• Copy number variation on ABCC2-DNMBP loci affects the diversity and composition of the fecal microbiota in pigs

  Ramayo-Caldas, Yuliaxis; Crespo-Piazuelo, Daniel; Morata, Jordi; González-Rodríguez, Olga; Sebastià, Cristina; Castelló, Anna; Dalmau, Antoni; Ramos-Onsins, Sebastián; Alexiou, Konstantinos G.; Folch, Josep M.; Quintanilla, Raquel; Ballester Devís, Maria (American Society for Microbiology, 2023)

  Genetic variation in the pig genome partially modulates the composition of porcine gut microbial communities. Previous studies have been focused on the association between single nucleotide polymorphisms (SNPs) and the gut ...
• Beauveria bassiana rewires molecular mechanisms related to growth and defense in tomato

  Proietti, Silvia; Falconieri, Gaia Salvatore; Bertini, Laura; Pascale, Alberto; Bizzarri, Elisabetta; Morales Sanfrutos, Julia; Sabidó Aguadé, Eduard, 1981-; Ruocco, Michelina; Monti, Maurilia M.; Russo, Assunta; Dziurka, Kinga; Ceci, Marcello; Loreto, Francesco; Caruso, Carla (Oxford University Press, 2023)

  Plant roots can exploit beneficial associations with soil-inhabiting microbes, promoting growth and expanding the immune capacity of the host plant. In this work, we aimed to provide new information on changes occurring ...
• Chromosome-level genome assembly of Lilford’s wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

  Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Feiner, Nathalie; Uller, Tobias; Gut, Marta; Sanchez Escudero, Ignacio; Tavecchia, Giacomo; Rotger, Andreu; Otalora Acevedo, Katherin Eliana; Baldo, Laura (Oxford University Press, 2023)

  The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for ...
• Y chromosome sequence and epigenomic reconstruction across human populations

  Esteller Cucala, Paula; Palmada-Flores, Marc; Kuderna, Lukas F.K.; Fontseré Alemany, Clàudia, 1992-; Serres Armero, Aitor, 1992-; Dabad, Marc; Torralvo, María; Faella, Armida; Ferrández Peral, Luis, 1991-; Llovera Nadal, Laia; Fornas Carreño, Oscar; Julià, Eva; Ramírez, Erika; González, Irene; Hecht, Jochen; Lizano González, Esther, 1974-; Juan, David; Marquès i Bonet, Tomàs, 1975- (Nature Research, 2023)

  Recent advances in long-read sequencing technologies have allowed the generation and curation of more complete genome assemblies, enabling the analysis of traditionally neglected chromosomes, such as the human Y chromosome ...
• SOX17 enhancer variants disrupt transcription factor binding and enhancer inactivity drives pulmonary hypertension

  Walters, Rachel; Vasilaki, Eleni; Arman, Jurjan; Chen, Chien-Nien; Wu, Yukyee; Liang, Olin D.; Ashek, Ali; Dubois, Olivier; Zhao, Lin; Sabrin, Farah; Cebola, Inês; Ferrer, Jorge; Morrell, Nicholas W.; Klinger, James R.; Wilkins, Martin R.; Zhao, Lan; Rhodes, Christopher J. (Wolters Kluwer (LWW), 2023)

  Background: Pulmonary arterial hypertension (PAH) is a rare disease characterized by remodeling of the pulmonary arteries, increased vascular resistance, and right-sided heart failure. Genome-wide association studies of ...
• A Stenotrophomonas maltophilia TetR-like transcriptional regulator involved in fatty acid metabolism is controlled by quorum sensing signals

  Coves, Xavier; Bravo, Marc; Huedo, Pol; Conchillo-Solé, Òscar; Gómez, Andromeda-Celeste; Esteve-Codina, Anna; Dabad, Marc; Gut, Marta; Daura, Xavier; Yero, Daniel; Gibert, Isidre (American Society for Microbiology, 2023)

  Stenotrophomonas maltophilia is an environmental bacterium as well as an emerging opportunistic multidrug-resistant pathogen. They use the endogenous diffusible signal factor (DSF) quorum sensing (QS) system to coordinate ...
• Chromatin alternates between A and B compartments at kilobase scale for subgenic organization

