• Efficient and interpretable prediction of protein functional classes by correspondence analysis and compact set relations

  Chang, Jia-Ming, 1978-; Taly, Jean-Francois; Erb, Ionas; Sung, Ting-Yi; Hsu, Wen-Lian; Tang, Chuan Yi; Notredame, Cedric; Su, Emily Chia-Yu (Public Library of Science (PLoS), 2013)

  Predicting protein functional classes such as localization sites and modifications plays a crucial role in function annotation. Given a tremendous amount of sequence data yielded from high-throughput sequencing experiments, ...
• The RanGTP pathway: from nucleo-cytoplasmic transport to spindle assembly and beyond

  Cavazza, Tommaso, 1985-; Vernos, Isabelle, 1959- (Frontiers, 2016)

  The small GTPase Ran regulates the interaction of transport receptors with a number of cellular cargo proteins. The high affinity binding of the GTP-bound form of Ran to import receptors promotes cargo release, whereas its ...
• Automatic identification of informative regions with epigenomic changes associated to hematopoiesis

  Carrillo-de-Santa Pau, Enrique; Juan, David; Pancaldi, Vera; Were, Felipe; Martin-Subero, José Ignacio; Rico, Daniel; Valencia, Alfonso; BLUEPRINT Consortium (Oxford University Press, 2017)

  Hematopoiesis is one of the best characterized biological systems but the connection between chromatin changes and lineage differentiation is not yet well understood. We have developed a bioinformatic workflow to generate ...
• A phylogenomics approach for selecting robust sets of phylogenetic markers

  Capella Gutiérrez, Salvador Jesús, 1985-; Kauff, Frank; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2014)

  Reconstructing the evolutionary relationships of species is a major goal in biology. Despite the increasing number of completely sequenced genomes, a large number of phylogenetic projects rely on targeted sequencing and ...
• The acute effects of ultraviolet radiation on the blood transcriptome are independent

  Bustamante Pineda, Mariona; Hernandez-Ferrer, Carles, 1987-; Sarria-Trujillo, Yaris; Harrison, Graham I.; Nonell Mazelón, Lara; Kang, Wenjing; Friedländer, Marc R.; Estivill, Xavier, 1955-; González, Juan Ramón; Nieuwenhuijsen, Mark J.; Young, Antony R. (Elsevier, 2017)

  The molecular basis of many health outcomes attributed to solar ultraviolet radiation (UVR) is unknown. We tested the hypothesis that they may originate from transcriptional changes in blood cells. This was determined by ...
• Interaction between airborne copper exposure and ATP7B polymorphisms on inattentiveness in scholar children

  Alemany, Silvia; Vilor-Tejedor, Natàlia; Bustamante Pineda, Mariona; Álvarez Pedrerol, Mar, 1981-; Rivas, Ioar; Forns i Guzman, Joan, 1981-; Querol, Xavier; Pujol Martí, Jesús, 1981-; Sunyer Deu, Jordi (Elsevier, 2017)

  Recent research indicates that airborne copper exposure in scholar children negatively affects brain functioning. These effects are likely to be influenced by the efficiency of copper metabolism, which is partly regulated ...
• Progesterone receptor induces bcl-x expression through intragenic binding sites favoring RNA polymerase II elongation

  Bertucci, Paola Y.; Nacht, A. Silvina; Alló, Mariano; Rocha-Viegas, Luciana; Ballaré, Cecilia Julia; Soronellas, Daniel; Castellano, Giancarlo; Zaurín Quer, Roser; Kornblihtt, Alberto R.; Beato, Miguel; Vicent, Guillermo Pablo; Pecci, Adali (Oxford University Press, 2013)

  Steroid receptors were classically described for regulating transcription by binding to target gene promoters. However, genome-wide studies reveal that steroid receptors-binding sites are mainly located at intragenic ...
• Polystyrene nanoplastics target lysosomes interfering with lipid metabolism through the PPAR system and affecting macrophage functionalization

  Brandts, Irene; Solà, Roger; Garcia Ordoñez, Marlid; Gella, Alex; Quintana, Albert; Martin, Beatriz; Esteve-Codina, Anna; Teles, Mariana; Roher, Nerea (Royal Society of Chemistry, 2023)

  Nanoplastics (NPs) are currently a main concern for environmental, animal and human health due to their potential to accumulate in different environmental compartments and provoke effects in living organisms. Nevertheless, ...
• SMARCAD1 and TOPBP1 contribute to heterochromatin maintenance at the transition from the 2C-like to the pluripotent state

  Sebastián Pérez, Rubén; Nakagawa, Shoma; Tu, Xiaochuan; Aranda Aragón, Sergio; Pesaresi, Martina; Gómez García, Pablo; Alcoverro-Bertran, Marc; Gómez Vázquez, José Luis; Carnevali, Davide; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Martin, Laura; Nissim Rafinia, Malka; Meshorer, Eran; Neguembor, Maria Victoria; Di Croce, Luciano; Cosma, Maria Pia (eLife, 2023)

  Chromocenters are established after the 2-cell (2C) stage during mouse embryonic development, but the factors that mediate chromocenter formation remain largely unknown. To identify regulators of 2C heterochromatin ...
• Macrophage and neutrophil heterogeneity at single-cell spatial resolution in human inflammatory bowel disease

  Garrido Trigo, Alba; Marchese, Domenica, 1986-; Caratù, Ginevra; Heyn, Holger; Salas, Azucena (Nature Research, 2023)

  Ulcerative colitis and Crohn's disease are chronic inflammatory intestinal diseases with perplexing heterogeneity in disease manifestation and response to treatment. While the molecular basis for this heterogeneity remains ...
• ORC1 binds to cis-transcribed RNAs for efficient activation of replication origins

