Ferenc Müller

The paper integrates ATAC-seq and RNA-seq data from zebrafish osteoblasts to identify chromatin and transcriptomic signatures and mechanisms of entpd5a regulation.

The paper maps non-coding regulatory elements in common carp embryos, revealing subgenome-specific regulatory divergence during development.

The paper identifies functionally conserved regulatory elements across distantly related vertebrates despite sequence divergence using a synteny-based method.

This paper develops an embryonic zebrafish xenograft model to assess the efficacy of multi-receptor tyrosine kinase inhibitors in rhabdomyosarcoma, identifying VEGF-A as a potential biomarker for Regorafenib response.

This study shows that paternal starvation in zebrafish affects offspring metabolism and fitness, with lasting impacts on gene expression and development.

This study shows that partially assembled TFIID complexes can initiate RNA polymerase II transcription but cannot fully replace holo-TFIID over time.

The paper identifies a high-density miR-430 promoter cluster that forms a transcription body, enabling early gene activation during the minor wave of zygotic genome activation in zebrafish.

The paper creates a central repository for zebrafish developmental genomics data, identifies new cis-regulatory elements, and compares regulatory elements between zebrafish and mouse.

The paper identifies genes regulated by retinoic acid signaling in zebrafish endoderm using RNA-seq, ChIP-seq, and ATAC-seq, and finds conserved RAR binding sites across vertebrates.

The paper shows that the TBPL2/TFIIA complex establishes the oocyte transcriptome by using a specific TSS recognition code through oocyte-specific promoter usage.

This paper introduces a tool for segmenting and tracking lineage in noisy, low frame rate 4D fluorescence microscopy data from zebrafish embryos.

The paper identifies global regulatory transitions at core promoters during mammalian germline development, showing a shift from somatic to maternal promoter codes in oogenesis.

The paper functionally annotates human long non-coding RNAs by systematically knocking down 285 lncRNAs and analyzing molecular phenotypes using CAGE sequencing.

The paper identifies a conserved noncoding element in HOTAIR that functions both in cis and trans, regulating HOXC11 and HOXD11 expression.

The paper shows zebrafish primordial germ cells use germ plasm in two phases to regulate transcriptome divergence from somatic cells through post-transcriptional mechanisms and chromatin changes.

The paper identifies dual-initiation promoters in zebrafish that use both canonical and non-canonical initiation motifs, showing differential regulation during development and conservation across species.

The paper shows that during zebrafish embryonic development, core promoter architecture changes correlate with cell cycle dynamics and lineage-specific gene expression.

The paper identifies a nuclear transcription compartment that enables early gene expression before genome activation in metazoan embryos.

SLIC-CAGE enables high-resolution transcription start site mapping using nanogram-level total RNA, significantly reducing the required input compared to existing CAGE methods.