• Detection of differential bait proteoforms through immunoprecipitation-mass spectrometry data analysis

  Kourtis, Savvas; Cianferoni, Damiano; Serrano Pubull, Luis, 1982-; Sdelci, Sara (Nature Research, 2024)

  Proteins are often referred to as the workhorses of cells, and their interactions are necessary to facilitate specific cellular functions. Despite the recognition that protein-protein interactions, and thus protein functions, ...
• A dynamic in vitro model of Down syndrome neurogenesis with trisomy 21 gene dosage correction

  Bansal, Prakhar; Banda, Erin C.; Glatt-Deeley, Heather R.; Stoddard, Christopher E.; Linsley, Jeremy W.; Arora, Neha; Deleschaux, Cécile; Ahern, Darcy T.; Kondaveeti, Yuvabharath; Massey, Rachael E.; Nicouleau, Michael; Wang, Shijie; Sabariego Navarro, Miguel; Dierssen, Mara; Finkbeiner, Steven; Pinter, Stefan F. (American Association for the Advancement of Science (AAAS), 2024)

  Excess gene dosage from chromosome 21 (chr21) causes Down syndrome (DS), spanning developmental and acute phenotypes in terminal cell types. Which phenotypes remain amenable to intervention after development is unknown. ...
• An extension of the Walsh-Hadamard transform to calculate and model epistasis in genetic landscapes of arbitrary shape and complexity

  Faure, Andre J.; Lehner, Ben, 1978-; Miró Pina, Verónica; Serrano Colomé, Clàudia; Weghorn, Donate (Public Library of Science (PLoS), 2024)

  Accurate models describing the relationship between genotype and phenotype are necessary in order to understand and predict how mutations to biological sequences affect the fitness and evolution of living organisms. The ...
• Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images

  Wernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Mattsson Langseth, Christoffer; Verron, Quentin; Nguyen, Huy Q.; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Martí Renom, Marc A.; Wu, Chao-Ting; Crosetto, Nicola; Bienko, Magda (Nature Research, 2024)

  Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of ...
• A TdT-driven amplification loop increases CRISPR-Cas12a DNA detection levels

  Zwerus, Jordy T.; Berghuis, Nicole F.; Jacques, Jeroen M.; Mars-Groenendijk, Roos; Busker, Ruud W.; Paauw, Armand; de Jong, Ad L.; van Leeuwen, Hans C. (Elsevier, 2024)

  Recent findings on CRISPR-Cas enzymes with collateral DNAse/RNAse activity have led to new and innovative methods for pathogen detection. However, many CRISPR-Cas assays necessitate DNA pre-amplification to boost sensitivity, ...
• The hepatocyte epidermal growth factor receptor (EGFR) pathway regulates the cellular interactome within the liver fibrotic niche

  Gonzalez-Sanchez, Ester; Vaquero, Javier; Caballero Díaz, Daniel; Grzelak, Jan; Fusté, Noel P.; Bertran, Esther; Amengual, Josep; García Sáez, Juan; Martín-Mur, Beatriz; Gut, Marta; Esteve-Codina, Anna; Alay, Ania; Coulouarn, Cedric; Calero Pérez, Silvia; Valdecantos, Pilar; Valverde, Angela M.; Sánchez, Aránzazu; Herrera, Blanca; Fabregat, Isabel (Wiley, 2024)

  Liver fibrosis is the consequence of chronic liver injury in the presence of an inflammatory component. Although the main executors of this activation are known, the mechanisms that lead to the inflammatory process that ...
• Documenting the de-identification process of clinical and imaging data for AI for health imaging projects

  Kondylakis, Haridimos; Garcia Lezena, Teresa; Tsiknakis, Manolis (Springer, 2024)

  Artificial intelligence (AI) is revolutionizing the field of medical imaging, holding the potential to shift medicine from a reactive "sick-care" approach to a proactive focus on healthcare and prevention. The successful ...
• PHF2-mediated H3K9me balance orchestrates heterochromatin stability and neural progenitor proliferation

