Comparative Genomics

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Showing 1 - 30 results of 103

2024

New developments for the Quest for Orthologs benchmark service

NAR Genomics and Bioinformatics

A. Altenhoff, Y. Nevers, V. Tran, D. Jyothi, M. Martin, S. Cosentino, S. Majidian, M. Marcet-Houben, D. Fuentes-Palacios, E. Persson, T. Walsh, O. Lecompte, T. Gabaldón, S. Kelly, Y. Hu, W. Iwasaki, S. Capella-Gutierrez, C. Dessimoz, P. D. Thomas, I. Ebersberger, and E. Sonnhammer
Reconstructing the last common ancestor of all eukaryotes

PLOS Biology

T. A. Richards, L. Eme, J. M. Archibald, G. Leonard, S. M. Coelho, A. de Mendoza, C. Dessimoz, P. Dolezal, L. K. Fritz-Laylin, T. Gabaldón, V. Hampl, G. J. P. L. Kops, M. M. Leger, P. Lopez-Garcia, J. O. McInerney, D. Moreira, S. A. Muñoz-Gómez, D. J. Richter, I. Ruiz-Trillo, A. E. Santoro, A. Sebé-Pedrós, B. Snel, C. W. Stairs, E. C. Tromer, J. J. E. van Hooff, B. Wickstead, T. A. Williams, A. J. Roger, J. B. Dacks, and J. G. Wideman
Acquired amphotericin B resistance leads to fitness trade-offs that can be mitigated by compensatory evolution in Candida auris

Nature Microbiology

H. Carolus, D. Sofras, G. Boccarella, P. Sephton-Clark, V. Biriukov, N. C. Cauldron, C. Lobo Romero, R. Vergauwen, S. Yazdani, S. Pierson, S. Jacobs, P. Vandecruys, S. Wijnants, J. F. Meis, T. Gabaldón, P. van den Berg, J. M. Rybak, C. A. Cuomo, and P. Van Dijck
A multidimensional assessment of in-host fitness costs of drug resistance in the opportunistic fungal pathogen Candida glabrata

FEMS Yeast Research

A. Arastehfar, F. Daneshnia, H. Hovhannisyan, N. Cabrera, M. Ilkit, J. V. Desai, T. Gabaldón, E. Shor, and D. S. Perlin
Chromosome level assemblies of Nakaseomyces (Candida) bracarensis uncover two distinct clades and define its adhesin repertoire

BMC Genomics

M. Marcet-Houben, E. Ksiezopolska, and T. Gabaldón
Threats from the Candida parapsilosis complex: the surge of multidrug resistance and a hotbed for new emerging pathogens

Microbiology and Molecular Biology Reviews

T. Gabaldón
PhyKIT: A Multitool for Phylogenomics

Current Protocols

J. L. Steenwyk, G. I. Martínez‐Redondo, T. J. Buida, E. Gluck‐Thaler, X‐X. Shen, T. Gabaldón, A. Rokas, and R. Fernández
Collateral sensitivity counteracts the evolution of antifungal drug resistance in Candida auris

Nature Microbiology

H. Carolus, D. Sofras, G. Boccarella, S. Jacobs, V. Biriukov, L. Goossens, A. Chen, I. Vantyghem, T. Verbeeck, S. Pierson, C. Lobo Romero, H. Steenackers, K. Lagrou, P. van den Berg, J. Berman, T. Gabaldón, and P. Van Dijck
Quest for Orthologs in the Era of Biodiversity Genomics

Genome Biology and Evolution

F. Langschied, N. Bordin, S. Cosentino, D. Fuentes-Palacios, N. Glover, M. Hiller, Y. Hu, J. Huerta-Cepas, L. Pedro Coelho, W. Iwasaki, S. Majidian, S. Manzano-Morales, E. Persson, T. A. Richards, T. Gabaldón, E. Sonnhammer, P. D. Thomas, C. Dessimoz, and I. Ebersberger
The European Reference Genome Atlas: piloting a decentralised approach to equitable biodiversity genomics

npj Biodiversity

A. M. McCartney, G. Formenti, A. Mouton, D. De Panis, L. S. Marins, H. G. Leitão, G. Diedericks, J. Kirangwa, M. Morselli, J. Salces-Ortiz, et al.
Editorial overview: emerging avenues in antimicrobial research

