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Items: 1 to 50 of 185

1.

CROSSMAPPER: estimating cross-mapping rates and optimizing experimental design in multi-species sequencing studies.

Hovhannisyan H, Hafez A, Llorens C, Gabaldón T.

Bioinformatics. 2019 Aug 8. pii: btz626. doi: 10.1093/bioinformatics/btz626. [Epub ahead of print]

PMID:
31392323
2.

Post-exercise hypotension and skeletal muscle oxygenation is regulated by nitrate-reducing activity of oral bacteria.

Cutler C, Kiernan M, Willis JR, Gallardo-Alfaro L, Casas-Agustench P, White D, Hickson M, Gabaldon T, Bescos R.

Free Radic Biol Med. 2019 Jul 29. pii: S0891-5849(19)30761-0. doi: 10.1016/j.freeradbiomed.2019.07.035. [Epub ahead of print]

PMID:
31369841
3.

Advances and Applications in the Quest for Orthologs.

Glover N, Dessimoz C, Ebersberger I, Forslund SK, Gabaldón T, Huerta-Cepas J, Martin MJ, Muffato M, Patricio M, Pereira C, Sousa da Silva A, Wang Y, Sonnhammer E, Thomas PD; Quest for Orthologs Consortium .

Mol Biol Evol. 2019 Jun 26. pii: msz150. doi: 10.1093/molbev/msz150. [Epub ahead of print]

PMID:
31241141
4.

Skin microbiome modulation induced by probiotic solutions.

Paetzold B, Willis JR, Pereira de Lima J, Knödlseder N, Brüggemann H, Quist SR, Gabaldón T, Güell M.

Microbiome. 2019 Jun 24;7(1):95. doi: 10.1186/s40168-019-0709-3.

5.

Recent trends in molecular diagnostics of yeast infections: from PCR to NGS.

OPATHY Consortium, Gabaldón T.

FEMS Microbiol Rev. 2019 Jun 3. pii: fuz015. doi: 10.1093/femsre/fuz015. [Epub ahead of print]

PMID:
31158289
6.

Whole-Genome Sequencing of the Opportunistic Yeast Pathogen Candida inconspicua Uncovers Its Hybrid Origin.

Mixão V, Hansen AP, Saus E, Boekhout T, Lass-Florl C, Gabaldón T.

Front Genet. 2019 Apr 25;10:383. doi: 10.3389/fgene.2019.00383. eCollection 2019.

7.

Microbiome and colorectal cancer: Roles in carcinogenesis and clinical potential.

Saus E, Iraola-Guzmán S, Willis JR, Brunet-Vega A, Gabaldón T.

Mol Aspects Med. 2019 May 24. pii: S0098-2997(19)30032-9. doi: 10.1016/j.mam.2019.05.001. [Epub ahead of print] Review.

8.

Fungal evolution: major ecological adaptations and evolutionary transitions.

Naranjo-Ortiz MA, Gabaldón T.

Biol Rev Camb Philos Soc. 2019 Aug;94(4):1443-1476. doi: 10.1111/brv.12510. Epub 2019 Apr 25.

PMID:
31021528
9.

Candida parapsilosis: from Genes to the Bedside.

Tóth R, Nosek J, Mora-Montes HM, Gabaldon T, Bliss JM, Nosanchuk JD, Turner SA, Butler G, Vágvölgyi C, Gácser A.

Clin Microbiol Rev. 2019 Feb 27;32(2). pii: e00111-18. doi: 10.1128/CMR.00111-18. Print 2019 Mar 20. Review.

PMID:
30814115
10.

Genome Comparisons of Candida glabrata Serial Clinical Isolates Reveal Patterns of Genetic Variation in Infecting Clonal Populations.

Carreté L, Ksiezopolska E, Gómez-Molero E, Angoulvant A, Bader O, Fairhead C, Gabaldón T.

Front Microbiol. 2019 Feb 12;10:112. doi: 10.3389/fmicb.2019.00112. eCollection 2019.

11.

Utilization of selenocysteine in early-branching fungal phyla.

Mariotti M, Salinas G, Gabaldón T, Gladyshev VN.

Nat Microbiol. 2019 May;4(5):759-765. doi: 10.1038/s41564-018-0354-9. Epub 2019 Feb 11.

12.

Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis.

