Axel Visel

Network inference at single-cell resolution reveals morphoregulatory divergence and multilayered buffering in limb evolution

The paper compares gene regulatory networks in mouse and pig limb development to reveal conserved and divergent regulatory programs and mechanisms of developmental robustness.

PhageTAILor leverages machine learning for phage tail-like elements detection and classification in plant-associated bacteria

PhageTAILor uses LightGBM on 74 detector features to flag prophages and bacterial phage tail-like elements (tailocins, T6SS, eCIS), recovering 12 of 13 validated tailocins under leave-one-genus-out.

A genomic catalog of Earth's bacterial and archaeal symbionts

This study uses machine learning to predict symbiotic lifestyles in microbial genomes, identifying 15-23% of uncultivated microbes as potential symbionts and creating a new catalog of symbiont genomes.

Multi-season analysis reveals hundreds of drought-responsive genes in sorghum

This study identifies hundreds of drought-responsive genes in sorghum using multi-season transcriptomic data from field experiments.

Functional architecture of cardiac TF regulatory landscapes in control of mammalian heart development

The paper identifies essential cardiac enhancer modules and regulatory mechanisms governing heart development, revealing resilience in cis-regulatory architectures and the role of Hand2 upstream regulatory intervals.

Uncovering Hidden Enhancers Through Unbiased In Vivo Testing

The paper identifies hidden enhancers in mouse embryos that are not detected by conventional chromatin profiling methods, highlighting a significant gap in enhancer discovery.

Identification of functional non-coding variants associated with orofacial cleft

This study identifies functional non-coding variants associated with orofacial cleft by combining GWAS, reporter assays, and stem cell modeling.

Conserved Cis-Acting Range Extender Element Mediates Extreme Long-Range Enhancer Activity in Mammals

The paper identifies a conserved cis-acting element, REX, that enables extreme long-range enhancer-promoter interactions in mammals by increasing the genomic interaction range of enhancers.

Functional annotation of de novo variants found near GWAS loci associated with cleft lip with or without cleft palate

The paper annotates de novo variants near GWAS loci for cleft lip with or without cleft palate, finding noncoding variants in enhancer regions associated with craniofacial development genes.

Mutagenesis Sensitivity Mapping of HumanEnhancers In Vivo

The paper maps the mutagenic sensitivity of human enhancers in vivo by systematically mutating enhancer sequences and using predictive modeling to identify critical nucleotides.

An Expanded Registry of Candidate cis-Regulatory Elements for Studying Transcriptional Regulation

The paper expands the ENCODE Registry of candidate cis-regulatory elements (cCREs) to include 2.35 million human and 927 thousand mouse cCREs, revealing novel regulatory functions and identifying KLF1 as a causal gene for red blood cell traits.

Integrative analysis of the 3D genome and epigenome in mouse embryonic tissues

The paper maps chromatin interactions in mouse fetal tissues and links them to gene expression and disease risk variants in humans.

Interpreting variants associated with congenital heart disease with a regulatory map of the human fetal heart

This study creates a gene regulation map of the human fetal heart to interpret genetic variants associated with congenital heart disease and cardiac traits, identifying valvular interstitial cells as key regulators.

Combinatorial transcription factor binding encodes cis-regulatory wiring of forebrain GABAergic neurogenesis

The paper identifies combinatorial TF-cRE interactions in mouse basal ganglia development, revealing modules that drive GABAergic neurogenesis and suppress other fates.

High incidence and geographic distribution of cleft palate cases in Finland are associated with a regulatory variant in IRF6

The paper identifies a regulatory variant in IRF6 associated with increased cleft palate risk in Finland and shows it disrupts IRF6 enhancer function.

Chondrogenic Enhancer Landscape of Limb and Axial Skeleton Development

The paper maps chondrogenic enhancers in limb and axial skeleton development and shows their role in explaining human height heritability.

Increased Enhancer-Promoter Interactions during Developmental Enhancer Activation in Mammals

The paper examines 3D enhancer-promoter interactions during mammalian development, finding that most enhancers bypass neighboring genes and show tissue-specific conformations with increased interactions upon activation.

Identification of conserved skeletal enhancers associated with craniosynostosis risk genes

The paper identifies conserved skeletal enhancers near GWAS risk loci for craniosynostosis, linking sequence variants to altered gene expression and disease risk.

A spatio-temporally constrained gene regulatory network directed by PBX1/2 acquires limb patterning specificity via HAND2

The paper reconstructs a gene regulatory network directed by PBX1/2 and HAND2 in mouse limb development, showing their genetic interaction and tissue-specific function.

Cell Type- and Tissue-specific Enhancers in Craniofacial Development

The paper identifies 14,000 human craniofacial enhancers across developmental stages and shows 56% are conserved in mice, providing cell type- and stage-specific activity profiles.

Conserved enhancer logic controls the notochord expression of vertebrate Brachyury

The paper identifies conserved notochord-specific enhancers of Brachyury/T/TBXT in vertebrates and shows their role in notochord expression and development.

Genome-Wide Fetalization of Enhancer Architecture in Heart Disease

The paper identifies widespread epigenomic changes in idiopathic dilated cardiomyopathy, showing a shift toward fetal-like enhancer states and providing a data resource for further study.

Single cell, whole embryo phenotyping of pleiotropic disorders of mammalian development

The paper uses single-cell RNA sequencing to systematically phenotype mouse genetic models, identifying molecular and cellular changes across multiple mutants and wildtypes.

MusMorph, a database of standardized mouse morphology data for morphometric meta-analyses

MusMorph provides standardized mouse morphology data for meta-analyses, including craniofacial and brain structures across developmental stages and genotypes.

Transcriptional Network Orchestrating Regional Patterning of Cortical Progenitors

The paper identifies a transcription factor network and enhancers involved in cortical regional patterning using mouse embryonic data.

SMAD4 target genes are part of a transcriptional network that integrates the response to BMP and SHH signaling during early limb bud patterning

The paper identifies SMAD4 target genes and their role in integrating BMP and SHH signaling during early limb bud development, revealing opposing regulatory effects on anterior and posterior gene expression.

Long-read metagenomics of soil communities reveals phylum-specific secondary metabolite dynamics

This study uses long-read metagenomics and metatranscriptomics to analyze soil communities, revealing phylum-specific secondary metabolite dynamics during wetting events.

Topologically Associating Domain Boundaries are Commonly Required for Normal Genome Function

This study shows that deleting TAD boundaries in mice often causes molecular or developmental phenotypes, highlighting their importance for genome function.

Deletion of a non-canonical regulatory sequence causes loss of Scn1a expression and epileptic phenotypes in mice

This study shows that deleting a non-canonical regulatory region of Scn1a in mice leads to reduced Scn1a expression and epileptic symptoms.

Bi-fated tendon-to-bone attachment cells are regulated by shared enhancers and KLF transcription factors

The paper identifies bi-fated tendon-to-bone attachment cells regulated by shared enhancers and KLF transcription factors, revealing how these cells integrate chondrocyte and tenocyte features.