Júlia Perera‐Bel

RERE and the Mediator complex cooperate with EWSR1::FLI1 in the reprogramming of Translation and Alternative Splicing, the latter being a therapeutically targetable vulnerability in Ewing sarcoma

This paper identifies MED13L and RERE as genes regulated by EWSR1::FLI1 in Ewing sarcoma, showing their role in altering translation and alternative splicing, and demonstrates RBM39 inhibition as a therapeutic strategy.

Identification of a large class of cancer-germline microproteins as a source of immunotherapeutic targets

The paper identifies a large class of non-canonical cancer-germline antigens (ncCGAs) from lncRNAs and mRNA untranslated regions, showing their potential as immunotherapeutic targets.

Oncogenes and tumor suppressor genes are enriched in stop-loss mutations generating protein extensions

The paper identifies stop-loss mutations in cancer genomes, showing enrichment in cancer-related genes and potential immunological consequences.

Tumor B cell infiltration in platinum-treated advanced urothelial carcinoma

The paper examines how platinum-based chemotherapy affects tumor immune microenvironments in urothelial cancer, finding that memory B cell infiltration correlates with improved survival in cisplatin-treated patients.

Predicting immunotherapy response in advanced bladder cancer: a meta-analysis of six independent cohorts

This study identifies factors predicting immunotherapy response in advanced bladder cancer using data from six cohorts.

EWS-FLI1 Expression in Human Embryonic MSCs Leads to Transcriptional Reprograming, Defective DNA Damage Repair and Ewing Sarcoma

This study shows that EWS-FLI1 expression in human embryonic mesenchymal stem cells leads to an ES-like transcriptome and tumor formation, despite not preferentially binding promoters.

Transcriptomics-Driven Machine Learning Models Accurately Predict Chemotherapy Response in Muscle-invasive Bladder Cancer

The paper develops a machine learning model using transcriptomic data to predict chemotherapy response in muscle-invasive bladder cancer with high accuracy.

Non-canonical ORFs are an important source of tumor-specific antigens in a liver cancer meta-cohort

The paper identifies non-canonical ORFs as a significant source of tumor-specific antigens in liver cancer, showing they can trigger immune responses and are shared among a substantial proportion of patients.

Reproducible data integration and visualization of biological networks in R

The paper introduces R-based tools for reproducible integration, exploration, and visualization of biological networks, with available code and documentation.

Explaining decisions of Graph Convolutional Neural Networks: patient-specific molecular subnetworks responsible for metastasis prediction in breast cancer

The paper introduces GLRP, a method to explain Graph-CNN decisions in breast cancer metastasis prediction, identifying patient-specific molecular subnetworks that align with clinical knowledge.