• Blueprint of human thymopoiesis reveals molecular mechanisms of stage-specific TCR enhancer activation

  Cieslak, Agata; Gut, Marta; Gut, Ivo Glynne; Asnafi, Vahid (Rockefeller University Press, 2020)

  Cell differentiation is accompanied by epigenetic changes leading to precise lineage definition and cell identity. Here we present a comprehensive resource of epigenomic data of human T cell precursors along with an ...
• HypercubeME: two hundred million combinatorially complete datasets from a single experiment

  Esteban, Laura Avino; Lonishin, Lyubov R.; Bobrovskiy, Daniil; Leleytner, Gregory; Bogatyreva, Natalya S.; Kondrashov, Fyodor A., 1979-; Ivankov, Dmitry N. (Oxford University Press, 2020)

  Motivation: Epistasis, the context-dependence of the contribution of an amino acid substitution to fitness, is common in evolution. To detect epistasis, fitness must be measured for at least four genotypes: the reference ...
• The abundance of the long intergenic non-coding RNA 01087 differentiates between luminal and triple-negative breast cancers and predicts patient outcome

  Palma, Fatima Domenica Elisa de; Monaco, Valentina del; Pol, Jonathan G.; Kremer, Margerie; D'Argenio, Valeria; Stoll, Gautier; Montanaro, Donatella; Uszczynska-Ratajczak, Barbara; Klein, Cecilia C.; Vlasova, Anna; Botti, Gerardo; D'Aiuto, Massimiliano; Baldi, Alfonso; Guigó Serra, Roderic; Kroemer, Guido; Maiuri, Maria Chiara; Salvatore, Francesco (Elsevier, 2020)

  The molecular complexity of human breast cancer (BC) renders the clinical management of the disease challenging. Long non-coding RNAs (lncRNAs) are promising biomarkers for BC patient stratification, early detection, and ...
• Structural analysis of SARS-CoV-2 genome and predictions of the human interactome

  Vandelli, Andrea; Monti, Michele; Milanetti, Edoardo; Armaos, Alexandros, 1989-; Rupert, Jakob; Zacco, Elsa; Bechara, Elias; Delli Ponti, Riccardo, 1987-; Tartaglia, Gian Gaetano (Oxford University Press, 2020)

  Specific elements of viral genomes regulate interactions within host cells. Here, we calculated the secondary structure content of >2000 coronaviruses and computed >100 000 human protein interactions with severe acute ...
• Modulation-enhanced localization microscopy

  Reymond, Loïc; Huser, Thomas; Ruprecht, Verena; Wieser, Stefan (IOP Publishing Ltd., 2020)

  Super-resolution fluorescence microscopy has become a powerful tool in cell biology to observe sub-cellular organization and molecular details below the diffraction limit of light. Super-resolution methods are generally ...
• The value of mouse models of rare diseases: a spanish experience

  Murillo-Cuesta, Silvia; Artuch, Rafael; Asensio, Fernando; Villa, Pedro de la; Dierssen, Mara; Enríquez, Jose Antonio; Fillat i Fonts, Cristina; Fourcade, Stéphane; Ibáñez, Borja; Montoliu, Lluis; Oliver, Eduardo; Pujol, Aurora, 1968-; Salido, Eduardo; Vallejo, Mario; Varela Nieto, Isabel (Frontiers, 2020)

  Animal models are invaluable for biomedical research, especially in the context of rare diseases, which have a very low prevalence and are often complex. Concretely mouse models provide key information on rare disease ...
• The function of GORASPs in Golgi apparatus organization in vivo

  Grond, Rianne; Veenendaal, Tineke; Duran, Juan M.; Raote, Ishier; Van Es, Johan H.; Corstjens, Sebastiaan; Delfgou, Laura; El Haddouti, Benaissa; Malhotra, Vivek; Rabouille, Catherine (Rockefeller University Press, 2020)

  In vitro experiments have shown that GRASP65 (GORASP1) and GRASP55 (GORASP2) proteins function in stacking Golgi cisternae. However, in vivo depletion of GORASPs in metazoans has given equivocal results. We have generated ...
• Internationalization of read-across as a validated new approach method (NAM) for regulatory toxicology

  Rovida, Costanza; Pastor Maeso, Manuel; Hartung, Thomas (ALTEX, 2020)

  Read-across (RAx) translates available information from well-characterized chemicals to a substance for which there is a toxicological data gap. The OECD is working on case studies to probe general applicability of RAx, ...
• Cirugía de la pared abdominal después del SARS-CoV-2: ¿es hora de restablecer los procedimientos no esenciales pospuestos?

  López Cano, Manuel; Saludes Serra, Judit; Rosselló Jiménez, Daniel; Pereira Rodríguez, José Antonio; Rodrigues Gonçalves, Victor; García Alamino, Josep M. (Elsevier, 2020)

  La pandemia por el COVID-19 nos ha encontrado desprotegidos ante la dificultad para dar una respuesta sanitaria adecuada y rápida. La red de hospitales del sistema sanitario público ha dispuesto la mayoría de los recursos ...
• TANGO1 membrane helices create a lipid diffusion barrier at curved membranes

  Raote, Ishier; Ernst, Andreas M.; Campelo, Felix; Rothman, James E.; Pincet, Frederic; Malhotra, Vivek (eLife, 2020)

  We have previously shown TANGO1 organises membranes at the interface of the endoplasmic reticulum (ER) and ERGIC/Golgi (Raote et al., 2018). TANGO1 corrals retrograde membranes at ER exit sites to create an export conduit. ...
• Chromatin-bound proteome profiling by genome capture

