Michael Hackenberg Universidad de Granada Verified email at ugr.es Bioinformatics Computational Genomics microRNA DNA methylation An integrative framework identifies cooperative targeting of host pathways by tick salivary miRNAs JM Medina, G Barturen, M Kotsyfakis, M Hackenberg Computational and Structural Biotechnology Journal 35 (1), 0106, 2026 Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis S Sharma, MI Hackenberg, L Navarro, E Narbona, A Gonzalez-Megias, … bioRxiv, 2026.09. 08.750093, 2026 Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards M Hackenberg, P Kalogeropoulos, KJ Peterson, MR Friedländer, … Nucleic Acids Research 53 (19), gkaf1049, 2025 Circulating extracellular vesicle isomiR signatures predict therapy response in patients with multiple myeloma C Gómez-Martín, EEE Drees, MAJ Van Eijndhoven, NJ Groenewegen, … Cell Reports Medicine 6 (10), 2025 Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer M Antunes-Ferreira, I Glogovitis, D Fortunato, S D’Ambrosi, MC Saborit, … Non-coding RNA 11 (3), 38, 2025 Genome sequences of four Ixodes species expands understanding of tick evolution A Cerqueira de Araujo, B Noël, A Bretaudeau, K Labadie, M Boudet, … BMC biology 23 (1), 17, 2025 MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models AW Clarke, E Høye, AA Hembrom, VM Paynter, J Vinther, Ł Wyrożemski, … Nucleic acids research 53 (D1), D116-D128, 2025 Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles C Scheepbouwer, E Aparicio-Puerta, C Gómez-Martin, … bioRxiv, 2024 Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data S Giannoukakos, S D'Ambrosi, D Koppers-Lalic, C Gómez-Martín, … Heliyon 10 (6), 2024 Whole genome sequencing of fourIxodesspecies expands understanding of tick evolution A Cerqueira de Araujo, B Noël, A Bretaudeau, K Labadie, M Boudet, … IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution MAJ van Eijndhoven, C Scheepbouwer, E Aparicio-Puerta, … STAR protocols 4 (4), 2023 HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia A Zubković, C Gomes, A Parchure, M Cesarec, A Ferenčić, F Rokić, … Journal of virology 97 (10), e00730-23, 2023 Interferon-alpha decreases cancer stem cell properties and modulates exosomes in malignant melanoma MB García-Ortega, E Aparicio, C Griñán-Lisón, G Jiménez, E López-Ruiz, … Cancers 15 (14), 3666, 2023 NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods C Scheepbouwer, M Hackenberg, MAJ van Eijndhoven, A Gerber, … Nucleic acids research 51 (W1), W372-W378, 2023 Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing C Gómez-Martín, E Aparicio-Puerta, MAJ van Eijndhoven, JM Medina, … Cell Reports Methods 3 (5), 2023 Combinatorial blood platelets-derived circRNA and mRNA signature for early-stage lung cancer detection S D’Ambrosi, S Giannoukakos, M Antunes-Ferreira, C Pedraz-Valdunciel, … International journal of molecular sciences 24 (5), 4881, 2023 ALL-tRNAseq enables robust tRNA profiling in tissue samples C Scheepbouwer, E Aparicio-Puerta, C Gomez-Martin, H Verschueren, … Genes & development 37 (5-6), 243-257, 2023 Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits C Gómez-Martín, H Zhou, JM Medina, E Aparicio-Puerta, M Hackenberg, … Functional & Integrative Genomics 23 (1), 15, 2023 Genome-wide analysis of microRNA expression profile in roots and leaves of three wheat cultivars under water and drought conditions C Gómez-Martín, H Zhou, JM Medina, E Aparicio-Puerta, B Shi, … Biomolecules 13 (3), 440, 2023 sRNAtoolbox: Dockerized Analysis of Small RNA Sequencing Data in Model and Non-model Species C Gómez-Martín, E Aparicio-Puerta, M Hackenberg MicroRNA Detection and Target Identification: Methods and Protocols, 179-213, 2023 View All Publications
