Stefan Mundlos

Evolution and mechanism of MEIS2-mediated forelimb specialization in bats

This study uses deep learning and functional genomics to show that MEIS2 and TWIST1 co-regulation, along with changes in regulatory regions of PBX1, underlie bat forelimb specialization.

Enhancer-promoter compatibility is mediated by the promoter-proximal region

The paper shows that the promoter-proximal region is essential for enhancer-promoter compatibility in specific cell types.

Comparative single-cell analyses reveal evolutionary repurposing of a conserved gene program in bat wing development

The paper compares bat and mouse limb development using single-cell analyses to show how a conserved gene program is repurposed in bat wing formation.

Enhancer adoption by an LTR retrotransposongenerates viral-like particles causingdevelopmental limb phenotypes

The paper shows that activation of an LTR retrotransposon in the embryo leads to viral-like particle production, causing limb malformations through apoptotic cell death.

Accurate detection of pathogenic structural variants guided by multi-platform comparison

The paper introduces dicast, a machine-learning method that improves the detection of pathogenic structural variants from short-read sequencing by leveraging genomic context and alignment features.

Reconfiguration of genome-lamina interactions marks the commissioning of limb cell-fates

The paper shows that genome-lamina interactions are reconfigured during limb development to prime regulatory domains for gene activation and support cell-fate decisions.

Combined analysis of chromatin accessibility, promoter interactions and whole genome sequencing solved the missing heritability in gastric cancer

The paper identifies novel genetic mechanisms underlying missing heritability in HDGC-like families by integrating chromatin accessibility, promoter interactions, and whole-genome sequencing data.

Atheroprone Flow Activates SMAD-FOXO1 to drive Endothelial-to-Mesenchymal Transition and Atherosclerosis

This study identifies SMAD/FOXO1 complexes that mediate EndoMT in response to atheroprone flow, showing their role in atherosclerosis and suggesting targeting this interaction could reduce disease progression.

Temporal misexpression of En1 during limb development causes distinct phenotypes

The study identifies two enhancer elements that maintain En1 expression during later limb development and shows that misexpression timing leads to distinct phenotypes.

Failure of digit tip regeneration in the absence of suggests Lmx1b functions disparate from dorsoventral polarity

The paper shows that nail tissue, not dorsoventral polarity, is essential for digit tip regeneration, and identifies Lmx1b's role in this process through transcriptomic analysis.

Polycomb-mediated Genome Architecture Enables Long-range Spreading of H3K27 methylation

The paper investigates how Polycomb-mediated genome architecture facilitates long-range H3K27 methylation spreading in ESCs and iPSCs, revealing RNA-dependent DNA looping and developmental gene roles in chromatin organization.

Cell adhesion and immune response, two main functions altered in the transcriptome of seasonally regressed testes of two mammalian species

The paper compares transcriptomes of testes from two mammalian species during seasonal regression, identifying conserved changes in cell adhesion and immune response pathways.

TADA - a Machine Learning Tool for Functional Annotation based Prioritisation of Putative Pathogenic CNVs

TADA prioritizes pathogenic CNVs using functional annotations and machine learning, achieving high AUC scores for deletions and duplications.

GestaltMatcher: Overcoming the limits of rare disease matching using facial phenotypic descriptors

GestaltMatcher improves diagnosis of ultra-rare genetic disorders by matching facial phenotypes to molecular diagnoses using a deep learning model trained on a large dataset of patient photographs.

Combinatorial effects on gene expression at the Lbx1/Fgf8 locus resolve Split-Hand/Foot Malformation type 3

The paper investigates how genomic rearrangements at the Lbx1/Fgf8 locus cause SHFM3 by altering chromatin structure and gene expression in mice.

Distal and proximal cis-regulatory elements sense X-chromosomal dosage and developmental state at the Xist locus

The paper identifies distal and proximal cis-regulatory elements that respond to X-chromosomal dosage and developmental state to regulate Xist expression during XCI in mouse embryonic stem cells.

Promoter repression and 3D-restructuring resolves divergent developmental gene expression in TADs

The paper shows that divergent gene expression within TADs is resolved through TAD restructuring and DNA methylation, not enhancer-promoter compatibility or position.

A CRISPR-Cas9-engineered mouse model for GPI-anchor deficiency mirrors human phenotypes and exhibits hippocampal synaptic dysfunctions

This paper introduces a CRISPR-Cas9-engineered mouse model for GPI-anchor deficiency that mirrors human phenotypes, including cognitive impairments and epilepsy, and identifies synaptic transmission deficits.

VarFish - Collaborative and Comprehensive Variant Analysis for Diagnosis and Research

VarFish is a web application for variant analysis in rare disease genetics, offering quality control, filtering, annotation, and collaboration tools for diagnostic and research use.

Variants in the degron of AFF3 cause a multi-system disorder with mesomelic dysplasia, horseshoe kidney and developmental and epileptic encephalopathy

The paper identifies degron variants in AFF3 causing a multi-system disorder with specific clinical features and demonstrates phenotypic overlap with AFF4-related syndromes.

PEDIA: Prioritization of Exome Data by Image Analysis

The paper introduces an AI-driven method that uses facial images to prioritize exome data, achieving 99% top-10 accuracy in identifying disease-causing genes.

Preformed Chromatin Topology Assists TranscriptionalRobustness of Shh during Limb Development

The paper shows that preformed chromatin topology supports robust Shh transcription during limb development, with CTCF and ZRS alleles influencing enhancer-promoter communication.

Functional dissection of TADs reveals non-essential and instructive roles in regulating gene expression

The paper investigates TAD function in mice by editing TAD organization, finding that TADs provide robustness but are not essential for gene regulation, and that disease phenotypes arise from re-direction of regulatory contacts.

Identification of cis elements for spatio-temporal control of DNA replication

The paper identifies cis-regulatory elements (ERCEs) that control domain-wide replication timing, chromatin compartmentalization, and transcription in mouse embryonic stem cells.

Advances in computer-assisted syndrome recognition and differentiation in a set of metabolic disorders

This paper evaluates deep learning for syndrome recognition in metabolic disorders, finding improved accuracy with larger training sets but no significant effect from ethnicity or sex.

Characterization of Glycosylphosphatidylinositol Biosynthesis Defects by Clinical Features, Flow Cytometry, and Automated Image Analysis

The paper evaluates clinical features, flow cytometry, and facial image analysis to classify GPIBDs and identify gene-specific patterns, finding that facial recognition software is most effective for gene prediction.

Genome-wide binding of posterior HOXA/D transcription factors reveals subgrouping and association with CTCF

The paper identifies genome-wide binding sites of posterior HOX-TFs and reveals subgrouping based on sequence specificity and CTCF association.