• Integration and segregation manifolds in the brain ensure cognitive flexibility during tasks and rest

  Capouskova, Katerina; Zamora-López, Gorka; Kringelbach, Morten L.; Deco, Gustavo (Wiley, 2023)

  Adapting to a constantly changing environment requires the human brain to flexibly switch among many demanding cognitive tasks, processing both specialized and integrated information associated with the activity in functional ...
• Does the health impact of exposure to neighbourhood green space differ between population groups? An explorative study in four european cities

  Ruijsbroek, Annemarie; Droomers, Mariël; Kruize, Hanneke; Van Kempen, Elise; Gidlow, Christopher J.; Hurst, Gemma; Andrusaityte, Sandra; Nieuwenhuijsen, Mark J.; Maas, Jolanda; Hardyns, Wim; Stronks, Karien; Groenewegen, Peter P. (MDPI, 2017)

  It has been suggested that certain residents, such as those with a low socioeconomic status, the elderly, and women, may benefit more from the presence of neighbourhood green space than others. We tested this hypothesis ...
• ¿Es posible comparar el empleo informal en los países de América del Sur? Análisis de su definición, clasificación y medición

  Ruiz Contreras, Marisol E.; Tarafa, Gemma; Jódar, Pere; Benach, Joan (Elsevier, 2015)

  Objetivo. Caracterizar y analizar la situación del empleo informal respecto a su definición, medición y clasificación, en los países de América del Sur. Métodos. A través de una scoping review se realizó una revisión ...
• Long-term asymmetrical acceleration of protein evolution after gene duplication

  Pich Roselló, Oriol, 1992-; Kondrashov, Fyodor A., 1979- (Oxford University Press, 2014)

  Rapid divergence of gene copies after duplication is thought to determine the fate of the copies and evolution of novel protein functions. However, data on how long the gene copies continue to experience an elevated rate ...
• CARGO: effective format-free compressed storage of genomic information

  Roguski, Łukasz; Ribeca, Paolo (Oxford University Press, 2016)

  The recent super-exponential growth in the amount of sequencing data generated worldwide has put techniques for compressed storage into the focus. Most available solutions, however, are strictly tied to specific bioinformatics ...
• Glucose homeostasis changes and pancreatic β-cell proliferation after switching to cyclosporin in tacrolimus-induced diabetes mellitus

  Rodríguez-Rodríguez, Ana Elena; Triñanes, Javier; Porrini, Esteban; Velázquez-García, Silvia; Fumero, Cecilia; Vega-Prieto, María Jose; Díez-Fuentes, María Luisa; Lima, Sergio Luis; Salido, Eduardo; Torres, Armando (Elsevier, 2015)

  Background. Switching to cyclosporin A may result in a reversion of tacrolimus-induced diabetes mellitus. However, mechanisms underlying such a reversion are still unknown. Methods. Obese Zucker rats were used as a model ...
• eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts

  Chitneedi, Praveen Krishna; Hadlich, Frieder; Moreira, Gabriel C. M.; Espinosa-Carrasco, José; Li, Changxi; Plastow, Graham; Fischer, Daniel; Charlier, Carole; Rocha, Dominique; Chamberlain, Amanda J.; Kuehn, Christa (Oxford University Press, 2024)

  Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow ...
• The genetic architecture of protein interaction affinity and specificity

  Bendel, Alexandra M.; Faure, Andre J.; Klein, Dominique; Shimada, Kenji; Lyautey, Romane; Schiffelholz, Nicole; Kempf, Georg; Cavadini, Simone; Lehner, Ben, 1978-; Diss, Guillaume (Nature Research, 2024)

  The encoding and evolution of specificity and affinity in protein-protein interactions is poorly understood. Here, we address this question by quantifying how all mutations in one protein, JUN, alter binding to all other ...
• Theoretical assessment of indistinguishable peptides in mass spectrometry-based proteomics

  Elhamraoui, Zahra; Borràs, Eva; Wilhelm, Mathias; Sabidó Aguadé, Eduard, 1981- (American Chemical Society (ACS), 2024)

  Mass-spectrometry-based proteomics has advanced with the integration of experimental and predicted spectral libraries, which have significantly improved peptide identification in complex search spaces. However, challenges ...
• A research data management (RDM) community for ELIXIR

  D'Anna, Flora; D'Altri, Teresa, 1984-; Andrabi, Munazah (F1000Research, 2024)

  Research data management (RDM) is central to the implementation of the FAIR (Findable Accessible, Interoperable, Reusable) and Open Science principles. Recognising the importance of RDM, ELIXIR Platforms and Nodes have ...
• C/EBPα induces highly efficient macrophage transdifferentiation of B lymphoma and leukemia cell lines and impairs their tumorigenicity

  Rapino, Francesca, 1982-; Robles, Eloy F.; Richter-Larrea, Jose A.; Kallin, Eric M.; Martinez-Climent, Jose A.; Graf, T. (Thomas) (Cell Press, 2013)

  Earlier work demonstrated that the transcription factor C/EBPα can convert immature and mature murine B lineage cells into functional macrophages. Testing >20 human lymphoma and leukemia B cell lines, we found that most ...
• 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 ~ ...
• 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 ...
• What’s in a name? A large-scale computational study on how competition between names affects naming variation

  Gualdoni, Eleonora; Brochhagen, Thomas; Mädebach, Andreas; Boleda, Gemma (Elsevier, 2023)

  Different speakers often use different names to refer to the same entity (e.g., “woman” vs. “tennis player” for a given woman playing tennis). We study how visual typicality affects variation in naming behavior. We use a ...
• Five decades of occupational cancer epidemiology

  Turner, Michelle C.; Straif, Kurt; Kogevinas, Manolis; Schubauer-Berigan, Mary K. (Nordic Association of Occupational Safety and Health (NOROSH), 2024)

  Objective: In this discussion paper, we provide a narrative review of past and present occupational cancer studies in the journal with a viewpoint towards future occupational cancer research. Method: We reviewed all ...

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