Raúl Rabadán

Nucleosome-scale p53-hormone receptor grammar distributed by Alu elements

The paper identifies p53-hormone receptor regulatory grammars distributed by Alu elements in mammary and muscle cells, with implications for breast cancer and muscle aging.

NicheScribe: consistent and generalizable annotation of stromal cells in the murine bone marrow niche

The paper develops NicheScribe, a method for consistently annotating stromal cells in the murine bone marrow niche using scRNA-seq data, enabling comparative analysis across different conditions.

MAPK/ERK signaling in gliomas modulates interferon responses, T cell recruitment, enhances tumor-microglia crosstalk, and drives immune checkpoint blockade efficacy.

This study identifies the MAPK/ERK pathway as a key regulator of glioma susceptibility to immune checkpoint blockade, showing it modulates interferon responses, T cell recruitment, and tumor-microglia interactions.

Quantitative molecular cartography of emergency myelopoiesis reveals conserved modules of hematopoietic activation

The paper identifies shared and distinct molecular mechanisms of emergency myelopoiesis using scRNA-seq and develops tools to annotate and model hematopoietic differentiation.

Mapping the genetic landscape of the DNA damage response with Cas12a-based combinatorial knockout screens

This study uses Cas12a-based knockout screens to identify genetic interactions in the DNA damage response, revealing synthetic lethal and buffering interactions with therapeutic implications.

Transcriptome sequencing of Hodgkin lymphoma Hodgkin and Reed-Sternberg cells reveals escape from NK cell recognition and an unfolded protein response

This study identifies unique transcriptional features of Hodgkin lymphoma HRS cells, including immune evasion mechanisms and an unfolded protein response, distinguishing them from other B-cell lymphomas.

Mapping kinase-dependent tumor immune adaptation with multiplexed single-cell CRISPR screens

The paper develops a CRISPR screening framework to map kinase-dependent immune evasion mechanisms in glioblastoma by integrating single-cell transcriptomics and deep generative models.

A transposase-derived gene required for human brain development

This study identifies PGBD5 as a transposase-derived gene essential for brain development in humans and mice, with deficiency causing intellectual disability and seizures.

Decoding the gene regulatory landscape through multimodal learning of protein-DNA interactions

Chromnitron predicts protein-DNA binding landscapes across cell types and proteins using multimodal learning, revealing new regulators of T cell exhaustion and dynamic shifts during neurogenesis.

Aberrant pace of cortical neuron development in brain organoids from patients with 22q11.2 deletion syndrome-associated schizophrenia

This study identifies delayed cortical neuron development in 22q11.2DS-associated schizophrenia using brain organoids and single-cell RNA sequencing.

Genomic Touchstone: Benchmarking Genomic Language Models in the Context of the Central Dogma

Genomic Touchstone evaluates genomic language models across 36 tasks and 88 datasets, revealing insights on model performance, scaling, and pretraining strategies.

A computational framework for mapping isoform landscape and regulatory mechanisms from spatial transcriptomics data

This paper introduces SPLISOSM, a framework for analyzing spatial transcriptomics data to detect isoform-level patterns, identifying spatially variable transcript diversity and regulatory relationships in mouse and human brain tissues.

Ku suppresses RNA-mediated innate immune responses in human cells to accommodate primate-specific Alu expansion.

The paper shows Ku suppresses RNA-mediated innate immune responses in human cells, enabling primate-specific Alu element expansion by reducing dsRNA-induced inflammation.

Enhancer Dynamics and Spatial Organization Drive Anatomically Restricted Cellular States in the Human Spinal Cord

This study examines enhancer dynamics and spatial organization in the human spinal cord to understand cellular state transitions and identity.

GET: a foundation model of transcription across human cell types

GET is a foundation model that accurately predicts gene expression and regulatory interactions across 213 human cell types using chromatin accessibility and sequence data.

Smoother: A Unified and Modular Framework for Incorporating Structural Dependency in Spatial Omics Data

Smoother integrates positional information into non-spatial models for spatial omics data, enabling accurate imputation, deconvolution, and dimensionality reduction in simulated and real datasets.

Mechanisms of insertions at a DNA double-strand break

The paper develops Indel-Seq to study insertion mechanisms at DNA double-strand breaks, finding insertions arise from transcription and require DNA-PK and ssDNA overhangs.

ATR kinase supports normal proliferation in the early S phase by preventing replication resource exhaustion.

This study shows ATR kinase prevents replication resource exhaustion in early S phase, supporting normal cell proliferation by regulating origin firing.

ARP2/3- and resection-coupled genome reorganization facilitates translocations

The paper shows that ARP2/3-dependent nuclear actin polymerization and DNA end-resection coordinate genome reorganization to facilitate homology-directed repair and prevent translocations.

KINOMO: A non-negative matrix factorization framework for recovering intra- and inter-tumoral heterogeneity from single-cell RNA-seq data

KINOMO improves the analysis of single-cell RNA-seq data by recovering intra- and inter-tumoral heterogeneity through non-negative matrix factorization, outperforming existing methods in benchmarking.

Comprehensive characterization of protein-protein interaction network perturbations by human disease mutations

This study identifies disease mutations that perturb protein-protein interactions in the human 3D interactome, showing their association with cancer survival and drug response.

A single-cell atlas of the mouse and human prostate reveals heterogeneity and conservation of epithelial progenitors

This study creates a single-cell atlas of mouse and human prostate epithelium, identifying conserved progenitor populations and anatomical relationships between species.

arcasHLA: high resolution HLA typing from RNA seq

arcasHLA is a tool for high-resolution HLA typing from RNA sequencing data, achieving high accuracy and speed compared to existing methods.

Topological Data Analysis of Single-cell Hi-C Contact Maps

The paper applies topological data analysis techniques to single-cell Hi-C contact maps to quantify biological structures.

Quasi-universality in single-cell sequencing data

This paper identifies a universal pattern in single-cell sequencing data and proposes a method to denoise it by distinguishing biological signals from artifacts.

On statistical modeling of sequencing noise in high depth data to assess tumor evolution

This paper develops a statistical model for sequencing noise in high-depth data to identify mutations associated with tumor progression and recurrence.

High-resolution genomic surveillance of 2014 ebolavirus using shared subclonal variants

This study identifies shared subclonal variants in 2014 ebolavirus to improve phylogenetic resolution and transmission bottleneck estimation during an outbreak.