• Fasting shapes chromatin architecture through an mTOR/RNA Pol I axis

  Al-Refaie, Nada; Padovani, Francesco; Hornung, Johanna; Pudelko, Lorenz; Binando, Francesca; Carmen Fabregat, Andrea del; Zhao, Qiuxia; Towbin, Benjamin D.; Sarinay Cenik, Elif; Stroustrup, Nicholas; Padeken, Jan; Schmoller, Kurt M.; Cabianca, Daphne S. (Nature Research, 2024)

  Chromatin architecture is a fundamental mediator of genome function. Fasting is a major environmental cue across the animal kingdom, yet how it impacts three-dimensional (3D) genome organization is unknown. Here we show ...
• The genetic architecture of protein stability

  Faure, Andre J.; Martí Aranda, Aina; Hidalgo-Carcedo, Cristina; Beltran, Antoni; Schmiedel, Jörn M.; Lehner, Ben, 1978- (Nature Research, 2024)

  There are more ways to synthesize a 100-amino acid (aa) protein (20100) than there are atoms in the universe. Only a very small fraction of such a vast sequence space can ever be experimentally or computationally surveyed. ...
• High-resolution kinetics and cellular determinants of SARS-CoV-2 antibody response over two years after COVID-19 vaccination

  Rubio, Rocío; Macià, Dídac; Barrios, Diana; Vidal, Marta; Jiménez, Alfons; Molinos-Albert, Luis M.; Díaz, Natalia; Canyelles, Mar; Lara Escandell, Maria; Planchais, Cyril; Santamaria, Pere; Carolis, Carlo; Izquierdo, Luis; Aguilar, Ruth; Moncunill, Gemma; Dobaño, Carlota (Elsevier, 2024)

  Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) studies usually rely on cross-sectional data of large cohorts but limited repeated samples, overlooking significant inter-individual antibody kinetic differences. ...
• Surface conversion of the dynamics of bacteria escaping chemorepellents

  Braham, Asma; Lemelle, Laurence; Ducasse, Romain; Toukabri, Houyem; Mottin, Eleonore; Fabrèges, Benoit; Calvez, Vincent; Place, Christophe (Springer, 2024)

  Flagellar swimming hydrodynamics confers a recognized advantage for attachment on solid surfaces. Whether this motility further enables the following environmental cues was experimentally explored. Motile E. coli (OD ~ ...
• Reactive oxygen species activate the Drosophila TNF receptor Wengen for damage-induced regeneration

  Esteban-Collado, José; Fernández Mañas, Mar; Fernández-Moreno, Manuel; Maeso, Ignacio; Corominas Guiu, Montserrat; Serras Rigalt, Florenci (EMBO Press, 2024)

  Tumor necrosis factor receptors (TNFRs) control pleiotropic pro-inflammatory functions that range from apoptosis to cell survival. The ability to trigger a particular function will depend on the upstream cues, association ...
• Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data

  Marot-Lassauzaie, Valérie; Beneyto Calabuig, Sergi; Obermayer, Benedikt; Velten, Lars; Beule, Dieter; Haghverdi, Laleh (Oxford University Press, 2024)

  Motivation: Single-cell RNA sequencing (scRNA-seq) data are widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it ...
• The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming

  Barrero Asencio, Mercedes; Lazarenkov, Aleksey; Blanco, Enrique; Palma, Luis G.; López Rubio, Anna V.; Bauer, Moritz, 1987-; Bigas Salvans, Anna; Di Croce, Luciano; Sardina, Jose Luis; Payer, Bernhard (American Association for the Advancement of Science (AAAS), 2024)

  Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) requires activation of the pluripotency network and resetting of the epigenome by erasing the epigenetic memory of the somatic state. In female mouse ...
• The relationship between nanoscale genome organization and gene expression in mouse embryonic stem cells during pluripotency transition

  Garate,, Ximena; Gómez García, Pablo Aurelio; Fernández Merino, Manuel; Cadevall Anglès, Marta; Zhu, Chenggan; Castells García, Àlvaro, 1991-; Ed-Daoui, Ilyas; Martin, Laura; Ochiai, Hiroshi; Neguembor, Maria Victoria; Cosma, Maria Pia (Oxford University Press, 2024)

  During early development, gene expression is tightly regulated. However, how genome organization controls gene expression during the transition from naïve embryonic stem cells to epiblast stem cells is still poorly understood. ...
• A deep learning method that identifies cellular heterogeneity using nanoscale nuclear features

  Carnevali, Davide; Zhong, Limei; González-Almela, Esther; Viana, Carlotta; Rotkevich, Mikhail; Wang, Aiping; Franco-Barranco, Daniel; González-Marfil, Aitor; Neguembor, Maria Victoria; Castells García, Àlvaro, 1991-; Arganda-Carreras, Ignacio; Cosma, Maria Pia (Springer, 2024)

  Cellular phenotypic heterogeneity is an important hallmark of many biological processes and understanding its origins remains a substantial challenge. This heterogeneity often reflects variations in the chromatin structure, ...
• Genome-scale quantification and prediction of pathogenic stop codon readthrough by small molecules

  Toledano, Ignasi; Supek, Fran; Lehner, Ben (Nature Research, 2024)

  Premature termination codons (PTCs) cause ~10-20% of inherited diseases and are a major mechanism of tumor suppressor gene inactivation in cancer. A general strategy to alleviate the effects of PTCs would be to promote ...
• In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications

