Welcome to the UPF Digital Repository

Articles (Departament de Ciències Experimentals i de la Salut)

Articles (Departament de Ciències Experimentals i de la Salut)

 

Articles de recerca, en accés obert, del Departament de Ciències Experimentals i de la Salut de la UPF.

Recent Submissions

  • Blanco, Enrique; Di Croce, Luciano; Aranda Aragón, Sergio (Oxford University Press, 2021)
    In order to evaluate cell- and disease-specific changes in the interacting strength of chromatin targets, ChIP-seq signal across multiple conditions must undergo robust normalization. However, this is not possible using ...
  • Sánchez-Barreiro, Fátima; Gopalakrishnan, Shyam; Ramos-Madrigal, Jazmín; Westbury, Michael V.; Manuel Montero, Marc de, 1991-; Margaryan, Ashot; Ciucani, Marta M.; Vieira, Filipe Garrett; Patramanis, Yannis; Kalthoff, Daniela C.; Timmons, Zena; Sicheritz-Ponten, Thomas; Dalén, Love; Ryder, Oliver A.; Zhang, Guojie; Marquès i Bonet, Tomàs, 1975-; Moodley, Yoshan; Gilbert, M Thomas (Wiley, 2021)
    Large vertebrates are extremely sensitive to anthropogenic pressure, and their populations are declining fast. The white rhinoceros (Ceratotherium simum) is a paradigmatic case: this African megaherbivore has suffered a ...
  • Farré, Xavier; Molina, Ruben; Barteri, Fabio; Timmers, Paul R.H.J.; Joshi, Peter K.; Oliva Miguel, Baldomero; Acosta, Sandra; Esteve Altava, Borja; Navarro i Cuartiellas, Arcadi, 1969-; Muntané, Gerard (Oxford University Press, 2021)
    The enormous mammal's lifespan variation is the result of each species' adaptations to their own biological trade-offs and ecological conditions. Comparative genomics have demonstrated that genomic factors underlying both, ...
  • Grau Bové, Xavier; Sebé-Pedrós, Arnau (Oxford University Press, 2021)
    Possvm (Phylogenetic Ortholog Sorting with Species oVerlap and MCL [Markov clustering algorithm]) is a tool that automates the process of identifying clusters of orthologous genes from precomputed phylogenetic trees and ...
  • Ramsheh, Mohammadali Yavari; Esteve-Codina, Anna; Heath, Simon; Gut, Ivo Glynne; Brightling, Christopher E. (Elsevier, 2021)
    Background: Chronic obstructive pulmonary disease (COPD) is associated with airway inflammation and bacterial dysbiosis. The relationship between the airway microbiome and bronchial gene expression in COPD is poorly ...
  • Vandelli, Andrea; Cid Samper, Fernando, 1991-; Torrent Burgas, Marc; Sánchez de Groot, Natalia; Tartaglia, Gian Gaetano (Elsevier, 2021)
    Condensation, or liquid-like phase separation, is a phenomenon indispensable for the spatiotemporal regulation of molecules within the cell. Recent studies indicate that the composition and molecular organization of ...
  • Illouz, Tomer; Biragyn, Arya; Iulita, Maria Florencia; Flores-Aguilar, Lisi; Dierssen, Mara; De Toma, Ilario; Antonarakis, Stylianos E.; Yu, Eugene; Herault, Yann; Potier, Marie-Claude; Botté, Alexandra; Roper, Randall; Sredni, Benjamin; London, Jacqueline; Mobley, William; Strydom, Andre; Okun, Eitan (Frontiers, 2021)
    The risk of severe outcomes following respiratory tract infections is significantly increased in individuals over 60 years, especially in those with chronic medical conditions, i.e., hypertension, diabetes, cardiovascular ...
  • Lara-Chica, Maribel; Correa-Sáez, Alejandro; Jiménez-Izquierdo, Rafael; Garrido-Rodríguez, Martín; Ponce, Francisco J.; Moreno, Rita; Morrison, Kimberley; Di Vona, Chiara, 1981-; Arató, Krisztina, 1981-; Jiménez-Jiménez, Carla; Morrugares, Rosario; Schmitz, M. Lienhard; Luna, Susana de la; Vega, Laureano de la; Calzado, Marco A. (Nature Research, 2021)
    The cell division cycle 25A (CDC25A) phosphatase is a key regulator of cell cycle progression that acts on the phosphorylation status of Cyclin-Cyclin-dependent kinase complexes, with an emergent role in the DNA damage ...
  • Gallego-Paüls, Marta; Hernández-Ferrer, Carles; Bustamante Pineda, Mariona; Basagaña Flores, Xavier; Barrera Gómez, Jose; Vives Usano, Marta, 1990-; Ruiz Arenas, Carlos, 1990-; Casas Sanahuja, Maribel; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Estivill, Xavier, 1955-; Urquiza, José M.; González, Juan Ramón; Vrijheid, Martine; Maitre, Léa (BioMed Central, 2021)
    Background: Multiple omics technologies are increasingly applied to detect early, subtle molecular responses to environmental stressors for future disease risk prevention. However, there is an urgent need for further ...
  • Herman, Emily K.; Najle, Sebastián R.; Dacks, Joel B. (BioMed Central, 2021)
    Background: The opportunistic pathogen Naegleria fowleri establishes infection in the human brain, killing almost invariably within 2 weeks. The amoeba performs piece-meal ingestion, or trogocytosis, of brain material ...