  Harris, Hannah L.; Farabella, Irene; Rowley, M. Jordan (Nature Research, 2023)

  Nuclear compartments are prominent features of 3D chromatin organization, but sequencing depth limitations have impeded investigation at ultra fine-scale. CTCF loops are generally studied at a finer scale, but the impact ...
• Insplico: effective computational tool for studying splicing order of adjacent introns genome-wide with short and long RNA-seq reads

  Gohr, André; Iñiguez, Luis P.; Torres Méndez, Antonio, 1992-; Bonnal, Sophie; Irimia, Manuel (Oxford University Press, 2023)

  Although splicing occurs largely co-transcriptionally, the order by which introns are removed does not necessarily follow the order in which they are transcribed. Whereas several genomic features are known to influence ...
• Targeting lymphoid-derived IL-17 signaling to delay skin aging

  Solá, Paloma; Mereu, Elisabetta; Bonjoch, Júlia; Casado-Peláez, Marta; Prats, Neus; Aguilera, Mònica; Reina García, Óscar, 1976-; Blanco, Enrique; Esteller, Manel; Di Croce, Luciano; Heyn, Holger; Solanas, Guiomar; Aznar Benitah, Salvador (Nature Research, 2023)

  Skin aging is characterized by structural and functional changes that contribute to age-associated frailty. This probably depends on synergy between alterations in the local niche and stem cell-intrinsic changes, underscored ...
• Rare predicted loss-of-function variants of type I IFN immunity genes are associated with life-threatening COVID-19

  Matuozzo, Daniela; Gut, Marta; Cobat, Aurélie (BioMed Central, 2023)

  Background: We previously reported that impaired type I IFN activity, due to inborn errors of TLR3- and TLR7-dependent type I interferon (IFN) immunity or to autoantibodies against type I IFN, account for 15-20% of cases ...
• Combined loss of CDH1 and downstream regulatory sequences drive early-onset diffuse gastric cancer and increase penetrance of hereditary diffuse gastric cancer

  São José, Celina; Laurie, Steven, 1973-; Oliveira, Carla (Springer, 2023)

  Background: Germline CDH1 pathogenic or likely pathogenic variants cause hereditary diffuse gastric cancer (HDGC). Once a genetic cause is identified, stomachs' and breasts' surveillance and/or prophylactic surgery is ...
• Evaluation of circulating tumor DNA by electropherogram analysis and methylome profiling in high-risk neuroblastomas

  Trinidad, Eva María; Juan-Ribelles, Antonio; Pisano, Giulia; Castel, Victoria; Cañete, Adela; Gut, Marta; Heath, Simon; Font de Mora, Jaime (Frontiers, 2023)

  Background: Liquid biopsy has emerged as a promising, non-invasive diagnostic approach in oncology because the analysis of circulating tumor DNA (ctDNA) reflects the precise status of the disease at diagnosis, progression, ...
• Chromosome-level genome assembly of Lilford's wall lizard, Podarcis lilfordi (Günther, 1874) from the Balearic Islands (Spain)

  Gómez Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler; Feiner, Nathalie; Uller, Tobias; Sanchez Escudero, Ignacio; Tavecchia, Giacomo; Rotger, Andreu; Otalora Acevedo, Katherin Eliana; Baldo, Laura (Oxford University Press, 2023)

  The Mediterranean lizard Podarcis lilfordi is an emblematic species of the Balearic Islands. The extensive phenotypic diversity among extant isolated populations makes the species a great insular model system for ...
• Dynamics of gene expression profiling and identification of high-risk patients for severe COVID-19

  Rombauts, Alexander; Bódalo-Torruella, Marta; Abelenda-Alonso, Gabriela; Perera Bel, Júlia; Ferrer Salvador, Anna; Acedo-Terrades, Ariadna; Gabarrós-Subirà, Maria; Oriol, Isabel; Gudiol, Carlota; Nonell Mazelón, Lara; Carratalà, Jordi (MDPI, 2023)

