• Communicating genome architecture: biovisualization of the genome, from data analysis and hypothesis generation to communication and learning

  Goodstadt, Mike N.; Martí Renom, Marc A. (Elsevier, 2019)

  Genome discoveries at the core of biology are made by visual description and exploration of the cell, from microscopic sketches and biochemical mapping to computational analysis and spatial modeling. We outline the ...
• Specific contributions of cohesin-SA1 and cohesin-SA2 to TADs and polycomb domains in embryonic stem cells

  Cuadrado, Ana; Giménez-Llorente, Daniel; Kojic, Aleksandar; Rodríguez-Corsino, Miriam; Cuartero, Yasmina; Martín-Serrano, Guillermo; Gómez López, Gonzalo; Marti-Renom, Marc A.; Losada, Ana (Elsevier, 2019)

  Cohesin exists in two variants carrying either STAG/SA1 or SA2. Here we have addressed their specific contributions to the unique spatial organization of the mouse embryonic stem cell genome, which ensures super-enhancer-dependent ...
• A Model for evaluating popularity and semantic information variations in radio listening sessions

  Porcaro, Lorenzo; Gómez Gutiérrez, Emilia, 1975- (2019)

  Listening to music radios is an activity that since the 20th century is part of the cultural habits for people all over the world. While in the case of analog radios DJs are in charge of selecting the music to be ...
• Transcriptomic analyses reveal groups of co-expressed, syntenic lncRNAs in four species of the genus Caenorhabditis

  Pegueroles Queralt, Maria Cinta; Iraola Guzman, Susana; Chorostecki, Uciel; Ksiezopolska, Ewa; Saus Martínez, Ester; Gabaldón Estevan, Juan Antonio, 1973- (Taylor & Francis, 2019)

  Long non-coding RNAs (lncRNAs) are a heterogeneous class of genes that do not code for proteins. Since lncRNAs (or a fraction thereof) are expected to be functional, many efforts have been dedicated to catalog lncRNAs in ...
• Targeted therapies for congenital myasthenic syndromes: systematic review and steps towards a treatabolome

  Thompson, Rachel; Bonne, Gisèle; Missier, Paolo; Lochmüller, Hanns (Portland Press, 2019)

  Despite recent scientific advances, most rare genetic diseases - including most neuro-muscular diseases - do not currently have curative gene-based therapies available. However, in some cases, such as vitamin, cofactor or ...
• ya||a: GPU-Powered spheroid models for mesenchyme and epithelium

  Germann, Philipp; Marin-Riera, Miquel; Sharpe, James (Elsevier, 2019)

  Simulating morphogenesis of both mesenchyme and epithelium has typically required complex and computationally expensive models. To meet this challenge, we developed ya||a-yet another parallel agent-based model. Our model ...
• Personal exposure to particulate matter in peri-urban India: predictors and association with ambient concentration at residence

  Sanchez, Margaux; Milà, Carles; Sreekanth, V.; Balakrishnan, Kalpana; Sambandam, Sankar; Nieuwenhuijsen, Mark J.; Kinra, Sanjay; Marshall, Julian D.; Tonne, Cathryn (Nature Research, 2019)

  Scalable exposure assessment approaches that capture personal exposure to particles for purposes of epidemiology are currently limited, but valuable, particularly in low-/middle-income countries where sources of personal ...
• The role of blank filter mass in attenuation measurements using an off-line transmissometer

  Sreekanth, V.; Tonne, Cathryn; Salmon, Maëlle; Arulselvan, S.; Marshall, Julian D. (Elsevier, 2019)

  We describe how reference filter characteristics (unexposed weights) can influence instrument-reported attenuation (thereby black carbon concentrations) using the OT21 (SootScan Optical Transmissometer), in the case of ...
• Integrated assessment of exposure to PM2.5 in South India and its relation with cardiovascular risk: Design of the CHAI observational cohort study

  Tonne, Cathryn; Salmon, Maëlle; Sanchez, Margaux; Sreekanth, V.; Bhogadi, Santhi; Sambandam, Sankar; Balakrishnan, Kalpana; Kinra, Sanjay; Marshall, Julian D. (Elsevier, 2017)

  While there is convincing evidence that fine particulate matter causes cardiovascular mortality and morbidity, little of the evidence is based on populations outside of high income countries, leaving large uncertainties ...
• Empirical mean-noise fitness landscapes reveal the fitness impact of gene expression noise

  Schmiedel, Jörn M.; Carey, Lucas; Lehner, Ben, 1978- (Nature Research, 2019)

