• 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 ...
• PD-1 signaling affects cristae morphology and leads to mitochondrial dysfunction in human CD8+ T lymphocytes

  Ogando, Jesús; Sáez, María Eugenia; Santos, Javier; Nuevo-Tapioles, Cristina; Gut, Marta; Esteve-Codina, Anna; Heath, Simon; González-Pérez, Antonio; Cuezva, José M.; Lacalle, Rosa Ana; Mañes, Santos (BioMed Central, 2019)

  Background: Binding of the programmed death-1 (PD-1) receptor to its ligands (PD-L1/2) transduces inhibitory signals that promote exhaustion of activated T cells. Blockade of the PD-1 pathway is widely used for cancer ...
• EV-associated miRNAs from peritoneal lavage as potential diagnostic biomarkers in colorectal cancer

  Roman-Canal, Berta; Tarragona, Jordi; Moiola, Cristian Pablo; Gatius, Sònia; Bonnin, Sarah; Ruiz-Miró, Maria; Sierra, José Enrique; Rufas, Maria; González, Esperanza; Porcel, José M.; Gil-Moreno, Antonio; Falcón-Pérez, Juan M.; Ponomarenko, Julia; Matias-Guiu, Xavier; Colas, Eva (BioMed Central, 2019)

  Background: Colorectal cancer (CRC) is the third leading cause of cancer-related mortality worldwide. Current systematic methods for diagnosing have inherent limitations so development of a minimally-invasive diagnosis, ...
• Single-cell transcriptomics unveils gene regulatory network plasticity

  Iacono, Giovanni; Massoni-Badosa, Ramon; Heyn, Holger (BioMed Central, 2019)

  Background: Single-cell RNA sequencing (scRNA-seq) plays a pivotal role in our understanding of cellular heterogeneity. Current analytical workflows are driven by categorizing principles that consider cells as individual ...
• PRDM14 controls X-chromosomal and global epigenetic reprogramming of H3K27me3 in migrating mouse primordial germ cells

  Mallol, Anna; Guirola, Maria; Payer, Bernhard, 1975- (BioMed Central, 2019)

  Background: In order to prepare the genome for gametogenesis, primordial germ cells (PGCs) undergo extensive epigenetic reprogramming during migration toward the gonads in mammalian embryos. This includes changes on a ...
• 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 ...
• EV-associated miRNAs from peritoneal lavage are a source of biomarkers in endometrial cancer

  Roman-Canal, Berta; Pablo-Moiola, Cristian; Gatius, Sònia; Bonnin, Sarah; Ruiz-Miró, Maria; González, Esperanza; González-Tallada, Xavier; Llordella, Ivanna; Hernández, Isabel; Porcel, José M.; Gil-Moreno, Antonio; Falcón-Pérez, Juan M.; Ponomarenko, Julia; Matias-Guiu, Xavier; Colas, Eva (MDPI, 2019)

  Endometrial cancer (EC) is the sixth most common cancer in women worldwide and is responsible for more than 89,000 deaths every year. Mortality is associated with presence of poor prognostic factors at diagnosis, i.e., ...
• 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 ...
• Protein transport by vesicles and tunnels

  Raote, Ishier; Malhotra, Vivek (Rockefeller University Press, 2019)

  Palade's corpus placed small vesicles as the sole means to transport proteins across stable distinct compartments of the secretory pathway. We suggest that cargo, spatial organization of secretory compartments, and the ...
• 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 ...
• Yap/Taz-TEAD activity links mechanical cues to progenitor cell behavior during zebrafish hindbrain segmentation

  Voltes Cobo, Adrià, 1991-; Hevia, Covadonga F.; Engel-Pizcueta, Carolyn; Dingare, Chaitanya; Calzolari, Simone, 1983-; Terriente, Javier; Norden, Caren; Lecaudey, Virginie; Pujades Corbi, Cristina (Company of Biologists, 2019)

  Cells perceive their microenvironment through chemical and physical cues. However, how the mechanical signals are interpreted during embryonic tissue deformation to result in specific cell behaviors is largely unknown. The ...
• Human albumin impairs amyloid β-peptide fibrillation through its C-terminus: from docking modeling to protection against neurotoxicity in alzheimer's disease

  Picón-Pagès, Pol; Bonet Martínez, Jaume, 1982-; García-García, Javier, 1982-; Garcia-Buendia, Joan; Gutierrez, Daniela; Valle, Javier; Gómez-Casuso, Carmen E.S.; Sidelkivska, Valeriya; Alvarez, Alejandra; Perálvarez Marín, Alex; Suades, Albert; Fernàndez Busquets, Xavier; Andreu Martínez, David; Vicente García, Rubén, 1978-; Oliva Miguel, Baldomero; Muñoz López, Francisco José, 1964- (Elsevier, 2019)

  Alzheimer's disease (AD) is a neurodegenerative process characterized by the accumulation of extracellular deposits of amyloid β-peptide (Aβ), which induces neuronal death. Monomeric Aβ is not toxic but tends to aggregate ...
• 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 ...
• 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 ...
• Applicability of the mutation-selection balance model to population genetics of heterozygous protein-truncating variants in humans

  Weghorn, Donate; Balick, Daniel J.; Cassa, Christopher; Kosmicki, Jack A.; Daly, Mark J.; Beier, David R.; Sunyaev, Shamil R. (Oxford University Press, 2019)

  The fate of alleles in the human population is believed to be highly affected by the stochastic force of genetic drift. Estimation of the strength of natural selection in humans generally necessitates a careful modeling ...
• Extensive post-transcriptional buffering of gene expression in the response to severe oxidative stress in baker's yeast

  Blevins, William R.; Tavella, Teresa; Moro, Simone G.; Blasco Moreno, Bernat, 1986-; Closa-Mosquera, Adrià; Díez Antón, Juana, 1962-; Carey, Lucas; Albà Soler, Mar (Nature Research, 2019)

  Cells responds to diverse stimuli by changing the levels of specific effector proteins. These changes are usually examined using high throughput RNA sequencing data (RNA-Seq); transcriptional regulation is generally assumed ...
• Sugar-containing beverages consumption and obesity in children aged 4-5 years in Spain: the INMA study

  Gonzalez-Palacios, Sandra; Navarrete-Muñoz, Eva-María; García-de-la-Hera, Manoli; Torres-Collado, Laura; Santa Marina, Loreto; Amiano, Pilar; Lopez-Espinosa, Maria-José; Tardón, Adonina; Riano-Galan, Isolina; Vrijheid, Martine; Sunyer Deu, Jordi; Vioque, Jesus (MDPI, 2019)

  The consumption of sugar-containing beverages (SCB) has been associated with obesity although the evidence in preschool children is scarce. Cross-sectional analyses were performed to assess the association between obesity ...
• 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 ...

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