Michael Hackenberg
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View article: Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards
Knowing is not enough; we must apply: the case for rigorous microRNA annotation standards Open
MicroRNAs are by far the most extensively studied and best-characterized class of small RNAs. This depth of knowledge may partly explain the persistent eagerness in the field to classify new sequences as microRNAs—since labeling a molecule…
View article: Deploying machine learning models in clinical settings: a real-world feasibility analysis for a model identifying adult-onset type 1 diabetes initially classified as type 2
Deploying machine learning models in clinical settings: a real-world feasibility analysis for a model identifying adult-onset type 1 diabetes initially classified as type 2 Open
Objective This study evaluates the performance and deployment feasibility of a machine learning (ML) model to identify adult-onset type 1 diabetes (T1D) initially coded as type 2 on electronic medical records (EMRs) from a health informati…
View article: Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer
Small RNA Landscape of Platelet Dust: Platelet-Derived Extracellular Vesicles from Patients with Non-Small-Cell Lung Cancer Open
Background: Platelet-derived Extracellular Vesicles, or “Platelet Dust” (PD), are reported as the most-abundant extracellular vesicles in plasma. However, the PD molecular content, especially the small RNA profile, is still poorly characte…
View article: MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models
MirGeneDB 3.0: improved taxonomic sampling, uniform nomenclature of novel conserved microRNA families and updated covariance models Open
We present a major update of MirGeneDB (3.0), the manually curated animal microRNA gene database. Beyond moving to a new server and the creation of a computational mirror, we have expanded the database with the addition of 33 invertebrate …
View article: Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles
Full-length tRNAs lacking a functional CCA tail are selectively sorted into the lumen of extracellular vesicles Open
Small extracellular vesicles (sEVs) are heterogenous lipid membrane particles typically less than 200 nm in size and secreted by most cell types either constitutively or upon activation signals. sEVs isolated from biofluids contain RNAs, i…
View article: Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data
Assessing the complementary information from an increased number of biologically relevant features in liquid biopsy-derived RNA-Seq data Open
Liquid biopsy-derived RNA sequencing (lbRNA-seq) exhibits significant promise for clinic-oriented cancer diagnostics due to its non-invasiveness and ease of repeatability. Despite substantial advancements, obstacles like technical artefact…
View article: Genome sequences of four<i>Ixodes</i>species expands understanding of tick evolution
Genome sequences of four<i>Ixodes</i>species expands understanding of tick evolution Open
Ticks, hematophagous acari, pose a significant threat by transmitting various pathogens to their vertebrate hosts during feeding. Despite advances in tick genomics, high-quality genomes were lacking until recently, particularly in the genu…
View article: Rezension von: Hackenberg, Michael, Books in Artisan Homes of Sixteenth-Century Germany
Rezension von: Hackenberg, Michael, Books in Artisan Homes of Sixteenth-Century Germany Open
Michael Hackenberg: Books in Artisan Homes of Sixteenth-Century Germany. In: Journal of Library History 21, 1986, S. 72-91.
View article: IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution
IsoSeek for unbiased and UMI-informed sequencing of miRNAs from low input samples at single-nucleotide resolution Open
Besides canonical microRNAs (miRNAs), sequence-based variations called isomiRs have biological relevance and diagnostic potential; however, accurate calling of these post-transcriptional modifications is challenging, especially for low inp…
View article: HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia
HSV-1 miRNAs are post-transcriptionally edited in latently infected human ganglia Open
Viruses use miRNAs to enable efficient replication, control host defense mechanisms, and regulate latent infection. Herpes simplex virus 1 (HSV-1) expresses multiple miRNAs whose functions are largely unknown. The evolutionary conservation…
View article: Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma
Interferon-Alpha Decreases Cancer Stem Cell Properties and Modulates Exosomes in Malignant Melanoma Open
Malignant melanoma (MM) can spread to other organs and is resistant in part due to the presence of cancer stem cell subpopulations (CSCs). While a controversial high dose of interferon-alpha (IFN-α) has been used to treat non-metastatic hi…
View article: HSV-1 miRNAs are posttranscriptionaly edited in latently infected human ganglia
HSV-1 miRNAs are posttranscriptionaly edited in latently infected human ganglia Open
Viruses use miRNAs to enable efficient replication, control host defense mechanisms, and regulate latent infection. Herpes simplex virus 1 (HSV-1) expresses multiple miRNAs, whose functions are largely unknown. The evolutionary conservatio…
View article: NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods
NORMSEQ: a tool for evaluation, selection and visualization of RNA-Seq normalization methods Open
RNA-sequencing has become one of the most used high-throughput approaches to gain knowledge about the expression of all different RNA subpopulations. However, technical artifacts, either introduced during library preparation and/or data an…
View article: Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing
Reassessment of miRNA variant (isomiRs) composition by small RNA sequencing Open
