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Items: 1 to 20 of 35

1.

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.

2.

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.

3.

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.

4.

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.

5.

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.

6.

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.

7.

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.

8.

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.

9.

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.

10.

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.

11.

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.

12.

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.

13.

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.

14.

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.

15.

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.

16.

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.

17.

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.

18.

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.

19.

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.

20.

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.

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