Pegueroles C, Iraola-Guzmán S, Chorostecki U, Ksiezopolska E, Saus E, Gabaldón T.

RNA Biol. 2019 Mar;16(3):320-329. doi: 10.1080/15476286.2019.1572438. Epub 2019 Jan 31.

13.

Impact of Homologous Recombination on the Evolution of Prokaryotic Core Genomes.

González-Torres P, Rodríguez-Mateos F, Antón J, Gabaldón T.

MBio. 2019 Jan 22;10(1). pii: e02494-18. doi: 10.1128/mBio.02494-18.

14.

Citizen science charts two major "stomatotypes" in the oral microbiome of adolescents and reveals links with habits and drinking water composition.

Willis JR, González-Torres P, Pittis AA, Bejarano LA, Cozzuto L, Andreu-Somavilla N, Alloza-Trabado M, Valentín A, Ksiezopolska E, Company C, Onywera H, Montfort M, Hermoso A, Iraola-Guzmán S, Saus E, Labeeuw A, Carolis C, Hecht J, Ponomarenko J, Gabaldón T.

Microbiome. 2018 Dec 6;6(1):218. doi: 10.1186/s40168-018-0592-3.

15.

Genetically encodable bioluminescent system from fungi.

Kotlobay AA, Sarkisyan KS, Mokrushina YA, Marcet-Houben M, Serebrovskaya EO, Markina NM, Gonzalez Somermeyer L, Gorokhovatsky AY, Vvedensky A, Purtov KV, Petushkov VN, Rodionova NS, Chepurnyh TV, Fakhranurova LI, Guglya EB, Ziganshin R, Tsarkova AS, Kaskova ZM, Shender V, Abakumov M, Abakumova TO, Povolotskaya IS, Eroshkin FM, Zaraisky AG, Mishin AS, Dolgov SV, Mitiouchkina TY, Kopantzev EP, Waldenmaier HE, Oliveira AG, Oba Y, Barsova E, Bogdanova EA, Gabaldón T, Stevani CV, Lukyanov S, Smirnov IV, Gitelson JI, Kondrashov FA, Yampolsky IV.

Proc Natl Acad Sci U S A. 2018 Dec 11;115(50):12728-12732. doi: 10.1073/pnas.1803615115. Epub 2018 Nov 26.

16.

Echinocandin-Induced Microevolution of Candida parapsilosis Influences Virulence and Abiotic Stress Tolerance.

Papp C, Kocsis K, Tóth R, Bodai L, Willis JR, Ksiezopolska E, Lozoya-Pérez NE, Vágvölgyi C, Mora Montes H, Gabaldón T, Nosanchuk JD, Gácser A.

mSphere. 2018 Nov 14;3(6). pii: e00547-18. doi: 10.1128/mSphere.00547-18.

17.

MICU1 Confers Protection from MCU-Dependent Manganese Toxicity.

Wettmarshausen J, Goh V, Huang KT, Arduino DM, Tripathi U, Leimpek A, Cheng Y, Pittis AA, Gabaldón T, Mokranjac D, Hajnóczky G, Perocchi F.

Cell Rep. 2018 Nov 6;25(6):1425-1435.e7. doi: 10.1016/j.celrep.2018.10.037.

18.

Evolution of the Peroxisomal Proteome.

Gabaldón T.

Subcell Biochem. 2018;89:221-233. doi: 10.1007/978-981-13-2233-4_9. Review.

PMID:
30378025
19.

Relative timing of mitochondrial endosymbiosis and the "pre-mitochondrial symbioses" hypothesis.

Gabaldón T.

IUBMB Life. 2018 Dec;70(12):1188-1196. doi: 10.1002/iub.1950. Epub 2018 Oct 25. Review.

20.

Evolutionary Emergence of Drug Resistance in Candida Opportunistic Pathogens.

Ksiezopolska E, Gabaldón T.

Genes (Basel). 2018 Sep 19;9(9). pii: E461. doi: 10.3390/genes9090461. Review.

21.

Transcriptome Sequencing Approaches to Elucidate Host-Microbe Interactions in Opportunistic Human Fungal Pathogens.

Hovhannisyan H, Gabaldón T.

Curr Top Microbiol Immunol. 2018 Aug 21. doi: 10.1007/82_2018_122. [Epub ahead of print]

PMID:
30128828
22.

