Matthew T. Weirauch

This study identifies HIF-2 as a critical factor for the survival of cytokine-activated human NK cells, showing it is induced by IL-2/IL-15 and not hypoxia, and its inhibition reduces NK cell viability.

This study develops an EBV-infected tonsil organoid model to study B cell states and antiviral responses during primary infection, revealing unique transcriptional programs and immune interactions.

This study identifies DNA binding motifs for 98 human transcription factors using meSMiLE-seq, revealing methylation-sensitive binding preferences for some TFs.

The paper uses GHT-SELEX to show many human TFs have high intrinsic sequence specificity and complex DNA binding, often matching in vivo ChIP-seq results.

This study provides a reference genome and transcriptome atlas of the Rocky Mountain wood tick, identifying genes involved in blood feeding and developmental-stage-specific gene expression.

This study systematically investigates EBV transcriptional regulators' interactions with the human genome, identifying extensive gene expression alterations and chromatin changes.

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

The paper identifies a new bZIP protein motif, BPabZIP, that facilitates nucleosome displacement and binding near nucleosomes in human cells.

The paper characterizes gene regulatory networks in human airway epithelial cells and identifies cell type-specific responses to type I interferon.

This study uses single nucleus RNA sequencing to identify altered angiogenic signaling in JDM muscle, highlighting vascular and IFN pathways.

This study shows that EBNA2 activity is increased in MS patients, altering gene expression and chromatin accessibility in EBV-transformed B cells.

The paper identifies memory-specific AP-1 recruitment in T cells, driven by epigenetic changes and co-factor interactions, and links it to disease risk variants.

This study identifies locus-specific DNA methylation defects at bivalent chromatin as a common feature in growth disorders caused by DNMT3A or NSD1 mutations.

This study evaluates over 3,000 congenital heart disease-risk variants using SNP Bind-n-Seq and MPRA to identify variants with allelic TF binding and regulatory activity.

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.

This study shows that Ddx3x is essential for B-cell development in mice, with loss leading to developmental blocks and defects in immunoglobulin rearrangement.

The paper evaluates cross-platform DNA motif discovery tools using 4,237 experiments to identify reliable transcription factor binding motifs and highlights challenges in motif detection.

This study shows that TGFβ from cardiomyocytes programs fibroblast development and ECM environment to support cardiomyocyte maturation in the developing heart.

This study shows HCMV infection disrupts chromatin organization and reduces TEAD1 activity through multiple mechanisms, linking it to genetic risk loci for eye and ear development.

This study identifies nuclear factor I (NFI) as a driver of dysregulated purine metabolism in DIPG, showing that targeting ATIC reduces tumor progression in mice.

The paper shows that inter-species mRNA transfer from mouse embryonic stem cells to human pluripotent stem cells reprograms them to a naive-like state through specific transcription factors.

The paper systematically determines the sequence specificity of 332 poorly characterized human transcription factors, identifying over 4,000 experiments and revealing tens of thousands of new TF binding sites.

The paper introduces EuPRI, a resource of RNA motifs for 34,736 RBPs across 690 eukaryotes, expanding motif knowledge and enabling functional and evolutionary insights.

The paper identifies rare FOXF1 missense variants in PAH patients, shows dysregulated FOXF1 expression in PAH lungs, and identifies downstream targets linked to PAH pathogenesis.

The paper shows nutrient starvation activates ECM remodeling gene enhancers linked to IBD risk in fibroblasts, suggesting a mechanism for pathological fibroblast activation in IBD.

The paper identifies functional regulatory SNPs in SLE risk loci by testing their impact on transcription factor binding and gene expression.

The paper links IBD polygenic risk to TNFi response using multiome-seq and genetic data from pediatric IBD patients.

The paper identifies a splicing mechanism in AML independent of mutations, showing it drives poor prognosis and can be targeted with PRMT5 inhibition.