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

	Matthew Weber B.S. Molecular and Cellular Biology (2016) M.S. Bioinformatics (2018) Department of Crop Sciences, UIUC	Mutation profiles of cancer Mr. 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
	Matthew Kendzior B.S. Crop Science (2016) Plant Biotechnology, Molecular Biology M.S. Bioinformatics (2018) Department of Crop Sciences, UIUC	Genomic variant calling by assembly
	Jennie Zermeno BS Integrative Biology (2017)	Benchmarking performance and accuracy of genomic variant calling software Jennie and Tiffany collaborate to document our efforts in benchmarking variant calling on HPC systems. We have run variant calling experiments on 500 genomes in parallel, on Blue Waters, to identify performance bottlenecks when using the GATK best practices workflow. Jennie is documenting this work in a publication. We have also tested a number of alternative software, such as Isaac, Genalice, Sentieon, as well as Dragen - a hardware solution. Tiffany is documenting the pros and cons of each of these excellent approaches in a separate manuscript.
	Tiffany Li BS Integrative Biology (2018) minor in Computer Science
	Angela Chen Statistics	Accurate and scalable GWAS algorithms
	Khory Wagner	Accurate and scalable GWAS algorithms
	Jacob Heldenbrand	NCSA Industry program
	Ryan Chui Bioinformatics	NCSA Industry program
	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 genomics Ellen 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
	Morgan Taschuk Bioinformatics	OICR
	Paul Hatton	University of Birmingham