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) Department of Crop Sciences, UIUC advised by Dr. Matthew Hudson | 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) Department of Crop Sciences, UIUC advised by Dr. Matthew Hudson | ||
Jennie Zermeno BS Integrative Biology (2017) | Benchmarking performance and accuracy of genomic variant calling softwareJennie 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 M.S. Statistics (2017) Department of Statistics, UIUC advised by Dr. Alexander Lipka | Accurate and scalable GWAS algorithms | |
Khory Wagner | ||
Jacob Heldenbrand | NCSA Industry | |
Ryan Chui M.S. Bioinformatics (2017) | ||
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 |