Yasset Pérez‐Riverol

hvantk: an agentic multi-omics framework for variant annotation and analysis

hvantk is a framework for variant annotation and analysis that integrates multi-omic data, improving the recovery of disease genes in case-control cohorts.

onsite: An Integrated Framework for Phosphosite Localization and False Localization Rate Estimation

The paper introduces onsite, a framework for estimating false localization rates in phosphoproteomics, showing pyLucXor achieves high accuracy and localization count.

mzQC: a versatile way to communicate quality information for biological mass spectrometry

The paper introduces mzQC, a standard for representing quality control metrics in mass spectrometry, enabling interoperable and machine-readable QC reporting.

π-MSNet: A large-scale, AI-ready and continuously reprocessed proteomics data resource

The paper introduces π-MSNet, a large-scale proteomics dataset for AI training and benchmarking, showing performance improvements when models are retrained on it.

Assessing the contribution of rare variants to congenital heart disease through a large-scale case-control exome study

This study identifies rare variants and digenic interactions associated with congenital heart disease using a large-scale exome case-control analysis.

Quantifying data reuse in proteomics using PRIDE downloads statistics and a semi-supervised LLM-based framework

The paper analyzes proteomics dataset reuse using PRIDE download statistics and a semi-supervised LLM-based framework to classify download sources.

pmultiqc: An open-source, lightweight, and metadata-oriented QC reporting library for MS proteomics

pmultiqc generates metadata-aware QC reports for proteomics data using standardized metrics and integrates with existing workflows and cloud services.

LFQ Benchmark Dataset - Generation Beta: Assessing Modern Proteomics Instruments and Acquisition Workflows with High-Throughput LC Gradients

The paper generates a benchmark dataset to evaluate proteomics instruments and workflows using high-throughput LC gradients across multiple platforms and organisms.

quantms-rescoring enables deep proteome coverage across protein quantification, immunopeptidomics, and post-translational modifications experiments.

quantms-rescoring improves proteomics analysis by integrating multiple search engines and machine learning, increasing identified spectra and quantifying more phosphorylated peptides and modification sites.

ProteoBench: the community-curated platform for comparing proteomics data analysis workflows

ProteoBench provides a centralized platform for comparing proteomics data analysis workflows, enabling benchmarking and community collaboration.

ibaqpy: A scalable Python package for baseline quantification in proteomics leveraging SDRF metadata

ibaqpy computes iBAQ values for proteomics data using SDRF metadata, improving scalability and reproducibility in large-scale experiments.

Proteogenomics analysis of human tissues using pangenomes

The paper reanalyzes human tissue proteomics data using pangenome references to identify novel peptides and variants, demonstrating the effectiveness of proteogenomics approaches with pangenome data.

Phosphorylation in the Plasmodium falciparum proteome: A meta-analysis of publicly available data sets

This paper performs a meta-analysis of 11 phosphoproteomics datasets to identify phosphorylated sites in Plasmodium falciparum and related species, revealing sequence motifs, conservation patterns, and structural context of phosphosites.

A meta-analysis of rice phosphoproteomics data to understand variation in cell signalling across the rice pan-genome

This study analyzes rice phosphoproteomics data to identify phosphosite variations across the rice pan-genome and their functional implications.

A comprehensive evaluation of consensus spectrum generation methods in proteomics

The paper evaluates consensus spectrum generation methods in proteomics, finding BEST and BIN to be the most reliable for peptide identification.

A comprehensive LFQ benchmark dataset on modern day acquisition strategies in proteomics

The paper presents a comprehensive benchmark dataset for evaluating label-free quantification methods across various proteomics acquisition strategies.

Generation of ENSEMBL-based proteogenomics databases boosts the identification of non-canonical peptides.

The paper introduces tools to generate proteogenomics databases using ENSEMBL resources, revealing non-canonical peptides in public datasets.

A method for independent estimation of false localisation rate for phosphoproteomics

The paper introduces a method to independently estimate the false localisation rate in phosphoproteomics using decoy amino acids, showing that alanine and leucine provide reliable results.

A proteomics sample metadata representation for multiomics integration, and big data analysis.

The paper introduces a standardized metadata format for proteomics datasets to improve reusability and integration across public repositories.

Integrative analysis of genomic variants reveals new associations of candidate haploinsufficient genes with congenital heart disease

The paper identifies 21 candidate haploinsufficient genes associated with congenital heart disease through integrative analysis of CNVs and DNMs in CHD cases and controls.

Universal Spectrum Identifier for mass spectra

The paper introduces the Universal Spectrum Identifier (USI) to standardize referencing mass spectra in proteomics repositories, enabling transparent traceability of spectral evidence in publications.

Universal Spectrum Explorer: A standalone (web-)application for cross-resource spectrum comparison

The paper introduces a web-based tool for cross-resource peptide spectrum comparison and visualization, with a focus on integration and retrieval from spectral databases.

An integrated landscape of protein expression in human cancer

This study compiles a proteomics resource for cancer cell lines and tumour samples, finding that protein abundance in cell lines often reflects tumours but fails to capture subtype-specific variations.

User-friendly, scalable tools and workflows for single-cell analysis

The paper introduces an interactive scRNA-Seq analysis environment based on Galaxy, integrating ~70 functions for scalable and accessible single-cell data analysis.

BioContainers Registry: searching for bioinformatics tools, packages and containers

The paper introduces the BioContainers Registry and API to improve the findability, accessibility, interoperability, and reusability of bioinformatics tools and containers.

The Omics Discovery REST interface

The paper introduces the OmicsDI REST interface for programmatic access to omics datasets and provides R and Python libraries for interacting with the API.

Phoenix Enhancer: proteomics data mining using clustered spectra

Phoenix Enhancer improves proteomics data analysis by clustering spectra to identify potential mis-identifications and enhance peptide spectrum match confidence.

ThermoRawFileParser: modular, scalable and cross-platform RAW file conversion

ThermoRawFileParser converts Thermo RAW files to open formats like mzML, enabling broader use with workflow systems and providing a user-friendly interface.

Scalable data analysis in proteomics and metabolomics using BioContainers and workflows engines.

The paper introduces a scalable approach for reproducible proteomics and metabolomics analysis using BioContainers and workflows engines like Galaxy and Nextflow.

Quantifying the impact of public omics data

This paper explores how to quantify the impact of public omics data by examining usage patterns and the role of FAIR principles in data discovery and reuse.