• 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 ...
• Regulation of Cx36 trafficking through the early secretory pathway by COPII cargo receptors and Grasp55

  Tetenborg, Stephan; Ariakia, Fatemeh; Martinez Soler, Elizabeth; Shihabeddin, Eyad; Cebrian Lazart, Ignacio; Miller, Adam C.; O'Brien, John T. (Springer, 2024)

  Gap junctions formed by the major neuronal connexin Cx36 function as electrical synapses in the nervous system and provide unique functions such as synchronizing neuron activities or supporting network oscillations. Although ...
• 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 ...
• The senescence-associated secretory phenotype induces cellular plasticity and tissue regeneration

  Ritschka, Birgit,1985-; Storer, Mekayla, 1981-; Mas Malavila, Alba; Heinzmann, Florian; Ortells Campos, Mª Carmen, 1984-; Morton, Jennifer P.; Sansom, Owen J.; Zender, Lars; Keyes, William M., 1973- (Cold Spring Harbor Laboratory Press (CSHL Press), 2017)

  Senescence is a form of cell cycle arrest induced by stress such as DNA damage and oncogenes. However, while arrested, senescent cells secrete a variety of proteins collectively known as the senescence-associated secretory ...
• Selenoprotein gene nomenclature

  Gladyshev, Vadim N.; Guigó Serra, Roderic; Zhang, Yan (American Society for Biochemistry and Molecular Biology (ASBMB), 2016)

  The human genome contains 25 genes coding for selenocysteine-containing proteins (selenoproteins). These proteins are involved in a variety of functions, most notably redox homeostasis. Selenoprotein enzymes with known ...
• 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 ...
• Genetic diversity and population structure of rice varieties cultivated in temperate regions

  Reig-Valiente, Juan L.; Viruel, Juan; Sales, Ester; Marqués, Luis; Terol, Javier; Gut, Marta; Derdak, Sophia; Talón, Manuel; Domingo, Concha (Springer Open, 2016)

  Background. After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. ...
• 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 ~ ...
• Reactive oxygen species activate the Drosophila TNF receptor Wengen for damage-induced regeneration

  Esteban-Collado, José; Fernández Mañas, Mar; Fernández-Moreno, Manuel; Maeso, Ignacio; Corominas Guiu, Montserrat; Serras Rigalt, Florenci (EMBO Press, 2024)

  Tumor necrosis factor receptors (TNFRs) control pleiotropic pro-inflammatory functions that range from apoptosis to cell survival. The ability to trigger a particular function will depend on the upstream cues, association ...
• Identifying cancer cells from calling single-nucleotide variants in scRNA-seq data

  Marot-Lassauzaie, Valérie; Beneyto Calabuig, Sergi; Obermayer, Benedikt; Velten, Lars; Beule, Dieter; Haghverdi, Laleh (Oxford University Press, 2024)

  Motivation: Single-cell RNA sequencing (scRNA-seq) data are widely used to study cancer cell states and their heterogeneity. However, the tumour microenvironment is usually a mixture of healthy and cancerous cells and it ...
• The interferon γ pathway enhances pluripotency and X-chromosome reactivation in iPSC reprogramming

  Barrero Asencio, Mercedes; Lazarenkov, Aleksey; Blanco, Enrique; Palma, Luis G.; López Rubio, Anna V.; Bauer, Moritz, 1987-; Bigas Salvans, Anna; Di Croce, Luciano; Sardina, Jose Luis; Payer, Bernhard (American Association for the Advancement of Science (AAAS), 2024)

  Reprogramming somatic cells into induced pluripotent stem cells (iPSCs) requires activation of the pluripotency network and resetting of the epigenome by erasing the epigenetic memory of the somatic state. In female mouse ...
• 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 ...
• In silico RNA isoform screening to identify potential cancer driver exons with therapeutic applications

  Anglada-Girotto, Miquel; Ciampi, Ludovica; Bonnal, Sophie; Head, Sarah A.; Miravet Verde, Samuel, 1992-; Serrano Pubull, Luis, 1982- (Nature Research, 2024)

  Alternative splicing is crucial for cancer progression and can be targeted pharmacologically, yet identifying driver exons genome-wide remains challenging. We propose identifying such exons by associating statistically ...
• Mitoclone2: an R package for elucidating clonal structure in single-cell RNA-sequencing data using mitochondrial variants

  Story, Benjamin A.; Velten, Lars; Mönke, Gregor; Annan, Ahrmad; Steinmetz, Lars M. (Oxford University Press, 2024)

  Clonal cell population dynamics play a critical role in both disease and development. Due to high mitochondrial mutation rates under both healthy and diseased conditions, mitochondrial genomic variability is a particularly ...

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