Browsing by Author "Pryszcz, Leszek Piotr, 1985-"

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  • Ancient dispersal of the human fungal pathogen Cryptococcus gattii from the Amazon rainforest
    Hagen, Ferry; Ceresini, Paulo C.; Polacheck, Itzhack; Ma, Hansong; Nieuwerburgh, Filip van; Gabaldón Estevan, Juan Antonio, 1973-; Kagan, Sarah; Pursall, E. Rhiannon; Hoogveld, Hans L.; Iersel, Leo J. van; Klau, Gunnar W.; Kelk, Steven M.; Stougie, Leen; Bartlett, Karen H.; Voelz, Kerstin; Pryszcz, Leszek Piotr, 1985-; Castañeda, Elizabeth; Lazera, Marcia; Meyer, Wieland; Deforce, Dieter; Meis, Jacques F.; May, Robin C.; Klaassen, Corné H. W.; Boekhout, Teun (Public Library of Science (PLoS), 2013)
    Over the past two decades, several fungal outbreaks have occurred, including the high-profile 'Vancouver Island' and 'Pacific Northwest' outbreaks, caused by Cryptococcus gattii, which has affected hundreds of otherwise ...
  • Distinct roles of the polarity factors Boi1 and Boi2 in the control of exocytosis and abscission in budding yeast
    Masgrau Fortuny, Aina, 1986-; Battola, Andrea, 1987-; Sanmartín Olmo, Trinidad; Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Mendoza, Manuel (Mendoza Palomares) (American Society for Cell Biology, 2017)
    Boi1 and Boi2 (Boi1/2) are budding yeast plasma membrane proteins that function in polarized growth, and in cytokinesis inhibition in response to chromosome bridges via the NoCut abscission checkpoint. How Boi1/2 act in ...
  • Enhanced detection of RNA modifications and read mapping with high-accuracy nanopore RNA basecalling models
    Diensthuber, Gregor; Pryszcz, Leszek Piotr, 1985-; Llovera Nadal, Laia; Lucas, Morghan C.; Delgado-Tejedor, Anna; Cruciani, Sonia; Roignant, Jean-Yves; Begik, Oguzhan; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2024)
    In recent years, nanopore direct RNA sequencing (DRS) became a valuable tool for studying the epitranscriptome, due to its ability to detect multiple modifications within the same full-length native RNA molecules. While ...
  • Epigenetic response of yarrowia lipolytica to stress: tracking methylation level and search for methylation patterns via whole-genome sequencing
    Kubiak-Szymendera, Monika; Pryszcz, Leszek Piotr, 1985-; Biatas, Wojciech; Celinska, Ewelina (MDPI, 2021)
    DNA methylation is a common, but not universal, epigenetic modification that plays an important role in multiple cellular processes. While definitely settled for numerous plant, mammalian, and bacterial species, the genome ...
  • Eukaryotic transporters for hydroxyderivatives of benzoic acid
    Cillingová, Andrea; Zeman, Igor; Tóth, Renáta; Neboháčová, Martina; Dunčková, Ivana; Hölcová, Mária; Jakúbková, Michaela; Gérecová, Gabriela; Pryszcz, Leszek Piotr, 1985-; Tomáška, L'ubomír; Gabaldón Estevan, Juan Antonio, 1973-; Gácser, Attila; Nosek, Jozef (Nature Publishing Group, 2017)
    Several yeast species catabolize hydroxyderivatives of benzoic acid. However, the nature of carriers responsible for transport of these compounds across the plasma membrane is currently unknown. In this study, we analyzed ...
  • Genome analysis of Candida subhashii reveals its hybrid nature and dual mitochondrial genome conformations
    Mixão, Verónica; Hegedűsová, Eva; Saus Martínez, Ester; Pryszcz, Leszek Piotr, 1985-; Cillingová, Andrea; Nosek, Jozef; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2021)
    Candida subhashii belongs to the CUG-Ser clade, a group of phylogenetically closely related yeast species that includes some human opportunistic pathogens, such as Candida albicans. Despite being present in the environment, ...
  • Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex
    Mixão, Verónica de Pinho, 1991-; del Olmo, Valentina; Hegedűsová, Eva; Saus Martínez, Ester; Pryszcz, Leszek Piotr, 1985-; Cillingová, Andrea; Nosek, Jozef; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2022)
    Candida parapsilosis species complex comprises three important pathogenic species: Candida parapsilosis sensu stricto, Candida orthopsilosis and Candida metapsilosis. The majority of C. orthopsilosis and all C. metapsilosis ...
  • Genome comparison of Candida orthopsilosis clinical strains reveals the existence of hybrids between two distinct subspecies
    Pryszcz, Leszek Piotr, 1985-; Németh, Tibor; Gácser, Attila; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2014)
    The Candida parapsilosis species complex comprises a group of emerging human pathogens of varying virulence. This complex was recently subdivided into three different species: C. parapsilosis sensu stricto, C. metapsilosis, ...
  • Genome sequence of flavor-producing yeast saprochaete suaveolens NRRL Y-17571
    Lichancová, Hana; Hodorová, Viktória; Sienkiewicz, Karolina; Penir, Sarah Mae U.; Afanasyev, Philipp; Boceck, Dominic; Bonnin, Sarah; Hakobyan, Siras; Krawczyk, Pawel S.; Smyczynska, Urszula; Zhivkoplias, Erik; Zlatohurska, Maryna; Odrzywolski, Adrian; Tralle, Eugeniusz; Frolova, Alina; Pryszcz, Leszek Piotr, 1985-; Brejová, Broňa; Vinař, Tomáš; Nosek, Jozef (American Society for Microbiology, 2019)
    Saprochaete suaveolens is an ascomycetous yeast that produces a range of fruity flavors and fragrances. Here, we report the high-contiguity genome sequence of the ex-holotype strain, NRRL Y-17571 (CBS 152.25). The nuclear ...
