Juan I. Fuxman Bass

This study shows defective HIV proviruses trigger type I interferon responses in myeloid cells through MDA5-dependent pathways, contributing to chronic inflammation in people with HIV.

The paper uses peptide tiling to identify viral protein regions that modulate stress-induced cell death in U2OS cells, revealing modular regulatory functions.

fastCDS maps protein domains to genomic coordinates efficiently, enabling rapid analysis of exonic architecture and variant interpretation.

The paper identifies TF-DNA binding interactions at cytokine promoters, showing that TF cooperativity and antagonism significantly influence DNA-binding specificity.

The paper systematically identifies effector functions of pathogen ORFs across multiple pathways, revealing new roles for known effectors and uncharacterized proteins.

The paper maps chromatin dysregulation caused by viral transcriptional regulators using PROD-ATAC, identifying vTRs that remodel chromatin and reveal shared host transcription factor networks.

The paper investigates how human transcription factors bind specific DNA sites in yeast, finding that disordered regions influence binding selectivity beyond DNA motifs.

The paper creates a regulatory atlas of HIV-1 and HIV-2 by analyzing transcriptional variation across clades, isolates, and individuals using MPRAs and predictive models.

eSIG-Net predicts how single mutations affect protein interactions using a sequence-based interaction language model, outperforming existing methods.

This study systematically profiles 95 viral transcriptional regulators (vTRs) across multiple assays, revealing their diverse mechanisms of rewiring host pathways to promote viral replication and disease links.

The paper identifies ~2,000 cis-regulatory elements (CREs) across 27 dsDNA viruses using reporter assays and machine learning, revealing their regulatory features and associated transcription factors.

The paper identifies two categories of transcription factor isoforms with distinct molecular functions and shows they contribute to gene regulatory complexity.

This study constructs a large-scale cancer-specific TF-DNA interaction network and identifies potential therapeutic targets among oncogenes and TFs.

The paper introduces MACAW, a workflow for detecting errors in genome-scale metabolic models, showing that error types vary with curation methods and that pathway-level errors are particularly challenging.

The paper identifies conserved skeletal enhancers near GWAS risk loci for craniosynostosis, linking sequence variants to altered gene expression and disease risk.

The paper introduces paired yeast one-hybrid assays to detect DNA-binding cooperativity and antagonism between transcription factors and demonstrates their application across various TF pairs.

Epitope-Evaluator is a web tool that allows users to interactively analyze and filter predicted T-cell epitopes from immunoinformatic tools.

The paper characterizes human minisatellite VNTRs, identifies population-specific alleles, and links some VNTRs to gene expression differences.

The paper develops enhanced yeast one-hybrid assays to study TF binding to repetitive elements, variants, and novel motifs, identifying 75 TFs interacting with Alu elements and changes in TF binding associated with cancer-related mutations.