Browsing by Author "Novoa, Eva Maria"

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  • Wu, Ming-Ru; Nissim, Lior; Stupp, Doron; Pery, Erez; Binder-Nissim, Adina; Weisinger, Karen; Enghuus, Casper; Palacios, Sebastian R.; Humphrey, Melissa; Zhang, Zhizhuo; Novoa, Eva Maria; Kellis, Manolis; Weiss, Ron; Rabkin, Samuel D.; Tabach, Yuval; Lu, Timothy K. (Nature Research, 2019)
    Cell state-specific promoters constitute essential tools for basic research and biotechnology because they activate gene expression only under certain biological conditions. Synthetic Promoters with Enhanced Cell-State ...
  • Liu, Huanle; Begik, Oguzhan; Lucas, Morghan C.; Ramirez, Jose Miguel; Mason, Christopher E.; Wiener, David; Schwartz, Schraga; Mattick, John S.; Smith, Martin A.; Novoa, Eva Maria (Nature Research, 2019)
    The epitranscriptomics field has undergone an enormous expansion in the last few years; however, a major limitation is the lack of generic methods to map RNA modifications transcriptome-wide. Here, we show that using direct ...
  • Jungfleisch, Jennifer, 1986-; Böttcher, René; Talló Parra, Marc, 1992-; Pérez Vilaró, Gemma, 1985-; Merits, Andres; Novoa, Eva Maria; Díez Antón, Juana, 1962- (Nature Research, 2022)
    Ample evidence indicates that codon usage bias regulates gene expression. How viruses, such as the emerging mosquito-borne Chikungunya virus (CHIKV), express their genomes at high levels despite an enrichment in rare codons ...
  • Furlan, Mattia; Delgado-Tejedor, Anna; Mulroney, Logan; Pelizzola, Mattia; Novoa, Eva Maria; Leonardi, Tommaso (Taylor and Francis, 2021)
    The covalent modification of RNA molecules is a pervasive feature of all classes of RNAs and has fundamental roles in the regulation of several cellular processes. Mapping the location of RNA modifications transcriptome-wide ...
  • Milenkovic, Ivan; Santos Vieira, Helaine Graziele; Lucas, Morghan C.; Ruiz-Orera, Jorge; Patone, Giannino; Kesteven, Scott; Wu, Jianxin; Feneley, Michael; Espadas, Guadalupe; Sabidó Aguadé, Eduard, 1981-; Hübner, Norbert; van Heesch, Sebastiaan; Völkers, Mirko; Novoa, Eva Maria (Oxford University Press, 2023)
    The existence of naturally occurring ribosome heterogeneity is now a well-acknowledged phenomenon. However, whether this heterogeneity leads to functionally diverse 'specialized ribosomes' is still a controversial topic. ...
  • Liu, Huanle; Begik, Oguzhan; Novoa, Eva Maria (Springer, 2021)
    RNA modifications play pivotal roles in the RNA life cycle and RNA fate, and are now appreciated as a major posttranscriptional regulatory layer in the cell. In the last few years, direct RNA nanopore sequencing (dRNA-seq) ...
  • Begik, Oguzhan; Mattick, John S.; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2022)
    Chemical RNA modifications, collectively referred to as the "epitranscriptome," are essential players in fine-tuning gene expression. Our ability to analyze RNA modifications has improved rapidly in recent years, largely ...
  • Espadas, Guadalupe; Morales Sanfrutos, Julia; Medina, Rebeca; Lucas, Morghan C.; Novoa, Eva Maria; Sabidó Aguadé, Eduard, 1981- (Elsevier, 2022)
    Over 170 post-transcriptional RNA modifications have been described and are common in all kingdoms of life. These modifications range from methylation to complex chemical structures, with methylation being the most abundant. ...
  • Cao, Jicong; Novoa, Eva Maria; Zhang, Zhizhuo; Chen, William C. W.; Liu, Dianbo; Choi, Gigi C. G.; Wong, Alan S. L.; Wehrspaun, Claudia; Kellis, Manolis; Lu, Timothy K. (Nature Research, 2021)
    Despite significant clinical progress in cell and gene therapies, maximizing protein expression in order to enhance potency remains a major technical challenge. Here, we develop a high-throughput strategy to design, screen, ...
