J. Saez-Rodriguez

A system-wide analysis of lipid transfer proteins delineates lipid mobility in human cells

The paper identifies lipid cargoes for half of analyzed human LTPs, revealing selectivity for lipid head groups and acyl chains and new lipid-organelle relationships.

Characterizing and targeting glioblastoma neuron-tumor networks with retrograde tracing

This study uses retrograde tracing to characterize neuron-tumor networks in glioblastoma and shows that targeting these networks can enhance therapeutic outcomes.

Compartments in medulloblastoma with extensive nodularity are connected through differentiation along the granular precursor lineage

The paper uses single-cell transcriptomics to show how two compartments in medulloblastoma are connected through a migrating precursor stage, revealing spatial and developmental links between proliferating and differentiated tumor cells.

A single-sample workflow for joint metabolomic and proteomic analysis of clinical specimens

The paper introduces a single-sample workflow, MTBE-SP3, for simultaneous proteomic and metabolomic analysis, showing it reduces technical variation and enables consistent results across biological matrices.

Utilizing gene co-expression networks with the rat kidney TXG-MAPr tool to enhance safety assessment, biomarker identification and human translation

This study builds gene co-expression networks from rat kidney toxicogenomics data and integrates them into a web tool to improve safety assessment and biomarker identification for drug development.

Single-cell transcriptomics reveal distinctive patterns of fibroblast activation in murine heart failure with preserved ejection fraction

This study uses single-cell RNAseq to identify distinct fibroblast and macrophage activation patterns in murine HFpEF, revealing disease-specific transcriptional signatures and a potential biomarker.

Charting the Heterogeneity of Colorectal Cancer Consensus Molecular Subtypes using Spatial Transcriptomics

This study uses spatial transcriptomics and single-cell RNA sequencing to analyze colorectal cancer subtypes, revealing intratumoral heterogeneity and cell communication events in CMS2 carcinomas.

A Network-based Transcriptomic Landscape of HepG2 cells to Uncover Causal Gene Cytotoxicity Interactions Underlying Drug-Induced Liver Injury

This study uses network-based transcriptomic analysis of HepG2 cells exposed to DILI compounds to identify causally linked genes involved in drug-induced liver injury.

Deep Phosphoproteomic Elucidation of Metformin-Signaling in Heterogenous Colorectal Cancer Cells

This study uses phosphoproteomics to analyze metformin signaling in CRC cell lines, revealing heterogeneous responses and identifying potential drug interactions.

Pre-analytical processing of plasma and serum samples for combined proteome and metabolome analysis

This study evaluates pre-analytical factors affecting plasma and serum proteome and metabolome stability, recommending standardized protocols for clinical use.

The human hepatocyte TXG-MAPr: WGCNA transcriptomic modules to support mechanism-based risk assessment

The paper introduces TXG-MAPr, a tool for analyzing toxicogenomic data using WGCNA to identify stress response modules across species and platforms.

Nitrogen partitioning between branched-chain amino acids and urea cycle enzymes sustains renal cancer progression

This study identifies metabolic reprogramming in renal cancer cells, showing how branched-chain amino acid catabolism and urea cycle enzymes support tumor progression and metastasis.

Increasing triacylglycerol formation and lipid storage by unsaturated lipids protects renal proximal tubules in diabetes

This study shows that unsaturated lipids reduce renal damage in diabetes by increasing lipid storage and protecting against ER stress in proximal tubular cells.

Pan-Cancer landscape of protein activities identifies drivers of signalling dysregulation and patient survival

The paper analyzes protein activity changes in cancer using genomics and proteomics data to identify drivers of signaling dysregulation and their impact on patient survival.

Dissecting CD8+ T cell pathology of severe SARS-CoV-2 infection by single-cell epitope mapping

This study identifies an immunogenic CD8+ T cell epitope associated with severe SARS-CoV-2 infection and characterizes its pathological features.

A Community Challenge for Pancancer Drug Mechanism of Action Inference from Perturbational Profile Data

The paper hosts a DREAM Challenge to evaluate computational models for predicting drug polypharmacology using perturbational profile data from 32 kinase inhibitors.

PYCR1-dependent proline synthesis in cancer-associated fibroblasts is required for the deposition of pro-tumorigenic extracellular matrix

This study identifies PYCR1-dependent proline synthesis in cancer-associated fibroblasts as critical for collagen production and tumor progression, suggesting PYCR1 as a therapeutic target to inhibit pro-tumorigenic extracellular matrix deposition.

A statistical framework for assessing pharmacological response and biomarkers using uncertainty estimates

The paper introduces a statistical framework using uncertainty estimates to identify biomarkers from drug screening data, finding 24 known and 6 novel biomarkers in cancer cell lines.

Functional linkage of gene fusions to cancer cell fitness assessed by pharmacological and CRISPR/Cas9 screening

The paper functionally links gene fusions to cancer cell fitness using drug sensitivity and CRISPR-Cas9 data, identifying rare functional fusions and novel therapeutic targets.

A functional landscape of chronic kidney disease entities from public transcriptomic data

This paper integrates transcriptomic data from nine CKD entities to delineate their molecular differences and identify potential therapeutic targets.

Prioritisation of oncology therapeutic targets using CRISPR-Cas9 screening

This study uses CRISPR-Cas9 screens in cancer cell lines to identify and prioritize new oncology therapeutic targets based on gene fitness, biomarkers, and tractability.

In silico prioritization of transporter-drug relationships from drug sensitivity screens

The paper uses pharmacogenomics data and regression models to identify drug-transporter relationships, uncovering both known and novel associations.

GDSCTools for Mining Pharmacogenomic Interactions in Cancer

GDSCTools provides a software package for analyzing pharmacogenomic data to identify genomic markers of drug response in cancer.

Transcription factor activities enhance markers of drug response in cancer

The paper uses computational methods to infer transcription factor activities from RNA-seq data and shows their utility as markers for drug response in cancer.

Dissecting cancer resistance to therapies with cell-type-specific dynamic logic models

The paper uses dynamic logic models of signaling pathways to predict drug sensitivity in colorectal cancer cell lines and identifies drug combinations to overcome resistance.

Rapid identification of optimal drug combinations for personalized cancer therapy using microfluidics

This paper presents a microfluidics-based method to rapidly screen drug combinations on patient cancer cells, identifying personalized treatment options validated in pancreatic cancer cell lines.