René Maehr

Stepwise reorganization of chromosome conformation and nuclear organization during stem cell differentiation

The paper temporally maps nuclear reorganization during human stem cell differentiation and identifies three temporally ordered transitions in nuclear structure and function.

Haplotype-resolved genome architecture mapping uncovers pervasive structural heterogeneity between human homologous chromosomes

The paper introduces CoPhasing, a method to phase chromatin contacts with haplotype specificity, revealing structural differences between homologous chromosomes.

Resolving thyroid lineage cell trajectories merging into a dual endocrine gland in mammals

The paper uses single-cell transcriptomics to study thyroid lineage development in mice, identifying gene regulatory networks and lineage-specific processes that explain how thyroid and ultimobranchial cells merge into a dual endocrine organ.

Systematic assessment of long-read RNA-seq methods for transcript identification and quantification

Benchmarking six long-read RNA-seq protocol-platform combinations and 14 tools across human, mouse, and manatee shows read length and accuracy drive isoform detection, depth drives quantification.

Discovery and characterization of LNCSOX17 as an essential regulator in human endoderm formation

The paper identifies and characterizes LNCSOX17, a lncRNA essential for human endoderm formation, showing its role in regulating transcriptome and differentiation.

Systematic evaluation of chromosome conformation capture assays

This study evaluates 3C-based assays to understand how experimental parameters affect chromatin interaction detection and quantification, leading to the development of Hi-C 3.0.

Ultrastructural details of mammalian chromosome architecture

This study improves chromosome architecture mapping by using Micro-C to achieve nucleosome-resolution insights in human cells, revealing new looping interactions and structural patterns.

TALE and NF-Y co-occupancy marks enhancers of developmental control genes during zygotic genome activation in zebrafish

The paper identifies NF-Y and TALE co-occupancy at enhancers of developmental control genes during zebrafish zygotic genome activation, showing distinct gene regulatory roles for each TF.

Beyond pseudotime: Following T-cell maturation in single-cell RNAseq time series

The paper introduces pseudodynamics, a framework to model real-time cellular development using time-series and genetic knock-out data, applied to thymic T-cell maturation.

Pax9 is required for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to control 4th pharyngeal arch artery morphogenesis.

The paper shows Pax9 is essential for cardiovascular development and interacts with Tbx1 in the pharyngeal endoderm to regulate 4th pharyngeal arch artery formation.