Michael Hackenberg

The paper benchmarks long-read RNA sequencing pipelines for de novo transcriptome assembly in non-model plants, finding organ-specific optimal strategies for flower and leaf tissues.

The paper identifies conserved miRNA-mRNA interactions in ticks that cooperatively target host genes involved in immune and tissue responses.

MirGeneDB 3.0 updates the microRNA gene database with expanded species coverage, refined nomenclature, and improved covariance models for phylogenetic analysis.

The paper identifies that full-length tRNAs with truncated CCA tails are selectively sorted into extracellular vesicles, suggesting a new mechanism for EV cargo selection.

The paper presents genome sequences of four Ixodes species, revealing gene family amplifications and evolutionary patterns in ticks.

GeneCodis 4 extends functional enrichment analysis to regulatory elements like transcription factors, CpG sites, and miRNAs, with new databases and visualizations.

The paper introduces IsoSeek, a method for unbiased and UMI-informed sequencing of cell-free miRNAs, revealing extensive uridylation of disease-associated miRNAs and improving isomiR detection in extracellular vesicles.

MirGeneDB 2.0 expands curated microRNA gene annotations to 45 metazoan species, revealing many false positives and missing miRNAs in previous annotations.

The paper introduces mirGFF3, a standardized format for miRNA/isomiR analysis, and mirtop, a tool to convert outputs into this format, enabling data sharing and comparative analysis.

miRNAgFree predicts and profiles novel microRNAs without genome assembly by leveraging biogenesis features, achieving high accuracy in well-annotated species.