Comparative Genomics

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Showing 31 - 60 results of 73

2022

Secondary structure prediction of long noncoding RNA: review and experimental comparison of existing approaches

Briefings in Bioinformatics

L. A. Bugnon, A. A. Edera, S. Prochetto, M. Gerard, J. Raad, E. Fenoy, M. Rubiolo, U. Chorostecki, T. Gabaldón, F. Ariel, L. E. Di Persia, D. H. Milone, and G. Stegmayer
Patterns of Genomic Variation in the Opportunistic Pathogen Candida glabrata Suggest the Existence of Mating and a Secondary Association with Humans

Current Biology

L. Carreté, E. Ksiezopolska, C. Pegueroles, E. Gómez-Molero, E. Saus, S. Iraola-Guzmán, D. Loska, O. Bader, C. Fairhead, and T. Gabaldón
Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors

npj Biofilms and Microbiomes

J. R. Willis, E. Saus, S. Iraola-Guzmán, E. Ksiezopolska, L. Cozzuto, L. A. Bejarano, N. Andreu-Somavilla, M. Alloza-Trabado, A. Blanco, A. Puig-Sola, E. Broglio, C. Carolis, J. Ponomarenko, J. Hecht, and T. Gabaldón
Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex

DNA Research

V. Mixão, V. del Olmo, E. Hegedűsová, E. Saus, L. Pryszcz, A. Cillingová, J. Nosek, and T. Gabaldón
Changes in the stool and oropharyngeal microbiome in obsessive-compulsive disorder

Scientific Reports

L. Domènech, J. Willis, M. Alemany-Navarro, M. Morell, E. Real, G. Escaramis, S. Bertolín, D. Sánchez Chinchilla, S. Balcells, C. Segalàs, X. Estivill, J. M. Menchón, T. Gabaldón, P. Alonso, and R. Rabionet
Candidemia Among Coronavirus Disease 2019 Patients in Turkey Admitted to Intensive Care Units: A Retrospective Multicenter Study

Open Forum Infectious Diseases

A. Arastehfar, N. Ünal, T. Hoşbul, M. Alper Özarslan, A. Sultan Karakoyun, F. Polat, D. Fuentes, R. Gümral, T. Turunç, F. Daneshnia, D. S. Perlin, C. Lass-Florl, T. Gabaldón, M. Ilkit, and H. M Nguyen
Trends in yeast diversity discovery

Fungal Diversity

T. Boekhout, A. S. Amend, F. El Baidouri, T. Gabaldón, J. Geml, M. Mittelbach, V. Robert, C. Shuhui Tan, B. Turchetti, D. Vu, Q-M. Wang, and A. Yurkov
Lung microbiota predict invasive pulmonary aspergillosis and its outcome in immunocompromised patients

Thorax

A. Hérivaux, J. R. Willis, T. Mercier, K. Lagrou, S. M. Gonçalves, R. A. Gonçales, J. Maertens, A. Carvalho, T. Gabaldón, and C. Cunha
The era of reference genomes in conservation genomics

Trends in Ecology & Evolution

G. Formenti, K. Theissinger, C. Fernandes, I. Bista, A. Bombarely, C. Bleidorn, C. Ciofi, A. Crottini, J. A. Godoy, J. Höglund, et al.

2021

Ten Years of Collaborative Progress in the Quest for Orthologs

Molecular Biology and Evolution

B. Linard, I. Ebersberger, S. E. McGlynn, N. Glover, T. Mochizuki, M. Patricio, O. Lecompte, Y. Nevers, P. D. Thomas, T. Gabaldón, E. Sonnhammer, C. Dessimoz, I. Uchiyama, A. Altenhoff, A. Ouangraoua, A. Warwick Vesztrocy, B. Linard, C. Dessimoz, D. Szklarczyk, D. Durand, D. Emms, D. Moi, D. Thybert, E. Sonnhammer, E. Kriventseva, H. Tang, H. Chiba, I. Uchiyama, I. Ebersberger, J. Huerta-Cepas, J. Tomas Fernandez-Breis, J. A. Blake, L. Pryszcz, M-J. Martin, M. Marcet Houben, M. Patricio, M. Muffato, N. Glover, O. Lecompte, P. D. Thomas, P. Schiffer, S. Capella-Gutierrez, S. Cosentino, S. E. McGlynn, S. Kuraku, S. Forslund, S. Kelly, S. Lewis, T. Jones, T. Mendes de Farias, T. Maeda, T. Gabaldón, W. Iwasaki, W. Pearson, Y. Wang, Y. Nevers, and Y. Hara
Structural characterization of NORAD reveals a stabilizing role of spacers and two new repeat units

Computational and Structural Biotechnology Journal

U. Chorostecki, E. Saus, and T. Gabaldón
Correction to: The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

Fungal Diversity

T. Boekhout, C. M. Aime, D. Begerow, T. Gabaldón, J. Heitman, M. Kemler, K. Khayhan, M-A. Lachance, E. J. Louis, S. Sun, D. Vu, and A. Yurkov
Comparative genomic analysis of clinical Candida glabrata isolates identifies multiple polymorphic loci that can improve existing multilocus sequence typing strategy

Studies in Mycology

A.. Arastehfar, M.. Marcet-Houben, F.. Daneshnia, S.J.. Taj-Aldeen, D.. Batra, S.R.. Lockhart, E.. Shor, T. Gabaldón, and D.S.. Perlin
Human albumin enhances the pathogenic potential of Candida glabrata on vaginal epithelial cells