IsomiRs, sequence variants of mature microRNAs, are usually detected and quantified using high-throughput sequencing. Many examples of their biological relevance have been reported, but sequencing artifacts identified as artificial variant…
View article: Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection
Combinatorial Blood Platelets-Derived circRNA and mRNA Signature for Early-Stage Lung Cancer Detection Open
Despite the diversity of liquid biopsy transcriptomic repertoire, numerous studies often exploit only a single RNA type signature for diagnostic biomarker potential. This frequently results in insufficient sensitivity and specificity neces…
View article: Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions
Genome-Wide Analysis of microRNA Expression Profile in Roots and Leaves of Three Wheat Cultivars under Water and Drought Conditions Open
Wheat is one of the most important food sources on Earth. MicroRNAs (miRNAs) play important roles in wheat productivity. To identify wheat miRNAs as well as their expression profiles under drought condition, we constructed and sequenced sm…
View article: ALL-tRNAseq enables robust tRNA profiling in tissue samples
ALL-tRNAseq enables robust tRNA profiling in tissue samples Open
Transfer RNAs (tRNAs) are small adaptor RNAs essential for mRNA translation. Alterations in the cellular tRNA population can directly affect mRNA decoding rates and translational efficiency during cancer development and progression. To eva…
View article: Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean
Decoding Gene Expression Signatures Underlying Vegetative to Inflorescence Meristem Transition in the Common Bean Open
The tropical common bean (Phaseolus vulgaris L.) is an obligatory short-day plant that requires relaxation of the photoperiod to induce flowering. Similar to other crops, photoperiod-induced floral initiation depends on the differentiation…
View article: isomiRdb: microRNA expression at isoform resolution
isomiRdb: microRNA expression at isoform resolution Open
A significant fraction of mature miRNA transcripts carries sequence and/or length variations, termed isomiRs. IsomiRs are differentially abundant in cell types, tissues, body fluids or patients’ samples. Not surprisingly, multiple studies …
View article: Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer
Multiplex Analysis of CircRNAs from Plasma Extracellular Vesicle-Enriched Samples for the Detection of Early-Stage Non-Small Cell Lung Cancer Open
Background: The analysis of liquid biopsies brings new opportunities in the precision oncology field. Under this context, extracellular vesicle circular RNAs (EV-circRNAs) have gained interest as biomarkers for lung cancer (LC) detection. …
View article: Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs
Bioinformatic Analysis of Ixodes ricinus Long Non-Coding RNAs Predicts Their Binding Ability of Host miRNAs Open
Ixodes ricinus ticks are distributed across Europe and are a vector of tick-borne diseases. Although I. ricinus transcriptome studies have focused exclusively on protein coding genes, the last decade witnessed a strong increase in long non…
View article: Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host
Transcriptomic analysis of the tick midgut and salivary gland responses upon repeated blood-feeding on a vertebrate host Open
Ticks are blood-feeding arthropods that use the components of their salivary glands to counter the host’s hemostatic, inflammatory, and immune responses. The tick midgut also plays a crucial role in hematophagy. It is responsible for manag…
View article: 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
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 Open
Herpes simplex virus 1 (HSV-1) expresses a large number of miRNAs, and their function is still not completely understood. In addition, HSV-1 has been found to deregulate host miRNAs, which adds to the complexity of the regulation of effici…
View article: Selective isolation of extracellular vesicles from minimally processed human plasma as a translational strategy for liquid biopsies
Selective isolation of extracellular vesicles from minimally processed human plasma as a translational strategy for liquid biopsies Open
Background: Intercellular communication is mediated by extracellular vesicles (EVs), as they enclose selectively packaged biomolecules that can be horizontally transferred from donor to recipient cells. Because all cells constantly generat…
View article: The Virus-induced Upregulation of the miR-183/96/182 Cluster and the FoxO Family Protein Members are not Required for the Efficient Replication of HSV-1
The Virus-induced Upregulation of the miR-183/96/182 Cluster and the FoxO Family Protein Members are not Required for the Efficient Replication of HSV-1 Open
Herpes simplex virus 1 (HSV-1) expresses a large number of miRNAs, and their function is still not completely understood. In addition, HSV-1 has been found to deregulate host miRNAs, which adds to the complexity of regulation of efficient …
View article: sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms
sRNAbench and sRNAtoolbox 2022 update: accurate miRNA and sncRNA profiling for model and non-model organisms Open
The NCBI Sequence Read Archive currently hosts microRNA sequencing data for over 800 different species, evidencing the existence of a broad taxonomic distribution in the field of small RNA research. Simultaneously, the number of samples pe…
View article: Functional Enrichment Analysis of Regulatory Elements
Functional Enrichment Analysis of Regulatory Elements Open
Statistical methods for enrichment analysis are important tools to extract biological information from omics experiments. Although these methods have been widely used for the analysis of gene and protein lists, the development of high-thro…