Marc R. Friedländer

This study shows that male obesity affects adipose mitochondrial function in offspring via the let-7-DICER axis, with reversible effects observed in both mice and human semen.

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.

This study identifies mRNA stem-loops and their stability as key regulators of stop codon readthrough in Drosophila, refining computational predictions of this phenomenon.

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.

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.

agoTRIBE identifies miRNA-target interactions in single cells using a fusion protein approach, revealing differential targeting across the cell cycle.

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.

This study shows environmental enrichment alters chromatin structure, transcription factor binding, and 3D genome organization in mice, affecting cognitive function and gene regulation.

The paper identifies >80,000 gene pairs with intrinsic covariance in mouse embryonic stem cells, showing nuclear organization and protein interactions drive transcript covariances.

This study shows BRG1 affects alternative splicing by altering RNA binding factor interactions with RNA, with some effects independent of its ATPase activity.

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.

This study introduces a Bayesian model to identify cancer driver genes by integrating evolutionary signatures, revealing novel gene-tumor type associations and highlighting chromatin modifiers as key targets.