Toma Tebaldi

FoldARE improves RNA secondary structure prediction by using pseudo-SHAPE constraints from structural ensembles, achieving high accuracy across benchmark datasets.

The paper identifies female-specific m6A RNA methylation changes in mouse livers under high-fat diet that correlate with post-transcriptional metabolic adaptations and protein remodeling.

The paper investigates how centrosome architecture and m6A-dependent regulation influence p53 surveillance after whole-genome doubling, identifying key molecular mechanisms.

This study identifies the YAP/NNMT axis as a driver of innate sensitivity to NAMPT inhibition in stem-like mesenchymal prostate cancer, suggesting NNMT as a biomarker for NAD+-targeting therapies.

This study presents a spatiotemporal multi-omics analysis of aging neuromuscular junctions in mice, identifying genes with decoupled transcript and protein trajectories and highlighting post-transcriptional regulation in NMJ aging.

This study uses spatial transcriptomics to show that infiltrative glioblastoma cells differentiate toward an oligodendrocyte-like state, which may contribute to tumor invasion and recurrence.

The paper introduces Cell Marker Accordion, a tool for accurate and interpretable single-cell and spatial omics annotation across health and disease contexts.

This study shows that the RBM15-MKL1 fusion protein drives leukemia through m6A methylation and WNT pathway activation, with METTL3 inhibition reducing tumor growth.

This study investigates how TDP-43 dysregulation disrupts protein synthesis in ALS models by altering ribosome dynamics and mRNA homeostasis, revealing a conserved mechanism across in vitro and in vivo systems.

This study identifies NAT10 as a master regulator of brain metastasis through an in vivo shRNA screen and shows its role in promoting tumor growth and metastasis via downstream effectors.

The paper shows that pluripotent mouse embryonic stem cells silence MDA5 to avoid endogenous dsRNA recognition, preventing IFN activation and ensuring normal development.

This paper introduces Signature Distance, a statistical distance that improves upon energy distance for comparing empirical distributions in high-dimensional biological data, showing greater sensitivity to density changes and enabling model-free data expansion.

This study shows TERRA, a telomeric lncRNA, localizes to stress granules in human ALT cells under stress conditions.

This study identifies a nuclear role for AGO2 in spermatogenesis, showing it enhances protein expression by interacting with splicing and chromatin factors.

The paper introduces expressyouRcell, an R package that visualizes gene expression and protein level changes across time and space using dynamic cellular pictographs.

DBiT-seq enables high-spatial-resolution multi-omics mapping of mouse embryos by deterministic barcoding, revealing tissue types and fine features like retinal pigmented epithelium and microvasculature.

The paper shows SMN protein binds ribosomes and modulates translation of specific mRNAs in SMA, causing translational defects in motor neuron-related proteins.

The paper was withdrawn due to a duplicate posting and directs readers to the current version on bioRxiv.

This study investigates the developmental effects of hypomorphic mutations in the mouse HD gene orthologue, revealing varying degrees of lethality and developmental abnormalities depending on mutation severity.

riboWaltz optimizes P-site positioning in ribosome profiling data, improving accuracy and visualization of ribosome locations compared to existing tools.

The paper introduces RiboLace, a method to isolate active ribosomes for ribosome profiling, enabling high-resolution analysis of active translation.

The paper identifies early translational defects in SMA mice, showing reduced translational efficiency and ribosome numbers in motor neurons, which are rescued by SMN restoration.