Genome Variation in the Model Halophilic Bacterium Salinibacter ruber.

González-Torres P, Gabaldón T.

Front Microbiol. 2018 Jul 19;9:1499. doi: 10.3389/fmicb.2018.01499. eCollection 2018.

23.

Eicosanoid biosynthesis influences the virulence of Candida parapsilosis.

Chakraborty T, Thuer E, Heijink M, Tóth R, Bodai L, Vágvölgyi C, Giera M, Gabaldón T, Gácser A.

Virulence. 2018;9(1):1019-1035. doi: 10.1080/21505594.2018.1475797.

24.

Genomes shed light on the secret life of Candida glabrata: not so asexual, not so commensal.

Gabaldón T, Fairhead C.

Curr Genet. 2019 Feb;65(1):93-98. doi: 10.1007/s00294-018-0867-z. Epub 2018 Jul 19. Review.

25.

Gene flow contributes to diversification of the major fungal pathogen Candida albicans.

Ropars J, Maufrais C, Diogo D, Marcet-Houben M, Perin A, Sertour N, Mosca K, Permal E, Laval G, Bouchier C, Ma L, Schwartz K, Voelz K, May RC, Poulain J, Battail C, Wincker P, Borman AM, Chowdhary A, Fan S, Kim SH, Le Pape P, Romeo O, Shin JH, Gabaldon T, Sherlock G, Bougnoux ME, d'Enfert C.

Nat Commun. 2018 Jun 8;9(1):2253. doi: 10.1038/s41467-018-04787-4.

26.

Biological Processes Modulating Longevity across Primates: A Phylogenetic Genome-Phenome Analysis.

Muntané G, Farré X, Rodríguez JA, Pegueroles C, Hughes DA, de Magalhães JP, Gabaldón T, Navarro A.

Mol Biol Evol. 2018 Aug 1;35(8):1990-2004. doi: 10.1093/molbev/msy105.

27.

Adaptation of S. cerevisiae to Fermented Food Environments Reveals Remarkable Genome Plasticity and the Footprints of Domestication.

Legras JL, Galeote V, Bigey F, Camarasa C, Marsit S, Nidelet T, Sanchez I, Couloux A, Guy J, Franco-Duarte R, Marcet-Houben M, Gabaldon T, Schuller D, Sampaio JP, Dequin S.

Mol Biol Evol. 2018 Jul 1;35(7):1712-1727. doi: 10.1093/molbev/msy066.

28.

Genome Sequence of the Brown Rot Fungal Pathogen Monilinia laxa.

Naranjo-Ortíz MA, Rodríguez-Píres S, Torres R, De Cal A, Usall J, Gabaldón T.

Genome Announc. 2018 Apr 26;6(17). pii: e00214-18. doi: 10.1128/genomeA.00214-18.

29.

Phylogenomics of the olive tree (Olea europaea) reveals the relative contribution of ancient allo- and autopolyploidization events.

Julca I, Marcet-Houben M, Vargas P, Gabaldón T.

BMC Biol. 2018 Jan 25;16(1):15. doi: 10.1186/s12915-018-0482-y.

30.

Investigation of Candida parapsilosis virulence regulatory factors during host-pathogen interaction.

Tóth R, Cabral V, Thuer E, Bohner F, Németh T, Papp C, Nimrichter L, Molnár G, Vágvölgyi C, Gabaldón T, Nosanchuk JD, Gácser A.

Sci Rep. 2018 Jan 22;8(1):1346. doi: 10.1038/s41598-018-19453-4.

31.

nextPARS: parallel probing of RNA structures in Illumina.

Saus E, Willis JR, Pryszcz LP, Hafez A, Llorens C, Himmelbauer H, Gabaldón T.

RNA. 2018 Apr;24(4):609-619. doi: 10.1261/rna.063073.117. Epub 2018 Jan 22.

32.

Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications.

Stavrou AA, Mixão V, Boekhout T, Gabaldón T.

Yeast. 2018 Jun;35(6):425-429. doi: 10.1002/yea.3303. Epub 2018 Feb 22.

33.

Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans.

Carreté L, Ksiezopolska E, Pegueroles C, Gómez-Molero E, Saus E, Iraola-Guzmán S, Loska D, Bader O, Fairhead C, Gabaldón T.