  • Pryszcz, Leszek Piotr, 1985-; Novoa, Eva Maria (Oxford University Press, 2021)
    Motivation: DNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. ...
  • Milà Alomà, Marta; Shekari, Mahnaz; Salvadó, Gemma; Gispert López, Juan Domingo; Arenaza Urquijo, Eider M.; Operto, Grégory; Falcón, Carles; Vilor Tejedor, Natàlia, 1988-; Grau-Rivera, Oriol; Sala Vila, Aleix; Sánchez Benavides, Gonzalo; González de Echávarri, José Maria; Minguillón, Carolina; Suárez-Calvet, Marc; Molinuevo, José Luis; ALFA study (BioMed Central, 2021)
    Background: Understanding the changes that occur in the transitional stage between absent and overt amyloid-β (Aβ) pathology within the Alzheimer's continuum is crucial to develop therapeutic and preventive strategies. The ...
  • Bover, Jordi; Molina, Pablo; Ureña-Torres, Pablo; Arenas Jiménez, María Dolores (Elsevier, 2020)
  • Vara, Covadonga; Paytuví Gallart, Andreu; Cuartero, Yasmina; Álvarez-González, Lucía; Marín-Gual, Laia; Garcia, Francisca; Florit-Sabater, Beatriu; Capilla, Laia; Sanchéz-Guillén, Rosa Ana; Sarrate, Zaida; Cigliano, Riccardo Aiese; Sanseverino, Walter; Searle, Jeremy B.; Ventura, Jacint; Martí Renom, Marc A.; Le Dily, François; Ruiz Herrera, Aurora (Nature Research, 2021)
    The spatial folding of chromosomes inside the nucleus has regulatory effects on gene expression, yet the impact of genome reshuffling on this organization remains unclear. Here, we take advantage of chromosome conformation ...
  • Buitrago, Diana; Labrador, Mireia; Arcon, Juan Pablo; Lema, Rafael; Flores, Oscar; Esteve-Codina, Anna; Blanc, Julie; Villegas, Núria; Bellido, David; Gut, Marta; Dans, Pablo D.; Heath, Simon; Gut, Ivo Glynne; Brun-Heath, Isabelle; Orozco, Modesto (Nature Research, 2021)
    Determining the effect of DNA methylation on chromatin structure and function in higher organisms is challenging due to the extreme complexity of epigenetic regulation. We studied a simpler model system, budding yeast, ...
  • Willis, Jesse R.; Saus Martínez, Ester; Iraola Guzman, Susana; Cabello-Yeves, Elena; Ksiezopolska, Ewa; Cozzuto, Luca; Bejarano, Luis A.; Andreu Somavilla, Núria; Alloza-Trabado, Miriam; Blanco, Andrea; Puig-Sola, Anna; Broglio, Elisabetta; Carolis, Carlo; Ponomarenko, Julia; Hecht, Jochen; Gabaldón Estevan, Juan Antonio, 1973- (Taylor & Francis, 2021)
    Introduction: Cystic fibrosis (CF) is an autosomal genetic disease, associated with the production of excessively thick mucosa and with life-threatening chronic lung infections. The microbiota of the oral cavity can act ...
  • Bisceglie, Lavinia; Hopp, Ann-Katrin; Gunasekera, Kapila; Wright, Roni H.G.; Le Dily, François; Vidal, Enrique; Dall'Agnese, Alessandra; Caputo, Luca; Nicoletti, Chiara; Puri, Pier Lorenzo; Beato, Miguel; Hottiger, Michael O. (Elsevier, 2021)
    While protein ADP-ribosylation was reported to regulate differentiation and dedifferentiation, it has so far not been studied during transdifferentiation. Here, we found that MyoD-induced transdifferentiation of fibroblasts ...
  • Ramirez, Juanma; Prieto, Gorka; Olazabal-Herrero, Anne; Borràs, Eva; Fernandez-Vigo, Elvira; Alduntzin, Unai; Osinalde, Nerea; Beaskoetxea, Javier; Lectez, Benoit; Aloria, Kerman; Rodríguez, José Antonio; Paradela, Alberto; Sabidó Aguadé, Eduard, 1981-; Muñoz, Javier; Corrales, Fernando; Arizmendi, Jesús M.; Mayor, Ugo (MDPI, 2021)
    The human genome contains nearly 100 deubiquitinating enzymes (DUBs) responsible for removing ubiquitin moieties from a large variety of substrates. Which DUBs are responsible for targeting which substrates remain mostly ...
  • Espeso Gil, Sergio, 1985-; Holik, Aliaksei Z.; Bonnin, Sarah; Jhanwar, Shalu, 1986-; Chandrasekaran, Sandhya; Pique Regi, Roger; Albaigès-Ràfols, Júlia; Maher, Michael; Permanyer, Jon; Irimia, Manuel; Friedländer, Marc R.; Pons Espinal, Meritxell, 1986-; Akbarian, Schahram; Dierssen, Mara; Maass, Philipp G.; Hor, Charlotte N.; Ossowski, Stephan (Frontiers, 2021)
    In early development, the environment triggers mnemonic epigenomic programs resulting in memory and learning experiences to confer cognitive phenotypes into adulthood. To uncover how environmental stimulation impacts the ...
  • Esteve-Codina, Anna; Soler Artigas, María; Dabad, Marc; Fernández Callejo, Marcos; Griebel, Thasso; Heath, Simon; Gut, Ivo Glynne; Ziegler-Heitbrock, Loems (Nature Research, 2021)
    Chronic obstructive pulmonary disease (COPD) is a destructive inflammatory disease and the genes expressed within the lung are crucial to its pathophysiology. We have determined the RNAseq transcriptome of bronchial brush ...

View more