Bastian Fromm

MirMachine 2 annotates microRNAs across thousands of animal genomes, revealing methodological biases in apparent microRNA absence.

The paper studies microRNA and target expression variation in mouse embryonic stem cells using genetic perturbation and single-cell RNA-seq, finding four co-expression groups and mixed effects on target variation.

RNAcentral integrates literature and gene-level data to enhance non-coding RNA sequence analysis and functional understanding.

The paper analyzes genomic data from 32 animal species to explore how changes in regulatory genes and microRNAs relate to morphological complexity and disparity, finding no link between genome size and disparity but strong associations between gene loss and parasitism, and microRNA increases and complexity.

The paper introduces a reference-free computational method to discover cancer-unique small RNAs from sequencing data, identifying 1211 novel oncRNAs with potential clinical relevance.

This paper presents the first near chromosome-level genome of a sea spider, revealing a single Hox cluster without abdominal-A/Hox9, supporting shared evolutionary patterns in arthropods.

The paper shows that placental phenotypes in mammals can be predicted from miRNA repertoires with high accuracy, revealing constrained genetic pathways for convergent evolution.

The paper investigates the correlation between loss of microRNAs, protein-coding genes, and morphological complexity in syndermatan invertebrates, finding a strong association in regressive evolution.

The paper presents the chromosome-scale assembly of the giant Pleurodeles waltl genome, revealing insights into its expansion and regeneration-related genes.

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

The paper presents genome assemblies for three Platynereis species to support comparative genomic studies and explore their biology.

This paper re-examines the Expensive Tissue Hypothesis, finding a thermoregulatory tradeoff between liver and brain proportions in mammals, and proposes a model of brain size evolution based on metabolic rates and microRNA families.

Chromosome-scale inshore hagfish genome places 1R before the cyclostome-gnathostome split and 2R in the gnathostome stem, and reveals two cyclostome-specific duplications (CR1, CR2).

The paper introduces MirMachine, a tool that uses trained covariance models to annotate microRNA complements in genomes, enabling annotation of large and extinct genomes and assessing genome assembly completeness.

The paper evaluates newly sequenced T2T genomic regions for paralogous miRNA loci and novel miRNAs, finding no bona fide miRNAs and only questionable ones.

The paper introduces MapToCleave, a method to profile miRNA biogenesis in living cells, showing that stable lower basal stems enhance processing and expression across species.

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.

The paper shows miR-21-5p and miR-30a-5p are identical between human and bovine, and their presence in human blood after milk ingestion is likely due to endogenous regulation or technical issues, not xenomiR uptake.

The paper profiles circulating RNAs in human serum using RNA-seq and identifies potential biomarkers by analyzing biological and technical variation.

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

The paper presents genome, transcriptome, and metagenome data from Eisenia fetida to study regeneration dynamics, identifying differentially expressed genes and microbial communities.

GSuite HyperBrowser provides a platform for integrative analysis of genome and epigenome datasets with customizable statistical methods and a Galaxy-based interface.