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. Together we enable the use of advanced computing infrastructure in computational genomics. Explore this page to find out who is involved, how we are connected, and what projects are currently ongoing.
NCSA Press: Crossing over, branching out: Meet the NCSA Genomics team
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Technical Program Manager, National Center for Supercomputing Applications
Research Assistant Professor, Institute of Genomic Biology
217-300-0568
NCSA Genomics, September 2017. Credit: Steve Deunsing
Not pictured: Matt Weber, Ram Venkatakrishnan
Current People and Projects | ||
Jacob Heldenbrand, Research Programmer B.S. Biochemistry (2014) M.S. Bioinformatics (2016)
| NCSA IndustryJacob supports biomedical partners in the NCSA Industry program. Jacob provides a complementary mix of expertise in HPC and bioinformatics data analysis to enable Jacob and Azza Ahmed (Ph. D. candidate, University of Khartoum) are exploring and evaluating the | |
Ramshankar Venkatakrishnan, Research Programmer B.S. Electronics & Communications (2012) M.S. Electrical & Computer Engineering (2015) | Mayo Grand Challenge: evaluating and streamlining genomics workflowsRamshankar is working on computational improvements for the Mayo Grand Challenge, a genomics research Ram will also contribute his hardware expertise to the project, evaluating system architecture options to complement the team’s | |
Katherine Kendig, Associate Project Manager B.A. Anthropology (2012) M.F.A. Creative Writing (2017) | Project ManagementKatherine assists the team with research coordination, manuscript editing and preparation, and documentation. She benchmarked the Sentieon variant calling software for the Mayo Grand Challenge. She also contributes to NCSA’s Public Affairs team, writing articles about NCSA and XSEDE research: After the storm; Bringing supercomputing to psychology; DISSCO Tech; ECSS: Profiles in Consulting; NCSA Genomics; History was here | |
Brian Bliss, Research Programmer | Data compressionBrian will be working on data compression for the Mayo Grand Challenge project. | |
Graduate Students | ||
Weihao Ge B.S. Physics (2008) M.S. Physics (2011) Ph.D. Biophysics (2018) advised by Dr. Eric Jacobsson | Search Space ReductionWeihao is evaluating statistical methods for search space reduction in the analysis of GWAS data for genomic variant Her work is part of the CCBGM project "Scaling the Computation of Epistatic Interactions in GWAS Data." | |
B.S. Molecular and Cellular Biology (2016) M.S. Bioinformatics (2018) Department of Crop Sciences, UIUC CompGen fellow advised by Dr. Matthew Hudson | Mutation profiles of cancerMr. Weber is developing machine learning methods to effectively stratify cancers based on the Paper: Simulating Next-Generation Sequencing Datasets from Empirical Mutation and Sequencing Models Poster: Statistical models to capture mutational properties for NextGen Sequencing Data | |
B.S. Crop Science (2016) Plant Biotechnology, Molecular Biology M.S. Bioinformatics (2018) Department of Crop Sciences, UIUC Graduate Fellow in the College of ACES advised by Dr. Matthew Hudson | Genomic variant calling by assemblyMr. K is focusing on a method to detect genomic variants by assembly. He is employing the software Cortex-var, which constructs de-novo genome assembly on multiple Mr. K is also working with Tiffany on the genomic analysis of HLHS for the Mayo Grand Challenge. Poster: Variant Calling by Assembly Poster: Reference-guided variant calling for non-repetitive sequences in Glycine Max | |
Prakruthi Burra B. E. Computer Science (2018) M.S. Biological Sciences (2018) | Workflow management for variant callingPrakruthi is implementing a variant calling workflow in Nextflow (a workflow manager). She is also in charge of testing the workflow developed for the Mayo Grand Challenge before delivery. Human Heredity & Health in AfricaPrakruthi will be contributing to UIUC's work with the H3Africa Consortium. | |
Dave Istanto B.S. Crop Sciences (2018) | Workflow management for structural variant callingDave is creating a Nextflow workflow for structural variant calling using Cortex-var. | |
Undergraduate Students | ||
Aishwarya Raj B.S. Biochemistry (2019) minor in Bioinformatics | Evolution of molecular networks and persistence of organismsConstruct and compare gene, metabolic and signaling networks from organisms across the tree of life. The goal of the project is to provide support for the general framework of persistence strategies. It postulates that persistence is achieved by biological systems via a tradeoff of traits that serve either Poster: Persistence Strategies in Biomolecular Network Architecture NCUR Slides: Architecture and Dynamics of Biomolecular Networks Facilitate Evolution of Persistence Strategies in Living Organisms | |
Cynthia Liu B.S. Bioengineering (2019) minor in Computer Science | Workflow management comparisonsCynthia worked to learn the Nextflow system for workflow management and to compare and contrast three competing workflow management options for bioinformatics in association with the work Ram is performing for the Mayo Grand Challenge.
