Berthold Göttgens

This study develops an in vitro clonal competition model to identify preleukemic TET2-mutant clones that suppress wild-type cells through RAC1-GEF signalling inhibition.

HARP integrates PBMC data from multiple studies to create a reference atlas with consensus annotations and identifies age, sex, and disease-related cellular modules.

This paper uses single-cell proteo-transcriptomic profiling to reveal post-translational regulatory mechanisms in human hematopoiesis, showing that protein-RNA correlations and transcription factor dynamics provide insights into lineage commitment and fate decisions.

This paper introduces LabCompass, a generative inverse-modeling framework that optimizes culture conditions to steer human hematopoietic cell fate in vitro, demonstrating its effectiveness through iterative experimental validation.

This study creates a mouse model of myeloid neoplasm with spontaneous RTK-RAS mutations, showing a premalignant phase and lineage restriction in tumors.

This paper introduces wSIR, a scalable supervised dimensionality reduction method for spatial transcriptomics data, which retains predictive power of spatial coordinates and is demonstrated on breast cancer and embryonic development datasets.

The paper investigates how Axin1 and Axin2 regulate WNT signaling to specify distinct mesoderm lineages during gastrulation.

This study uses a cross-species bone marrow niche model to show that plasticity in the murine niche supports human HSC engraftment, highlighting its role in stem cell function.

Human Developmental Cell Atlas integrates ~4.6 million cells/nuclei from 4-22 post-conception weeks into 454 refined cell types and maps 114 spatial niches across 6PCW whole-embryo sections.

Tripso, a self-supervised transformer model, identifies gene program-specific embeddings and discovers novel gene programs, revealing biological insights in hematopoietic development and disease.

PerturbGen predicts how genetic perturbations affect cellular trajectories across time in human datasets, showing effects on immune responses, hematopoiesis, and skin development.

RIMA enables cross-species comparison of transcriptomic atlases, identifying conserved developmental programs and revealing species-specific differences in gene expression timing.

Pseudodynamics+ reconstructs population dynamics from time-resolved single-cell data using physics-informed neural networks, revealing dynamic changes in cell state parameters.

The paper identifies two bone marrow compartments and shows inflammation affects them differently, with type I interferon causing changes in mesenchymal stromal cells.

This paper introduces a double reporter strategy to identify a non-migratory subset of hematopoietic stem cells in the bone marrow niche and shows their dynamic interactions during stress and aging.

diffGEK compares transcriptional kinetics across biological conditions to identify mechanistic differences in gene expression dynamics.

The paper identifies two HSC subsets with distinct responses to Plasmodium infection, showing that BiotinHi HSCs remain functional by maintaining a stemness-associated metabolic profile despite sensing inflammation.

This study shows MLL2 stabilizes 3D chromatin loops during pluripotent cell differentiation without requiring its enzymatic activity.

This study identifies Sema4A as an extrinsic factor that protects myeloid-biased HSCs from inflammatory stress, preserving functional diversity in the hematopoietic stem cell pool.

This study shows that DNMT3A R882H mutant HSCs resist inflammatory stress through delayed p53 activation, leading to clonal expansion and increased AML risk.

The paper characterizes Tet2-mutant HSCs using multi-omic data and identifies ECM molecules as regulators of self-renewal in pre-leukemic HSCs.

This study creates a spatiotemporal atlas of mouse gastrulation and early organogenesis using spatial transcriptomics and scRNA-seq, revealing gene expression dynamics and mesodermal fate decisions.

This study shows that STAT3 signaling is crucial for tissue expansion during postimplantation mouse development by promoting cell proliferation and differentiation.

This study shows that JAK inhibition increases uSTAT5 levels, which promotes HSC maintenance and stemness, and reveals a new role for uSTAT5 in controlling HSC function.

The paper identifies Eomes's role in directing the formation of distinct extra-embryonic hematovascular tissues in mice, revealing functional and mechanistic diversity in their development.

CLADES estimates clone-specific kinetics and fate bias in human cord blood LT-scSeq data using a NeuralODE-Gillespie hybrid approach, improving meta-clone fate prediction accuracy.

This study identifies conserved and species-specific cis-regulatory elements in human and mouse blood cells using integrative epigenomic analysis and clustering.

This study shows that DNA methylation is critical for restricting neural differentiation but not germline fate in ESCs, with TKO ESCs capable of germline specification.

The paper uses scRNA-Seq and computational methods to predict and validate differentiation trajectories during early mammalian organogenesis, showing agreement between computational predictions and experimental outcomes.

The paper develops statistical tools to analyze gene knockouts in mouse embryos and applies them to study developmental disruptions and cancer therapy responses.