Almudena Espín-Pérez

Multi-Sample and Multi-Group Spatial Colocalization Analysis Using PANORAMIC

PANORAMIC improves spatial colocalization analysis by accounting for within-sample uncertainty, revealing stronger immune cell colocalization in specific colorectal cancer subtypes.

Multi-modal benchmarking of the Ultima UG100 and Illumina NovaSeq sequencing platforms using clinically relevant FFPE tissues

This paper benchmarks the Ultima UG100 and Illumina NovaSeq platforms on FFPE tissues for various sequencing modalities, finding they produce comparable results with subtle discrepancies in non-coding transcripts.

Deciphering Cellular Ecosystems Driving Tumor Progression and Immune Escape from Spatial Transcriptomics and Single-Cell with COMPOTES

The paper introduces a machine-learning method to identify recurrent cell-cell communication patterns across tumor samples using spatial transcriptomics and single-cell data, revealing key immune and genetic programs in bladder cancer.

Multiple instance learning with spatial transcriptomics for interpretable patient-level predictions: application in glioblastoma

This paper introduces SpaMIL, a spatial transcriptomics-based multiple instance learning framework for patient-level outcome prediction in glioblastoma, achieving high prognostic accuracy.

Histology and spatial transcriptomic integration revealed infiltration zone with specific cell composition as a prognostic hotspot in glioblastoma

The paper identifies a prognostic infiltration zone in glioblastoma using histology and spatial transcriptomic integration, revealing specific cell composition associated with long-term survival.

Joint probabilistic modeling of pseudobulk and single-cell transcriptomics enables accurate estimation of cell type composition

The paper introduces MixupVI, a deep generative model for reference-free deconvolution of bulk RNA-seq data using single-cell transcriptomics, and releases PyDeconv for benchmarking deconvolution algorithms.

Transcriptome Analysis of Archived Tumor Tissues by Visium, GeoMx DSP, and Chromium Methods Reveals Inter- and Intra-Patient Heterogeneity

The paper compares three transcriptomic methods on FFPE tumor samples to assess their ability to detect inter- and intra-patient heterogeneity.

High Resolution Single Cell Maps Reveals Distinct Cell Organization and Function Across Different Regions of the Human Intestine

The paper maps cell organization and function across human intestine regions using single nuclear RNA and open chromatin assays, revealing distinct cell neighborhoods and regulatory differences.