Publications & public media
Publications
Here are some publications that have benefited from the use of Garnatxa:
2025 - Context-Aware Biosensor Design Through Biology-Guided Machine Learning and Dynamical Modeling Jonathan Tellechea-Luzardo, Hector Martin Lazaro, Christian Fernandez Perez, David Henriques, Irene Otero-Muras and Pablo Carbonell.
2025 - Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation Carolina Monzó , Adam Frankish and Ana Conesa.
2025 - Genome data artifacts and functional studies of deletion repair in the BA.1 SARS-CoV-2 spike protein Miguel Álvarez-Herrera, Paula Ruiz-Rodriguez, Beatriz Navarro-Domínguez, Joao Zulaica, Brayan Grau, María Alma Bracho, Manuel Guerreiro, Cristóbal Aguilar‐Gallardo, Fernando González-Candelas, Iñaki Comas, Ron Geller and Mireia Coscollá.
2025 - Organ-level gene regulatory network models enable the identification of central transcription factors in Solanum lycopersicum José D. Fernández, David Navarro-Payá, Antonio Santiago, Jonathan Canan, Sebastián Contreras-Riquelme, Ariel Cerda, Tomás C. Moyano, Lorena Melet, Nathan R. Johnson, Javier Canales, José M. Álvarez, José Tomás Matus and Elena A. Vidal.
2025 - Developing the Grapevine Hydric Stress Atlas: A Meta-Analysis Resource for Exploring Transcriptome Responses to Drought Álvaro Vidal Valenzuela, David Navarro-Payá, Antonio Santiago, Paolo Sonego, Felipe Gainza-Cortés, Mickael Malnoy and José Tomás Matus.
2025 - Metrics of Genomic Complexity in the Evolution of Bacterial Endosymbiosis Pablo Román-Escrivá, Moisès Bernabeu, Eleonora Paganin, Wladimiro Diaz, Miguel Verdú, José L. Oliver, Vicente Arnau and Andrés Moya.
2024 - Chronic infection of Caenorhabditis elegans by Orsay virus induces age-dependent immunity and superinfection exclusion Victoria G. Castiglioni, Ana Villena-Giménez, Antonio González-Sánchez, Christina Toft, Gustavo G. Gómez and Santiago F. Elena.
2024 - The Plantae Visualization Platform: a comprehensive web-based tool for the integration, visualization, and analysis of omic data across plant and related species Antonio Santiago, Luis Orduña, José David Fernández, Álvaro Vidal, Iñigo de Martín-Agirre, Purificación Lisón, Elena A. Vidal, David Navarro-Payá and José Tomás Matus.
2024 - Microgravity and low muon radiation affect viral pathogenesis and physiology in Caenorhabditis elegans Ana Villena-Giménez, Victoria G. Castiglioni Esmeralda G. Legarda1, Juan C.Muñoz-Sánchez, Rubén González and Santiago F. Elena.
2024 - SQANTI-reads: a tool for the quality assessment of long read data in multi-sample lrRNA-seq experiments Netanya Keil, Carolina Monzó, Lauren McIntyre and Ana Conesa
2024 - Towards understanding post-COVID-19 condition: A systematic meta-analysis of transcriptomic alterations with sex-specific insights Elena Cristina Rusu, Pablo Monfort-Lanzas, Laia Bertran, Andrea Barrientos-Riosalido, Emilia Sol, Razieh Mahmoudian, Carmen Aguilar, Silvia Brianso, Fadel Mohamed, Susana Garcia, Javier Camaron and Teresa Auguet.
2024 - Quantifying defective and wild-type viruses from high-throughput RNA sequencing Juan C. Muñoz-Sánchez, María J. Olmo-Uceda, José-Ángel Oteo and Santiago F. Elena
2024 - Mapping mutational fitness effects across the coxsackievirus B3 proteome reveals distinct profiles of mutation tolerability Beatriz Álvarez-Rodríguez, Sebastian Velandia-Álvarez, Christina Toft and Ron Geller
2024 - Transcriptomic Insights into the Epigenetic Modulation of Turnip Mosaic Virus Evolution in Arabidopsis thaliana María J. Olmo-Uceda, Silvia Ambrós, Régis L. Corrêa and Santiago F. Elena
2024 - Experimental evolution of an RNA virus in Caenorhabditis elegans Victoria G. Castiglioni, María J. Olmo-Uceda, Susana Martín, Marie-Anne Félix, Rubén González and Santiago F. Elena
2024 - Biosynthesis of oxyresveratrol in mulberry (Morus alba L.) is mediated by a group of p-coumaroyl-CoA 2’-hydroxylases acting upstream of stilbene synthases Antonio Santiago, Pablo Romero, Ascensión Martínez, María José Martínez, Jone Echeverría, Susana Selles, Raquel Alvarez-Urdiola, Chen Zhang, David Navarro-Payá, Gastón A. Pizzio, Estel·la Micó, Antonio Samper, Jaime Morante, Riccardo Aiese Cigliano, David Manzano, Roque Bru and José Tomás Matus
2024 - Host-strain compatibility influences transcriptional responses in Mycobacterium tuberculosis infections Paula Ruiz-Rodriguez, Marta Caballer-Gual, Guillem Santamaria, Hellen Hiza y Mireia Coscolla.
