Allen Institute · 19 hours ago
Bioinformatics Intern – Exploration of Alternative Splicing and Clonal Expansion
Seattle, WA
Internship
Hybrid
Intern
$35.58/hr - $35.58/hrThe Allen Institute is dedicated to understanding the principles of life and advancing health through innovative research. They are seeking a Bioinformatics Intern to investigate alternative splicing and clonal expansion in the immune system using long-read RNA-seq data, contributing to the development of new analysis tools and AI models for gene regulation.
Neuroscience
No H1B
Responsibilities
Investigating alternative splicing and clonal expansion in the normal immune system
Using data from the long-read RNA-seq, this project will investigate clonal expansion and somatic mutations in multiple dimensions
Using long-read sequence data from a bulk analysis of bone marrow (BM) and peripheral blood mononuclear cells (PBMCs) will allow us to identify germ line SNPs
Having established an individual map over germline encoded SNPs, we can search subpopulations of cells, or even single cells to identify additional mutations that has been acquired at some time during the life of the individual (somatic mutations)
Having data from both BM and PBMCs should allow us to trace somatic mutations from early progenitors in the BM into the peripheral immune system
The data generated from normal cells can also be combined with existing data from multiple myeloma cells to explore the propagation of somatic mutations in the transformed cells
The long-read sequencing data should also identify BCR/TCR receptor sequences in both blood and BM allowing for an extensive analysis of clonal expansion of lymphoid cells in both the BM and in the periphery
It will be used to develop new analysis tools that can be explored in future projects and generation of AI based models for gene regulation
Aim 1: Study patterns of alternative splicing and alternative starting sites across healthy immune cell types using long read scRNA-seq data and potentially scATAC-seq data to identify alternative starting sites
Aim 2: Study allele-specific transcription and link it to polymorphisms in promoter and/or enhancer sites
In addition to imputations to long-read scRNA-seq data, we may also analyze scATAC-seq data to identify polymorphisms in promoter and/or enhancer sites
Aim 3: Identify BCR/TCR receptor sequences associated with expanded clones of lymphoid cells
Aim 4: Identify somatic mutations associated with expanded clones of immune cells
Qualification
Required
Currently enrolled in the Bioinformatics and Genomics Master's Program at University of Oregon, or in an equivalent Master's degree program
Write scripts in Python or R
Use Jupyter Notebook environments to perform and explore data analysis methods
Use Git and Github for version control
Perform analysis with command-line scripting and tools
Use Linux/Unix-like systems for data analysis
Benefits
Medical
Dental
Vision
Basic life insurance
401k plan
Paid time off
Company
Allen Institute
The Allen Institute is dedicated to answering some of the biggest questions in bioscience and accelerating research worldwide.
Founded in 2003
501-1000 employees
Funding
Current Stage
Late StageLeadership Team
Rui Costa
President and CEO
Andy Hickl
Chief Technology Officer
Recent News
2025-12-25
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