Post Doc Fellow

Description

About the lab

We are a newly established computational research group at the Translational Genomics Research Institute developing and applying pangenome methods to study genome variation and evolution. Our work builds on experience developing pangenome graph construction and analysis tools (PGGB, ODGI, IMPG) and contributions to the Telomere-to-Telomere Consortium and Human Pangenome Reference Consortium.

We use long-read sequencing and de novo genome assembly to construct personalized pangenomes for cancer samples, detecting somatic structural variation that reference-based methods miss. We also aim to reduce the cost and complexity of germline genome assembly to make personalized pangenomics more routine in clinical and research settings. Additionally, we are developing pangenome-based approaches for genome-wide association studies.

We are looking for a passionate and highly motivated postdoctoral fellow to join our team.

Position summary

The postdoctoral fellow will develop and apply computational methods for cancer pangenomics using long-read sequencing data. Through our collaboration with the Barthel Lab, we have access to in-house PacBio Revio and Oxford Nanopore PromethION platforms with skilled library preparation support, ensuring ample data. The candidate will also be encouraged to identify and pursue new research areas and ideas.

This position offers flexibility:  hybrid arrangements with on-site time at TGen in Phoenix are possible for the right candidate. 

Responsibilities

• Developing computational tools for analyzing and visualizing long-read sequencing data and genome assemblies in normal and tumor samples
• Constructing personalized pangenomes to characterize somatic structural variation
• Contributing to pangenome-based variant calling and association study pipelines
• Working with large-scale genomic, epigenomic, and transcriptomic data
• Contributing to genome assembly and comparative genomics analyses
• Collaborating with internal and external partners, including consortium colleagues (e.g., Telomere-to-Telomere Consortium, Human Pangenome Reference Consortium)
• Building and maintaining reproducible workflows (e.g., Snakemake, Nextflow)
• Presenting research internally and externally (e.g., conferences)

Requirements

Required:

• PhD in Bioinformatics, Computer Science, Computational Biology, or related field
• Experience analyzing DNA sequencing data
• Proficiency in Python and/or R
• Familiarity with Linux/Unix and HPC systems (SLURM)
• Experience with version control (Git/GitHub)
• Understanding of statistics for genomic analysis

Preferred:

• Long-read sequencing analysis experience
• Proficiency in a compiled language (C, C++, Rust)
• Track record of software development (include a link to the software project you are most proud of)
• Familiarity with genome assembly, structural variant calling, or pangenome methods
• Experience with workflow managers
• Knowledge of cancer genomics databases (TCGA, ICGC)
• Experience with GWAS or variant-phenotype association analysis
• Familiarity with controlled-access genomic databases (e.g., dbGaP)

Location

The Guarracino Lab is located at the Translational Genomics Research Institute, a non-profit research institute in Phoenix, Arizona. Phoenix is the 5th largest city in the nation, ranked 5th as an Emerging Life Science Market, with over $3.25 billion in recent capital investment in biosciences. TGen sits at the center of the Phoenix Biomedical Campus, a 30-acre urban life sciences hub. Phoenix offers over 300 sunny days a year, multiple mountain ranges nearby, and access to some of the nation's most stunning national and state parks. The airport is a 10-minute drive from TGen with consistently high passenger satisfaction ratings.

Benefits

• BC/BS of Arizona health coverage
• Dental, Vision, Life, Short and Long Term Disability
• 401k with 6% match
• Generous time off
• Commuter benefits
• Employee Assistance Program

Application

Please direct questions to aguarracino@tgen.org. Submit a cover letter describing your research interests and motivation for joining the group, along with a CV detailing your research experience, publications, conference presentations, and contact information for at least two references. Review of applications will begin immediately and continue until the position is filled.