Michiel Vermeulen

The paper uses a microfluidics and proteomics approach to study dynamic protein gradients in mouse embryos, revealing antagonistic ligand-receptor patterns that regulate Wnt oscillations and somite formation.

The paper identifies proteomic regulators of T cell functionality in cancer using proteomic and transcriptomic profiling of tumor-infiltrating T cells.

This study identifies prolyl hydroxylation as essential for ZIKV NS1 maturation and secretion, with mutations affecting viral replication and protein stability.

The paper identifies rs3769823 as a functional variant near CASP8 influencing its expression in a cell-type specific manner and associated with multiple cancers.

The paper identifies a new SET1B complex and shows SET1/MLL complexes control transcription independently of H3K4me3 by counteracting promoter-proximal termination and supporting transcription burst size.

The paper identifies heparan sulfate (HS) as a key factor for cell-surface RNA (csRNA) presentation and reveals a ternary complex of HS, RNA, and RNA-binding proteins that recruits immune receptors.

This study identifies Pfs230 Domain 12 as a potent malaria transmission-blocking vaccine candidate that induces antibodies reducing parasite transmission to mosquitoes.

The paper presents a proteomic characterization of chromatin states in Plasmodium falciparum using proximity-labelling approaches, identifying 214 proteins and validating new chromatin components and functions.

The paper identifies a regulatory variant driving microphthalmia by analyzing its effects in mouse models and linking it to FOXE3 expression and ocular development.

The paper determines the structure of the Pfs230:Pfs48/45 complex bound to transmission-blocking antibodies, revealing molecular interactions and epitopes that inform vaccine development.

This study shows that Nodal and Wnt signalling act antagonistically during mammalian gastrulation, with Nodal promoting anterior structures and Wnt driving posterior development.

This paper introduces PARM, a deep learning model trained on MPRA data to predict human promoter activity and identify TF binding preferences, revealing positional and functional differences in regulatory grammar.

The paper identifies breast cancer risk SNPs that overlap with estrogen receptor binding sites, showing their role in altering estrogen signaling through chromatin interactions.

This study investigates how varying ratios of HspB2 and HspB3 affect their phase behavior, revealing reversible condensates and aggregates with distinct molecular compositions.

This study uses multi-omics to show ONECUT2 restricts M cell differentiation in mouse intestinal organoids by acting downstream of RANK/RANKL signaling.

The paper quantifies how chromatin context affects transcription factor binding affinities genome-wide and shows DNA accessibility is the main determinant.

The paper identifies SALL4 as a protein that interprets DNA base composition by binding to AT-rich motifs, and shows its role in controlling cell fate through regulation of AT-rich gene expression.

The paper identifies biallelic mutations in CENATAC as a cause of constitutional aneuploidy by disrupting minor intron splicing and causing chromosome segregation errors.

This study compares NuRD's role in human and mouse pluripotent stem cells, finding that NuRD is required for transcriptional responses to differentiation signals in both, but with distinct functional differences between species.

The paper identifies multiple melanoma susceptibility genes and variants by integrating MPRA with eQTL data, revealing MX2's role in melanoma promotion.

This study shows that the m6A reader Ythdf limits axonal growth in Drosophila by modulating Fmr1 target selection.

The paper shows that Polycomb-mediated repression maintains spatial gene expression in zebrafish after body plan formation, with minimal global changes in gene expression.

This study identifies EZHIP as a novel cofactor of PRC2 that limits its activity in germ cells, leading to altered H3K27me2/3 deposition and impaired fertility in female mice.

The paper identifies over 30,000 SNPs affecting regulatory element activity using SuRE reporter technology, linking them to gene regulation and potential human traits.

The paper shows that MTA proteins in ES cell NuRD complex are functionally redundant, and NuRD is essential for maintaining differentiation trajectory during early lineage commitment.

The paper identifies GBAF as an enhancer-associated chromatin remodeler that interacts with H3K27ac and is essential for enhancer transcription.

The paper identifies ZMAT2 as a regulator of human epidermal differentiation through interactions with epigenetic modifiers and the pre-spliceosome, highlighting joint control of cell adhesion genes.

The paper introduces ID-seq, a technology that measures multiple molecular and cellular phenotypes in parallel, and uses it to study kinase inhibitor effects on human epidermal stem cells.