Publications by authors named "Michael Hackenberg"

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Circulating extracellular vesicle isomiR signatures predict therapy response in patients with multiple myeloma.
Cristina Gómez-Martín, Esther E E Drees, Monique A J van Eijndhoven, Nils J Groenewegen, Steven Wang, Michael Hackenberg

Cell Rep Med· October 2025

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Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards.
Michael Hackenberg, Panagiotis Kalogeropoulos, Kevin J Peterson, Marc R Friedländer, Bastian Fromm

Nucleic Acids Res· October 2025

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Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer.
Mafalda Antunes-Ferreira, Ilias Glogovitis, Diogo Fortunato, Silvia D'Ambrosi, Mariona Colom Saborit, Michael Hackenberg

Noncoding RNA· May 2025

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MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models.
Alexander W Clarke, Eirik Høye, Anju Angelina Hembrom, Vanessa Molin Paynter, Jakob Vinther, Michael Hackenberg

Nucleic Acids Res· January 2025

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Genome sequences of four Ixodes species expands understanding of tick evolution.
Alexandra Cerqueira de Araujo, Benjamin Noel, Anthony Bretaudeau, Karine Labadie, Matéo Boudet, Michael Hackenberg

BMC Biol· January 2025

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Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles.
Chantal Scheepbouwer, Ernesto Aparicio-Puerta, Cristina Gómez-Martin, Monique A J van Eijndhoven, Esther E E Drees, Michael Hackenberg

bioRxiv· May 2024

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Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data.
Stavros Giannoukakos, Silvia D'Ambrosi, Danijela Koppers-Lalic, Cristina Gómez-Martín, Alberto Fernandez, Michael Hackenberg

Heliyon· March 2024

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IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution.
Monique A J van Eijndhoven, Chantal Scheepbouwer, Ernesto Aparicio-Puerta, Michael Hackenberg, D Michiel Pegtel

STAR Protoc· December 2023

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HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia.
Andreja Zubković, Cristina Gomes, Adwait Parchure, Mia Cesarec, Antun Ferenčić, Michael Hackenberg

J Virol· October 2023

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NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods.
Chantal Scheepbouwer, Michael Hackenberg, Monique A J van Eijndhoven, Alan Gerber, Michiel Pegtel

Nucleic Acids Res· July 2023

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Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma.
María Belén García-Ortega, Ernesto Aparicio, Carmen Griñán-Lisón, Gema Jiménez, Elena López-Ruiz, Michael Hackenberg

Cancers (Basel)· July 2023

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Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing.
Cristina Gómez-Martín, Ernesto Aparicio-Puerta, Monique A J van Eijndhoven, José M Medina, Michael Hackenberg

Cell Rep Methods· May 2023

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ALL-tRNAseq enables robust tRNA profiling in tissue samples.
Chantal Scheepbouwer, Ernesto Aparicio-Puerta, Cristina Gomez-Martin, Heleen Verschueren, Monique van Eijndhoven, Michael Hackenberg

Genes Dev· March 2023

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Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection.
Silvia D'Ambrosi, Stavros Giannoukakos, Mafalda Antunes-Ferreira, Carlos Pedraz-Valdunciel, Jillian W P Bracht, Michael Hackenberg

Int J Mol Sci· March 2023

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Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions.
Cristina Gómez-Martín, Hui Zhou, José María Medina, Ernesto Aparicio-Puerta, Bujun Shi, Michael Hackenberg

Biomolecules· February 2023

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isomiRdb: microRNA expression at isoform resolution.
Ernesto Aparicio-Puerta, Pascal Hirsch, Georges P Schmartz, Tobias Fehlmann, Verena Keller, Michael Hackenberg

Nucleic Acids Res· January 2023

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sRNAtoolbox: Dockerized Analysis of Small RNA Sequencing Data in Model and Non-model Species.
Cristina Gómez-Martín, Ernesto Aparicio-Puerta, Michael Hackenberg

Methods Mol Biol· January 2023

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Comprehensive, integrative genomic analysis of microRNA expression profiles in different tissues of two wheat cultivars with different traits.
Cristina Gómez-Martín, Hui Zhou, José Maria Medina, Ernesto Aparicio-Puerta, Michael Hackenberg

Funct Integr Genomics· December 2022

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Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean.
Ana M González, Ricardo Lebrón, Fernando J Yuste-Lisbona, Cristina Gómez-Martín, Ana Ortiz-Atienza, Michael Hackenberg

Int J Mol Sci· November 2022

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Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer.
Carlos Pedraz-Valdunciel, Stavros Giannoukakos, Ana Giménez-Capitán, Diogo Fortunato, Martyna Filipska, Michael Hackenberg

Pharmaceutics· September 2022

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Quantitative proteomics analysis reveals core and variable tick salivary proteins at the tick-vertebrate host interface.
Chaima Bensaoud, Stefan Tenzer, Alicia Poplawski, José María Medina, Mohamed Amine Jmel, Michael Hackenberg

Mol Ecol· August 2022

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Selective isolation of extracellular vesicles from minimally processed human plasma as a translational strategy for liquid biopsies.
Diogo Fortunato, Stavros Giannoukakos, Ana Giménez-Capitán, Michael Hackenberg, Miguel A Molina-Vila

Biomark Res· August 2022

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Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host.
José María Medina, Mohamed Amine Jmel, Brent Cuveele, Cristina Gómez-Martín, Ernesto Aparicio-Puerta, Michael Hackenberg

Front Cell Infect Microbiol· August 2022

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Bioinformatic Analysis of Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs.
José María Medina, Muhammad Nadeem Abbas, Chaima Bensaoud, Michael Hackenberg, Michail Kotsyfakis

Int J Mol Sci· August 2022

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The Virus-Induced Upregulation of the miR-183/96/182 Cluster and the FoxO Family Protein Members Are Not Required for Efficient Replication of HSV-1.
Andreja Zubković, Ines Žarak, Ivana Ratkaj, Filip Rokić, Maja Jekić, Michael Hackenberg

Viruses· July 2022

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