• Exploring the therapeutic potential of defective interfering particles in reducing the replication of SARS-CoV-2

  Locke, Macauley; Grebennikov, Dmitry; Sazonov, Igor; López García, Martín; Loguinova, Marina; Meyerhans, Andreas; Bocharov, Gennady A.; Molina-París, Carmen (MDPI, 2024)

  SARS-CoV-2 still presents a global threat to human health due to the continued emergence of new strains and waning immunity among vaccinated populations. Therefore, it is still relevant to investigate potential therapeutics, ...
• The human VGLUT3-pT8I mutation elicits uneven striatal DA signaling, food or drug maladaptive consumption in male mice

  Favier, Mathieu; Martín García, Elena, 1975-; Maldonado, Rafael, 1961-; El Mestikawy, Salah (Nature Research, 2024)

  Cholinergic striatal interneurons (ChIs) express the vesicular glutamate transporter 3 (VGLUT3) which allows them to regulate the striatal network with glutamate and acetylcholine (ACh). In addition, VGLUT3-dependent ...
• CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing

  Carbonell Sala, Silvia; Perteghella, Tamara; Lagarde, Julien; Nishiyori, Hiromi; Palumbo, Emilio; Arnan Ros, Carme; Takahashi, Hazuki; Carninci, Piero; Uszczynska-Ratajczak, Barbara; Guigó Serra, Roderic (Nature Research, 2024)

  Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts ...
• The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

  Corominas Guiu, Montserrat; Guigó Serra, Roderic (Oxford University Press, 2024)

  The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories ...
• PyAMPA: a high-throughput prediction and optimization tool for antimicrobial peptides

  Ramos Llorens, Marc; Bello Madruga, Roberto; Valle, Javier; Andreu Martínez, David; Torrent Burgas, Marc (American Society for Microbiology, 2024)

  The alarming rise of antibiotic-resistant bacterial infections is driving efforts to develop alternatives to conventional antibiotics. In this context, antimicrobial peptides (AMPs) have emerged as promising candidates for ...
• PromptSMILES: prompting for scaffold decoration and fragment linking in chemical language models

  Thomas, Morgan; Ahmad, Mazen; Tresadern, Gary; De Fabritiis, Gianni (BioMed Central, 2024)

  SMILES-based generative models are amongst the most robust and successful recent methods used to augment drug design. They are typically used for complete de novo generation, however, scaffold decoration and fragment linking ...
• Premature death, suicide, and nonlethal intentional self-harm after psychiatric discharge

  Mortier, Philippe; Conde, Susana; Alayo, Itxaso; Amigo, Franco; Ballester, Laura; Cirici, Roser; Guinart, Dani; Ferrer Forés, Maria Montserrat; Leis Machín, Angela 1974-; Mayer, Miguel Ángel, 1960-; Portillo-Van Diest, Ana; Puértolas Gracia, Beatriz; Ramírez Anguita, Juan Manuel; Sanz, Ferran; Pérez Solá, Victor; Vilagut Saiz, Gemma, 1975-; Alonso Caballero, Jordi (American Medical Association, 2024)

  Importance: There is a need for representative research on serious adverse outcomes following discharge from psychiatric hospitalization. Objective: To compare rates of premature death, suicide, and nonlethal intentional ...
• Psychometric examination of the Multidimensional Psychological Flexibility Inventory Short Form (MPFI-24) and the Psy-Flex Spanish versions in individuals with chronic pain

  Navarrete, Jaime; Rodríguez Freire, Carla; Sanabria-Mazo, Juan P.; Martínez Rubio, David; McCracken, Lance M.; Gallego Alonso, Ana; Sundstrom, Felicia T. A.; Serrat, Mayte; Alonso Caballero, Jordi; Feliu-Soler, Albert; Nieto, Rubén; Luciano, Juan V. (Wiley, 2024)

  Background: Acceptance and Commitment Therapy (ACT) has been found to be beneficial for individuals dealing with chronic pain. The theoretical mechanisms of change proposed by ACT are based on the Hexaflex model. To ...
• Implications of noncoding regulatory functions in the development of insulinomas

  Ramos-Rodríguez, Mireia; Subirana-Granés, Marc; Norris, Richard; Fernández Ruiz, Ángel; Fuentes Páez, Georgina; Pérez-González, Beatriz; Berenguer Balaguer, Clara; Raurell Vila, Helena; López Bigas, Núria; González-Pérez, Abel; Pasquali, Lorenzo (Elsevier, 2024)

  Insulinomas are rare neuroendocrine tumors arising from pancreatic β cells, characterized by aberrant proliferation and altered insulin secretion, leading to glucose homeostasis failure. With the aim of uncovering the role ...
• Sex differences in the effects of N-ethylpentylone in young CD1 mice: Insights on behaviour, thermoregulation and early gene expression

