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Items: 1 to 20 of 95

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.

Secondary structure impacts patterns of selection in human lncRNAs.

Pegueroles C, Gabaldón T.

BMC Biol. 2016 Jul 25;14:60. doi: 10.1186/s12915-016-0283-0.

3.

Correction: The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T.

PLoS Genet. 2016 Jul 14;12(7):e1006202. doi: 10.1371/journal.pgen.1006202.

4.

Lokiarchaeota Marks the Transition between the Archaeal and Eukaryotic Selenocysteine Encoding Systems.

Mariotti M, Lobanov AV, Manta B, Santesmasses D, Bofill A, Guigó R, Gabaldón T, Gladyshev VN.

Mol Biol Evol. 2016 Sep;33(9):2441-53. doi: 10.1093/molbev/msw122.

5.

Genome sequence of the olive tree, Olea europaea.

Cruz F, Julca I, Gómez-Garrido J, Loska D, Marcet-Houben M, Cano E, Galán B, Frias L, Ribeca P, Derdak S, Gut M, Sánchez-Fernández M, García JL, Gut IG, Vargas P, Alioto TS, Gabaldón T.

Gigascience. 2016 Jun 27;5:29. doi: 10.1186/s13742-016-0134-5.

6.

spongeScan: A web for detecting microRNA binding elements in lncRNA sequences.

Furió-Tarí P, Tarazona S, Gabaldón T, Enright AJ, Conesa A.

Nucleic Acids Res. 2016 Jul 8;44(W1):W176-80. doi: 10.1093/nar/gkw443.

7.

Long Non-Coding RNAs As Potential Novel Prognostic Biomarkers in Colorectal Cancer.

Saus E, Brunet-Vega A, Iraola-Guzmán S, Pegueroles C, Gabaldón T, Pericay C.

Front Genet. 2016 Apr 12;7:54. doi: 10.3389/fgene.2016.00054. Review.

8.

Redundans: an assembly pipeline for highly heterozygous genomes.

Pryszcz LP, Gabaldón T.

Nucleic Acids Res. 2016 Jul 8;44(12):e113. doi: 10.1093/nar/gkw294.

9.

Standardized benchmarking in the quest for orthologs.

Altenhoff AM, Boeckmann B, Capella-Gutierrez S, Dalquen DA, DeLuca T, Forslund K, Huerta-Cepas J, Linard B, Pereira C, Pryszcz LP, Schreiber F, da Silva AS, Szklarczyk D, Train CM, Bork P, Lecompte O, von Mering C, Xenarios I, Sjölander K, Jensen LJ, Martin MJ, Muffato M; Quest for Orthologs consortium., Gabaldón T, Lewis SE, Thomas PD, Sonnhammer E, Dessimoz C.

Nat Methods. 2016 May;13(5):425-30. doi: 10.1038/nmeth.3830.

10.

Whole genome sequencing of turbot (Scophthalmus maximus; Pleuronectiformes): a fish adapted to demersal life.

Figueras A, Robledo D, Corvelo A, Hermida M, Pereiro P, Rubiolo JA, Gómez-Garrido J, Carreté L, Bello X, Gut M, Gut IG, Marcet-Houben M, Forn-Cuní G, Galán B, García JL, Abal-Fabeiro JL, Pardo BG, Taboada X, Fernández C, Vlasova A, Hermoso-Pulido A, Guigó R, Álvarez-Dios JA, Gómez-Tato A, Viñas A, Maside X, Gabaldón T, Novoa B, Bouza C, Alioto T, Martínez P.

DNA Res. 2016 Jun;23(3):181-92. doi: 10.1093/dnares/dsw007.

11.

Genome and transcriptome analysis of the Mesoamerican common bean and the role of gene duplications in establishing tissue and temporal specialization of genes.

