• Hybridization and emergence of virulence in opportunistic human yeast pathogens

  Mixão, Verónica; Gabaldón Estevan, Juan Antonio, 1973- (Wiley, 2018)

  Hybridization between different species can result in the emergence of new lineages and adaptive phenotypes. Occasionally, hybridization in fungal organisms can drive the appearance of opportunistic lifestyles or shifts ...
• Misidentification of genome assemblies in public databases: The case of Naumovozyma dairenensis and proposal of a protocol to correct misidentifications

  Stavrou, Aimilia A.; Mixão, Verónica; Boekhout, Teun; Gabaldón Estevan, Juan Antonio, 1973- (Wiley, 2018)

  Online sequence databases such as NCBI GenBank serve as a tremendously useful platform for researchers to share and reuse published data. However, submission systems lack control for errors such as organism misidentification, ...
• Eicosanoid biosynthesis influences the virulence of Candida parapsilosis

  Chakraborty, Tanmoy; Thuer, Ernst, 1986-; Heijink, Marieke; Tóth, Renáta; Bodai, László; Vágvölgyi, Csaba; Giera, Martin; Gabaldón Estevan, Juan Antonio, 1973-; Gácser, Attila (Taylor & Francis, 2018)

  Lipid mediators, derived from arachidonic acid metabolism, play an important role in immune regulation. The functions of bioactive eicosanoids range from modulating cytokine signaling and inflammasome formation to ...
• Investigation of Candida parapsilosis virulence regulatory factors during host-pathogen interaction

  Tóth, Renáta; Cabral, Vitor; Thuer, Ernst, 1986-; Bohner, Flóra; Németh, Tibor; Papp, Csaba; Nimrichter, Leonardo; Molnár, Gergő; Vágvölgyi, Csaba; Gabaldón Estevan, Juan Antonio, 1973-; Nosanchuk, Joshua D.; Gácser, Attila (Nature Research, 2018)

  Invasive candidiasis is among the most life-threatening infections in patients in intensive care units. Although Candida albicans is the leading cause of candidaemia, the incidence of Candida parapsilosis infections is ...
• Deciphering the mechanism of action of 089, a compound impairing the fungal cell cycle

  Stefanini, Irene; Rizzetto, Lisa; Rivero, Damariz; Carbonell, Silvia; Gut, Marta; Heath, Simon; Gut, Ivo Glynne; Trabocchi, Andrea; Guarna, Antonio; Ben Ghazzi, Nagwa; Bowyer, Paul; Kapushesky, Misha; Cavalieri, Duccio (Nature Research, 2018)

  Fungal infections represent an increasingly relevant clinical problem, primarily because of the increased survival of severely immune-compromised patients. Despite the availability of active and selective drugs and of ...
• Knock-down of AHCY and depletion of adenosine induces DNA damage and cell cycle arrest

  Belužić, Lucija; Grbeša, Ivana; Belužić, Robert; Park, Jong Hoon; Kong, Hyun Kyung; Kopjar, Nevenka; Espadas, Guadalupe; Sabidó Aguadé, Eduard, 1981-; Lepur, Adriana; Rokić, Filip; Jerić, Ivanka; Brkljačić, Lidija; Vugrek, Oliver (Nature Research, 2018)

  Recently, functional connections between S-adenosylhomocysteine hydrolase (AHCY) activity and cancer have been reported. As the properties of AHCY include the hydrolysis of S-adenosylhomocysteine and maintenance of the ...
• Somatic alterations compromised molecular diagnosis of DOCK8 hyper-IgE syndrome caused by a novel intronic splice site mutation

  Hagl, Beate; Spielberger, Benedikt D.; Thoene, Silvia; Bonnal, Sophie; Mertes, Christian; Winter, Christof; Nijman, Isaac J.; Verduin, Shira; Eberherr, Andreas C.; Puel, Anne; Schindler, Detlev; Ruland, Jürgen; Meitinger, Thomas; Gagneur, Julien; Orange, Jordan S.; van Gijn, Marielle E.; Renner, Ellen D. (Nature Research, 2018)

  In hyper-IgE syndromes (HIES), a group of primary immunodeficiencies clinically overlapping with atopic dermatitis, early diagnosis is crucial to initiate appropriate therapy and prevent irreversible complications. ...
• Music recommendation diversity: a tentative framework and preliminary results

  Porcaro, Lorenzo; Castillo, Carlos; Gómez Gutiérrez, Emilia, 1975- (International Society for Music Information Retrieval (ISMIR), 2019)

  Music recommendations are increasingly part of the listening experience of people all over the world, especially in the context of streaming services. In this scenario, recommender systems’ role is to help users in ...
• nextPARS: parallel probing of RNA structures in Illumina

  Saus Martínez, Ester; Willis, Jesse R.; Pryszcz, Leszek Piotr, 1985-; Hafez, Ahmed; Llorens, Carlos; Himmelbauer, Heinz; Gabaldón Estevan, Juan Antonio, 1973- (Cold Spring Harbor Laboratory Press (CSHL Press), 2018)

  RNA molecules play important roles in virtually every cellular process. These functions are often mediated through the adoption of specific structures that enable RNAs to interact with other molecules. Thus, determining ...
• Genetically encodable bioluminescent system from fungi