  Aguirre, Samuel; Pappa, Stella; Serna Pujol, Núria; Padilla, Natàlia; Iacobucci, Simona; Nacht, A. Silvina; Vicent, Guillermo Pablo; Jordan Vallès, Albert; Cruz, Xavier de la; Martínez Balbás, Marian A. (EMBO Press, 2024)

  Heterochromatin stability is crucial for progenitor proliferation during early neurogenesis. It relays on the maintenance of local hubs of H3K9me. However, understanding the formation of efficient localized levels of H3K9me ...
• Targeting the autophagy-NAD axis protects against cell death in Niemann-Pick type C1 disease models

  Kataura, Tetsushi; Sedlackova, Lucia; Sun, Congxin; Kocak, Gamze; Wilson, Niall; Banks, Peter; Hayat, Faisal; Trushin, Sergey; Trushina, Eugenia; Maddocks, Oliver D. K.; Oblong, John E.; Miwa, Satomi; Imoto, Masaya; Saiki, Shinki; Erskine, Daniel; Migaud, Marie E.; Sarkar, Sovan; Korolchuk, Viktor I. (Nature Research, 2024)

  Impairment of autophagy leads to an accumulation of misfolded proteins and damaged organelles and has been implicated in plethora of human diseases. Loss of autophagy in actively respiring cells has also been shown to ...
• The Wnt-dependent master regulator NKX1-2 controls mouse pre-implantation development

  Nakagawa, Shoma; Carnevali, Davide; Tan, Xiangtian; Alvarez, Mariano J.; Parfitt, David-Emlyn; Di Vicino, Umberto; Arumugam, Karthik; Shin, William; Aranda, Sergi; Normanno, Davide; Sebastián Pérez, Rubén; Cannatá, Chiara; Cortes, Paola; Neguembor, Maria Victoria; Shen, Michael M.; Califano, Andrea; Cosma, Maria Pia (Elsevier, 2024)

  Embryo size, specification, and homeostasis are regulated by a complex gene regulatory and signaling network. Here we used gene expression signatures of Wnt-activated mouse embryonic stem cell (mESC) clones to reverse ...
• TANGO1 inhibitors reduce collagen secretion and limit tissue scarring

  Raote, Ishier; Häkkinen, Hanna-Maria; Vibe, Carine; Broadbent, Katrina; Carolis, Carlo; Ruprecht, Verena; Malhotra, Vivek (Nature Research, 2024)

  Uncontrolled secretion of ECM proteins, such as collagen, can lead to excessive scarring and fibrosis and compromise tissue function. Despite the widespread occurrence of fibrotic diseases and scarring, effective therapies ...
• Active transcription and epigenetic reactions synergistically regulate meso-scale genomic organization

  Kant, Aayush; Guo, Zixian; Vinayak, Vinayak; Neguembor, Maria Victoria; Li, Wing Shun; Agrawal, Vasundhara; Pujadas, Emily; Almassalha, Luay; Backman, Vadim; Lakadamyali, Melike; Cosma, Maria Pia; Shenoy, Vivek B. (Nature Research, 2024)

  In interphase nuclei, chromatin forms dense domains of characteristic sizes, but the influence of transcription and histone modifications on domain size is not understood. We present a theoretical model exploring this ...
• Developing a platform for secretion of biomolecules in Mycoplasma feriruminatoris

  Gonzalez de Miguel, Javier; Montero-Blay, Ariadna, 1994-; Ciampi, Ludovica; Rodriguez-Arce, Irene; Serrano Pubull, Luis, 1982- (BioMed Central, 2024)

  Background: Having a simple and fast dividing organism capable of producing and exposing at its surface or secreting functional complex biomolecules with disulphide bridges is of great interest. The mycoplasma bacterial ...
• Engineering Mycoplasma pneumoniae to bypass the association with Guillain-Barré syndrome

  Broto, Alicia; Piñero-Lambea, Carlos; Segura-Morales, Carolina; Tio-Gillen, Anne P.; Unger, Wendy W. J.; Burgos, Raul; Mazzolini, Rocco; Miravet Verde, Samuel; Jacobs, Bart C.; Casas, Josefina; Huizinga, Ruth; Lluch-Senar, Maria 1982-; Serrano Pubull, Luis, 1982- (Elsevier, 2024)

