This group is a host for research into the use of high performance computing (HPC) for primary genomics analyses, such as alignment, variant calling, genome assembly, and RNASeq. By its nature, this research is highly collaborative. Every member of our team is affiliated with multiple departments or campus initiatives. The student participants in this group serve as a bond between the campus faculty using computational genomics analyses in their research, and the NCSA experts in HPC, storage, networking, databases, etc. Explore this page to find out who is involved, how we are connected, and what projects are currently ongoing.
Senior Research Scientist, National Center for Supercomputing Applications
Research Assistant Professor, Institute of Genomic Biology
217-300-0568
Projects
B.S. Molecular and Cellular Biology (2016) M.S. Bioinformatics (2018) | Mutation profiles of cancerMr. Weber is developing machine learning methods to effectively stratify cancers based on the statistical properties of mutations found in afflicted individuals. Cancer stratification is predictive of disease outcomes, drug response and drug metabolism. Effective computational approaches based on total data acquired to-date can make this process cheaper in the clinic. Matt collaborates with the Ontario Institute for Cancer research to make sure his models are realistic | |
Junyu Li B.S. Molecular and Cellular Biology (2017) minor in Computer Science
| Genomic variant calling by assembly | |
B.S. Crop Science (2016) Plant Biotechnology, Molecular Biology M.S. Bioinformatics (2018) | ||
Jennie Zermeno | Benchmarking performance and accuracy of genomic variant calling software | |
Tiffany Li | ||
Angela Chen Statistics | Accurate and scalable GWAS algorithms | |
Khory Wagner | ||
Jacob Heldenbrand | NCSA Industry | |
Ryan Chui Bioinformatics | ||
Noah Flynn Bioengineering | Evolution of molecular networks and persistence of organisms | |
Aishwarya Raj | ||
Ellen Nie BS. Biochemistry (2018), minor in Computer Science | Big data network transfers for genomicsEllen is benchmarking the network transfers of genomic data across multiple sites. She wants to understand the limitations of modern network backbone for big data genomics, and to facilitate correct configuration of the endpoints to resolve those limitations. Ellen is looking at the sites of our collaborators in Toronto, South Africa, Sudan, and the UK. | |
Nainika Roy Molecular and Cellular Biology | Data formats and data structures in computational genomics |
Other Collaborations
Matthew Hudson Bioinformatics Crop Science | HPCBio, Carver Biotechnology Center | |
Elliott Rodriguez Computer Science
| NCSA Scientific Software and Applications + University of Khartoum
Portable variant calling workflow
H3Africa Consortium | |
Azza Ahmed Computer Science Bioinformatics
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Morgan Taschuk Bioinformatics | OICR | |
Paul Hatton | University of Birmingham |