Current Opinion in Microbiology

T. Gabaldón, and L. Pedro Sór de Carvalho
Long-term stability of acquired drug resistance and resistance associated mutations in the fungal pathogen Nakaseomyces glabratus (Candida glabrata)

Frontiers in Cellular and Infection Microbiology

E. Ksiezopolska, M. Àngel Schikora-Tamarit, J. Carlos Nunez-Rodriguez, and T. Gabaldón
Comparison between 16S rRNA and shotgun sequencing in colorectal cancer, advanced colorectal lesions, and healthy human gut microbiota

BMC Genomics

D. Bars-Cortina, E. Ramon, B. Rius-Sansalvador, E. Guinó, A. Garcia-Serrano, N. Mach, O. Khannous-Lleiffe, E. Saus, T. Gabaldón, G. Ibáñez-Sanz, L. Rodríguez-Alonso, A. Mata, A. García-Rodríguez, M. Obón-Santacana, and V. Moreno
Symmetric and asymmetric DNA N6-adenine methylation regulates different biological responses in Mucorales

Nature Communications

C. Lax, S. J. Mondo, M. Osorio-Concepción, A. Muszewska, M. Corrochano-Luque, G. Gutiérrez, R. Riley, A. Lipzen, J. Guo, H. Hundley, M. Amirebrahimi, V. Ng, D. Lorenzo-Gutiérrez, U. Binder, J. Yang, Y. Song, D. Cánovas, E. Navarro, M. Freitag, T. Gabaldón, I. V. Grigoriev, L. M. Corrochano, F. E. Nicolás, and V. Garre
The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

NAR Genomics and Bioinformatics

M. Corominas, T. Marques-Bonet, M. A. Arnedo, M. Bayés, J. Belmonte, H. Escrivà, R. Fernández, T. Gabaldón, T. Garnatje, J. Germain, M. Niell, F. Palero, J. Pons, P. Puigdomènech, L. Aguilera, F. Cámara, J. Gómez-Garrido, F. Cruz, I. Sánchez-Escudero, C. R. Altaba, R. Alves, E. Arboleda, M. Capa, L. Triginer, V. Arbona, C. Avila, L. Baldo, A. Enguidanos, A. Prófumo, O. S. Wangesteen, M. Barceló-Serra, L. Botigué, A. Monfort, B. Burriel-Carranza, S. Carranza, J. del Campo, G. Mochales-Riaño, M. Palmada-Flores, H. Candela, C. Cañestro, C. Carreras, M. Domènech, C. Galià-Camps, S. Guirao-Rico, J. Lozano-Fernández, M. Pascual, C. Pegueroles, A. Sánchez-Gracia, M. A. Carretero, O. Grau, R. Garrido, X. Grau-Bové, T. Hermoso, I. Kim, J. A. Jurado-Rivera, C. Lalueza-Fox, J-B. Ledoux, R. Logares, R. Massana, F. Piferrer, J. Mauri, F. Mesquita-Joanes, J. S. Monrós, J. Pellicer, J. Peñuelas, C. Roquet, A. Ruiz-Herrera, G. Torruella, X. Turón, M. Ventura, V. Arroyo, C. Cuevas-Caballé, J. Ferrer Obiol, I. Gut, M. Gut, O. Hidalgo, G. Izquierdo-Arànega, L. Pérez-Sorribes, E. Righi, M. Riutort, J. Vallès, J. Rozas, T. Alioto, and R. Guigó
The Effect of Dietary Nitrate on the Oral Microbiome and Salivary Biomarkers in Individuals with High Blood Pressure

The Journal of Nutrition

L. duToit, M. L. Sundqvist, A. Redondo-Rio, Z. Brookes, P. Casas-Agustench, M. Hickson, A. Benavente, G. Montagut, E. Weitzberg, T. Gabaldón, J. O. Lundberg, and R. Bescos
Assessing Diagnosis of Candida Infections: A Study on Species Prevalence and Antifungal Resistance in Northern Morocco

