• Inborn errors of OAS-RNase L in SARS-CoV-2-related multisystem inflammatory syndrome in children

  Lee, Danyel; COVID Human Genetic Effort; Zhang, Shen-Ying (American Association for the Advancement of Science (AAAS), 2023)

  Multisystem inflammatory syndrome in children (MIS-C) is a rare and severe condition that follows benign COVID-19. We report autosomal recessive deficiencies of OAS1, OAS2, or RNASEL in five unrelated children with MIS-C. ...
• A chromosome‐level genome assembly enables the identification of the follicule stimulating hormone receptor as the master sex‐determining gene in the flatfish Solea senegalensis

  de la Herrán, Roberto; Gómez-Garrido, Jèssica; Cruz, Fernando; Alioto, Tyler S; Martínez, Paulino (Wiley, 2023)

  Sex determination (SD) shows huge variation among fish and a high evolutionary rate, as illustrated by the Pleuronectiformes (flatfishes). This order is characterized by its adaptation to demersal life, compact genomes and ...
• Liquidhope: methylome and genomic profiling from very limited quantities of plasma-derived DNA

  Trinidad, Eva María; Vidal, Enrique; Coronado, Esther; Esteve-Codina, Anna; Castel, Victoria; Cañete, Adela; Gut, Marta; Heath, Simon; Font de Mora, Jaime (Oxford University Press, 2023)

  Analysis of the methylome of tumor cell-free deoxyribonucleic acid (DNA; cfDNA) has emerged as a powerful non-invasive technique for cancer subtyping and prognosis. However, its application is frequently hampered by the ...
• Effects of microtubule length and crowding on active microtubule network organization

  Chew, Wei-Xiang; Henkin, Gil; Nédélec, François; Surrey, Thomas (Elsevier, 2023)

  Active filament networks can organize into various dynamic architectures driven by cross-linking motors. Densities and kinetic properties of motors and microtubules have been shown previously to determine active microtubule ...
• RBD-Based ELISA and luminex predict Anti-SARS-CoV-2 surrogate-neutralizing activity in two longitudinal cohorts of German and Spanish health care workers

  Aguilar, Ruth; Vidal, Marta; Rubio, Rocío; Jiménez, Alfons; Carolis, Carlo; Mayor, Alfredo; Izquierdo, Luis; Garcia Basteiro, Alberto L.; Moncunill, Gemma; Dobaño, Carlota; Gerhard, Markus (American Society for Microbiology, 2023)

  The ability of antibodies to neutralize severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) is an important correlate of protection. For routine evaluation of protection, however, a simple and cost-efficient ...
• A community-based participatory framework to co-develop Patient Education Materials (PEMs) for rare diseases: A model transferable across diseases

  Falcão, Marta; Allocca, Mariateresa; Rodrigues, Ana Sofia; Granjo, Pedro; Francisco, Rita; Pascoal, Carlota; Rossi, Maria Grazia; Marques-da-Silva, Dorinda; Magrinho, Salvador C. M.; Jaeken, Jaak; Castro, Larisa Aragon; Freitas, Cláudia de; Videira, Paula A.; Andrés-Aguayo, Luísa de; Ferreira, Vanessa Miriam dos Reis (MDPI, 2023)

  At least 50% of chronic disease patients don't follow their care plans, leading to lower health outcomes and higher medical costs. Providing Patient Education Materials (PEMs) to individuals living with a disease can help ...
• The power of geohistorical boundaries for modeling the genetic background of human populations: The case of the rural catalan Pyrenees

  Fibla, Joan; Maceda Porto, Iago, 1986-; Laplana, Marina; Guerrero, Montserrat; Martín Álvarez, Miguel; Burgueño, Jesús; Camps, Agustí; Fàbrega, Jordi; Felisart, Josefina; Grané, Joan; Remón, José Luis; Serra, Jordi; Moral, Pedro; Lao Grueso, Oscar, 1976- (Frontiers, 2023)

  The genetic variation of the European population at a macro-geographic scale follows genetic gradients which reflect main migration events. However, less is known about factors affecting mating patterns at a micro-geographic ...
• Remote visualization of large-scale genomic alignments for collaborative clinical research and diagnosis of rare diseases

  Corvò, Alberto; Matalonga, Leslie; Laurie, Steven, 1973-; Picó-Amador, Daniel; Fernández Callejo, Marcos; Paramonov, Ida; Gut, Ivo Glynne; Piscia, Davide; Beltran, Sergi (Elsevier, 2023)

  The Solve-RD project objectives include solving undiagnosed rare diseases (RD) through collaborative research on shared genome-phenome datasets. The RD-Connect Genome-Phenome Analysis Platform (GPAP), for data collation ...
• Divergent sensory and immune gene evolution in sea turtles with contrasting demographic and life histories

  Bentley, Blair P.; Pawar, Harvinder; Kuhlwilm, Martin; Marquès i Bonet, Tomàs, 1975-; Komoroske, Lisa M. (National Academy of Sciences, 2023)

  Sea turtles represent an ancient lineage of marine vertebrates that evolved from terrestrial ancestors over 100 Mya. The genomic basis of the unique physiological and ecological traits enabling these species to thrive in ...
• Day-night and seasonal variation of human gene expression across tissues