  Aranda Aragón, Sergio; Borràs, Eva; Sabidó Aguadé, Eduard, 1981-; Di Croce, Luciano (Elsevier, 2020)

  De novo identification of chromatin interactors can reveal unexpected pathways relevant to physiology and human disease. Inspired by the DNA mediated chromatin pull-down (Dm-ChP) technology (also known as iPOND [isolation ...
• RING1B recruits EWSR1-FLI1 and cooperates in the remodeling of chromatin necessary for Ewing sarcoma tumorigenesis

  Sánchez Molina, Sara; Figuerola, Elisabeth; Blanco, Enrique; Sánchez Jiménez, María; Táboas, Pablo; Gómez, Soledad; Ballaré, Cecilia Julia; García-Domínguez, Daniel J.; Prada, Estela; Hontecillas-Prieto, Lourdes; Carcaboso, Angel M.; Tirado, Oscar M.; Hernández Muñoz, Inmaculada; Alava, Enrique de; Lavarino, Cinzia; Di Croce, Luciano; Mora, Jaume (American Association for the Advancement of Science (AAAS), 2020)

  Ewing sarcoma (EwS) is an aggressive tumor that affects adolescents and young adults. EwS is defined by a chromosomal translocation, EWSR1-FLI1 being the most common, that causes genome reprogramming through remodeling of ...
• Determination of primary microRNA processing in clinical samples by targeted pri-miR-sequencing

  Conrad, Thomas; Ntini, Evgenia; Lang, Benjamin; Cozzuto, Luca; Andersen, Jesper B.; Marquardt, Jens U.; Ponomarenko, Julia; Tartaglia, Gian Gaetano; Vang Ørom, Ulf A. (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)

  MicroRNA expression is important for gene regulation and deregulated microRNA expression is often observed in diseases such as cancer. The processing of primary microRNA transcripts is an important regulatory step in ...
• Novel loci for childhood body mass index and shared heritability with adult cardiometabolic traits

  Vogelezang, Suzanne; Vilor Tejedor, Natàlia, 1988-; Bustamante Pineda, Mariona; Vrijheid, Martine; Sunyer Deu, Jordi; Felix, Janine Frédérique (Public Library of Science (PLoS), 2020)

  The genetic background of childhood body mass index (BMI), and the extent to which the well-known associations of childhood BMI with adult diseases are explained by shared genetic factors, are largely unknown. We performed ...
• PyHIST: A Histological Image Segmentation Tool

  Muñoz-Aguirre, Manuel; Ntasis, Vasilis F.; Rojas, Santiago; Guigó Serra, Roderic (Public Library of Science (PLoS), 2020)

  The development of increasingly sophisticated methods to acquire high-resolution images has led to the generation of large collections of biomedical imaging data, including images of tissues and organs. Many of the current ...
• Model-driven design allows growth of Mycoplasma pneumoniae on serum-free media

  Gaspari, Erika; Malachowski, Antoni; García Morales, Luis; Burgos, Raul; Serrano Pubull, Luis, 1982-; Martins dos Santos, Vitor; Suarez-Diez, Maria (Nature Research, 2020)

  Mycoplasma pneumoniae is a slow-growing, human pathogen that causes atypical pneumonia. Because it lacks a cell wall, many antibiotics are ineffective. Due to its reduced genome and dearth of many biosynthetic pathways, ...
• Framework for quality assessment of whole genome cancer sequences

  Whalley, Justin P.; Stobbe, Miranda D.; Beltran, Sergi; Gut, Marta; Trotta, Jean-Remi; Gut, Ivo Glynne (Nature Research, 2020)

  Bringing together cancer genomes from different projects increases power and allows the investigation of pan-cancer, molecular mechanisms. However, working with whole genomes sequenced over several years in different ...
• Nuclear gene proximity and protein interactions shape transcript covariations in mammalian single cells

  Tarbier, Marcel; Mackowiak, Sebastian D.; Frade, João; Catuara Solarz, Silvina, 1986-; Biryukova, Inna; Gelali, Eleni; Bárcena Menéndez, Diego, 1984-; Zapata Ortiz, Luis, 1985-; Ossowski, Stephan; Bienko, Magda; Gallant, Caroline J.; Friedländer, Marc R. (Nature Research, 2020)

  Single-cell RNA sequencing studies on gene co-expression patterns could yield important regulatory and functional insights, but have so far been limited by the confounding effects of differentiation and cell cycle. We apply ...
• The altered transcriptome of pediatric myelodysplastic syndrome revealed by RNA sequencing

  Zubovic, Lorena; Piazza, Silvano; Tebaldi, Toma; Cozzuto, Luca; Palazzo, Giuliana; Sidarovich, Viktoryia; Sanctis, Verónica de; Bertorelli, Roberto; Lammens, Tim; Hofmans, Mattias; Moerloose, Bárbara de; Ponomarenko, Julia; Pigazzi, Martina; Masetti, Riccardo; Mecucci, Cristina; Basso, Giuseppe; Macchi, Paolo (BioMed Central, 2020)

  Pediatric myelodysplastic syndrome (PMDS) is a very rare and still poorly characterized disorder. In this work, we identified novel potential targets of PMDS by determining genes with aberrant expression, which can be ...
• Characterization of an eutherian gene cluster generated after transposon domestication identifies Bex3 as relevant for advanced neurological functions

  Navas Pérez, Enrique; Cuscó Pons, Pol, 1987-; García Fernàndez, Jordi (BioMed Central, 2020)

  Background: One of the most unusual sources of phylogenetically restricted genes is the molecular domestication of transposable elements into a host genome as functional genes. Although these kinds of events are sometimes ...

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