Eric M. Bindels

scRIPT: a rapid, high-coverage single-cell lineage-tracing method applied to the hematoendothelial differentiation of embryonic stem cells

scRIPT is a single-cell lineage-tracing method that improves coverage and reliability in differentiation protocols by integrating rapid barcoding, sorting, and sequencing with quality control.

Time-resolved single-cell state tracing exposes bidirectional state dynamics during differentiation

The paper uses single-cell state tracing to show bidirectional differentiation dynamics and rare transcriptome conversions across lineage boundaries in both in vivo and in vitro settings.

Impact of Enteric Neuronal Loss on Intestinal Cell Composition

This study investigates how loss of the enteric nervous system in zebrafish affects intestinal cell composition and identifies similar changes in human HSCR tissues.

NicheSphere reveals Spp1⁺ macrophages as central hubs coordinating fibrotic remodeling in myeloproliferative neoplasms

This study identifies Spp1⁺ macrophages as key hubs coordinating fibrotic remodeling in myeloproliferative neoplasms using NicheSphere, a novel computational method for cell communication analysis.

Insights from pooled CRISPRi single-cell screens in K562 cells reveal gene functions, regulatory networks, and highlight opportunities and limitations

This study applies a modified CRISPRi-CROP-seq protocol to knockdown six TFs in K562 cells, revealing gene functions, regulatory networks, and highlighting technical limitations of pooled CRISPRi screens.

Wnt-dependent spatiotemporal reprogramming ofbone marrow niches drives fibrosis

The paper shows that Wnt-dependent reprogramming of bone marrow niches drives fibrosis by activating osteolineage cells and altering hematopoietic support.

Prime-Target neoantigen vaccination unleashes unprecedented T cell immunity within ''cold'' immunosuppressive tumors

This study demonstrates that Prime-Target neoantigen vaccination effectively overcomes immunosuppression in 'cold' tumors by enhancing T cell infiltration and reshaping the tumor microenvironment.

Single-Cell Roadmap of Early Hemato-Endothelial Development: Functions of Atf3, Zfp711 and Bcl6b

The paper investigates the roles of Atf3, Zfp711, and Bcl6b in early hemato-endothelial lineage specification using scRNA-seq and KO mESCs, finding distinct effects on mesodermal and hematopoietic lineages.

MECOM is a master repressor of myeloid differentiation through dose control of CEBPA in acute myeloid leukemia

This study shows MECOM represses myeloid differentiation by inhibiting CEBPA, and its overexpression in AML reduces CEBPA levels, maintaining stem cell state.

Targeting mitochondria mitigates chemotherapy-induced bone marrow dysfunction

This paper shows that chemotherapy causes long-term bone marrow dysfunction by impairing hematopoietic stem cells, which can be reversed by mitochondrial-targeted treatment.

CSF single-cell RNA sequencing reveals clonally expanded CD4+ stem cell-like memory T cells in GAD65-antibody associated neurological syndromes

The paper uses single-cell RNA sequencing to identify clonally expanded CD4+ stem cell-like memory T cells in the CSF of anti-GAD65 AINS patients, suggesting their role in disease pathogenesis.

Hematological phenotypes in GATA2 deficiency syndrome arise from secondary injuries and maladaptation to proliferation

This study shows that GATA2 deficiency leads to hematological issues through bone marrow failure and maladaptation, with leukemia arising from genomic instability and proliferation defects.

Decoding primitive endoderm - epiblast interactions using mouse ICM embryoids

This paper introduces two mouse embryoid models to study interactions between primitive endoderm and epiblast during early development, showing they replicate in vivo dynamics and cell fate decisions.

Rapid specification of human pluripotent stem cells to functional astrocytes

This study develops a method to differentiate human pluripotent stem cells into functional astrocytes in 28 days, validated by marker expression and network activity support.

CSF plasma cell expansion in LGI1-/CASPR2-autoimmune encephalitis is associated with loss of regulatory MAIT cells

The paper uses single-cell transcriptomics to show CSF-specific plasma cell expansion and systemic loss of MAIT cells in anti-LGI1/CASPR2 autoimmune encephalitis.

Gata2-regulated Gfi1b expression controls endothelial programming during endothelial-to-hematopoietic transition

This study shows that Gata2 regulates Gfi1b to control endothelial-to-hematopoietic transition and HSPC maturation, with reduced Gata2 leading to impaired hematopoietic programming.

Unbiased intestinal single cell transcriptomics reveals previously uncharacterized enteric nervous system populations in larval zebrafish

The paper performs single-cell RNA sequencing on larval zebrafish ENS to identify previously uncharacterized neuronal and glial populations and reveals a binary neurogenic branching mechanism.

Spatial multi-omic map of human myocardial infarction

This study generates a high-resolution spatial multi-omic map of human myocardial infarction by integrating single-cell gene expression, chromatin accessibility, and spatial transcriptomic data to reveal cellular zones of injury, repair, and remodeling.

Causal integration of multi-omics data with prior knowledge to generate mechanistic hypotheses

COSMOS integrates multi-omics data with prior knowledge to generate mechanistic hypotheses about biological processes in renal cell carcinoma.