Tomek Swigut

The paper introduces SPIE-seq to study enhancer target selection, finding that genomic context and distance-weighted competition, not enhancer identity, determine target choice.

This study shows that SNAI1 and SNAI2 repressors tune enhancer activity by shifting chromatin states, affecting enhancer function and evolution.

TCOF1 dosage is limiting for transitional human neural crest cells; its enhancers buffer promoter output against MYC fluctuations rather than amplifying it, a pattern seen across 14 dosage-sensitive promoters.

The paper investigates the role of HERVK LTR5Hs elements in human preimplantation development, showing their cis-regulatory impact on the epiblast transcriptome and their essential role in blastoid formation through ZNF729 activation.

This study investigates how promoter strength and position influence promoter competition by inserting diverse promoters into the Sox2 locus and measuring their effect on endogenous Sox2 expression.

The paper shows that enhancer-promoter communication scales with genomic distance in a gene-specific manner, independent of 3D contact frequency or chromatin state.

The paper identifies a SNP that regulates facial shape and disease risk by affecting PKDCC expression during chondrogenesis, showing its impact on both normal variation and clefting.

The paper shows how DNA motifs guide transcription factor cooperativity in embryonic face and limb mesenchyme, shaping cell identity and morphology.

The paper modulates SOX9 levels in human facial progenitors to study dosage sensitivity and identifies regulatory elements and genes that are sensitive to SOX9 changes.

The paper investigates how structural elements regulate SOX9 expression over long genomic distances in PRS patients by analyzing chromatin topology and modeling interactions.

This study identifies 203 genomic regions associated with facial variation using GWAS on multivariate shape phenotypes, revealing novel regions and epistatic interactions.

qDRIP quantitatively compares RNA:DNA hybrids in different conditions to estimate their absolute counts and half-lives.