publications

* denotes equal contribution. For an updated publication list visit my Google Scholar .

2023

  1. NAR
    isomiRdb: microRNA expression at isoform resolution
    Ernesto* Aparicio-Puerta, Pascal* Hirsch, Georges P Schmartz, Tobias Fehlmann, Verena Keller, and 4 more authors
    Nucleic Acids Research, 2023
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  2. G&D
    ALL-tRNAseq enables robust tRNA profiling in tissue samples
    Chantal Scheepbouwer, Ernesto Aparicio-Puerta, Cristina Gomez-Martin, Heleen Verschueren, Monique Eijndhoven, and 6 more authors
    Genes \& Development, 2023
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  3. sRNAtoolbox: Dockerized Analysis of Small RNA Sequencing Data in Model and Non-model Species
    Cristina Gómez-Martı́n, Ernesto Aparicio-Puerta, and Michael Hackenberg
    In MicroRNA Detection and Target Identification: Methods and Protocols, 2023
  4. Biomol
    Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions
    Cristina Gómez-Martı́n, Hui Zhou, José Marı́a Medina, Ernesto Aparicio-Puerta, Bujun Shi, and 1 more author
    Biomolecules, 2023
  5. Funct&Integr Gen
    Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits
    Cristina Gómez-Martı́n, Hui Zhou, José Maria Medina, Ernesto Aparicio-Puerta, Michael Hackenberg, and 1 more author
    Functional \& Integrative Genomics, 2023
  6. NAR
    miEAA 2023: updates, new functional microRNA sets and improved enrichment visualizations
    Ernesto Aparicio-Puerta, Pascal Hirsch, Georges P Schmartz, Fabian Kern, Tobias Fehlmann, and 1 more author
    Nucleic Acids Research, 2023
  7. Cell Rep Meths
    Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing
    Cristina Gómez-Martı́n, Ernesto Aparicio-Puerta, Monique AJ Eijndhoven, José M Medina, Michael Hackenberg, and 1 more author
    Cell Reports Methods, 2023
  8. RNA Biol
    Ageing-associated small RNA cargo of extracellular vesicles
    Fabian Kern, Thomas Kuhn, Nicole Ludwig, Martin Simon, Laura Gröger, and 6 more authors
    RNA Biology, 2023
  9. Cancers
    Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma
    Marı́a Belén Garcı́a-Ortega, Ernesto Aparicio, Carmen Gri\~nán-Lisón, Gema Jiménez, Elena López-Ruiz, and 6 more authors
    Cancers, 2023

2022

  1. NAR
    MirGeneDB 2.1: toward a complete sampling of all major animal phyla
    Bastian Fromm, Eirik Høye, Diana Domanska, Xiangfu Zhong, Ernesto Aparicio-Puerta, and 6 more authors
    Nucleic acids research, 2022
  2. Biomedicines
    Functional Enrichment Analysis of Regulatory Elements
    Adrian Garcia-Moreno, Raul López-Domı́nguez, Juan Antonio Villatoro-Garcı́a, Alberto Ramirez-Mena, Ernesto Aparicio-Puerta, and 3 more authors
    Biomedicines, 2022
  3. NAR
    sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
    Ernesto Aparicio-Puerta*, Cristina Gómez-Martı́n, Stavros Giannoukakos, José Marı́a Medina, Chantal Scheepbouwer, and 6 more authors
    Nucleic Acids Research, 2022
  4. Mol Ecol
    Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface
    Chaima Bensaoud, Stefan Tenzer, Alicia Poplawski, José Marı́a Medina, Mohamed Amine Jmel, and 6 more authors
    Molecular Ecology, 2022
  5. Front Cell Infect
    Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host
    José Marı́a Medina, Mohamed Amine Jmel, Brent Cuveele, Cristina Gómez-Martı́n, Ernesto Aparicio-Puerta, and 6 more authors
    Frontiers in Cellular and Infection Microbiology, 2022
  6. Antioxidants
    MicroRNA-4732-3p Is Dysregulated in Breast Cancer Patients with Cardiotoxicity, and Its Therapeutic Delivery Protects the Heart from Doxorubicin-Induced Oxidative Stress in Rats
    Rafael Sánchez-Sánchez, Ignacio Reinal, Esteban Peiró-Molina, Marc Buigues, Sandra Tejedor, and 6 more authors
    Antioxidants, 2022

2021

  1. JMB
    geno5mC: A Database to Explore the Association between Genetic Variation (SNPs) and CpG Methylation in the Human Genome
    Cristina Gómez-Martı́n, Ernesto Aparicio-Puerta, JM Medina, Guillermo Barturen, JL Oliver, and 1 more author
    Journal of Molecular Biology, 2021
  2. NAR
    Validation of human microRNA target pathways enables evaluation of target prediction tools
    Fabian Kern, Lena Krammes, Karin Danz, Caroline Diener, Tim Kehl, and 6 more authors
    Nucleic acids research, 2021
  3. In Silico Analysis of Micro-RNA Sequencing Data.
    Ernesto Aparicio-Puerta, Bastian Fromm, Michael Hackenberg, and Marc K Halushka
    In RNA Bioinformatics, 2021
  4. NAR
  5. JEV
    Extracellular vesicle miRNA predict FDG-PET status in patients with classical Hodgkin Lymphoma
    Esther EE Drees, Margaretha GM Roemer, Nils J Groenewegen, Jennifer Perez-Boza, Monique AJ Eijndhoven, and 6 more authors
    Journal of Extracellular Vesicles, 2021

2020

  1. NAR
    mirnaQC: a webserver for comparative quality control of miRNA-seq data
    Ernesto Aparicio-Puerta, Cristina Gómez-Martı́n, Stavros Giannoukakos, José Marı́a Medina, Juan Antonio Marchal, and 1 more author
    Nucleic Acids Research, 2020
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2019

  1. NAR
    sRNAbench and sRNAtoolbox 2019: intuitive fast small RNA profiling and differential expression
    Ernesto Aparicio-Puerta, Ricardo Lebrón, Antonio Rueda, Cristina Gómez-Martı́n, Stavros Giannoukakos, and 6 more authors
    Nucleic acids research, 2019
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  2. NAR
    liqDB: a small-RNAseq knowledge discovery database for liquid biopsy studies
    Ernesto Aparicio-Puerta, David Jáspez, Ricardo Lebrón, Danijela Koppers-Lalic, Juan A Marchal, and 1 more author
    Nucleic acids research, 2019
  3. NAR
    MirGeneDB 2.0: the metazoan microRNA complement
    Bastian Fromm, Diana Domanska, Eirik Høye, Vladimir Ovchinnikov, Wenjing Kang, and 6 more authors
    Nucleic Acids Research, 2019
  4. Bioinformatics
    Unification of miRNA and isomiR research: the mirGFF3 format and the mirtop API
    Thomas Desvignes, Phillipe Loher, Karen Eilbeck, Jeffery Ma, Gianvito Urgese, and 6 more authors
    Bioinformatics, 2019

2017

  1. bioRxiv
    miRNAgFree: prediction and profiling of novel microRNAs without genome assembly
    Ernesto L Aparicio, Antonio Rueda, Bastian Fromm, Cristina Gómez-Martin, Ricardo Lebrón, and 4 more authors
    bioRxiv, 2017