Guillermo Parada · Computational Biology

Publications

A selection of my peer-reviewed publications. A complete list is available on my Google Scholar profile.

Notation: * denotes equal contribution; # denotes corresponding author.

Selected publications

  • Alu-mediated RNA duplexes are associated with widespread exon skipping across primate transcriptomes

    Lee, H.*; Cao, X.*; Parada, G.E.*#; Li, J.D.; Iosub, I.A.; Braunschweig, U.; Rebelo, K.; Ule, J.; Wan, Y.#; Blencowe, B.J.#

    Genome Biology · 2026

    Co-first and co-corresponding author; helped establish RNA duplexes as a major layer of primate-specific splicing regulation.

    DOI

  • Alternative splicing modulation by G-quadruplexes

    Georgakopoulos-Soares, I.*; Parada, G.E.*; Wong, H.Y.; Medhi, R.; Furlan, G.; Munita, R.; et al.

    Nature Communications · 2022

    Co-led the study and analyses; showed that G-quadruplex structures modulate alternative splicing transcriptome-wide.

    DOI

  • MicroExonator enables systematic discovery and quantification of microexons across mouse embryonic development

    Parada, G.E.; Munita, R.; Georgakopoulos-Soares, I.; Fernandes, H.J.R.; Kedlian, V.R.; Metzakopian, E.; et al.

    Genome Biology · 2021

    Sole first author; developed MicroExonator and generated a systematic microexon atlas across mouse development.

    DOI Code

  • A comprehensive survey of non-canonical splice sites in the human transcriptome

    Parada, G.E.*; Munita, R.*; Cerda, C.A.; Gysling, K.#

    Nucleic Acids Research · 2014

    Co-first author; mapped high-confidence non-canonical splice sites in the human transcriptome.

    DOI

Additional selected publications

  • Dupas, S.J.; Parada, G.E.; Li, J.D.; Brown, K.R.; Moffat, J.; Blencowe, B.J. Splice isoform perturbation coupled to single-cell transcriptome profiling reveals functions of microexons in neurogenesis and autism-linked pathways. Nature Communications, 2026.
  • Georgakopoulos-Soares, I.; Yizhar-Barnea, O.; Mouratidis, I.; …; Parada, G.E.; et al. Leveraging sequences missing from the human genome to diagnose cancer. Communications Medicine, 2025.
  • Song, Y.; Parada, G.E.; Lee, J.T.H.; Hemberg, M. Mining alternative splicing patterns in scRNA-seq data using scASfind. Genome Biology, 2024.
  • Salmen, F.*; De Jonghe, J.*; Kaminski, T.; Alemany, A.; Parada, G.E.; …; Hemberg, M.; Hollfelder, F.; van Oudenaarden, A. High-throughput total RNA sequencing in single cells. Nature Biotechnology, 2022.
  • Han, H.; Best, A.J.; Braunschweig, U.; Mikolajewicz, N.; Li, J.L.; …; Parada, G.E.; et al. Systematic exploration of dynamic splicing networks reveals conserved multistage regulators of neurogenesis. Molecular Cell, 2022.
  • Parada, G.E.; Hemberg, M. Identification and Quantification of Microexons Using Bulk and Single-Cell RNA-Seq Data. Methods in Molecular Biology, 2022.
  • Georgakopoulos-Soares, I.; Parada, G.E.; Hemberg, M. Secondary structures in RNA synthesis, splicing and translation. Computational and Structural Biotechnology Journal, 2022.
  • Georgakopoulos-Soares, I.; Victorino, J.; Parada, G.E.; Agarwal, V.; Zhao, J.; et al. High-throughput characterization of the role of non-B DNA motifs on promoter function. Cell Genomics, 2022.
  • Parada, G.E.; Hemberg, M. Bridge over troubled transcripts. Nature Computational Science, 2022.
  • Gapp, K.; Parada, G.E.; Gross, F.; Corcoba, A.; Kaur, J.; Grau, E.; Hemberg, M.; Bohacek, J.; Miska, E.A. Single paternal dexamethasone challenge programs offspring metabolism and reveals multiple candidates in RNA-mediated inheritance. iScience, 2021.
  • Urbonaite, G.; Lee, J.T.H.; Liu, P.; Parada, G.E.; Hemberg, M.; Acar, M. A yeast-optimized single-cell transcriptomics platform elucidates how mycophenolic acid and guanine alter global mRNA levels. Communications Biology, 2021.
  • Georgakopoulos-Soares, I.; Mouratidis, I.; Parada, G.E.; Matharu, N.; Hemberg, M.; Ahituv, N. Asymmetron: a toolkit for the identification of strand asymmetry patterns in biological sequences. Nucleic Acids Research, 2021.
  • Akay, A.; Di Domenico, T.; Suen, K.M.; Nabih, A.; Parada, G.E.; et al. The helicase Aquarius/EMB-4 is required to overcome intronic barriers to allow nuclear RNAi pathways to heritably silence transcription. Developmental Cell, 2017.
  • Sáez, J.E.; Gómez, A.V.; Barrios, Á.P.; Parada, G.E.; Galdames, L.; González, M.; Andrés, M.E. Decreased expression of CoREST1 and CoREST2 together with LSD1 and HDAC1/2 during neuronal differentiation. PLOS ONE, 2015.
  • Gómez, A.V.; Córdova, G.; Munita, R.; Parada, G.E.; Barrios, Á.P.; Cancino, G.I.; Álvarez, A.R.; Andrés, M.E. Characterizing HSF1 binding and post-translational modifications of the hsp70 promoter in cultured cortical neurons. PLOS ONE, 2015.
  • von Bernhardi, R.; Cornejo, F.; Parada, G.E.; Eugenín, J. Role of TGF-β signalling in the pathogenesis of Alzheimer's disease. Frontiers in Cellular Neuroscience, 2015.