  Wucher, Valentin; Sodaei, Reza, 1988-; Amador, Raziel; Irimia, Manuel; Guigó Serra, Roderic (Public Library of Science (PLoS), 2023)

  Circadian and circannual cycles trigger physiological changes whose reflection on human transcriptomes remains largely uncharted. We used the time and season of death of 932 individuals from GTEx to jointly investigate ...
• Global analysis of the association between pig muscle fatty acid composition and gene expression using RNA-Seq

  Valdés-Hernández, Jesús; Ramayo-Caldas, Yuliaxis; Passols, Magí; Sebastià, Cristina; Criado-Mesas, Lourdes; Crespo-Piazuelo, Daniel; Esteve-Codina, Anna; Castelló, Anna; Sánchez, Armand; Folch, Josep M. (Nature Research, 2023)

  Fatty acids (FAs) play an essential role as mediators of cell signaling and signal transduction, affecting metabolic homeostasis and determining meat quality in pigs. However, FAs are transformed by the action of several ...
• High ambient temperature impacts on flowering time in Brassica napus through both H2A.Z-dependent and independent mechanisms

  Abelenda, José A.; Trabanco, Noemí; Olmo, Iván del; Pozas, Jenifer; Martín-Trillo, María del Mar; Gómez Garrido, Jèssica; Esteve-Codina, Anna; Pernas, Mónica; Jarillo, José A.; Piñeiro, Manuel (Wiley, 2022)

  Knowledge concerning the integration of genetic pathways mediating the responses to environmental cues controlling flowering initiation in crops is scarce. Here, we reveal the diversity in oilseed rape (OSR) flowering ...
• SEGCOND predicts putative transcriptional condensate-associated genomic regions by integrating multi-omics data

  Klonizakis, Antonios; Nikolaou, Christoforos; Graf, T. (Thomas) (Oxford University Press, 2023)

  Motivation: The compartmentalization of biochemical reactions, involved in the activation of gene expression in the eukaryotic nucleus, leads to the formation of membraneless bodies through liquid-liquid phase separation. ...
• A computational pipeline to learn gene expression predictive models from epigenetic information at enhancers or promoters

  González Ramírez, Mar, 1991-; Blanco, Enrique; Di Croce, Luciano (Elsevier, 2023)

  Here, we present a computational pipeline to obtain quantitative models that characterize the relationship of gene expression with the epigenetic marking at enhancers or promoters in mouse embryonic stem cells. Our protocol ...
• SURE editing: combining oligo-recombineering and programmable insertion/deletion of selection markers to efficiently edit the Mycoplasma pneumoniae genome

  Piñero-Lambea, Carlos; Garcia Ramallo, Eva; Miravet Verde, Samuel; Burgos, Raul; Scarpa, Margherita; Serrano Pubull, Luis, 1982-; Lluch-Senar, Maria 1982- (Oxford University Press, 2022)

  The development of advanced genetic tools is boosting microbial engineering which can potentially tackle wide-ranging challenges currently faced by our society. Here we present SURE editing, a multi-recombinase engineering ...
• Discovery of drug-omics associations in type 2 diabetes with generative deep-learning models

  Allesøe, Rosa Lundbye; IMI DIRECT Consortium (Nature Research, 2023)

  The application of multiple omics technologies in biomedical cohorts has the potential to reveal patient-level disease characteristics and individualized response to treatment. However, the scale and heterogeneous nature ...
• Karyon: a computational framework for the diagnosis of hybrids, aneuploids, and other nonstandard architectures in genome assemblies

  Naranjo Ortiz, Miguel Ángel, 1989-; Molina, Manuel; Fuentes Palacios, Diego; Mixão, Verónica; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2022)

  Background: Recent technological developments have made genome sequencing and assembly highly accessible and widely used. However, the presence in sequenced organisms of certain genomic features such as high heterozygosity, ...
• Genomic adaptations to an endoparasitic lifestyle in the morphologically atypical crustacean sacculina carcini (Cirripedia: Rhizocephala)

  Martin, Sebastian; Lesny, Peter; Glenner, Henrik; Hecht, Jochen; Vilcinskas, Andreas; Bartolomaeus, Thomas; Podsiadlowski, Lars (Oxford University Press, 2022)

  The endoparasitic crustacean Sacculina carcini (Cirripedia: Rhizocephala) has a much simpler morphology than conventional filter-feeding barnacles, reflecting its parasitic lifestyle. To investigate the molecular basis of ...
• Proteomic profiling reveals mitochondrial dysfunction in the cerebellum of transgenic mice overexpressing DYRK1A, a Down syndrome candidate gene

  Ortega, Mireia; De Toma, Ilario; Fernández-Blanco, Álvaro; Calderón Moruno, Anna; Barahona, Lucía; Trullàs, Ramón; Sabidó Aguadé, Eduard, 1981-; Dierssen, Mara (Frontiers, 2022)

  Introduction: DYRK1A is a dual-specificity kinase that is overexpressed in Down syndrome (DS) and plays a key role in neurogenesis, neuronal differentiation and function, cognitive phenotypes, and aging. Dyrk1A has also ...
• Wnt genes in colonic polyposis predisposition

  Quintana, Isabel; Tonda, Raúl; Parra Farré, Genís; Piscia, Davide; Beltran, Sergi; Valle, Laura (Elsevier, 2022)

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