Lorenzo Calviello

Accelerating discovery and integration from RNA to Protein with R2T2P

R2T2P integrates transcriptomics and proteomics data to study FSHD, revealing novel RNAs and their impact on translation and protein levels.

The human RNA-DNA interactome is cell type-specific and dynamic

The paper maps RNA-DNA interactions in 16 human cell types, showing cell-type-specific and dynamic networks that correlate with gene regulation and disease traits.

High-quality peptide evidence for annotating non-canonical open reading frames as human proteins

The paper identifies 25% of 7,264 non-canonical open reading frames (ncORFs) as producing translated gene products, supported by over 3,000 peptides from 3.8 billion mass spectra.

Genomic codes governing enhancer RNA fate

This paper introduces CFC-seq and SALA to sequence non-poly(A) RNAs, identifies 39,425 novel transcriptional units, and reveals a genomic code governing enhancer RNA fate based on promoter architecture.

A ubiquitous GC content signature underlies multimodal mRNA regulation by DDX3X

The paper identifies GC content in coding sequences as a key factor in mRNA stabilization following DDX3X depletion, supported by analysis of RNA-seq data and ENCODE datasets.

Truncated RNA-binding protein production by DUX4-induced systemic inhibition of nonsense-mediated RNA decay

The paper shows that inhibiting NMD in FSHD leads to widespread production of truncated RNA-binding proteins, some of which are toxic and can be detected in patient samples.

A community-driven roadmap to advance research on translated open reading frames detected by Ribo-seq

This paper outlines a community-driven initiative to create a consolidated catalog of human Ribo-seq ORFs, addressing the lack of standardized annotation for these features.

Aberrant cortical development is driven by impaired cell cycle and translational control in a DDX3X syndrome model

This study investigates DDX3X syndrome using a mouse model, showing that DDX3X regulates cell cycle and translation in neural progenitors, leading to cortical malformations and neurodevelopmental issues.

DDX3X and DDX3Y are redundant in protein synthesis

This study shows DDX3X and DDX3Y redundantly regulate translation, with DDX3Y compensating for DDX3X loss in human cells, explaining sex-bias in DDX3X-related diseases.

DDX3 depletion represses translation of mRNAs with complex 5' UTRs

This study identifies mRNAs regulated by DDX3 depletion using ribosome profiling and RNA-seq, showing DDX3 preferentially affects a subset of transcripts with complex 5' UTRs.

Control of ribosomal protein synthesis by Microprocessor complex

The paper shows the Microprocessor complex regulates ribosomal protein synthesis by binding TOP motifs and promoting transcription elongation, linking ribosome biogenesis to cell growth.

Quantification of translation uncovers the functions of the alternative transcriptome

ORFquant quantifies translation at the open reading frame level using Ribo-seq, revealing alternative ORFs and gene-specific protein production differences across human cell lines.

A SARS-CoV-2-Human Protein-Protein Interaction Map Reveals Drug Targets and Potential Drug-Repurposing

Affinity-purification mass spectrometry of 26 SARS-CoV-2 proteins in HEK293T cells yields 332 high-confidence host interactions and 67 druggable human proteins with known compounds.

Ribo-seQC: comprehensive analysis of cytoplasmic and organellar ribosome profiling data

Ribo-seQC is a software package that evaluates ribosome profiling data quality and translational profiles across cytoplasmic and organellar ribosomes, outputting shareable platform-independent HTML reports.

Integrative classification of human coding and non-coding genes based on RNA metabolism profiles

The paper classifies human coding and non-coding genes based on RNA metabolism profiles, revealing distinct metabolic patterns and functional subsets of lncRNAs.

Comprehensive identification and characterization of conserved small ORFs in animals

The paper identifies and characterizes conserved small ORFs in multiple animal species, finding novel micropeptides with evidence of translation and functional potential.

A spectral analysis approach to detect actively translated open reading frames in high-resolution ribosome profiling data

RiboTaper identifies actively translated open reading frames using spectral analysis of Ribo-seq data, revealing novel ORFs and validating peptide products in HEK293 cells.