Resources

Data and Analyses

TARGETING TRANSLATION

2026 | Using the eIF4A inhibitor zotatifin with the BCL2 inhibitor venetoclax to target AML cells.

  • Paper: Lee YS et al. Synergistic targeting of eIF4A-mediated translation initiation and apoptosis in acute myeloid leukemia. Blood Neoplasia, 2026
  • reanalyze-aml2019: Expression of translation initiation factors including EIF4A1 in healthy bone marrow and AML cell subpopulations (folder: 2026_Lee).
  • AML-DepMap-Insights-2024: From DepMap and PRISM, evaluate EIF4A expression and zotatifin sensitivity in AML cell lines (folder: 2026_Lee).
  • DrugSynergy_2026: RNA- and ribosome-sequencing analysis as described in the paper.
  • GEO: RNA- and ribosome-sequencing data.

HUMAN HSC AGING

2026 | Using consensus non-negative matrix factorization to discover programs driving HSC aging.

  • Paper: Safina KR et al. An inflammatory and quiescent HSC subpopulation expands with age in humans. Genome Biology, 2026
  • Aging_HSCs_2025: Scripts to reproduce analyses including differential gene expression, cNMF, and GSEA.
  • GEO: Single-cell RNA-seq data (additional datasets are described in paper’s data availability section).

BPDCN EVOLUTION

2023 | How pre-leukemic cells in the bone marrow can evolve to a full-blown dendritic cell leukemia after acquiring DNA mutations in the skin.

  • Paper: Griffin GK et al. Ultraviolet radiation shapes dendritic cell leukaemia transformation in the skin. Nature, 2023
  • Single-cell_BPDCN: R scripts to analyze the single-cell gene expression and genotyping data.
  • GEO: Raw and processed sequencing data.
  • Figshare: Seurat objects with single-cell sequencing data.

MAESTER

2022 | How mitochondrial DNA mutations can be used to determine the clonal relationships between single cells.

  • Paper: Miller TE et al. Mitochondrial variant enrichment from high-throughput single-cell RNA sequencing resolves clonal populations. Nat Biotechnol, 2022
  • MAESTER-2021: Scripts used to analyze the data and generate figures.
  • maegatk: Mitochondrial Alteration Enrichment and Genome Analysis Toolkit to process .bam files with mitochondrial reads to generate heteroplasmy estimation in single cells.
  • Mitochondrial_variants: A table of mitochondrial variants, their effects on the resultant proteins, and the potential beneficial/detrimental consequences of mutations.
  • GEO: Raw and processed sequencing data.

WAT3R

2022 | Recovering T cell receptors (TCRs) from 3’ single-cell RNA-sequencing.

  • Paper: Ainciburu M et al. WAT3R: recovery of T-cell receptor variable regions from 3’ single-cell RNA-sequencing. Bioinformatics, 2022
  • WAT3R: Pipeline to process data generated by the protocol T-cell Receptor Enrichment to linK clonotypes by sequencing (TREK-seq).
  • Docker: Image to run the pipeline
  • GEO: Raw and processed single-cell RNA and TCR-seq sequencing data.

T CELLS IN BPDCN

2022 | Here we explore the mechanisms of immune dysfuction in a rare dendritic cell leukemia.

  • Paper: DePasquale EAK et al. Single-cell multiomics reveals clonal T-cell expansions and exhaustion in blastic plasmacytoid dendritic cell neoplasm. Front Immunol, 2022
  • BPDCN: Scripts used to analyze the data and generate figures for the paper.
  • GEO: Raw and processed single-cell RNA and TCR-seq sequencing data.

SINGLE-CELL AML

2019 | Analysis of acute myeloid leukemia cell heterogeneity.

  • Paper: van Galen P et al. Single-cell RNA-seq reveals AML hierarchies relevant to disease progression and immunity. Cell, 2019
  • aml2019: Original code largely written by Volker Hovestadt.
  • reanalyze-AML2019: Scripts that facilitate the visualization of genes of interest in barplots, violin/sina plots, and heatmaps.
  • GEO: Raw and processed single-cell RNA and TCR-seq sequencing data.
  • Figshare: Seurat object with single-cell sequencing data.

MINT-CHIP

2016 | Here we introduce a new method to enable chromatin immunoprecipitation + sequencing (ChIP-seq) on small cell numbers.

  • Paper: van Galen P et al. A multiplexed system for quantitative comparisons of chromatin landscapes. Mol Cell, 2016
  • Protocol: Step-by-step protocol to carry out Mint-ChIP.

Addgene Plasmids

Plasmid Gene/Insert Description Reference
pSMALB-ATF4.5 ATF4 5’ UTR, ATF4-eGFP fusion ORF, TagBFP ATF4 reporter van Galen P, Kreso A, Mbong N, et al. The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress. Nature, 2014.
pSMALB-ATF4.12 ATF4 5’ UTR, ATF4-eGFP fusion ORF, TagBFP ATF4 reporter (negative control) van Galen P, Kreso A, Mbong N, et al. The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress. Nature, 2014.
pSMALB-ATF4.14 ATF4 5’ UTR, ATF4-eGFP fusion ORF, TagBFP ATF4 reporter (positive control) van Galen P, Kreso A, Mbong N, et al. The unfolded protein response governs integrity of the haematopoietic stem-cell pool during stress. Nature, 2014.
pMAL Gateway cloning element Bidirectional expression vector (pPGK promoter, GFP) van Galen P, Kreso A, Wienholds E, et al. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell, 2014.
pMALB Gateway cloning element Bidirectional expression vector (hPGK promoter, TagBFP) van Galen P, Kreso A, Wienholds E, et al. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell, 2014.
pSMAL Gateway cloning element Bidirectional expression vector (SFFV promoter, GFP) van Galen P, Kreso A, Wienholds E, et al. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell, 2014.
pSMALB Gateway cloning element Bidirectional expression vector (SFFV promoter, TagBFP) van Galen P, Kreso A, Wienholds E, et al. Reduced lymphoid lineage priming promotes human hematopoietic stem cell expansion. Cell Stem Cell, 2014.

For Trainees

Learning

R for Statistical Computing

Python

  • Think Python, How to Think Like a Computer Scientist (book)
  • A Byte of Python (book)
  • Introduction to Python (videos)

Bash

  • O’Reilly – Bash Scripting and Shell Programming (videos)

Other sources

Cell Type Annotation

Packages for automated cell type annotation.