  The clinical manifestations of SARS-CoV-2 infection vary widely, from asymptomatic infection to the development of acute respiratory distress syndrome (ARDS) and death. The host response elicited by SARS-CoV-2 plays a key ...
• Comparative genomics reveals the hybrid origin of a macaque group

  Zhang, Bao-Lin; Marquès i Bonet, Tomàs, 1975-; Wu, Dong-Dong (American Association for the Advancement of Science (AAAS), 2023)

  Although species can arise through hybridization, compelling evidence for hybrid speciation has been reported only rarely in animals. Here, we present phylogenomic analyses on genomes from 12 macaque species and show that ...
• A metabolic map of the DNA damage response identifies PRDX1 in the control of nuclear ROS scavenging and aspartate availability

  Moretton, Amandine; Kourtis, Savvas; Gañez-Zapater, Antoni; Calabrò, Chiara; Espinar Calvo, Maria Lorena; Fontaine, Frédéric; Darai, Evangelia; Abad Cortel, Etna; Block, Samuel; Pascual-Reguant, Laura, 1990-; Pardo-Lorente, Natalia; Ghose, Ritobrata; Vander Heiden, Matthew G.; Janic, Ana; Müller, André C.; Loizou, Joanna I.; Sdelci, Sara (EMBO Press, 2023)

  While cellular metabolism impacts the DNA damage response, a systematic understanding of the metabolic requirements that are crucial for DNA damage repair has yet to be achieved. Here, we investigate the metabolic enzymes ...
• Somatic mutations detected in Parkinson disease could affect genes with a role in synaptic and neuronal processes

  Lobon, Irene; Solís Moruno, Manuel, 1993-; Juan, David; Muhaisen, Ashraf; Abascal, Federico; Esteller Cucala, Paula; García Pérez, Raquel, 1989-; Martí, Maria Josep; Tolosa, Eduard; Ávila, Jesús; Rahbari, Raheleh; Marquès i Bonet, Tomàs, 1975-; Casals López, Ferran; Soriano, Eduardo (Frontiers, 2022)

  The role of somatic mutations in complex diseases, including neurodevelopmental and neurodegenerative disorders, is becoming increasingly clear. However, to date, no study has shown their relation to Parkinson disease's ...
• Identification of ALK gene alterations in urothelial carcinoma

  Bellmunt Molins, Joaquim, 1959-; Selvarajah, Shamini; Rodig, Scott; Salido Galeote, Marta; Muga, Silvia de; Costa, Irmgard; Bellosillo Paricio, Beatriz; Werner, Lillian; Mullane, Stephanie A.; Fay, André P.; O’Brien, Robert; Barretina, Jordi; Minoche, André E.; Signoretti, Sabina; Montagut Viladot, Clara; Himmelbauer, Heinz; Berman, David M.; Kantoff, Philip; Choueiri, Toni K.; Rosenberg, Jonathan E. (Public Library of Science (PLoS), 2014)

  Anaplastic lymphoma kinase (ALK) genomic alterations have emerged as a potent predictor of benefit from treatment with ALK inhibitors in several cancers. Currently, there is no information about ALK gene alterations in ...
• Tuneable endogenous mammalian target complementation via multiplexed plasmid-based recombineering

  Beltran-Sastre, Violeta; Benisty, Hannah, 1986-; Burnier, Julia; Berger, Imre; Serrano Pubull, Luis, 1982-; Kiel, Christina (Nature Research, 2015)

  Understanding the quantitative functional consequences of human disease mutations requires silencing of endogenous genes and expression of mutants at close to physiological levels. Changing protein levels above or below ...
• The conformation of yeast chromosome III is mating type dependent and controlled by the recombination enhancer

  Belton, Jon-Matthew; Lajoie, Bryan R.; Audibert, Sylvain; Cantaloube, Sylvain; Lassadi, Imen; Goiffon, Isabelle; Baù, Davide; Marti-Renom, Marc A.; Bystricky, Kerstin; Dekker, Job (Cell Press, 2015)

  Mating-type switching in yeast occurs through gene conversion between the MAT locus and one of two silent loci (HML or HMR) on opposite ends of the chromosome. MATa cells choose HML as template, whereas MATα cells use HMR. ...

View more