2024 - DetSpace: a web server for engineering detectable pathways for bio-based chemical production Hèctor Martín Lázaro, Ricardo Marín Bautista, Pablo Carbonell.
2024 - Accumulation dynamics of defective genomes during experimental evolution of two betacoronaviruses Julia Hillung, María J. Olmo-Uceda, Juan C. Muñoz-Sánchez and Santiago F. Elena.
2024 - Cellular receptors for mammalian viruses Ana Valero-Rello, Carlos Baeza-Delgado, Iván Andreu-Moreno and Rafael Sanjuán.
2024 - Quasineutral multistability in an epidemiological-like model for defective-helper betacoronavirus infection in cell cultures Juan C. Muñoz-Sánchez, J. Tomás Lázaro, Julia Hillung, María J. Olmo-Uceda, Josep Sardanyés and Santiago F. Elena.
2024 - Adaptive advantage of deletion repair in the N-terminal domain of the SARS-CoV-2 spike protein in variants of concern Miguel Álvarez-Herrera, Paula Ruiz-Rodriguez, Beatriz Navarro-Domínguez, Joao Zulaica, Brayan Grau, María Alma Bracho, Manuel Guerreiro, Cristóbal Aguilar Gallardo, Fernando González-Candelas, Iñaki Comas, Ron Geller and Mireia Coscollá.
2024 - MOSim: bulk and single-cell multi-layer regulatory network simulator Carolina Monzó, Carlos Martínez-Mira, Ángeles Arzalluz-Luque, Ana Conesa and Sonia Tarazona.
2023 - Emergence of two distinct spatial folds in a pair of plant virus proteins encoded by nested genes Esmeralda G. Legarda, Santiago F. Elena and Arcady R. Mushegian.
2023 - Trends of genome’s complexity metrics in endosymbiont organisms and their free-living counterparts Eleonora Paganina, Pablo Román-Escrivá, Moisès Bernabéu, Vicente Arnau, Wladimiro Díaz-Villanueva and Andrés Moya.
2023 - Exploring the Common Human Gut Eukaryotic Microbiota around the World Enrique Roig-Tormoa, Samuel Piquer-Estebana, Wladimiro Diaz-Villanueva, Vicente Arnau and Andrés Moya.
2023 - Calculating genomic signature distances between phages and their bacterial host for distinguishing lytic and lysogenic phage Vicente Arnau, Wladimiro Diaz-Villanueva, Jorge Mifsut, Paula Villasante, Pablo Román and Mária Džunková.
2023 - MYB24 orchestrates terpene and flavonol metabolism as light responses to anthocyanin depletion in variegated grape berries Chen Zhang, Zhanwu Dai, Thilia Ferrier, Luis Orduña, Antonio Santiago, Arnau Peris, Darren C.J. Wong, Christian Kappel, Stefania Savoi, Rodrigo Loyola, Alessandra Amato, Bartosz Kozak, Miaomiao Li, Akun Liang, David Carrasco, Carlos Meyer-Regueiro, Carmen Espinoza, Ghislaine Hilbert, Rosa Figueroa-Balderas, Dario Cantu, Rosa Arroyo-Garcia, Patricio Arce-Johnson, Patricia Claudel, Daniel Errandonea, Manuel Rodríguez-Concepción, Eric Duchêne, Shao-shan Carol Huang, Simone Diego Castellarin, Giovanni Battista Tornielli, Francois Barrieu and José Tomás Matus.
2023 - NAC61 regulates late-and post-ripening associated processes in grapes involving a NAC60-dependent regulatory network Chiara Foresti, Luis Orduña, José Tomás Matus, Elodie Vandelle, Davide Danzi, Oscar Bellon, Giovanni Battista Tornielli, Alessandra Amato and Sara Zenoni.
2023 - Story of an infection: viral dynamics and host responses in the Caenorhabditis elegans-Orsay virus pathosystem Victoria G. Castiglioni, Maria J. Olmo-Uceda, Ana Villena-Giménez, Juan C. Muñoz-Sánchez and Santiago F. Elena.
2023 - Aggregated gene co-expression networks predict transcription factor regulatory landscapes in grapevine Luis Orduña, Antonio Santiago, David Navarro-Payá, Chen Zhang, Darren C J Wong and José Tomás Matus.
2023 - VIPERA: Viral Intra-Patient Evolution Reporting and Analysis Miguel Álvarez-Herrera, Jordi Sevilla, Paula Ruiz-Rodriguez, Andrea Vergara, Jordi Vila, Pablo Cano-Jiménez, Fernando González-Candelas, Iñaki Comas and Mireia Coscollá.
2023 - Inference of the Life Cycle of Environmental Phages from Genomic Signature Distances to Their Hosts. Vicente Arnau, Wladimiro Díaz-Villanueva, Jorge Mifsut-Benet, Paula Villasante, Beatriz Beamud, Paula Mompó, Rafael Sanjuan, Fernando González Candelas, Pilar Domingo Calap and Mária Džunková.