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sjessa/README.md

👩‍💻 Hi, I'm Selin, a computational biologist and post-doctoral scientist

Here are the key research projects I worked on during my PhD:

A single-cell RNAseq atlas for the developing mouse forebrain and brainstem

We assembled a scRNAseq reference dataset of >100k cells from nine timepoints in the developing mouse brain to profile cell types and their expression patterns and dynamics.

A data-driven approach to identify the cell-of-origin in pediatric brain tumors

Leveraging our brain reference atlas, we designed approaches to computationally integrate primary patient tumor omics data (scRNAseq, scATACseq, bulk RNAseq, ChIPseq, HiC) with the atlas in order to identify, for each subtype of pediatric brain tumors, their most likely cell-of-origin.

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  1. fungenomics/braindex fungenomics/braindex Public

    A web portal for exploring scRNAseq data in the developing brain, including our in-house atlas of the E10-P6 forebrain and brainstem

    R 1

  2. fungenomics/HGG-oncohistones fungenomics/HGG-oncohistones Public

    Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)

    HTML 7 2

  3. fungenomics/G34-gliomas fungenomics/G34-gliomas Public

    Cell-of-origin analysis for "Histone H3.3G34-mutant interneuron progenitors co-opt PDGFRA for gliomagenesis" (Chen*, Deshmukh*, Jessa*, Hadjadj*, et al, Cell, 2020)

    HTML

  4. rr rr Public template

    Custom, lightweight template workflow for reproducible research projects in R

    HTML 3

  5. chromswitch chromswitch Public

    An R/Bioconductor package for detecting chromatin state switches

    R 3 1

  6. chromswitch-analysis chromswitch-analysis Public

    Code and data to accompany the chromswitch paper, "chromswitch: A flexible method for detecting chromatin state switches" (Jessa and Kleinman, Bioinformatics, 2018)

    R 1