Recent Submissions

  • Design and characterization of in-one protease-esterase pluriZyme 

    Fernandez Lopez, Laura; Roda, Sergi; Gonzalez Alfonso, Jose L.; Plou, Francisco J.; Guallar, Victor; Ferrer, Manuel (MDPI, 2022)
    Article
    Open Access
    Proteases are abundant in prokaryotic genomes (~10 per genome), but their recovery encounters expression problems, as only 1% can be produced at high levels; this value differs from that of similarly abundant esterases ...
  • Epigenome-wide analysis of T-cell large granular lymphocytic leukemia identifies BCL11B as a potential biomarker 

    Johansson, Patricia; Laguna, Teresa; Ossowski, Julio; Pancaldi, Vera; Brauser, Martina (BioMed Central (BMC), 2022-11)
    Article
    Open Access
    Background The molecular pathogenesis of T-cell large granular lymphocytic leukemia (T-LGLL), a mature T-cell leukemia arising commonly from T-cell receptor αβ-positive CD8+ memory cytotoxic T cells, is only partly ...
  • Chromosome-level assemblies from diverse clades reveal limited structural and gene content variation in the genome of Candida glabrata 

    Marcet Houben, Marina; Alvarado, María; Ksiezopolska, Ewa; Saus, Ester; de Groot, Piet W. J.; Gabaldón, Toni (BioMed Central (BMC), 2022)
    Article
    Open Access
    Background Candida glabrata is an opportunistic yeast pathogen thought to have a large genetic and phenotypic diversity and a highly plastic genome. However, the lack of chromosome-level genome assemblies representing ...
  • Computational analysis of sense-antisense chimeric transcripts reveals their potential regulatory features and the landscape of expression in human cells 

    Mukherjee, Sumit; Detroja, Rajesh; Balamurali, Deepak; Matveishina, Elena; Medvedeva, Yulia A; Valencia, Alfonso; Gorohovski, Alessandro; Frenkel-Morgenstern, Milana (Oxford University Press, 2021-08)
    Article
    Open Access
    Many human genes are transcribed from both strands and produce sense-antisense gene pairs. Sense-antisense (SAS) chimeric transcripts are produced upon the coalescing of exons/introns from both sense and antisense transcripts ...
  • EP-Pred: A machine learning tool for bioprospecting promiscuous ester hydrolases 

    Xiang, Ruite; Fernandez Lopez, Laura; Robles Martín, Ana; Ferrer, Manuel; Guallar, Victor (MDPI, 2022)
    Article
    Open Access
    When bioprospecting for novel industrial enzymes, substrate promiscuity is a desirable property that increases the reusability of the enzyme. Among industrial enzymes, ester hydrolases have great relevance for which the ...
  • Pre-trained biomedical language models for clinical NLP in Spanish 

    Pio Carrino, Casimiro; Llop, Joan; Pàmies, Marc; Gutiérrez Fandiño, Asier; Armengol Estapé, Jordi; Silveira Ocampo, Joaquín; Valencia, Alfonso; Gonzalez Agirre, Aitor; Villegas, Marta (Association for Computational Linguistics, 2022-05)
    Conference lecture
    Open Access
    This work presents the first large-scale biomedical Spanish language models trained from scratch, using large biomedical corpora consisting of a total of 1.1B tokens and an EHR corpus of 95M tokens. We compared them against ...
  • Challenges and opportunities for mining adverse drug reactions: perspectives from pharma, regulatory agencies, healthcare providers and consumers 

    Gonzalez Hernandez, Graciela; Krallinger, Martin; Muñoz, Monica; Rodriguez Esteban, Raul; Uzuner, Özlem; Hirschman, Lynette (Oxford University Press, 2022-09)
    Article
    Open Access
    Monitoring drug safety is a central concern throughout the drug life cycle. Information about toxicity and adverse events is generated at every stage of this life cycle, and stakeholders have a strong interest in applying ...
  • Genetic regulation of RNA splicing in human pancreatic islets 

    Atla, Goutham; Bonàs Guarch, Silvia; Cuenca Ardura, Mirabai; Beucher, Anthony; Crouch, Daniel J. M.; Moran, Ignasi (BioMed Central (BMC), 2022)
    Article
    Open Access
    Background Non-coding genetic variants that influence gene transcription in pancreatic islets play a major role in the susceptibility to type 2 diabetes (T2D), and likely also contribute to type 1 diabetes (T1D) risk. For ...
  • Overview of the COVID-19 text mining tool interactive demonstration track in BioCreative VII 

    Chatr-aryamontri, Andrew; Hirschman, Lynette; Ross, Karen E; Oughtred, Rose; Krallinger, Martin; Dolinski, Kara; Tyers, Mike; Korves, Tonia; Arighi, Cecilia N (Oxford University Press, 2022)
    Article
    Open Access
    The coronavirus disease 2019 (COVID-19) pandemic has compelled biomedical researchers to communicate data in real time to establish more effective medical treatments and public health policies. Nontraditional sources such ...
  • Discovery and validation of clinically relevant long non-coding RNAs in colorectal cancer 

    Snyder, Madison; Iraola Guzmán, Susana; Saus, Ester; Gabaldón, Toni (MDPI, 2022-08)
    Article
    Open Access
    Colorectal cancer (CRC) is the third most prevalent cancer worldwide, with nearly two million newly diagnosed cases each year. The survival of patients with CRC greatly depends on the cancer stage at the time of diagnosis, ...
  • Structural elucidation and engineering of a bacterial carbohydrate oxidase 

    Boverio, Alessandro; Widodo, Wahyu S.; Santema, Lars L.; Rozeboom, Henriëtte J.; Xiang, Ruite; Guallar, Victor; Mattevi, Andrea; Fraaije, Marco W. (American Chemical Society, 2022-07)
    Article
    Open Access
    Flavin-dependent carbohydrate oxidases are valuable tools in biotechnological applications due to their high selectivity in the oxidation of carbohydrates. In this study, we report the biochemical and structural characterization ...
  • Citizen-science reveals changes in the oral microbiome in Spain through age and lifestyle factors 

    Willis, Jesse R.; Saus, Ester; Iraola Guzmán, Susana; Ksiezopolska, Ewa; Cozzuto, Luca; Gabaldón, Toni (Nature Research, 2022)
    Article
    Open Access
    The relevance of the human oral microbiome to our understanding of human health has grown in recent years as microbiome studies continue to develop. Given the links of the oral cavity with the digestive, respiratory and ...

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