• bwtool: a tool for bigWig files

  Pohl, Andy, 1979-; Beato, Miguel (Oxford University Press, 2014)

  BigWig files are a compressed, indexed, binary format for genome-wide signal data for calculations (e.g. GC percent) or experiments (e.g. ChIP-seq/RNA-seq read depth). bwtool is a tool designed to read bigWig files rapidly ...
• Linking off-target kinase pharmacology to the differential cellular effects observed among PARP inhibitors

  Antolín Hernández, Albert, 1984-; Mestres i López, Jordi (Impact Journals, 2014)

  PARP inhibitors hold promise as a novel class of targeted anticancer drugs. However, their true mechanism of action is still not well understood following recent reports that show marked differences in cellular effects. ...
• ΔNp63α is an oncogene that targets chromatin remodeler Lsh to drive skin stem cell proliferation and tumorigenesis

  Keyes, William M., 1973-; Pecoraro, Matteo, 1984-; Aranda, Victoria; Vernersson Lindahl, Emma; Li, Wangzhi; Vogel, Hannes; Guo, Xuecui; Garcia, Elvin L.; Michurina, Tatyana V.; Enikolopov, Grigori; Muthuswamy, Senthil K.; Mills, Alea A. (Elsevier, 2011)

  The p53 homolog p63 is essential for development, yet its role in cancer is not clear. We discovered that p63 deficiency evokes the tumor-suppressive mechanism of cellular senescence, causing a striking absence of stratified ...
• XTACC3-XMAP215 association reveals an asymmetric interaction promoting microtubule elongation

  Mortuza, Gulnahar; Cavazza, Tommaso, 1985-; García Mayoral, María Flor; Hermida, Dario; Peset, Isabel; Pedrero, Juan G.; Merino, Nekane; Blanco, Francisco; Lyngsø, Jeppe; Bruix, Marta; Pedersen, Jan Skov; Vernos, Isabelle, 1959-; Montoya, Guillermo (Nature Research, 2014)

  chTOG is a conserved microtubule polymerase that catalyses the addition of tubulin dimers to promote microtubule growth. chTOG interacts with TACC3, a member of the transforming acidic coiled-coil (TACC) family. Here we ...
• Phosphorylation of the transcription factor Atf1 at multiple sites by the MAP kinase Sty1 controls homologous recombination and transcription

  Sánchez Mir, Laura; Fraile Beneitez, Rodrigo; Ayté del Olmo, José; Hidalgo Hernando, Elena (Elsevier, 2020)

  Transcription factors are often the downstream effectors of signaling cascades. In fission yeast, the transcription factor Atf1 is phosphorylated by the MAP kinase Sty1 under several environmental stressors to promote ...
• Genome-wide identification of Fas/CD95 alternative splicing regulators reveals links with iron homeostasis

  Tejedor Vaquero, Juan Ramón, 1984-; Papasaikas, Panagiotis; Valcárcel, J. (Juan) (Elsevier, 2015)

  Alternative splicing of Fas/CD95 exon 6 generates either a membrane-bound receptor that promotes, or a soluble isoform that inhibits, apoptosis. Using an automatized genome-wide siRNA screening for alternative splicing ...
• Functional splicing network reveals extensive regulatory potential of the core spliceosomal machinery

  Papasaikas, Panagiotis; Tejedor Vaquero, Juan Ramón, 1984-; Vigevani, Luisa, 1985-; Valcárcel, J. (Juan) (Elsevier, 2015)

  Pre-mRNA splicing relies on the poorly understood dynamic interplay between >150 protein components of the spliceosome. The steps at which splicing can be regulated remain largely unknown. We systematically analyzed the ...
• 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 ...

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