Liudmila Mainzer

Mayo Grand Challenge Storage

(bavz)
Dec 2018 - Dec 2019

BRAIN GWAS Benchmarking

(jpe)
Sep 2013 - Dec 2013

2020

D. P. Wickland, Y. Ren, J. P. Sinnwell, J. S. Reddy, C. Pottier, V. Sarangi, S. Tian, S. G. Younkin, M. M. Carasquillo, O. A. Ross, S. G. Younkin, N. Ertekin-Taner, R. Rademakers, M. E. Hudson, L. S. Mainzer, J.M. Biernacka, and Y. W. Asman (2020): Impact of variant-level hidden batch effects on identification of genetic risk factors in large sequencing studies, (submitted)

2019

Azza Ahmed, Jacob Heldenbrand, Yan Asmann, Faisal Fadlelmola, Daniel S. Katz, Katherine Kendig, Matthew Kendzior, Tiffany Li, Yingxue Ren, Elliott Rodriguez, Matthew Weber, Justin M. Wozniak, Jennie Zermeno, and Liudmila S. Mainzer (2019): Managing genomic variant calling workflows with Swift/T, PLoS ONE, Vol 14, Num 7, ppe0211608

2018

Yingxue Ren, Joseph S. Reddy, Cyril Pottier, Vivekananda Sarangi, Shulan Tian, Jason P. Sinnwell, Shannon K. McDonnell, Joanna M. Biernacka, Minerva M. Carrasquillo, Owen A. Ross, Nilüfer Ertekin-Taner, Rosa Rademakers, Matthew Hudson, Liudmila Sergeevna Mainzer, and Yan W. Asmann (2018): Identification of Missing Variants by Combining Multiple Analytic Pipelines, BMC Bioinformatics, Springer Nature, Vol 19, Num 1, pp139

2017

Jacob Heldenbrand, Yingxue Ren, Yan Asmann, and Liudmila S. Mainzer (2017): Step-by-Step Guide for Downloading Very Large Datasets to a Supercomputer Using the SRA Toolkit V1 (protocols.io.kb6csre), ZappyLab, Inc., Protocols.io

2016

Subho S. Banerjee, Arjun P. Athreya, Liudmila S. Mainzer, C. Victor Jongeneel, Wen-Mei Hwu, Zbigniew T. Kalbarczyk, and Ravishankar K. Iyer (2016): Efficient and Scalable Workflows for Genomic Analyses, Association for Computing Machinery, Proceedings of the ACM International Workshop on Data-Intensive Distributed Computing (DIDC '16), pp27-36, Kyoto, Japan

2019

Matthew E. Hudson, Yan W. Asmann, Liudmila Sergeevna Mainzer (2019): Impact of Batch Effect and Study Design Biases on Identification of Genetic Risk Factors in Sequencing Data, 2019 Blue Waters Annual Report, pp266-267

2018

Liudmila Mainzer, Yan Asmann, Matthew Hudson (2018): Identification of Missing Variants in Alzheimer's Disease, and the New Standards for Genomic Variant Identification in Large Cohorts, 2018 Blue Waters Annual Report, pp232-233

2016

Liudmila Mainzer (2016): Instrumenting Human Variant Calling Workflow at Scale, 2016 Blue Waters Annual Report, pp225-227
Liudmila Mainzer (2016): Custom Genotyping Chip for African Populations, 2016 Blue Waters Annual Report, pp224-225

2015

Liudmila Mainzer (2015): Instrumenting Human Variant Calling Workflow, 2015 Blue Waters Annual Report, pp158-159

Yingxue Ren: Rescue the missing variants: lessons learned from large sequencing projects


25th Annual Conference Intelligent Systems for Molecular Biology (ISMB) and 16th annual European Conference on Computational Biology (ECCB); Prague, Czech Republic, Jul 25, 2017

Yan Asmann: Genotyping for Very Large Cohorts


Blue Waters Symposium 2017, May 16, 2017

Yingxue Ren: Rescue the missing variants: lessons learned from large sequencing projects


Pacific Symposium on Biocomputing 2017; Big Island of Hawaii, Hawaii, U.S.A., Jan 5, 2017

Gerrit Botha: Custom Genotyping Chip for African Populations


Blue Waters Symposium 2016, Jun 14, 2016

Blue Waters Illinois allocations awarded to 26 research teams


Mar 7, 2017

Twenty-six research teams at the University of Illinois at Urbana-Champaign have been allocated computation time on the National Center for Supercomputing Application's (NCSA) sustained-petascale Blue Waters supercomputer after applying in Fall 2016. These allocations range from 25,000 to 600,000 node-hours of compute time over a time span of either six months or one year. The research pursuits of these teams are incredibly diverse, ranging anywhere from physics to political science.


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Supercomputing Genetic Medicine in Africa


Jun 15, 2016

The National Center for Supercomputing Applications at the University of Illinois at Urbana-Champaign is helping change the way genetic medicine is researched and practiced in Africa. Members of the Blue Waters team recently made it possible to discover genomic variants in over 300 deeply sequenced human samples to help construct a genotyping chip specific for African populations. ... Much of what is known about the genetics of diseases is based on people with European ancestry. The Consortium for Human Heredity and Health in Africa — H3Africa — aims to change that by promoting health research that takes into account the genetic diversity of African populations.


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Uncovering Alzheimer's complex genetic networks


Feb 3, 2015

The release of the film, "Still Alice," in September 2014 shone a much-needed light on Alzheimer's disease, a debilitating neurological disease that affects a growing number of Americans each year. ... "We re interested in studying the genetics of Alzheimer's disease," said Mariet Allen, a post-doctoral fellow at the Mayo Clinic in Florida. "Can we identify genetic risk factors and improve our understanding of the biological pathways and cellular mechanisms that can play a role in the disease process?" Allen is part of a team of researchers from the Mayo Clinic who are using Blue Waters, one of the most powerful supercomputers in the world, to decode the complicated language of genetic pathways in the brain. In doing so, they hope to provide insights into what genes and proteins are malfunctioning in the brain, causing amyloid beta plaques, tau protein tangles and brain atrophy due to neuronal cell loss--the telltale signs of the disease--and how these genes can be detected and addressed.


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18 general, 9 exploratory allocations on Blue Waters awarded to Illinois researchers


Nov 24, 2014

Eighteen researchers at the University of Illinois at Urbana-Champaign received allocations on the Blue Waters petascale supercomputer at the National Center for Supercomputing Applications (NCSA). A portion of available time on Blue Waters is reserved for University faculty and staff projects like these that require the system’s unique capabilities. Ten of the awards will continue projects already running on Blue Waters, related to a wide variety of topics like tornadoes, steel casting, and cell function, among others. Eight allocations are for new projects.


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