PLOS Pathogens

M. Pekmezovic, A-K. Kaune, S. Austermeier, S. U. J. Hitzler, S. Mogavero, H. Hovhannisyan, T. Gabaldón, M. S. Gresnigt, and B. Hube
Sex-Specific Effects of Synbiotic Exposure in Mice on Addictive-Like Behavioral Alterations Induced by Chronic Alcohol Intake Are Associated With Changes in Specific Gut Bacterial Taxa and Brain Tryptophan Metabolism

Frontiers in Nutrition

N. Pizarro, E. Kossatz, P. González, A. Gamero, E. Veza, C. Fernández, T. Gabaldón, R. de la Torre, and P. Robledo
Methods in Molecular BiologyRNA BioinformaticsProfiling of RNA Structure at Single-Nucleotide Resolution Using nextPARS

U. Chorostecki, J. R. Willis, E. Saus, and T. Gabaldón
OCT1 – a yeast mitochondrial thiolase involved in the 3-oxoadipate pathway

FEMS Yeast Research

R. Vrzoňová, R. Tóth, B. Siváková, A. Moťovská, K. Gaplovská-Kyselá, P. Baráth, Ľ. Tomáška, A. Gácser, T. Gabaldón, J. Nosek, and M. Neboháčová
Citizen-science based study of the oral microbiome in Cystic fibrosis and matched controls reveals major differences in diversity and abundance of bacterial and fungal species

Journal of Oral Microbiology

J. R. Willis, E. Saus, S. Iraola-Guzmán, E. Cabello-Yeves, E. Ksiezopolska, L. Cozzuto, L. A. Bejarano, N. Andreu-Somavilla, M. Alloza-Trabado, A. Blanco, A. Puig-Sola, E. Broglio, C. Carolis, J. Ponomarenko, J. Hecht, and T. Gabaldón
Human tRNAs with inosine 34 are essential to efficiently translate eukarya-specific low-complexity proteins

Nucleic Acids Research

A. GabrielTorres, M. Rodríguez-Escribà, M. Marcet-Houben, H. Graziele S. Vieira, N. Camacho, H. Catena, M. Murillo Recio, À. Rafels-Ybern, O. Reina, F. Miguel Torres, A. Pardo-Saganta, T. Gabaldón, E. Maria Novoa, and L. Ribas de Pouplana
The long non-coding RNA landscape of Candida yeast pathogens

Nature Communications

H. Hovhannisyan, and T. Gabaldón
Transient Mitochondria Dysfunction Confers Fungal Cross-Resistance against Phagocytic Killing and Fluconazole

mBio

S. Siscar-Lewin, T. Gabaldón, A. M. Aldejohann, O. Kurzai, B. Hube, and S. Brunke
The transposable element-rich genome of the cereal pest Sitophilus oryzae

BMC Biology

N. Parisot, C. Vargas-Chávez, C. Goubert, P. Baa-Puyoulet, S. Balmand, L. Beranger, C. Blanc, A. Bonnamour, M. Boulesteix, N. Burlet, F. Calevro, P. Callaerts, T. Chancy, H. Charles, S. Colella, A. Da Silva Barbosa, E. Dell’Aglio, A. Di Genova, G. Febvay, T. Gabaldón, M. Galvão Ferrarini, A. Gerber, B. Gillet, R. Hubley, S. Hughes, E. Jacquin-Joly, J. Maire, M. Marcet-Houben, F. Masson, C. Meslin, N. Montagné, A. Moya, A. Tereza Rib de Vasconcelos, G. Richard, J. Rosen, M-F. Sagot, A. F. A. Smit, J. M. Storer, C. Vincent-Monegat, A. Vallier, A. Vigneron, A. Zaidman-Rémy, W. Zamoum, C. Vieira, R. Rebollo, A. Latorre, and A. Heddi
Origin and Early Evolution of the Eukaryotic Cell

Annual Review of Microbiology

T. Gabaldón
Comparative Genomics Used to Predict Virulence Factors and Metabolic Genes among Monilinia Species

Journal of Fungi

M. Marcet-Houben, M. Villarino, L. Vilanova, A. De Cal, J. A. L. van Kan, J. Usall, T. Gabaldón, and R. Torres
Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations

DNA Research

V. Mixão, E. Hegedűsová, E. Saus, L. P. Pryszcz, A. Cillingová, J. Nosek, and T. Gabaldón
Narrow mutational signatures drive acquisition of multidrug resistance in the fungal pathogen Candida glabrata

Current Biology

E. Ksiezopolska, M. Àngel Schikora-Tamarit, R. Beyer, J. Carlos Nunez-Rodriguez, C. Schüller, and T. Gabaldón
Oral microbiome in down syndrome and its implications on oral health

Journal of Oral Microbiology

J. R. Willis, S. Iraola-Guzmán, E. Saus, E. Ksiezopolska, L. Cozzuto, L. A. Bejarano, N. Andreu-Somavilla, M. Alloza-Trabado, A. Puig-Sola, A. Blanco, E. Broglio, C. Carolis, J. Hecht, J. Ponomarenko, and T. Gabaldón
Extreme diversification driven by parallel events of massive loss of heterozygosity in the hybrid lineage of Candida albicans

Genetics

V. Mixão, E. Saus, T. Boekhout, and T. Gabaldón
The evolving species concepts used for yeasts: from phenotypes and genomes to speciation networks

Fungal Diversity

T. Boekhout, C. M. Aime, D. Begerow, T. Gabaldón, J. Heitman, M. Kemler, K. Khayhan, M-A. Lachance, E. J. Louis, S. Sun, D. Vu, and A. Yurkov
Timing the origin of eukaryotic cellular complexity with ancient duplications

Nature Ecology & Evolution

J. Vosseberg, J. J. E. van Hooff, M. Marcet-Houben, A. van Vlimmeren, L. M. van Wijk, T. Gabaldón, and B. Snel

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