  Anglada-Girotto, Miquel; Ciampi, Ludovica; Bonnal, Sophie; Head, Sarah A.; Miravet Verde, Samuel, 1992-; Serrano Pubull, Luis, 1982- (Nature Research, 2024)

  Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically ...
• Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants

  Story, Benjamin A.; Velten, Lars; Mönke, Gregor; Annan, Ahrmad; Steinmetz, Lars M. (Oxford University Press, 2024)

  Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly ...
• Alzheimer's disease genetic pathways impact cerebrospinal fluid biomarkers and imaging endophenotypes in non-demented individuals

  Lorenzini, Luigi; Vilor Tejedor, Natàlia, 1988-; Gispert López, Juan Domingo; Barkhof, Frederik (Wiley, 2024)

  Introduction: Unraveling how Alzheimer's disease (AD) genetic risk is related to neuropathological heterogeneity, and whether this occurs through specific biological pathways, is a key step toward precision medicine. ...
• Gut microbiota signatures of vulnerability to food addiction in mice and humans

  Samulenaite, Solveiga; García Blanco, Alejandra; Mayneris Perxachs, Jordi; Domingo Rodriguez, Laura, 1992-; Cabana-Domínguez, Judit; Fernàndez-Castillo, Noèlia; Gago-García, Edurne; Pineda-Cirera, Laura; Burokas, Aurelijus, 1982-; Espinosa-Carrasco, José; Arboleya, Silvia; Latorre, Jessica; Stanton, Catherine; Hosomi, Koji; Kunisawa, Jun; Cormand, Bru; Fernández Real, Jose M.; Maldonado, Rafael, 1961-; Martín García, Elena, 1975- (BMJ Publishing Group, 2024)

  Objective: Food addiction is a multifactorial disorder characterised by a loss of control over food intake that may promote obesity and alter gut microbiota composition. We have investigated the potential involvement of ...
• NFAT5 counters long-term IFN-1 responses in hematopoietic stem cells to preserve reconstitution potential

  Traveset Martínez, Laia; Cerdán Porqueras, Víctor; Huerga Encabo, Hector, 1989-; Avalle, Silvia; Esteve-Codina, Anna; Fornas Carreño, Oscar; Aramburu, José (Aramburu Beltrán); López Rodríguez, M. Cristina (American Society of Hematology, 2024)

  Hematopoietic stem cells (HSCs) readily recover from acute stress, but persistent stress can reduce their viability and long-term potential. Here, we show that the nuclear factor of activated T cells 5 (NFAT5), a transcription ...
• Whole genomes from the extinct Xerces Blue butterfly can help identify declining insect species

  Dios Martínez, Toni de; Fontseré Alemany, Clàudia, 1992-; Renom, Pere; Stiller, Josefin; Llovera Nadal, Laia; Uliano-Silva, Marcela; Sánchez-Gracia, Alejandro; Wright, Charlotte; Lizano González, Esther, 1974-; Caballero, Berta; Navarro i Cuartiellas, Arcadi, 1969-; Civit, Sergi; Robbins, Robert K.; Blaxter, Mark; Marquès i Bonet, Tomàs, 1975-; Vila, Roger; Lalueza Fox, Carles, 1965- (eLife, 2024)

  The Xerces Blue (Glaucopsyche xerces) is considered to be the first butterfly to become extinct in historical times. It was notable for its chalky lavender wings with conspicuous white spots on the ventral wings. The last ...
• Genomic adaptation to small population size and saltwater consumption in the critically endangered Cat Ba langur

  Zhang, Liye; Marquès i Bonet, Tomàs, 1975-; Roos, Christian (Nature Research, 2024)

  Many mammal species have declining populations, but the consequences of small population size on the genomic makeup of species remain largely unknown. We investigated the evolutionary history, genetic load and adaptive ...
• Intravital imaging of hair-cell development and regeneration in the zebrafish

  Pinto-Teixeira, Filipo; Muzzopappa, Mariana; Swoger, Jim; Mineo, Alessandro; Sharpe, James; López-Schier, Hernán (Frontiers, 2013)

  Direct videomicroscopic visualization of organ formation and regeneration in toto is a powerful strategy to study cellular processes that often cannot be replicated in vitro. Intravital imaging aims at quantifying changes ...
• The genomic aftermath of hybridization in the opportunistic pathogen candida metapsilosis

  Pryszcz, Leszek Piotr, 1985-; Németh, Tibor; Saus Martínez, Ester; Ksiezopolska, Ewa; Hegedűsová, Eva; Nosek, Jozef; Wolfe, Kenneth H.; Gacser, Attila; Gabaldín Estevan, Juan Antonio, 1973- (Public Library of Science (PLoS), 2015)

  Candida metapsilosis is a rarely-isolated, opportunistic pathogen that belongs to a clade of pathogenic yeasts known as the C. parapsilosis sensu lato species complex. To gain insight into the recent evolution of C. ...
• Inter-laboratory evaluation of instrument platforms and experimental workflows for quantitative accuracy and reproducibility assessment

  Percy, Andrew J.; Espadas, Guadalupe; Sabidó Aguadé, Eduard, 1981-; Borchers, Christoph H. (Elsevier, 2015)

  The reproducibility of plasma protein quantitation between laboratories and between instrument types was examined in a large-scale international study involving 16 laboratories and 19 LC–MS/MS platforms, using two kits ...

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