Career Opportunity

Bioinformatics Engineer

The Sgourakis lab at the Children’s Hospital of Philadelphia (CHOP) and the University of Pennsylvania (UPenn) is recruiting a Bioinformatics Engineer to assist and support computational studies done by members of the lab. Our highly productive team is developing computational tools to predict tumor antigens and neoantigens from cancer patient sequencing data, and use these predictions to model the structures of peptide:HLA protein complexes using an in-house modeling suite, RosettaMHC. We apply these technologies in the field of cancer immunology, providing valuable feedback for the development of targeted immunotherapies. A synergistic research direction of the group is to develop software (MAUS) for analyzing Nuclear Magnetic Resonance (NMR) spectroscopy data, and to coordinate drug discovery applications in collaboration with other research groups (see https://sgourakislab.org/publications/). 

Specifically, the Bioinformatics Engineer will use an existing software pipeline, ProTECT (Prediction of T cell epitopes for Cancer Therapy), that has been further fine-tuned for high-performance computing at CHOP, to predict potential neoantigens expressed in a range of tumors directly from patient sequencing data. Working in close collaboration with Dr. Sgourakis and his team, the engineer will develop and apply computational protocols to parse the massive amount of data produced by ProTECT, as well efficient methods to summarize it. The Engineer will then use a special-purpose software developed at the Sgourakis Lab, RosettaMHC, to model the structures of neoantigens obtained from genomic sequencing data, to further refine and rank ProTECT’s predictions, and to correlate specific structural features with immunotherapy outcome.

Successful candidates should have a demonstrated experience in C++  code development. Additional experience in Python programming and high-performance computing is favorably considered.

Interested candidates should send a CV and names of three referees to Dr. Nik Sgourakis, at sgourakisn@chop.edu. For more details of the lab, please visit https://sgourakislab.org

Relevant publications

1. Cross-HLA targeting of intracellular oncoproteins with peptide-centric CARs. Nature, 2021
2. Backbone-independent NMR resonance assignments of methyl probes in large proteins. Nature Communications, 2021
3. A Recurrent mutation in anaplastic lymphoma kinase with distinct neoepitope conformations Frontiers in Immunology, 2018

Facilities  

The Center for Computational and Genomic Medicine at CHOP has routine access to a 90 Node HPC which also include 4 NVIDIA Tesla M60 GPU 16GB GPUs. Combined, the cluster has 12.5TB RAM, 4,496 Cores, and direct access to over 3PB of Network Attached Storage over dedicated 80Gb inter-switch connections. The CHOP Research Institute has a significant investment in a VMware Virtual environment comprised of 50 servers with a total 10 TB of RAM, 1640 GHZ of processing power and 100 Terabytes of disk space.