Journal of Fungi

I. Ahaik, J. Carlos Nunez-Rodriguez, J. Abrini, S. Bouhdid, and T. Gabaldón
Proof of Concept Study: Comparability of Microbiome Diversity in Self- and Physician-Collected HPV-Positive and HPV-Negative Cervicovaginal Samples

International Journal of Molecular Sciences

L. Asensio-Puig, Á. de Andrés-Pablo, O. Khannous-Lleiffe, R. Ibáñez, A. Acera, S. de Sanjosé, T. Gabaldón, L. Alemany, L. Bruni, and M. Àngel Pavón
Several secondary metabolite gene clusters in the genomes of ten Penicillium spp. raise the risk of multiple mycotoxin occurrence in chestnuts

Food Microbiology

M. Garello, E. Piombo, F. Buonsenso, S. Prencipe, S. Valente, G. Roberta Meloni, M. Marcet-Houben, T. Gabaldón, and D. Spadaro
Hybrids unleashed: exploring the emergence and genomic insights of pathogenic yeast hybrids

Current Opinion in Microbiology

V. del Olmo, and T. Gabaldón
An inconspicuous identification: Isolation and identification of a novel Pichia species presenting as fungemia following cardiac surgery

International Journal of Infectious Diseases

A. T. Caldwell, T. Gabaldón, V. Mixão, N. L. Wengenack, B. P. Westley, and R. W. Stevens
On the impact of incomplete taxon sampling on the relative timing of gene transfer events

PLOS Biology

M. Bernabeu, S. Manzano-Morales, and T. Gabaldón
Noncontiguous operon atlas for the Staphylococcus aureus genome

microLife

P. Iturbe, A. San Martín, H. Hamamoto, M. Marcet-Houben, T. Galbaldón, C. Solano, and I. Lasa
Probing RNA structural landscapes across Candida yeast genomes

Frontiers in Microbiology

U. Chorostecki, E. Saus, and T. Gabaldón
Genomics of the expanding pine pathogen Lecanosticta acicola reveals patterns of ongoing genetic admixture

mSystems

M. Marcet-Houben, F. Cruz, J. Gómez-Garrido, T. S. Alioto, J. Carlos Nunez-Rodriguez, N. Mesanza, M. Gut, E. Iturritxa, and T. Gabaldón
Performance of a Shotgun Prediction Model for Colorectal Cancer When Using 16S rRNA Sequencing Data

International Journal of Molecular Sciences

E. Ramon, M. Obón-Santacana, O. Khannous-Lleiffe, E. Saus, T. Gabaldón, E. Guinó, D. Bars-Cortina, G. Ibáñez-Sanz, L. Rodríguez-Alonso, A. Mata, A. García-Rodríguez, and V. Moreno
Positive selection in gamete interaction proteins in Carnivora

Molecular Ecology

F. Pisciottano, M. Clara Campos, C. Penna, C. David Bruque, T. Gabaldón, and P. Saragüeta
Profiling Bacteria in the Lungs of Patients with Severe Influenza Versus COVID-19 with or without Aspergillosis

American Journal of Respiratory and Critical Care Medicine

S. Feys, M. Cardinali-Benigni, H. Moon Lauwers, C. Jacobs, A. Stevaert, S. M. Gonçalves, C. Cunha, Y. Debaveye, G. Hermans, J. Heylen, S. Humblet-Baron, K. Lagrou, L. Maessen, P. Meersseman, M. Peetermans, A. Redondo-Rios, L. Seldeslachts, M. R. Starick, K. Thevissen, G. Vande Velde, C. Vandenbriele, L. Vanderbeke, A. Wilmer, L. Naesens, F. L. van de Veerdonk, J. Van Weyenbergh, T. Gabaldón, J. Wauters, and A. Carvalho
Recent gene selection and drug resistance underscore clinical adaptation across Candida species

Nature Microbiology

M. ÀngelSchikora-Tamarit, and T. Gabaldón

2023

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