  Kotlobay, Alexey A.; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973-; Yampolsky, Ilia V. (National Academy of Sciences, 2018)

  Bioluminescence is found across the entire tree of life, conferring a spectacular set of visually oriented functions from attracting mates to scaring off predators. Half a dozen different luciferins, molecules that emit ...
• RES complex is associated with intron definition and required for zebrafish early embryogenesis

  Fernández, Juan Pablo; Moreno Mateos, Miguel Ángel; Gohr, André; Miao, Liyun; Chan, Shun Hang; Irimia, Manuel; Giraldez, Antonio J. (Public Library of Science (PLoS), 2018)

  Pre-mRNA splicing is a critical step of gene expression in eukaryotes. Transcriptome-wide splicing patterns are complex and primarily regulated by a diverse set of recognition elements and associated RNA-binding proteins. ...
• The Integrator complex regulates differential snRNA processing and fate of adult stem cells in the highly regenerative planarian Schmidtea mediterranea

  Schmidt, David; Reuter, Hanna; Hüttner, Katja; Ruhe, Larissa; Rabert, Franziska; Seebeck, Florian; Irimia, Manuel; Solana, Jordi; Bartscherer, Kerstin (Public Library of Science (PLoS), 2018)

  In multicellular organisms, cell type diversity and fate depend on specific sets of transcript isoforms generated by post-transcriptional RNA processing. Here, we used Schmidtea mediterranea, a flatworm with extraordinary ...
• Walking along chromosomes with super-resolution imaging, contact maps, and integrative modeling

  Nir, Guy; Farabella, Irene; Soler-Vila, Paula; Martí Renom, Marc A.; Wu, C.-ting (Public Library of Science (PLoS), 2018)

  Chromosome organization is crucial for genome function. Here, we present a method for visualizing chromosomal DNA at super-resolution and then integrating Hi-C data to produce three-dimensional models of chromosome ...
• Hair cell identity establishes labeled lines of directional mechanosensation

  Lozano Ortega, Marta; Valera, Gema; Xiao, Yan; Faucherre, Adèle; López-Schier, Hernán (Public Library of Science (PLoS), 2018)

  Directional mechanoreception by hair cells is transmitted to the brain via afferent neurons to enable postural control and rheotaxis. Neuronal tuning to individual directions of mechanical flow occurs when each peripheral ...
• Genome sequence of the brown rot fungal pathogen Monilinia laxa

  Naranjo Ortiz, Miguel Ángel, 1989-; Rodríguez-Píres, Silvia; Torres, Rosario; De Cal, Antonieta; Usall, Josep; Gabaldón Estevan, Juan Antonio, 1973- (American Society for Microbiology, 2018)

  Monilinia laxa (phylum Ascomycota) is a plant pathogen responsible for the brown rot blossom blight disease in stone fruit trees of the Rosaceae family, such as apricots. We report here the genome sequence of strain 8L of ...
• Key features of turing systems are determined purely by network topology

  Diego, Xavier; Marcon, Luciano, 1983-; Müller, Patrick; Sharpe, James (American Physical Society, 2018)

  Turing’s theory of pattern formation is a universal model for self-organization, applicable to many systems in physics, chemistry, and biology. Essential properties of a Turing system, such as the conditions for the existence ...
• A damped oscillator imposes temporal order on posterior gap gene expression in Drosophila

  Verd Fernández, Berta, 1984-; Clark, Erik; Wotton, Karl R.; Janssens, Hilde; Jiménez Guri, Eva; Crombach, Anton; Jaeger, Johannes, 1973- (Public Library of Science (PLoS), 2018)

  Insects determine their body segments in two different ways. Short-germband insects, such as the flour beetle Tribolium castaneum, use a molecular clock to establish segments sequentially. In contrast, long-germband insects, ...
• HMC-reliefF: feature ranking for hierarchical multi-label classification

  Slavkov, Ivica; Karcheska, Jana; Kocev, Dragi; Džeroski, Sašo (ComSIS Consortium, 2018)

  In machine learning, the growing complexity of the available data poses an increased challenge for its analysis. The rising complexity is both in terms of the data becoming more high-dimensional as well as the data having ...
• ResMarkerDB: a database of biomarkers of response to antibody therapy in breast and colorectal cancer

  Pérez-Granado, Judith; Piñero González, Janet, 1977-; Furlong, Laura I., 1971- (Oxford University Press, 2019)

  The clinical efficacy of therapeutic monoclonal antibodies for breast and colorectal cancer has greatly contributed to the improvement of patients' outcomes by individualizing their treatments according to their genomic ...
• A nomenclature and classification for the congenital myasthenic syndromes: preparing for FAIR data in the genomic era

  Thompson, Rachel; Abicht, Angela; Beeson, David; Engel, Andrew G.; Eymard, Bruno; Maxime, Emmanuel; Lochmüller, Hanns (BioMed Central, 2018)

  Background: Congenital myasthenic syndromes (CMS) are a heterogeneous group of inherited neuromuscular disorders sharing the common feature of fatigable weakness due to defective neuromuscular transmission. Despite rapidly ...

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