• Pitfalls in assessing stromal tumor infiltrating lymphocytes (sTILs) in breast cancer

  Kos, Zuzana; Comerma Blesa, Laura, 1983-; Salgado, Roberto; International Immuno-Oncology Biomarker Working Group (Nature Research, 2020)

  Stromal tumor-infiltrating lymphocytes (sTILs) are important prognostic and predictive biomarkers in triple-negative (TNBC) and HER2-positive breast cancer. Incorporating sTILs into clinical practice necessitates reproducible ...
• 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 ...
• DualSeqDB: the host-pathogen dual RNA sequencing database for infection processes

  Macho Rendón, Javier; Lang, Benjamin; Ramos Llorens, Marc; Tartaglia, Gian Gaetano; Torrent Burgas, Marc (Oxford University Press, 2020)

  Despite antibiotic resistance being a matter of growing concern worldwide, the bacterial mechanisms of pathogenesis remain underexplored, restraining our ability to develop new antimicrobials. The rise of high-throughput ...
• RNA as the stone guest of protein aggregation

  Louka, Alexandra; Zacco, Elsa; Temussi, Piero Andrea; Tartaglia, Gian Gaetano; Pastore, Annalisa (Oxford University Press, 2020)

  The study of prions as infectious aggregates dates several decades. From its original formulation, the definition of a prion has progressively changed to the point that many aggregation-prone proteins are now considered ...
• 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 ...
• Quantifying the monomer-dimer equilibrium of tubulin with mass photometry

  Fineberg, Adam; Surrey, Thomas; Kukura, Philipp (Elsevier, 2020)

  The αβ-tubulin heterodimer is the fundamental building block of microtubules, making it central to several cellular processes. Despite the apparent simplicity of heterodimerisation, the associated energetics and kinetics ...
• Neural sensitivity to syllable frequency and mutual information in speech perception and production

  Tremblay, Pascale; Deschamps, Isabelle; Baroni, Marco; Hasson, Uri (Elsevier, 2016)

  Many factors affect our ability to decode the speech signal, including its quality, the complexity of the elements that compose it, as well as their frequency of occurrence and co-occurrence in a language. Syllable frequency ...
• 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 ...
• Web-based embodied conversational agents and older people

  Llorach, Gerard; Agenjo, Javier; Blat, Josep; Sayago Barrantes, Sergio (Springer, 2019)

  Within Human-Computer Interaction, there has recently been an important turn to embodied and voice-based interaction. In this chapter, we discuss our ongoing research on building online Embodied Conversational Agents (ECAs), ...
• 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 ...
• Hierarchical multi-scale set-class analysis

  Martorell Domínguez, Agustín; Gómez Gutiérrez, Emilia, 1975- (Taylor & Francis, 2015)

  This work presents a systematic methodology for set-class surface analysis using temporal multi-scale techniques. The method extracts the set-class content of all the possible temporal segments, addressing the representational ...
• Mapping between dynamic markings and performed loudness: a machine learning approach

  Kosta, Katerina; Ramírez, Rafael,1966-; Bandtlow, Oscar F.; Chew, Elaine (Taylor & Francis, 2016)

  Loudness variation is one of the foremost tools for expressivity in music performance. Loudness is frequently notated as dynamic markings such as p (piano, meaning soft) or f (forte, meaning loud). While dynamic markings ...
• 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 ...
• 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 ...
• Metabolic shift underlies recovery in reversible infantile respiratory chain deficiency

  Hathazi, Denisa; Lochmüller, Hanns; Horvath, Rita (EMBRO Press, 2020)

  Reversible infantile respiratory chain deficiency (RIRCD) is a rare mitochondrial myopathy leading to severe metabolic disturbances in infants, which recover spontaneously after 6-months of age. RIRCD is associated with ...
• Brain states and transitions: insights from computational neuroscience

  Kringelbach, Morten L.; Deco, Gustavo (Elsevier, 2020)

  Within the field of computational neuroscience there are great expectations of finding new ways to rebalance the complex dynamic system of the human brain through controlled pharmacological or electromagnetic perturbation. ...

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