Eduard Porta‐Pardo

Spatial transcriptomics unveils the in situ cellular and molecular hallmarks of the lung in fatal COVID-19

This study uses spatial transcriptomics to analyze lung tissue from fatal COVID-19 cases, identifying cellular and molecular changes during disease progression.

RNA and protein are not interchangeable in single-cell spatial multi-omics

This study shows that spatial RNA and protein measurements are largely overlapping for lineage markers and abundance but discordant for specific molecules and spatial features, indicating they are complementary rather than interchangeable.

A pan-cancer single-cell atlas of pericytes

The paper constructs a pan-cancer single-cell RNA sequencing atlas of pericytes, revealing a common transcriptional program in tumour-associated pericytes and their specialised subtypes across multiple cancers.

Convergent stromal and immune remodeling defines spatial tumor dynamics in PARP inhibitor-resistant high-grade serous ovarian cancer

This study identifies spatial tumor microenvironment changes in PARP inhibitor-resistant high-grade serous ovarian cancer using spatial transcriptomics.

Benchmarking of spatial transcriptomics platforms across six cancer types

This study benchmarks spatial transcriptomics and proteomics platforms across six cancer types, identifying platform-specific strengths and limitations in data quality and biological insights.

3Dmapper: A Command Line Tool For BioBank-scale Mapping Of Variants To Protein Structures

3Dmapper maps annotated protein positions and variants to protein structures efficiently and reliably for large-scale genomic data analysis.

Brewpitopes: a pipeline to refine B-cell epitope predictions during public health emergencies

Brewpitopes refines B-cell epitope predictions by integrating protein features, improving neutralizing epitope identification in SARS-CoV-2.

Radical fringe facilitates NOTCH1 and JAG1 cis interactions to sustain Hematopoietic stem cell fate

The paper identifies NOTCH1-JAG1 cis interactions regulated by RADICAL FRINGE that maintain hematopoietic stem cell fate during development.

The structural coverage of the human proteome before and after AlphaFold

This study quantifies how AlphaFold's structural models increase human proteome coverage from 48% to 76% and reduce the dark proteome from 26% to 10%.

The landscape of interactions between cancer polygenic risk scores and somatic alterations in cancer cells

This study examines how cancer polygenic risk scores correlate with somatic alterations in tumors from The Cancer Genome Atlas, revealing associations with specific molecular subtypes and driver events.

The consequences of variant calling decisions in secondary analyses of cancer sequencing data

This study evaluates how variant calling decisions affect downstream cancer genomics analyses and finds that different callers and strategies yield significant differences in driver gene identification, mutational signatures, and actionable variant detection.

Cancer3D 2.0: interactive analysis of 3D patterns of cancer mutations in cancer subsets

Cancer3D 2.0 provides an interactive platform to analyze 3D mutation patterns in cancer subsets, enabling identification of novel driver regions in specific patient subgroups.