Computational biologist applying methods in data science to biomedical and translational research at Ospedale Pediatrico Bambino Gesù.

Expertise of over 9 years in genomics and next generation sequencing (NGS) data.

Bambino Gesu, Seattle Children's, Fred Hutch

Most of my work lives in two organization accounts:

Meshinchi-Lab — Pediatric cancer genomics at Ospedale Pediatrico Bambino Gesù and Fred Hutch: pediatric AML, T-ALL, and rhabdomyosarcoma. Bulk and single-cell RNA-seq, gene fusion detection, Oxford Nanopore long-read WGS and structural variant calling, and immunotherapy target discovery. Active project repositories are private; the pipelines, packages, and templates below are public.

RSC-RP — Research Scientific Computing at Seattle Children's: shared Nextflow pipelines, HPC and cloud infrastructure, and analysis support spanning pediatric leukemia (ALL), developmental biology in iPSC-derived motor neurons, and infectious disease (Plasmodium falciparum). Code repositories for internal SCRI analytical work were hosted on a private organizational Bitbucket.

Pipelines and workflows — Nextflow and WDL, on Slurm HPC and AWS

• bulk_rnaseq_fusion_nf — Gene fusion detection with STAR-Fusion, FusionInspector, and CICERO
• rnaseq_count_nf — Bulk RNA-seq alignment and quantification
• cutandrun_nf — Cut&Run alignment, QC, and peak calling
• batch_pipeline — Multi-step array jobs on AWS Batch
• Isoseq3_workflow — PacBio long-read Iso-Seq transcript characterization

R packages

• DeGSEA — Associating clinical data with transcriptome sequencing data
• fusBreakpoint — Sequence search in BAM files with Bioconductor

Analysis

• mack_d_2023.04.13_iPSC_neuromuscular_scRNAseq — Time-course scRNA-seq of iPSC-derived motor neurons
• kappe_s_2022.04_PF_LiverStage — Bulk RNA-seq of hepatocytes infected with Plasmodium falciparum

Reproducibility and standards

• contributing_guidelines — Lab-wide standards for creating, maintaining, and contributing to analysis software
• r_analysis_template and py_analysis_template — Quarto project templates for exploratory analysis
• renv_bioc_rstudio_docker — RStudio Server with Bioconductor and renv, containerized
• nextflow_scri_config — Institutional nf-core profile for Seattle Children's compute

• Website: jennylsmith.github.io

• LinkedIn: jenny-leopoldina-smith