An integrative framework identifies cooperative targeting of host pathways by tick salivary miRNAs JM Medina, G Barturen, M Kotsyfakis, M Hackenberg Computational and Structural Biotechnology Journal 35 (1), 0106, 2026
Benchmarking long-read RNA sequencing for de novo transcriptome assembly in non-model plant species: insights from Moricandia arvensis S Sharma, MI Hackenberg, L Navarro, E Narbona, A Gonzalez-Megias, … bioRxiv, 2026.09. 08.750093, 2026
Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards M Hackenberg, P Kalogeropoulos, KJ Peterson, MR Friedländer, … Nucleic Acids Research 53 (19), gkaf1049, 2025
Circulating extracellular vesicle isomiR signatures predict therapy response in patients with multiple myeloma C Gómez-Martín, EEE Drees, MAJ Van Eijndhoven, NJ Groenewegen, … Cell Reports Medicine 6 (10), 2025
Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer M Antunes-Ferreira, I Glogovitis, D Fortunato, S D’Ambrosi, MC Saborit, … Non-coding RNA 11 (3), 38, 2025
Genome sequences of four Ixodes species expands understanding of tick evolution A Cerqueira de Araujo, B Noël, A Bretaudeau, K Labadie, M Boudet, … BMC biology 23 (1), 17, 2025
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models AW Clarke, E Høye, AA Hembrom, VM Paynter, J Vinther, Ł Wyrożemski, … Nucleic acids research 53 (D1), D116-D128, 2025
Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles C Scheepbouwer, E Aparicio-Puerta, C Gómez-Martin, … bioRxiv, 2024
Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data S Giannoukakos, S D'Ambrosi, D Koppers-Lalic, C Gómez-Martín, … Heliyon 10 (6), 2024
Whole genome sequencing of fourIxodesspecies expands understanding of tick evolution A Cerqueira de Araujo, B Noël, A Bretaudeau, K Labadie, M Boudet, …
IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution MAJ van Eijndhoven, C Scheepbouwer, E Aparicio-Puerta, … STAR protocols 4 (4), 2023
HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia A Zubković, C Gomes, A Parchure, M Cesarec, A Ferenčić, F Rokić, … Journal of virology 97 (10), e00730-23, 2023
Interferon-alpha decreases cancer stem cell properties and modulates exosomes in malignant melanoma MB García-Ortega, E Aparicio, C Griñán-Lisón, G Jiménez, E López-Ruiz, … Cancers 15 (14), 3666, 2023
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods C Scheepbouwer, M Hackenberg, MAJ van Eijndhoven, A Gerber, … Nucleic acids research 51 (W1), W372-W378, 2023
Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing C Gómez-Martín, E Aparicio-Puerta, MAJ van Eijndhoven, JM Medina, … Cell Reports Methods 3 (5), 2023
Combinatorial blood platelets-derived circRNA and mRNA signature for early-stage lung cancer detection S D’Ambrosi, S Giannoukakos, M Antunes-Ferreira, C Pedraz-Valdunciel, … International journal of molecular sciences 24 (5), 4881, 2023
ALL-tRNAseq enables robust tRNA profiling in tissue samples C Scheepbouwer, E Aparicio-Puerta, C Gomez-Martin, H Verschueren, … Genes & development 37 (5-6), 243-257, 2023
Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits C Gómez-Martín, H Zhou, JM Medina, E Aparicio-Puerta, M Hackenberg, … Functional & Integrative Genomics 23 (1), 15, 2023
Genome-wide analysis of microRNA expression profile in roots and leaves of three wheat cultivars under water and drought conditions C Gómez-Martín, H Zhou, JM Medina, E Aparicio-Puerta, B Shi, … Biomolecules 13 (3), 440, 2023
sRNAtoolbox: Dockerized Analysis of Small RNA Sequencing Data in Model and Non-model Species C Gómez-Martín, E Aparicio-Puerta, M Hackenberg MicroRNA Detection and Target Identification: Methods and Protocols, 179-213, 2023
