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Browsing Center for Genomic Regulation (CRG) by Subject "Software"

Browsing Center for Genomic Regulation (CRG) by Subject "Software"

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  • Accurate detection of m6A RNA modifications in native RNA sequences
    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 ...
  • Deconwolf enables high-performance deconvolution of widefield fluorescence microscopy images
    Wernersson, Erik; Gelali, Eleni; Girelli, Gabriele; Wang, Su; Castillo, David; Mattsson Langseth, Christoffer; Verron, Quentin; Nguyen, Huy Q.; Chattoraj, Shyamtanu; Martinez Casals, Anna; Blom, Hans; Lundberg, Emma; Nilsson, Mats; Martí Renom, Marc A.; Wu, Chao-Ting; Crosetto, Nicola; Bienko, Magda (Nature Research, 2024)
    Microscopy-based spatially resolved omic methods are transforming the life sciences. However, these methods rely on high numerical aperture objectives and cannot resolve crowded molecular targets, limiting the amount of ...
  • Differential metabolic activity and discovery of therapeutic targets using summarized metabolic pathway models
    Çubut, Cankut; Hidalgo, Marta R.; Amadoz, Alicia; Rian, Kinza; Salavert, Francisco; Pujana, Miguel Angel; Mateo, Francesca; Herranz Ors, Carmen, 1992-; Carbonell-Caballero, Jose; Dopazo, Joaquín (Nature Research, 2019)
    In spite of the increasing availability of genomic and transcriptomic data, there is still a gap between the detection of perturbations in gene expression and the understanding of their contribution to the molecular ...
  • MassIVE.quant: a community resource of quantitative mass spectrometry-based proteomics datasets
    Choi, Meena; Chiva, Cristina; Sabidó Aguadé, Eduard, 1981-; Vitek, Olga (Nature Research, 2020)
    MassIVE.quant is a repository infrastructure and data resource for reproducible quantitative mass spectrometry-based proteomics, which is compatible with all mass spectrometry data acquisition types and computational ...
  • 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 ...
  • Systematic assessment of long-read RNA-seq methods for transcript identification and quantification
    Pardo Palacios, Francisco J.; Carbonell Sala, Silvia; Lagarde, Julien; Guigó Serra, Roderic; Brooks, Angela N. (Nature Research, 2024)
    The Long-read RNA-Seq Genome Annotation Assessment Project Consortium was formed to evaluate the effectiveness of long-read approaches for transcriptome analysis. Using different protocols and sequencing platforms, the ...

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