Anthony Mathelier

HiFIseek identifies gene-specific enrichment of high-impact mutations in genomic regions associated with cancer and breast cancer risk SNPs, showing limited agreement across CRR-score combinations.

The paper shows that transient SUMOylation inhibition in human pre-adipocytes leads to stable beige differentiation when combined with PPARG activation.

This study integrates multi-omics data with gene regulatory networks to improve survival predictions in ten cancer types, showing improved associations with patient survival when GRNs are included.

COBIND identifies TF co-binding patterns using NMF on TFBS data, revealing both known and novel co-binding configurations across species.

MoDLE is a computational tool that rapidly simulates DNA loop extrusion contact patterns, matching existing methods and Micro-C data with high accuracy.

The paper identifies cis-regulatory mutations in cancer that disrupt gene regulatory programs by affecting both transcriptional and post-transcriptional regulation.

UniBind compiles high-confidence TF-DNA interactions from ChIP-seq data across nine species, predicting 56 million TFBSs and cis-regulatory modules.

MirGeneDB 2.0 expands curated microRNA gene annotations to 45 metazoan species, revealing many false positives and missing miRNAs in previous annotations.

The paper identifies copy number motifs in breast cancer genomes that predict disease outcome and driver events, outperforming existing clinical and genomic markers.

The paper shows that the choice of metric significantly affects genomic co-occurrence analysis and proposes alternative approaches to guide this choice.

The paper develops a method to predict direct TF-DNA interactions from ChIP-seq data and provides a resource of these interactions and cis-regulatory modules.

The paper compares super-enhancers and stretch enhancers across ten human cell types, finding super-enhancers are more transcriptionally active and cell-type-specific.

The paper identifies two classes of human enhancers distinguished by sequence composition, activity, and genome organization, with one class specifically linked to immune response genes.

The paper introduces a RESTful API for accessing JASPAR data, enabling programmatic retrieval in multiple formats and supporting DNA binding domain sequence analysis.

Intervene is a tool for intersecting and visualizing multiple gene or genomic region sets, offering Venn diagrams, UpSet plots, and heat maps for analysis.

CAGEd-oPOSSUM analyzes CAGE-derived TSSs to identify transcription factors regulating gene expression in specific cell types and conditions.

The paper identifies YY1's role in X-linked gene escape from inactivation by analyzing promoter activity and allelic binding in human datasets.