Poster: Comparative Analysis of Genomic Sequencing Workflow Management Systems | |
High School StudentsWe have several high school students working with our team to gain skills and complete projects in a real-world environment. | ||
Sophia Torrellas | Sophia and Angelynn are benchmarking the performance and accuracy of Minimap2 (Li, 2018) - a program used for analyzing sequencing read data in genomics. Minimap2 maps the sequencing reads against the reference genome for the species. Currently, BWA MEM (Li, 2013) is the most widely used tool for this purpose, with Novoalign (Hercus and Albertyn, 2012) coming as a close second. However, recent research (Li, 2018) suggests that Minimap2 is equally accurate yet also faster than BWA MEM. Are these claims true? Can we validate them independently using our own measurements? Sophia and Angelynn are running tests in AWS to answer these questions. | |
Angelynn Huang is testing minimap2, a bioinformatics software, in the cloud. |
Former Group Members | ||
Ellen Nie B.S. Computer Science (2018) | Big data network transfers for genomicsEllen is benchmarking the network transfers of genomic data across multiple sites. Poster: Benchmarking and Optimization of Long Distance Big Data Transfers Validation of Sentieon - the fast alternative to GATKEllen is also collaborating with OICR to validate the speed and accuracy of the new software Convert Java-based GWAS code for SparkIn a project described below (Accurate and scalable GWAS algorithms) we are improving performance of We would like to deploy this Java code on Spark, to see if the necessary performance gains could be obtained. A successful student applicant will use Java Spark API to adapt the current code for a Spark platform that Poster: Scaling the Computation of Epistatic Interactions in GWAS Data | |
Tiffany Li B.S. Integrative Biology (2018) minor in Computer Science | Benchmarking performance and accuracy of genomic variant calling softwareTiffany collaborates to document our efforts in benchmarking variant calling on HPC We have also tested a number of alternative software, such as Isaac, Genalice, and Sentieon, Validation and benchmarking on ParFu - a parallel file packaging utilityTiffany is also involved in testing and benchmarking of ParFu, an MPI tool for creating or extracting | |
Sijia Huo B.S. Mathematics & Computer Science (2018) second major in Statistics third major in Economics | Parallelization of RSijia is working with NCSA Faculty Fellow Dr. Zeynep Madak-Erdogan to introduce parallel R code into her research. Dr. Madak-Erdogan is exploring racial disparities in breast cancer occurrence through the lens of diet and nutrition. | |
Ryan Chui B.S. Biochemistry (2016) M.S. Bioinformatics (2017) | NCSA IndustryRyan performed software installation, benchmarking, and development for a variety of industry partners. To investigate how the training time for deep neural networks (DNN’s) can be affected, Ryan worked On Github: EpiQuant: Hadoop, C, Tensorflow - epistasis software prototypes MLCC - multi-label cancer classification q2b - binary representation of nucleotides ptgz - parallel tar gzip Usage Analyzer - log analyzer for HPC schedulers | |
Jennie Zermeno B.S. Integrative Biology (2017) | Benchmarking performance and accuracy of genomic variant calling softwareJennie collaborated to document our efforts in benchmarking variant calling on HPC Bioinformatics in the CloudJennie is investigating the issues of portability, reproducibility and scaling of bioinformatics workflows Students Capitalize on Computational Genomics Research Using AWS | |
Angela Chen M.S. Statistics (2017) Department of Statistics, UIUC CompGen fellow advised by Dr. Alexander Lipka | Accurate and scalable GWAS algorithmsAngela and Khory collaborated to improve the scalability and parallelization of the statistical software Angela wrote a manuscript to demonstrate that her new stepwise epistatic model selection Khory provided the expertise in computer science to convert this Java code into C++ and parallelize | |
Khory Wagner advised by Dr. Vologymyr Kindratenko | ||
Nainika Roy B.S. Molecular and Cellular Biology (2017) minor in Informatics and Chemistry SPIN fellow | Data formats and data structures in computational genomics | |
Junyu Li B.S. Molecular and Cellular Biology (2017) minor in Computer Science SPIN fellow | Genomic variant calling by assemblyJunyu worked with Mr. K in an interdisciplinary team, providing the expertise in math and computer Poster: Reference-guided variant calling for novel non-repetitive sequences in Glycine max | |
Noah Flynn B.S. Bioengineering, Mathematics (2017) minor in computer science SPIN fellow | Evolution of molecular networks and persistence of organisms |
Other Collaborations
Dr. Matthew Hudson Bioinformatics Crop Science | HPCBio, Carver Biotechnology Center | |
Dan Wickland Ph.D. Informatics (2019) | ||
Computer Science | NCSA Scientific Software and ApplicationsPortable variant calling workflow in Swift
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Azza Ahmed Computer Science advised by Dr. Faisal Fadlelmola | ||
Dr. Zeynep Madak-Erdogan Food Science & Human Nutrition | Madak-Erdogan LabSystems Biology of Estrogen Signaling
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Brandi Smith Ph.D. Food Science and Human Nutrition (2021) | ||
H3Africa Consortium
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Morgan Taschuk Bioinformatics | OICR
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Paul Hatton HPC / Visualisation
| University of Birmingham |
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