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drgideonobeng/README.md

Gideon Obeng

Computational biologist and cell biologist uncovering disease mechanisms through bulk and single-cell genomics and epigenomics. I design reproducible pipelines to transform complex sequencing data into mechanistic insights and biological discoveries. PhD in Molecular Pathobiology (Mie University); Postdoctoral Associate and AHA Fellow at Rutgers NJMS

Featured work

Tbx1-depleted-Tbx1cre-lineage — Four-phase Nextflow pipeline characterizing cell-autonomous Tbx1 loss in cardiopharyngeal progenitors. scVI integration (batch correction with preserved KO phenotype), pseudobulk DESeq2, GO enrichment. Identifies neural crest loss, cardiac maturation impairment, and KO-specific neuronal fate adoption at single-cell resolution.

Mesp1cre-lineage-developmental-atlas — Phased Nextflow pipeline for Mesp1 cardiopharyngeal lineage analysis across E8.0→E10.5. fastMNN integration into a developmental atlas with documented artifact recovery. Explore it live: mesp1 Atlas Explorer — deployed R Shiny app, ~22k cells across 15 cell types.

Mouse-embryonic-brain-multiome-analysis — Joint scRNA-seq + scATAC-seq integration (Seurat v5 WNN + Signac) resolving 13 cell types, with ATAC coverage tracks and motif enrichment linking chromatin state to lineage identity.

Kdr-depleted-Mef2cAHFcre-lineage-seurat — Conditional-knockout lineage analysis with validated cloud execution on AWS Batch + S3 via the Nextflow executor.

Stack

Nextflow DSL2 · Docker · AWS (Batch, EC2, S3) · R/Seurat · Signac · scVI · scanpy · DESeq2 · clusterProfiler · Cell Ranger · STAR · GATK4 · Python · Bash

Contact

obgideon@gmail.com · LinkedIn

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  1. Mesp1cre-lineage-developmental-atlas Mesp1cre-lineage-developmental-atlas Public

    Developmental atlas pipeline integrating Mesp1-lineage scRNA-seq across four mouse embryonic timepoints (E8.0-E10.5). Nextflow DSL2 + Seurat + fastMNN.

    R

  2. Mouse-embryonic-brain-multiome-analysis Mouse-embryonic-brain-multiome-analysis Public

    Single-cell multiome (RNA + ATAC) analysis pipeline applied to E18 mouse brain. Nextflow DSL2 + Seurat v5 + Signac with WNN integration. 13 cell types resolved, ATAC coverage tracks for lineage mar…

    R

  3. Tbx1-depleted-Tbx1cre-lineage Tbx1-depleted-Tbx1cre-lineage Public

    Four-phase scRNA-seq pipeline characterizing Tbx1 conditional knockout in cardiopharyngeal progenitors. Nextflow DSL2 + Seurat + scVI + DESeq2 + clusterProfiler.

    R

  4. RNAseq-analysis-Tamoxifen-Mouse-Embryonic-ECs RNAseq-analysis-Tamoxifen-Mouse-Embryonic-ECs Public

    Bulk RNA-seq DE analysis of tamoxifen effects on E15.5 mouse embryonic endothelial cells (GSE247449). Nextflow DSL2 + DESeq2 + clusterProfiler.

    R