Ana Conesa

SQANTI-evidence annotates genomes from long-read RNA-seq without a reference, achieving high precision in gene and isoform prediction across species.

TensorPLS is an R package for analyzing longitudinal omics data using PLS-DA, handling missing data and providing temporal insights through VIP scores and cross-validation.

The paper evaluates normalization methods and quantification pipelines for long-read RNA sequencing across PacBio and ONT platforms, showing platform-specific impacts on accuracy.

SQANTI-browser converts SQANTI3 classifications into UCSC Genome Browser Track Hubs for visualizing and curating long-read transcriptomes with metadata and filtering capabilities.

This study compares two strategies for combining biologically replicated long-read RNA-seq data to identify transcripts, finding that 'Join & Call' is better for novel isoforms while 'Call & Join' is more efficient for large datasets.

The paper investigates the YMC phase transitions by integrating metabolic, chromatin, and transcriptional data, finding that metabolite accumulation mediates the shift between HOC and LOC phases.

The paper introduces TUSCO, a framework for evaluating transcriptome reconstruction quality using long-read sequencing by assessing precision and sensitivity with a curated set of single-isoform genes.

SQANTI-reads assesses long-read RNA-seq data quality using SQANTI3 metrics, identifying under-annotated genes and splicing site variation across samples.

MOSim generates synthetic bulk and single-cell multi-omics datasets for benchmarking methods that analyze regulatory networks across various omics layers.

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

SQANTI3 extends long-read transcriptome quality control with transcript-end subcategories, a short-read TSS ratio, rules or random-forest filters and a rescue module, raising SIRV-benchmarked F-score stepwise.

MORE constructs phenotype-specific multi-omic regulatory networks using regression-based modeling and variable selection, showing improved accuracy and efficiency over existing tools.

This paper introduces TranD, a tool for comparing transcriptome structures using nucleotide-level distance metrics to assess transcript complexity and structural differences between species or annotations.

SQANTI-SIM simulates controlled transcript novelty for long-read RNA-seq data to benchmark transcriptome reconstruction pipelines.

MAMBA integrates semi-quantitative metabolomic data with gene-centric omics to improve metabolic network characterization and metabolite prediction in yeast under heat stress.

The paper introduces immuneREF, a method to quantify immune repertoire similarity across health and disease, finding that healthy and diseased repertoires are more similar than previously thought.

The paper examines how gene regulation, not gene content, contributes to maize genotypes' sensitivity to ozone stress by analyzing gene expression across diverse inbred lines.

The paper introduces GAIT-GM, a Galaxy tool for multi-omics analysis, and finds a link between branched-chain amino acid metabolism and cholinergic neuron defects in a C. elegans Parkinson's disease model.

Acorde identifies co-expression networks of alternative isoforms from single-cell data and detects co-differential isoform usage in neural cell types.

The paper introduces a conceptual framework and bioinformatics pipeline for multi-omics data integration, validated on TCGA datasets to enhance feature identification compared to single-omics analysis.

GAIT-GM provides Galaxy tools for integrating gene expression and metabolomics data through pathway-based analysis and flexible modeling of metabolite changes.

The paper introduces tappAS, a framework for analyzing the functional impact of differential splicing, showing AltTP plays a major role in neural development by altering protein function and regulation.

The paper introduces a method to build gene regulatory networks from scATAC-seq and scRNA-seq data using linked self-organizing maps, demonstrating its application in mouse pre-B cell differentiation.

The paper presents STATegra, a multi-omics dataset of mouse B-cell differentiation combining 10 omics technologies to study dynamic cellular processes.

PaintOmics 3 provides a web tool for integrated visualization and pathway analysis of multi-omics data, supporting various omic types and offering interactive features for biological interpretation.

SQANTI characterizes long-read transcript sequences to assess quality and improve quantification of full-length transcriptomes.

The paper introduces Iso-maSigPro, a tool for identifying differential isoform expression in RNA-seq time series and provides clustering and visualization functions for analyzing isoform-level gene expression patterns.

This study benchmarks nine workflows for detecting differential splicing and isoform expression in RNA-seq, finding that workflow performance depends on replicates and heterogeneity, with Limma, DESeq2, and DEXSeq performing well.