Eva Maria Novoa

Declines in mRNA synthesis set the rate of organismal aging

The paper shows that declining mRNA synthesis capacity during aging reduces mRNA abundance, driving organismal aging, and that manipulating this decline affects healthspan and lifespan.

Evolutionary and biological insights into the paternally expressed Snord116-Ipw-Snord115 gene array at the imprinted Prader-Willi syndrome domain

The paper investigates the role of Snord116 and Snord115 genes in Prader-Willi syndrome using knockout mice and comparative genomics, finding their impact on growth, metabolism, and gene regulation.

Harmonized nucleoside mass spectrometry enables reproducible cross-platform RNA modification quantification

The paper benchmarks cross-platform RNA modification quantification using LC-MS/MS and finds that harmonized workflows and SILIS normalization improve reproducibility across different instrument types.

Single-molecule m6A profiling reveals position-dependent mRNA regulation and non-canonical roles for Ythdf2 in early embryogenesis

The paper uses single-molecule m6A profiling to study mRNA regulation during zebrafish MZT, finding m6A's role in mRNA decay and poly(A) tail dynamics.

AMaNITA: an end-to-end workflow for native tRNA nanopore sequencing data analysis

AMaNITA provides an end-to-end workflow for analyzing nanopore native tRNA sequencing data, enabling differential abundance and modification stoichiometry analysis.

FIRST-seq: a nanopore-based cDNA sequencing platform for RNA modification and structure profiling

FIRST-seq uses nanopore cDNA sequencing to profile RNA modifications and structures by analyzing RT errors, achieving single-nucleotide resolution without PCR or second-strand synthesis.

Host tRNA modifications drive efficient translation of influenza A virus genome and impact host antiviral stress responses

The paper shows that host tRNA modifications are critical for efficient influenza A virus translation and antiviral responses, with ELP3 loss impairing viral propagation.

Systematic benchmarking of basecalling models for RNA modification detection with highly multiplexed nanopore sequencing

This study benchmarks RNA modification detection models using synthetic and biological data, finding high reliability but issues with false positives and cross-reactivity.

Selective profiling of translationally active tRNAs and their dynamics under stress

The paper introduces tRIBO-seq, a nanopore-based method to profile ribosome-associated tRNAs, revealing stress-induced changes in tRNA abundance, modification, and fragmentation.

Nano3P-seq: charting the coding and non-coding transcriptome at single molecule resolution

The paper introduces Nano3P-seq, a nanopore-based method to analyze RNA polyA tail composition and length at single-molecule resolution, along with software PolyTailor for accurate estimation of transcript abundances and tail dynamics.

SeqTagger, a rapid and accurate tool to demultiplex direct RNA nanopore sequencing datasets

SeqTagger demultiplexes direct RNA nanopore sequencing datasets with high precision and recall, supporting multiple chemistries and library types.

De novo basecalling of m6A modifications at single molecule and single nucleotide resolution

This paper introduces m6ABasecaller, a method for de novo basecalling of m6A modifications at single molecule and single nucleotide resolution using nanopore sequencing.

Epitranscriptomic rRNA fingerprinting reveals tissue-of-origin and tumor-specific signatures

The paper uses rRNA modification patterns to identify tissue and tumor-specific signatures, showing their potential as diagnostic biomarkers.

Unbiased functional genetic screens reveal essential RNA modifications in human cancer and drug resistance

The paper identifies essential RNA modifications in cancer using CRISPR screens and finds that mitochondrial metabolic plasticity influences drug resistance through specific RNA modifications.

Single nucleus RNA-seq in the hippocampus of a Down syndrome mouse model reveals new key players in memory

The paper uses single nucleus RNA-seq to analyze the hippocampus of a Down syndrome mouse model, identifying transcriptomic changes and a novel long-non-coding gene involved in cognitive phenotypes.

Comprehensive map of ribosomal 2'-O-methylation and C/D box snoRNAs in Drosophila melanogaster

This study maps 2'-O-methylation sites and identifies C/D box snoRNAs in Drosophila rRNAs, showing limited stress-induced variation in methylation levels.

Enhanced detection of RNA modifications and mappability with high-accuracy nanopore RNA basecalling models

This paper shows that using high-accuracy nanopore RNA basecalling models improves detection of RNA modifications, read mappability, and basecalling accuracy.

Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart

This study investigates the role of RPL3L in ribosome heterogeneity and mitochondrial activity in cardiomyocytes, finding that its depletion increases ribosome-mitochondria interactions and ATP levels.

Nano3P-seq: transcriptome-wide analysis of gene expression and tail dynamics using end-capture nanopore cDNA sequencing

Nano3P-seq quantifies RNA abundance, tail composition, and tail length dynamics at single-read resolution without PCR or adapters.

ModPhred: an integrative toolkit for the analysis and storage of nanopore sequencing DNA and RNA modification data

ModPhred provides a toolkit for analyzing and storing nanopore sequencing DNA and RNA modification data, enabling efficient encoding, visualization, and analysis.

High-Throughput 5' UTR Engineering for Enhanced Protein Production in Non-Viral Gene Therapies

This study develops a high-throughput method to engineer 5' UTRs that enhance protein expression in non-viral gene therapies, identifying synthetic 5 UTRs that outperform existing plasmids.

Quantitative profiling of native RNA modifications and their dynamics using nanopore sequencing

The paper introduces a method to quantify RNA modifications using nanopore sequencing, revealing novel modification sites and dynamics in yeast under environmental stress.

Subcellular relocalization and nuclear redistribution of the RNA methyltransferases TRMT1 and TRMT1L upon neuronal activation

The paper investigates the subcellular relocalization of TRMT1 and TRMT1L during neuronal activation and identifies their role in RNA modification dynamics and neuronal plasticity.

Barcoding and demultiplexing Oxford Nanopore native RNA sequencing reads with deep residual learning

This paper introduces a deep learning method for barcoding and demultiplexing direct RNA sequencing reads without base-calling or additional library steps, achieving high specificity and read demultiplexing rates.

Integrative analyses of the RNA modification machinery reveal tissue- and cancer-specific signatures

The paper identifies tissue- and cancer-specific RNA modification machinery (RMP) expression patterns and dysregulation across 32 tissues, 10 species, and 13,358 tumor-normal samples.

Best practices for genome-wide RNA structure analysis: combination of mutational profiles and drop-off information

This paper shows that combining mutational profiles and drop-off information improves RNA structure analysis by capturing complementary structural information and reducing false positives.

Parallel and scalable workflow for the analysis of Oxford Nanopore direct RNA sequencing datasets

The paper introduces a scalable workflow for analyzing Oxford Nanopore direct RNA sequencing data, enabling RNA modification detection and polyA tail length estimation.

Accurate detection of m6A RNA modifications in native RNA sequences

This paper demonstrates the detection of m6A RNA modifications in native RNA sequences using Oxford Nanopore Technologies with high accuracy.

mRNA structure dynamics identifies the embryonic RNA regulome

The paper characterizes mRNA structure dynamics during zebrafish development and identifies ribosome-mediated RNA remodeling and 3-UTR structures as key regulators of gene expression and decay.