  • Torres, Adrian Gabriel; Rodríguez-Escribà, Marta; Marcet Houben, Marina; Santos Vieira, Helaine Graziele; Camacho, Noelia; Catena, Helena; Murillo Recio, Marina; Rafels-Ybern, Àlbert; Reina García, Óscar, 1976-; Torres, Francisco Miguel; Pardo Saganta, Ana; Gabaldón Estevan, Juan Antonio, 1973-; Novoa, Eva Maria; Ribas de Pouplana, Lluís (Oxford University Press, 2021)
    The modification of adenosine to inosine at the wobble position (I34) of tRNA anticodons is an abundant and essential feature of eukaryotic tRNAs. The expansion of inosine-containing tRNAs in eukaryotes followed the ...
  • Begik, Oguzhan; Lucas, Morghan C.; Liu, Huanle; Ramírez, José Miguel; Mattick, John S.; Novoa, Eva Maria (BioMed Central, 2020)
    Background: RNA modifications play central roles in cellular fate and differentiation. However, the machinery responsible for placing, removing, and recognizing more than 170 RNA modifications remains largely uncharacterized ...
  • Lucas, Morghan C. (Universitat Pompeu Fabra, 2023-05-03)
    The aim of this thesis is to delve into sperm RNA dynamics during maturation and paternal inheritance. To obtain an integrative multi-omics view of sperm RNA during these processes, I turned to the new direct RNA sequencing ...
  • 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 ...
  • Picchioni, Daria; Antolin-Fontes, Albert; Camacho, Noelia; Schmitz, Claus; Pons-Pons, Alba; Rodríguez-Escribà, Marta; Machallekidou, Antoni; Güler, Merve Nur; Siatra, Panagiota; Carretero-Junquera, Maria; Serrano, Alba; Hovde, Stacy L.; Knobel, Philip A.; Novoa, Eva Maria; Solà-Vilarrubias, Maria; Kaguni, Laurie S.; Stracker, Travis; Ribas de Pouplana, Lluís (Elsevier, 2019)
    The aminoacylation of tRNAs by aminoacyl-tRNA synthetases (ARSs) is a central reaction in biology. Multiple regulatory pathways use the aminoacylation status of cytosolic tRNAs to monitor and regulate metabolism. The ...
  • 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. ...
  • Smith, Martin A.; Ersavas, Tansel; Ferguson, James M.; Liu, Huanle; Lucas, Morghan C.; Begik, Oguzhan; Bojarski, Lilly; Barton, Kirston; Novoa, Eva Maria (Cold Spring Harbor Laboratory Press (CSHL Press), 2020)
    Nanopore sequencing enables direct measurement of RNA molecules without conversion to cDNA, thus opening the gates to a new era for RNA biology. However, the lack of molecular barcoding of direct RNA nanopore sequencing ...
  • Baquero Pérez, Belinda; Yonchev, Ivaylo D.; Delgado-Tejedor, Anna; Medina, Rebeca; Puig-Torrents, Mireia; Sudbery, Ian; Begik, Oguzhan; Wilson, Stuart A.; Novoa, Eva Maria; Díez Antón, Juana, 1962- (Nature Research, 2024)
    Despite the nuclear localization of the m6A machinery, the genomes of multiple exclusively-cytoplasmic RNA viruses, such as chikungunya (CHIKV) and dengue (DENV), are reported to be extensively m6A-modified. However, these ...
  • Begik, Oguzhan; Diensthuber, Gregor; Liu, Huanle; Delgado-Tejedor, Anna; Kontur, Cassandra; Niazi, Adnan Muhammad; Valen, Eivind; Giraldez, Antonio J.; Beaudoin, Jean-Denis; Mattick, John S.; Novoa, Eva Maria (Nature Research, 2023)
    RNA polyadenylation plays a central role in RNA maturation, fate, and stability. In response to developmental cues, polyA tail lengths can vary, affecting the translation efficiency and stability of mRNAs. Here we develop ...
  • 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 ...
  • 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 ...

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