  The effects of cell-to-cell variation (noise) in gene expression have proven difficult to quantify because of the mechanistic coupling of noise to mean expression. To independently quantify the effects of changes in mean ...
• Characterization of the non-stationary nature of steady-state visual evoked potentials using echo state networks

  Ibáñez Soria, David, 1983-; Soria Frisch, Aureli; García Ojalvo, Jordi; Ruffini, Giulio (Public Library of Science (PLoS), 2019)

  State Visual Evoked Potentials (SSVEPs) arise from a resonance phenomenon in the visual cortex that is produced by a repetitive visual stimulus. SSVEPs have long been considered a steady-state response resulting from purely ...
• Blockade of the sigma-1 receptor relieves cognitive and emotional impairments associated to chronic osteoarthritis pain

  Carcolé, Mireia; Zamanillo, Daniel; Merlos, Manuel; Fernández-Pastor, Begoña; Cabañero Ferri, David; Maldonado, Rafael, 1961- (Frontiers, 2019)

  Osteoarthritis is the most common musculoskeletal disease worldwide, often characterized by degradation of the articular cartilage, chronic joint pain and disability. Cognitive dysfunction, anxiety and depression are common ...
• Community assessment to advance computational prediction of cancer drug combinations in a pharmacogenomic screen

  Menden, Michael P.; AstraZeneca-Sanger Drug Combination DREAM Consortium; Saez-Rodriguez, Julio (Nature Research, 2019)

  The effectiveness of most cancer targeted therapies is short-lived. Tumors often develop resistance that might be overcome with drug combinations. However, the number of possible combinations is vast, necessitating data-driven ...
• The role of socioeconomic status in the association of lung function and air pollution-A pooled analysis of three adult ESCAPE cohorts

  Keidel, Dirk; Antó i Boqué, Josep Maria; Basagaña Flores, Xavier; Burte, Marthe-Emilie, 1989-; Carsin, Anne-Elie; Sunyer Deu, Jordi; Jacquemin Leonard, Bénédicte; Probst-Hensch, Nicole (MDPI, 2019)

  Ambient air pollution is a leading environmental risk factor and its broad spectrum of adverse health effects includes a decrease in lung function. Socioeconomic status (SES) is known to be associated with both air pollution ...
• Identification of potential Music Information Retrieval technologies for computer-aided jingju singing training

  Gong, Rong; Serra, Xavier (2017)

  Music Information Retrieval (MIR) technologies have been proven useful in assisting western classical singing training. Jingju (also known as Beijing or Peking opera) singing is different from western singing in terms ...
• Early positivity signals changes in an abstract linguistic pattern

  Monte Ordoño, Julia, 1989-; Toro Soto, Juan Manuel, 1976- (Public Library of Science (PLoS), 2017)

  The extraction of abstract structures from speech (or from gestures in the case of sign languages) has been claimed to be a fundamental mechanism for language acquisition. In the present study we registered the neural ...
• Early neural responses underlie advantages for consonance over dissonance

  Crespo Bojorque, Paola, 1985-; Monte Ordoño, Julia, 1989-; Toro Soto, Juan Manuel, 1976- (Elsevier, 2018)

  Consonant musical intervals tend to be more readily processed than dissonant intervals. In the present study, we explore the neural basis for this difference by registering how the brain responds after changes in consonance ...
• Learning a new selection rule in visual and frontal cortex

  van der Togt, Chris; Stănişor, Liviu; Pooresmaeili, Arezoo; Albantakis, Larissa; Deco, Gustavo; Roelfsema, Pieter R. (Oxford University Press, 2016)

  How do you make a decision if you do not know the rules of the game? Models of sensory decision-making suggest that choices are slow if evidence is weak, but they may only apply if the subject knows the task rules. Here, ...
• Human consciousness is supported by dynamic complex patterns of brain signal coordination

  Demertzi, A.; Tagliazucchi, Enzo; Dehaene, Stanislas; Deco, Gustavo; Barttfeld, P.; Raimondo, F.; Martial, C.; Fernández-Espejo, D.; Rohaut, B.; Voss, H. U.; Schiff, N. D.; Owen, A. M.; Laureys, S.; Naccache, L.; Sitt, J. D. (American Association for the Advancement of Science (AAAS), 2019)

  Adopting the framework of brain dynamics as a cornerstone of human consciousness, we determined whether dynamic signal coordination provides specific and generalizable patterns pertaining to conscious and unconscious states ...
• Data augmentation for instrument classification robust to audio effects

  Ramires, António; Serra, Xavier (2019)

  Reusing recorded sounds (sampling) is a key component in Electronic Music Production (EMP), which has been present since its early days and is at the core of genres like hip-hop or jungle. Commercial and non-commercial ...

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