  Espinosa Velasco, María; Castro Zavala, Adriana, 1988-; Reguilón, Marina D.; Gallego-Landin, Ines; Bellot, Marina; Rublinetska, Olga; Valverde Granados, Olga; Rodríguez-Arias, Marta; Nadal Gratacós, Núria; Berzosa, Xavier; Gómez Canela, Cristian; Lí Carbó, Marcel; Camarasa, Jorge; Escubedo, Elena; López Arnau, Raúl; Pubill, David (Wiley, 2024)

  Background and purpose: New psychoactive substances such as N-ethylpentylone (NEP) are continuously emerging in the illicit drug market, and knowledge of their effects and risks, which may vary between sexes, is scarce. ...
• Genopyc: a Python library for investigating the functional effects of genomic variants associated to complex diseases

  Gualdi, Francesco; Oliva Miguel, Baldomero; Piñero González, Janet, 1977- (Oxford University Press, 2024)

  Motivation: Integrative Biomedicl Informatics, Research Program on Biomedical Informatics (IBI - GRIB), Hospital Del Mar Medical Research Institute (IMIM), Department of Experimental and Health Sciences, Universitat Pompeu ...
• Biological computation through recurrence

  Vidal-Saez, María Sol; Vilarroya, Óscar; García Ojalvo, Jordi (Elsevier, 2024)

  One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to ...
• A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction

  Bansal, Prakhar; Banda, Erin C.; Glatt-Deeley, Heather R.; Stoddard, Christopher E.; Linsley, Jeremy W.; Arora, Neha; Deleschaux, Cécile; Ahern, Darcy T.; Kondaveeti, Yuvabharath; Massey, Rachael E.; Nicouleau, Michael; Wang, Shijie; Sabariego Navarro, Miguel; Dierssen, Mara; Finkbeiner, Steven; Pinter, Stefan F. (American Association for the Advancement of Science (AAAS), 2024)

  Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. ...
• An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

  Faure, Andre J.; Lehner, Ben, 1978-; Miró Pina, Verónica; Serrano Colomé, Clàudia; Weghorn, Donate (Public Library of Science (PLoS), 2024)

  Accurate models describing the relationship between genotype and phenotype are necessary in order to understand and predict how mutations to biological sequences affect the fitness and evolution of living organisms. The ...
• Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

  Wernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Mattsson Langseth, Christoffer; Verron, Quentin; Nguyen, Huy Q.; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Martí Renom, Marc A.; Wu, Chao-Ting; Crosetto, Nicola; Bienko, Magda (Nature Research, 2024)

  Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of ...
• The hepatocyte epidermal growth factor receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche

  Gonzalez-Sanchez, Ester; Vaquero, Javier; Caballero Díaz, Daniel; Grzelak, Jan; Fusté, Noel P.; Bertran, Esther; Amengual, Josep; García Sáez, Juan; Martín-Mur, Beatriz; Gut, Marta; Esteve-Codina, Anna; Alay, Ania; Coulouarn, Cedric; Calero Pérez, Silvia; Valdecantos, Pilar; Valverde, Angela M.; Sánchez, Aránzazu; Herrera, Blanca; Fabregat, Isabel (Wiley, 2024)

  Liver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that ...
• PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation

  Aguirre, Samuel; Pappa, Stella; Serna Pujol, Núria; Padilla, Natàlia; Iacobucci, Simona; Nacht, A. Silvina; Vicent, Guillermo Pablo; Jordan Vallès, Albert; Cruz, Xavier de la; Martínez Balbás, Marian A. (EMBO Press, 2024)

  Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me ...
• The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

  Nakagawa, Shoma; Carnevali, Davide; Tan, Xiangtian; Alvarez, Mariano J.; Parfitt, David-Emlyn; Di Vicino, Umberto; Arumugam, Karthik; Shin, William; Aranda, Sergi; Normanno, Davide; Sebastián Pérez, Rubén; Cannatá, Chiara; Cortes, Paola; Neguembor, Maria Victoria; Shen, Michael M.; Califano, Andrea; Cosma, Maria Pia (Elsevier, 2024)

  Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse ...
• TANGO1 inhibitors reduce collagen secretion and limit tissue scarring

  Raote, Ishier; Häkkinen, Hanna-Maria; Vibe, Carine; Broadbent, Katrina; Carolis, Carlo; Ruprecht, Verena; Malhotra, Vivek (Nature Research, 2024)

  Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring and fibrosis and compromise tissue function. Despite the widespread occurrence of fibrotic diseases and scarring, effective therapies ...
• Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization

  Kant, Aayush; Guo, Zixian; Vinayak, Vinayak; Neguembor, Maria Victoria; Li, Wing Shun; Agrawal, Vasundhara; Pujadas, Emily; Almassalha, Luay; Backman, Vadim; Lakadamyali, Melike; Cosma, Maria Pia; Shenoy, Vivek B. (Nature Research, 2024)

  In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this ...

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