• Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models

  Diensthuber, Gregor; Pryszcz, Leszek Piotr, 1985-; Llovera Nadal, Laia; Lucas, Morghan C.; Delgado-Tejedor, Anna; Cruciani, Sonia; Roignant, Jean-Yves; Begik, Oguzhan; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2024)

  In recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, due to its ability to detect multiple modifications within the same full-length native RNA molecules. While ...
• The pluripotency state of human embryonic stem cells derived from single blastomeres of eight-cell embryos

  Massafret, Ot; Barragán, Montserrat; Álvarez-González, Lucía; Aran, Begoña; Martín-Mur, Beatriz; Esteve-Codina, Anna; Ruiz Herrera, Aurora; Ibáñez, Elena; Santaló, Josep (Elsevier, 2024)

  Human embryonic stem cells (hESCs) derived from blastocyst stage embryos present a primed state of pluripotency, whereas mouse ESCs (mESCs) display naïve pluripotency. Their unique characteristics make naïve hESCs more ...
• An activity-specificity trade-off encoded in human transcription factors

  Naderi, Julian; Magalhaes, Alexandre P.; Kibar, Gözde; Stik, Grégoire; Zhang, Yaotian; Mackowiak, Sebastian D.; Wieler, Hannah M.; Rossi, Francesca; Buschow, Rene; Christou-Kent, Marie; Alcoverro-Bertran, Marc; Graf, T. (Thomas); Vingron, Martin; Hnisz, Denes (Nature Research, 2024)

  Transcription factors (TFs) control specificity and activity of gene transcription, but whether a relationship between these two features exists is unclear. Here we provide evidence for an evolutionary trade-off between ...
• CSF glial biomarkers are associated with cognition in individuals at risk of Alzheimer's disease

  Warmenhoven, Noëlle; Sánchez Benavides, Gonzalo; González Escalante, Armand; Milà Alomà, Marta; Shekari, Mahnaz; López Martos, David; Ortiz Romero, Paula, 1994-; Kollmorgen, Gwendlyn; Quijano Rubio, Clara; Minguillón, Carolina; Gispert López, Juan Domingo; Vilor Tejedor, Natàlia, 1988-; Arenaza Urquijo, Eider M.; Palpatzis, Eleni; Ashton, Nicholas J.; Zetterberg, Henrik; Blennow, Kaj; Suárez-Calvet, Marc; Grau-Rivera, Oriol; ALFA Study (Wiley, 2024)

  Introduction: We examined whether baseline glial markers soluble triggering receptor expressed on myeloid cell 2 (sTREM2), chitinase 3-like protein 1 (YKL-40), and glial fibrillary acidic protein (GFAP) in cerebrospinal ...
• Reverse phenotyping after whole-exome sequencing in children with developmental delay/intellectual disability-An exception or a necessity?

  Ilic, Nikola; Maric, Nina; Maver, Ales; Armengol i Dulcet, Lluís; Kravljanac, Ruzica; Cirkovic, Jana; Krstic, Jovana; Radivojevic, Danijela; Cirkovic, Sanja; Ostojic, Slavica; Krasic, Stasa; Paripovic, Aleksandra; Vukomanovic, Vladislav; Peterlin, Borut; Maric, Gorica; Sarajlija, Adrijan (MDPI, 2024)

  This study delves into the diagnostic yield of whole-exome sequencing (WES) in pediatric patients presenting with developmental delay/intellectual disability (DD/ID), while also exploring the utility of Reverse Phenotyping ...
• Temporally resolved proteomics identifies nidogen-2 as a cotarget in pancreatic cancer that modulates fibrosis and therapy response

  Pereira, Brooke A.; Lucas, Morghan C.; Timpson, Paul (American Association for the Advancement of Science (AAAS), 2024)

  Pancreatic ductal adenocarcinoma (PDAC) is characterized by increasing fibrosis, which can enhance tumor progression and spread. Here, we undertook an unbiased temporal assessment of the matrisome of the highly metastatic ...
• Three-dimensional genome architecture persists in a 52,000-year-old woolly mammoth skin sample

  Sandoval Velasco, Marcela; Martí Renom, Marc A.; Lieberman Aiden, Erez (Elsevier, 2024)

  Analyses of ancient DNA typically involve sequencing the surviving short oligonucleotides and aligning to genome assemblies from related, modern species. Here, we report that skin from a female woolly mammoth (†Mammuthus ...
• DNA methylation enables recurrent endogenization of giant viruses in an animal relative

