 1997 May 2;272(18):12052-6.

47.
48.

Activation of cell growth inhibitor by ectoprotein kinase-mediated phosphorylation in transformed mouse fibroblasts.

Friedberg I, Belzer I, Oged-Plesz O, Kuebler D.

J Biol Chem. 1995 Sep 1;270(35):20560-7.

49.

Growth inhibition of breast cancer cells induced by exogenous ATP.

Spungin B, Friedberg I.

J Cell Physiol. 1993 Dec;157(3):502-8.

PMID:
8253861
50.

Effect of ionophore A23187 on the membrane permeability in mouse fibroblasts.

De BK, Friedberg I.

Biochem Biophys Res Commun. 1991 Aug 15;178(3):830-41.

PMID:
1651721

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