  • Genome sequence of the yeast Saprochaete ingens CBS 517.90
    Hodorová, Viktória; Lichancová, Hana; Zubenko, Stanislav; Sienkiewicz, Karolina; Penir, Sarah Mae U.; Afanasyev, Philipp; Boceck, Dominic; Bonnin, Sarah; Hakobyan, Siras; Smyczynska, Urszula; Zhivkoplias, Erik; Zlatohurska, Maryna; Tralle, Eugeniusz; Frolova, Alina; Pryszcz, Leszek Piotr, 1985-; Brejová, Broňa; Vinař, Tomáš; Nosek, Jozef (American Society for Microbiology, 2019)
    Chromosome-scale genome assembly of the yeast Saprochaete ingens CBS 517.90 was determined by a combination of technologies producing short (HiSeq X; Illumina) and long (MinION; Oxford Nanopore Technologies) reads. The ...
  • MasterOfPores: A workflow for the analysis of Oxford nanopore direct RNA sequencing datasets
    Cozzuto, Luca; Liu, Huanle; Pryszcz, Leszek Piotr, 1985-; Hermoso Pulido, Antonio; Delgado-Tejedor, Anna; Ponomarenko, Julia; Novoa, Eva Maria (Frontiers Media, 2020)
    The direct RNA sequencing platform offered by Oxford Nanopore Technologies allows for direct measurement of RNA molecules without the need of conversion to complementary DNA, fragmentation or amplification. As such, it is ...
  • MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life
    Chorostecki, Uciel; Molina, Manuel; Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2020)
    Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases ...
  • MetaPhOrs: orthology and paralogy predictions from multiple phylogenetic evidence using a consistency-based confidence score
    Pryszcz, Leszek Piotr, 1985-; Huerta Cepas, Jaime; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2011)
    Reliable prediction of orthology is central to comparative genomics. Approaches based on phylogenetic analyses closely resemble the original definition of orthology and paralogy and are known to be highly accurate. However, ...
  • Mitochondrial Carriers Link the Catabolism of Hydroxyaromatic Compounds to the Central Metabolism in Candida parapsilosis
    Zeman, Igor; Neboháčová, Martina; Gérecová, Gabriela; Katonová, Kornélia; Jánošíková, Eva; Jakúbková, Michaela; Centárová, Ivana; Dunčková, Ivana; Tomáška, L'ubomír; Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973-; Nosek, Jozef (Genetics Society of America, 2016)
    The pathogenic yeast Candida parapsilosis metabolizes hydroxyderivatives of benzene and benzoic acid to compounds channeled into central metabolism, including the mitochondrially localized tricarboxylic acid cycle, via the ...
  • ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data
    Pryszcz, Leszek Piotr, 1985-; Novoa, Eva Maria (Oxford University Press, 2022)
    Motivation: DNA and RNA modifications can now be identified using Nanopore sequencing. However, we currently lack a flexible software to efficiently encode, store, analyze and visualize DNA and RNA modification data. ...
  • nextPARS: parallel probing of RNA structures in Illumina
    Saus Martínez, Ester; Willis, Jesse R.; Pryszcz, Leszek Piotr, 1985-; Hafez Khafaga, Ahmed Ibrahem, 1987-; Llorens, Carlos, 1968-; 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 ...
  • PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome
    Huerta Cepas, Jaime; Capella Gutiérrez, Salvador Jesús, 1985-; Pryszcz, Leszek Piotr, 1985-; Marcet Houben, Marina; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2014)
    Phylogenetic trees representing the evolutionary relationships of homologous genes are the entry point for many evolutionary analyses. For instance, the use of a phylogenetic tree can aid in the inference of orthology and ...
  • Quantitative analysis of tRNA abundance and modifications by nanopore RNA sequencing
    Lucas, Morghan C.; Pryszcz, Leszek Piotr, 1985-; Medina, Rebeca; Milenkovic, Ivan; Camacho, Noelia; Marchand, Virginie; Motorin, Yuri; Ribas de Pouplana, Lluís; Novoa, Eva Maria (Nature Research, 2024)
    Transfer RNAs (tRNAs) play a central role in protein translation. Studying them has been difficult in part because a simple method to simultaneously quantify their abundance and chemical modifications is lacking. Here we ...
  • Quantitative profiling of pseudouridylation dynamics in native RNAs with nanopore sequencing
    Begik, Oguzhan; Lucas, Morghan C.; Pryszcz, Leszek Piotr, 1985-; Ramirez, Jose Miguel; Medina, Rebeca; Milenkovic, Ivan; Cruciani, Sonia; Liu, Huanle; Santos Vieira, Helaine Graziele; Sas Chen, Aldema; Mattick, John S.; Schwartz, Schraga; Novoa, Eva Maria (Nature Research, 2021)
    Nanopore RNA sequencing shows promise as a method for discriminating and identifying different RNA modifications in native RNA. Expanding on the ability of nanopore sequencing to detect N6-methyladenosine, we show that ...
  • Redundans: an assembly pipeline for highly heterozygous genomes
    Pryszcz, Leszek Piotr, 1985-; Gabaldón Estevan, Juan Antonio, 1973- (Oxford University Press, 2016)
    Many genomes display high levels of heterozygosity (i.e. presence of different alleles at the same loci in homologous chromosomes), being those of hybrid organisms an extreme such case. The assembly of highly heterozygous ...

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