Vlasova A, Capella-Gutiérrez S, Rendón-Anaya M, Hernández-Oñate M, Minoche AE, Erb I, Câmara F, Prieto-Barja P, Corvelo A, Sanseverino W, Westergaard G, Dohm JC, Pappas GJ Jr, Saburido-Alvarez S, Kedra D, Gonzalez I, Cozzuto L, Gómez-Garrido J, Aguilar-Morón MA, Andreu N, Aguilar OM, Garcia-Mas J, Zehnsdorf M, Vázquez MP, Delgado-Salinas A, Delaye L, Lowy E, Mentaberry A, Vianello-Brondani RP, García JL, Alioto T, Sánchez F, Himmelbauer H, Santalla M, Notredame C, Gabaldón T, Herrera-Estrella A, Guigó R.

Genome Biol. 2016 Feb 25;17:32. doi: 10.1186/s13059-016-0883-6.

12.

Contrasting Patterns of Evolutionary Diversification in the Olfactory Repertoires of Reptile and Bird Genomes.

Vandewege MW, Mangum SF, Gabaldón T, Castoe TA, Ray DA, Hoffmann FG.

Genome Biol Evol. 2016 Feb 9;8(3):470-80. doi: 10.1093/gbe/evw013.

13.

Late acquisition of mitochondria by a host with chimaeric prokaryotic ancestry.

Pittis AA, Gabaldón T.

Nature. 2016 Mar 3;531(7592):101-4. doi: 10.1038/nature16941.

14.

Genome sequencing and secondary metabolism of the postharvest pathogen Penicillium griseofulvum.

Banani H, Marcet-Houben M, Ballester AR, Abbruscato P, González-Candelas L, Gabaldón T, Spadaro D.

BMC Genomics. 2016 Jan 5;17:19. doi: 10.1186/s12864-015-2347-x.

15.

Horizontal acquisition of toxic alkaloid synthesis in a clade of plant associated fungi.

Marcet-Houben M, Gabaldón T.

Fungal Genet Biol. 2016 Jan;86:71-80. doi: 10.1016/j.fgb.2015.12.006.

16.

Contrasting Genomic Diversity in Two Closely Related Postharvest Pathogens: Penicillium digitatum and Penicillium expansum.

Julca I, Droby S, Sela N, Marcet-Houben M, Gabaldón T.

Genome Biol Evol. 2015 Dec 14;8(1):218-27. doi: 10.1093/gbe/evv252.

17.

The Leishmania metaphylome: a comprehensive survey of Leishmania protein phylogenetic relationships.

Valdivia HO, Scholte LL, Oliveira G, Gabaldón T, Bartholomeu DC.

BMC Genomics. 2015 Oct 30;16:887. doi: 10.1186/s12864-015-2091-2.

18.

The Genomic Aftermath of Hybridization in the Opportunistic Pathogen Candida metapsilosis.

Pryszcz LP, Németh T, Saus E, Ksiezopolska E, Hegedűsová E, Nosek J, Wolfe KH, Gacser A, Gabaldón T.

PLoS Genet. 2015 Oct 30;11(10):e1005626. doi: 10.1371/journal.pgen.1005626. Erratum in: PLoS Genet. 2016 Jul;12(7):e1006202.

19.

Molecular signatures of plastic phenotypes in two eusocial insect species with simple societies.

Patalano S, Vlasova A, Wyatt C, Ewels P, Camara F, Ferreira PG, Asher CL, Jurkowski TP, Segonds-Pichon A, Bachman M, González-Navarrete I, Minoche AE, Krueger F, Lowy E, Marcet-Houben M, Rodriguez-Ales JL, Nascimento FS, Balasubramanian S, Gabaldon T, Tarver JE, Andrews S, Himmelbauer H, Hughes WO, Guigó R, Reik W, Sumner S.

Proc Natl Acad Sci U S A. 2015 Nov 10;112(45):13970-5. doi: 10.1073/pnas.1515937112.

20.

Interactions between closely related bacterial strains are revealed by deep transcriptome sequencing.

González-Torres P, Pryszcz LP, Santos F, Martínez-García M, Gabaldón T, Antón J.

Appl Environ Microbiol. 2015 Dec;81(24):8445-56. doi: 10.1128/AEM.02690-15.

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