  Sarre, Luke A.; Kim, Iana V.; Ovchinnikov, Vladimir; Olivetta, Marine; Suga, Hiroshi; Dudin, Omaya; Sebé-Pedrós, Arnau; Mendoza, Alex de (American Association for the Advancement of Science (AAAS), 2024)

  5-Methylcytosine (5mC) is a widespread silencing mechanism that controls genomic parasites. In eukaryotes, 5mC has gained complex roles in gene regulation beyond parasite control, yet 5mC has also been lost in many lineages. ...
• The structure and mechanics of the cell cortex depend on the location and adhesion state

  Flormann, Daniel; Kainka, Lucina; Montalvo, Gala; Rheinlaender, Johannes; Thalla, D.; Vesperini, Doriane; Pohland, M. O.; Kaub, K. H.; Schu, M.; Pezzano, Fabio; Ruprecht, Verena; Terriac, Emmanuel; Hawkins, Rhoda; Lautenschläger, Franziska (National Academy of Sciences, 2024)

  Cells exist in different phenotypes and can transition between them. A phenotype may be characterized by many different aspects. Here, we focus on the example of whether the cell is adhered or suspended and choose particular ...
• Common genetic variants associated with urinary phthalate levels in children: A genome-wide study

  Bustamante Pineda, Mariona; Balagué-Dobón, Laura; Casas Sanahuja, Maribel; Maitre, Léa; Nurtdinov, Ramil; González, Juan Ramón; Vrijheid, Martine (Elsevier, 2024)

  Introduction: Phthalates, or dieters of phthalic acid, are a ubiquitous type of plasticizer used in a variety of common consumer and industrial products. They act as endocrine disruptors and are associated with increased ...
• Long non-coding RNAs involved in Drosophila development and regeneration

  Camilleri Robles, Carlos; Amador, Raziel; Tiebe, Marcel; Teleman, Aurelio A.; Serras, Florenci; Guigó Serra, Roderic; Corominas Guiu, Montserrat (Oxford University Press, 2024)

  The discovery of functional long non-coding RNAs (lncRNAs) changed their initial concept as transcriptional noise. LncRNAs have been identified as regulators of multiple biological processes, including chromatin structure, ...
• Elucidation of the epitranscriptomic RNA modification landscape of Chikungunya Virus

  Baquero Pérez, Belinda; Bortoletto, Enrico; Rosani, Umberto; Delgado-Tejedor, Anna; Medina, Rebeca; Novoa, Eva Maria; Venier, Paola; Díez Antón, Juana, 1962- (MDPI, 2024)

  The genomes of positive-sense (+) single-stranded RNA (ssRNA) viruses are believed to be subjected to a wide range of RNA modifications. In this study, we focused on the chikungunya virus (CHIKV) as a model (+) ssRNA virus ...
• Modeling the impact of neuromorphological alterations in Down syndrome on fast neural oscillations

  Clusella, Pau; Manubens-Gil, Linus, 1989-; García Ojalvo, Jordi; Dierssen, Mara (Public Library of Science (PLoS), 2024)

  Cognitive disorders, including Down syndrome (DS), present significant morphological alterations in neuron architectural complexity. However, the relationship between neuromorphological alterations and impaired brain ...
• CapTrap-seq: a platform-agnostic and quantitative approach for high-fidelity full-length RNA sequencing

  Carbonell Sala, Silvia; Perteghella, Tamara; Lagarde, Julien; Nishiyori, Hiromi; Palumbo, Emilio; Arnan Ros, Carme; Takahashi, Hazuki; Carninci, Piero; Uszczynska-Ratajczak, Barbara; Guigó Serra, Roderic (Nature Research, 2024)

  Long-read RNA sequencing is essential to produce accurate and exhaustive annotation of eukaryotic genomes. Despite advancements in throughput and accuracy, achieving reliable end-to-end identification of RNA transcripts ...
• The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics

  Corominas Guiu, Montserrat; Guigó Serra, Roderic (Oxford University Press, 2024)

  The Catalan Initiative for the Earth BioGenome Project (CBP) is an EBP-affiliated project network aimed at sequencing the genome of the >40 000 eukaryotic species estimated to live in the Catalan-speaking territories ...
• 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, ...

View more