Curr Biol. 2018 Jan 8;28(1):15-27.e7. doi: 10.1016/j.cub.2017.11.027. Epub 2017 Dec 14.

34.

Characterization of ecologically diverse viruses infecting co-occurring strains of cosmopolitan hyperhalophilic Bacteroidetes.

Villamor J, Ramos-Barbero MD, González-Torres P, Gabaldón T, Rosselló-Móra R, Meseguer I, Martínez-García M, Santos F, Antón J.

ISME J. 2018 Feb;12(2):424-437. doi: 10.1038/ismej.2017.175. Epub 2017 Nov 3.

35.

Gearing up to handle the mosaic nature of life in the quest for orthologs.

Forslund K, Pereira C, Capella-Gutierrez S, Sousa da Silva A, Altenhoff A, Huerta-Cepas J, Muffato M, Patricio M, Vandepoele K, Ebersberger I, Blake J, Fernández Breis JT; Quest for Orthologs Consortium, Boeckmann B, Gabaldón T, Sonnhammer E, Dessimoz C, Lewis S.

Bioinformatics. 2017 Aug 30. doi: 10.1093/bioinformatics/btx542. [Epub ahead of print]

36.

Regulatory Mechanisms of a Highly Pectinolytic Mutant of Penicillium occitanis and Functional Analysis of a Candidate Gene in the Plant Pathogen Fusarium oxysporum.

Bravo-Ruiz G, Sassi AH, Marcet-Houben M, Di Pietro A, Gargouri A, Gabaldon T, Roncero MIG.

Front Microbiol. 2017 Sep 8;8:1627. doi: 10.3389/fmicb.2017.01627. eCollection 2017.

37.

Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast.

Masgrau A, Battola A, Sanmartin T, Pryszcz LP, Gabaldón T, Mendoza M.

Mol Biol Cell. 2017 Nov 1;28(22):3082-3094. doi: 10.1091/mbc.E17-06-0404. Epub 2017 Sep 13.

38.

Eukaryotic transporters for hydroxyderivatives of benzoic acid.

Cillingová A, Zeman I, Tóth R, Neboháčová M, Dunčková I, Hölcová M, Jakúbková M, Gérecová G, Pryszcz LP, Tomáška Ľ, Gabaldón T, Gácser A, Nosek J.

Sci Rep. 2017 Aug 21;7(1):8998. doi: 10.1038/s41598-017-09408-6.

39.

Genome-wide signatures of complex introgression and adaptive evolution in the big cats.

Figueiró HV, Li G, Trindade FJ, Assis J, Pais F, Fernandes G, Santos SHD, Hughes GM, Komissarov A, Antunes A, Trinca CS, Rodrigues MR, Linderoth T, Bi K, Silveira L, Azevedo FCC, Kantek D, Ramalho E, Brassaloti RA, Villela PMS, Nunes ALV, Teixeira RHF, Morato RG, Loska D, Saragüeta P, Gabaldón T, Teeling EC, O'Brien SJ, Nielsen R, Coutinho LL, Oliveira G, Murphy WJ, Eizirik E.

Sci Adv. 2017 Jul 19;3(7):e1700299. doi: 10.1126/sciadv.1700299. eCollection 2017 Jul.

40.

Hybridization and emergence of virulence in opportunistic human yeast pathogens.

Mixão V, Gabaldón T.

Yeast. 2018 Jan;35(1):5-20. doi: 10.1002/yea.3242. Epub 2017 Sep 14.

41.

Lack of the PGA exopolysaccharide in Salmonella as an adaptive trait for survival in the host.

Echeverz M, García B, Sabalza A, Valle J, Gabaldón T, Solano C, Lasa I.

PLoS Genet. 2017 May 24;13(5):e1006816. doi: 10.1371/journal.pgen.1006816. eCollection 2017 May.

42.

Erratum to: Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Apr 4;18(1):63. doi: 10.1186/s13059-017-1202-6. No abstract available.

43.

Genomic history of the origin and domestication of common bean unveils its closest sister species.

Rendón-Anaya M, Montero-Vargas JM, Saburido-Álvarez S, Vlasova A, Capella-Gutierrez S, Ordaz-Ortiz JJ, Aguilar OM, Vianello-Brondani RP, Santalla M, Delaye L, Gabaldón T, Gepts P, Winkler R, Guigó R, Delgado-Salinas A, Herrera-Estrella A.

