Jonas Simon Fleck

Decoding morphogen patterning of human neural organoids with a multiplexed single-cell transcriptomic screen

The paper uses a multiplexed single-cell transcriptomic screen to study how morphogen cues affect regional specification in human neural organoids, finding that timing, concentration, and combination of morphogens strongly influence cell type and regional composition.

CellFlow enables generative single-cell phenotype modeling with flow matching

CellFlow predicts single-cell phenotypes from complex perturbations using flow matching, demonstrating accuracy in cytokine stimulation, drug treatments, and developmental modeling.

An integrated transcriptomic cell atlas of human neural organoids

This paper integrates 36 single-cell transcriptomics datasets from human neural organoids into a unified atlas to assess cell type coverage and compare organoid protocols with primary brain tissue.

Single-cell epigenomic reconstruction of developmental trajectories in human neural organoid systems from pluripotency

The paper reconstructs epigenomic trajectories in human neural organoids from pluripotency to terminal cell states using single-cell histone modification profiling.

Single-cell brain organoid screening identifies developmental defects in autism

The paper uses CRISPR and single-cell transcriptomics to screen ASD risk genes in brain organoids, identifying developmental defects and regulatory modules linked to autism.

Single-cell analyses of axolotl forebrain organization, neurogenesis, and regeneration

This study uses single-cell genomics to analyze axolotl forebrain cell types, neurogenesis, and regeneration, identifying conserved neuron classes and injury responses.

Multimodal spatiotemporal phenotyping of human organoid development

This paper develops a multimodal approach to study human retinal organoid development, integrating spatial, transcriptomic, and chromatin accessibility data to create a virtual atlas of retinal development.

Inferring and perturbing cell fate regulomes in human cerebral organoids

The paper uses single-cell genomic data from human cerebral organoids to infer gene regulatory networks and assess transcription factor roles in brain development.

Accurate de novo identification of biosynthetic gene clusters with GECCO

A linear conditional random field over ordered protein-domain annotations finds biosynthetic gene clusters de novo more precisely than DeepBGC and runs over three times faster on one CPU.

Resolving brain organoid heterogeneity by mapping single cell genomic data to a spatial reference

This paper introduces VoxHunt, a computational method that maps single-cell genomic data from brain organoids to spatial reference data to assess patterning and cell composition.

Single-cell genomic atlas of great ape cerebral organoids uncovers human-specific features of brain development

This study uses single-cell genomics to compare brain development in humans, chimpanzees, and macaques, identifying human-specific gene regulatory features.