  Mas, Aina Maria; Goñi, Enrique; Ruiz de Los Mozos, Igor; Arcas Mantas, Aida; Statello, Luisa; González, Jovanna; Blázquez, Lorea; Lee, Wei Ting Chelsea; Gupta, Dipika; Sejas, Álvaro; Hoshina, Shoko; Armaos, Alexandros, 1989-; Tartaglia, Gian Gaetano; Waga, Shou; Ule, Jernej; Rothenberg, Eli; Gómez, María; Huarte, Maite (Nature Research, 2023)

  Cells must coordinate the activation of thousands of replication origins dispersed throughout their genome. Active transcription is known to favor the formation of mammalian origins, although the role that RNA plays in ...
• Metabolic rewiring induced by ranolazine improves melanoma responses to targeted therapy and immunotherapy

  Redondo Muñoz, Marta; Heyn, Holger; Arozarena, Imanol (Nature Research, 2023)

  Resistance of melanoma to targeted therapy and immunotherapy is linked to metabolic rewiring. Here, we show that increased fatty acid oxidation (FAO) during prolonged BRAF inhibitor (BRAFi) treatment contributes to acquired ...
• microRNA sequencing for biomarker detection in the diagnosis, classification and prognosis of Diffuse Large B Cell Lymphoma

  Larrabeiti Etxebarria, Ane; Bilbao Aldaiturriaga, Nerea; Arzuaga Mendez, Javier; Martin Arruti, Maialen; Cozzuto, Luca; Gaafar, Ayman; Ruiz Diaz, Irune; Guerra, Isabel; Martin Guerrero, Idoia; Lopez-Lopez, Elixabet; Gutierrez Camino, Angela (Nature Research, 2023)

  Despite being considered a single disease, Diffuse Large B Cell Lymphoma (DLBCL) presents with variable backgrounds, which results in heterogeneous outcomes among patients, with 40% of them still having primary refractory ...
• The minus-end depolymerase KIF2A drives flux-like treadmilling of γTuRC-uncapped microtubules

  Henkin, Gil; Brito, Cláudia; Thomas, Claire; Surrey, Thomas (Rockefeller University Press, 2023)

  During mitosis, microtubules in the spindle turn over continuously. At spindle poles, where microtubule minus ends are concentrated, microtubule nucleation and depolymerization, the latter required for poleward microtubule ...
• SUNi mutagenesis: Scalable and uniform nicking for efficient generation of variant libraries

  Mighell, Taylor L.; Toledano, Ignasi; Lehner, Ben, 1978- (Public Library of Science (PLoS), 2023)

  Multiplexed assays of variant effects (MAVEs) have made possible the functional assessment of all possible mutations to genes and regulatory sequences. A core pillar of the approach is generation of variant libraries, but ...
• Updated MS²PIP web server supports cutting-edge proteomics applications

  Declercq, Arthur; Bouwmeester, Robbin; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Hirschler, Aurélie; Carapito, Christine; Martens, Lennart; Degroeve, Sven; Gabriels, Ralf (Oxford University Press, 2023)

  Interest in the use of machine learning for peptide fragmentation spectrum prediction has been strongly on the rise over the past years, especially for applications in challenging proteomics identification workflows such ...
• Tetraspanin-8 sequesters syntaxin-2 to control biphasic release propensity of mucin granules

  Wojnacki, José; Lujan, Agustin Leonardo; Brouwers, Nathalie; Aranda Vallejo, Carla; Bigliani, Gonzalo; Pena Rodriguez, Maria; Foresti, Ombretta; Malhotra, Vivek (Nature Research, 2023)

  Agonist-mediated stimulated pathway of mucin and insulin release are biphasic in which rapid fusion of pre-docked granules is followed by slow docking and fusion of granules from the reserve pool. Here, based on a cell-culture ...
• Single-cell profiling of lncRNA expression during Ebola virus infection in rhesus macaques

  Santus, Luisa; Sopena Rios, Maria; García Pérez, Raquel, 1989-; Lin, Aaron E.; Adams, Gordon C.; Barnes, Kayla G.; Siddle, Katherine J.; Wohl, Shirlee; Reverter, Ferran; Rinn, John L.; Bennett, Richard S.; Hensley, Lisa E.; Sabeti, Pardis C.; Melé Messeguer, Marta, 1982- (Nature Research, 2023)

  Long non-coding RNAs (lncRNAs) are involved in numerous biological processes and are pivotal mediators of the immune response, yet little is known about their properties at the single-cell level. Here, we generate a ...
• Genetic analysis of blood molecular phenotypes reveals common properties in the regulatory networks affecting complex traits

  Brown, Andrew A.; DIRECT Consortium; Viñuela, Ana (Nature Research, 2023)

  We evaluate the shared genetic regulation of mRNA molecules, proteins and metabolites derived from whole blood from 3029 human donors. We find abundant allelic heterogeneity, where multiple variants regulate a particular ...
• A new chromosome-assigned Mongolian gerbil genome allows characterization of complete centromeres and a fully heterochromatic chromosome

  Brekke, Thomas D.; Papadopulos, Alexander S. T.; Julià, Eva; Fornas Carreño, Oscar; Fu, Beiyuan; Yang, Fengtang; Fuente, Roberto de la; Page, Jesus; Baril, Tobias; Hayward, Alexander; Mulley, John F. (Oxford University Press, 2023)

  Chromosome-scale genome assemblies based on ultralong-read sequencing technologies are able to illuminate previously intractable aspects of genome biology such as fine-scale centromere structure and large-scale variation ...

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