  A non-pathogenic Mycoplasma pneumoniae-based chassis is leading the development of live biotherapeutic products (LBPs) for respiratory diseases. However, reports connecting Guillain-Barré syndrome (GBS) cases to prior M. ...
• Systematic mapping of organism-scale gene-regulatory networks in aging using population asynchrony

  Eder, Matthias; Martin, Olivier M. F.; Oswal, Natasha; Sedlackova, Lucia; Moutinho, Catia; Carmen Fabregat, Andrea del; Menéndez Bravo, Simón; Sebé-Pedrós, Arnau; Heyn, Holger; Stroustrup, Nicholas (Elsevier, 2024)

  In aging, physiologic networks decline in function at rates that differ between individuals, producing a wide distribution of lifespan. Though 70% of human lifespan variance remains unexplained by heritable factors, little ...
• Staying on track - Keeping things running in a high-end scientific imaging core facility

  Renaud, Oliver; Aulner, Nathalie; Salles, Audrey; Halidi, Nadia; Brunstein, Maia; Mallet, Adeline; Aumayr, Karin; Terjung, Stefan; Levy, Daniel; Lippens, Saskia; Verbavatz, Jean-Marc; Heuser, Thomas; Santarella-Mellwig, Rachel; Tinevez, Jean-Yves; Woller, Tatiana; Botzki, Alexander; Cawthorne, Christopher; Core4Life Consortium; Munck, Sebastian (Wiley, 2024)

  Modern life science research is a collaborative effort. Few research groups can single-handedly support the necessary equipment, expertise and personnel needed for the ever-expanding portfolio of technologies that are ...
• Non-canonical role for the BAF complex subunit DPF3 in mitosis and ciliogenesis

  Verrillo, Giulia; Obeid, Anna Maria; Genco, Alexia; Scrofani, Jacopo, 1984-; Orange, François; Hanache, Sarah; Mignon, Julien; Leyder, Tanguy; Michaux, Catherine; Kempeneers, Céline; Bricmont, Noëmie; Herkenne, Stephanie; Vernos, Isabelle, 1959-; Martin, Maud; Mottet, Denis (Company of Biologists, 2024)

  DPF3, along with other subunits, is a well-known component of the BAF chromatin remodeling complex, which plays a key role in regulating chromatin remodeling activity and gene expression. Here, we elucidated a non-canonical ...
• Characterization of the common genetic variation in the spanish population of Navarre

  Maillo, Alberto; Beltran, Sergi; Gómez Cabrero, David (MDPI, 2024)

  Large-scale genomic studies have significantly increased our knowledge of genetic variability across populations. Regional genetic profiling is essential for distinguishing common benign variants from disease-causing ones. ...
• Multiple genetic variants at the SLC30A8 locus affect local super-enhancer activity and influence pancreatic β-cell survival and function

  Hu, Ming; Kim, Innah; Morán, Ignasi; Peng, Weicong; Sun, Orien; Bonnefond, Amélie; Khamis, Amna; Bonàs-Guarch, Silvia; Froguel, Philippe; Rutter, Guy A. (Wiley, 2024)

  Variants at the SLC30A8 locus are associated with type 2 diabetes (T2D) risk. The lead variant, rs13266634, encodes an amino acid change, Arg325Trp (R325W), at the C-terminus of the secretory granule-enriched zinc transporter, ...
• Population genetics and phylogeographic history of the insular lizard Podarcis lilfordi (Gunther, 1874) from the Balearic Islands based on genome-wide polymorphic data

  Otalora Acevedo, Katherin Eliana; Riera, Joan Lluís; Tavecchia, Giacomo; Rotger, Andreu; Igual, José Manuel; Trotta, Jean-Remi Paul; Baldo, Laura (Wiley, 2024)

  Islands provide a great system to explore the processes that maintain genetic diversity and promote local adaptation. We explored the genomic diversity of the Balearic lizard Podarcis lilfordi, an endemic species characterized ...

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