Genome Biol. 2017 Mar 29;18(1):60. doi: 10.1186/s13059-017-1190-6.

44.

Rapid transcriptional plasticity of duplicated gene clusters enables a clonally reproducing aphid to colonise diverse plant species.

Mathers TC, Chen Y, Kaithakottil G, Legeai F, Mugford ST, Baa-Puyoulet P, Bretaudeau A, Clavijo B, Colella S, Collin O, Dalmay T, Derrien T, Feng H, Gabaldón T, Jordan A, Julca I, Kettles GJ, Kowitwanich K, Lavenier D, Lenzi P, Lopez-Gomollon S, Loska D, Mapleson D, Maumus F, Moxon S, Price DR, Sugio A, van Munster M, Uzest M, Waite D, Jander G, Tagu D, Wilson AC, van Oosterhout C, Swarbreck D, Hogenhout SA.

Genome Biol. 2017 Feb 13;18(1):27. doi: 10.1186/s13059-016-1145-3. Erratum in: Genome Biol. 2017 Apr 4;18(1):63.

45.

Widespread Inter- and Intra-Domain Horizontal Gene Transfer of d-Amino Acid Metabolism Enzymes in Eukaryotes.

Naranjo-Ortíz MA, Brock M, Brunke S, Hube B, Marcet-Houben M, Gabaldón T.

Front Microbiol. 2016 Dec 20;7:2001. doi: 10.3389/fmicb.2016.02001. eCollection 2016.

46.

Extreme genomic erosion after recurrent demographic bottlenecks in the highly endangered Iberian lynx.

Abascal F, Corvelo A, Cruz F, Villanueva-Cañas JL, Vlasova A, Marcet-Houben M, Martínez-Cruz B, Cheng JY, Prieto P, Quesada V, Quilez J, Li G, García F, Rubio-Camarillo M, Frias L, Ribeca P, Capella-Gutiérrez S, Rodríguez JM, Câmara F, Lowy E, Cozzuto L, Erb I, Tress ML, Rodriguez-Ales JL, Ruiz-Orera J, Reverter F, Casas-Marce M, Soriano L, Arango JR, Derdak S, Galán B, Blanc J, Gut M, Lorente-Galdos B, Andrés-Nieto M, López-Otín C, Valencia A, Gut I, García JL, Guigó R, Murphy WJ, Ruiz-Herrera A, Marques-Bonet T, Roma G, Notredame C, Mailund T, Albà MM, Gabaldón T, Alioto T, Godoy JA.

Genome Biol. 2016 Dec 14;17(1):251.

47.

Correction: Gene Expansion Shapes Genome Architecture in the Human Pathogen Lichtheimia corymbifera: An Evolutionary Genomics Analysis in the Ancient Terrestrial Mucorales (Mucoromycotina).

Schwartze VU, Winter S, Shelest E, Marcet-Houben M, Horn F, Wehner S, Linde J, Valiante V, Sammeth M, Riege K, Nowrousian M, Kaerger K, Jacobsen ID, Marz M, Brakhage AA, Gabaldón T, Böcker S, Voigt K.

PLoS Genet. 2016 Dec 5;12(12):e1006491. doi: 10.1371/journal.pgen.1006491. eCollection 2016 Dec.

48.

The Case of the Missing Ancient Fungal Polyploids.

Campbell MA, Ganley AR, Gabaldón T, Cox MP.

Am Nat. 2016 Dec;188(6):602-614. Epub 2016 Sep 26. Review.

PMID:
27860510
49.

High-Throughput Proteomics Reveals the Unicellular Roots of Animal Phosphosignaling and Cell Differentiation.

Sebé-Pedrós A, Peña MI, Capella-Gutiérrez S, Antó M, Gabaldón T, Ruiz-Trillo I, Sabidó E.

Dev Cell. 2016 Oct 24;39(2):186-197. doi: 10.1016/j.devcel.2016.09.019. Epub 2016 Oct 13.

50.

Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis.

Zeman I, Neboháčová M, Gérecová G, Katonová K, Jánošíková E, Jakúbková M, Centárová I, Dunčková I, Tomáška L, Pryszcz LP, Gabaldón T, Nosek J.

G3 (Bethesda). 2016 Dec 7;6(12):4047-4058. doi: 10.1534/g3.116.034389.

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