Spring through the gateway - Deploying genomic workflows with XSEDE

David Rhee, Joseph Hargitai, R. Brent Calder, Pilib Ó Broin, Kevin Shieh, Aaron Golden

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Abstract

The use of sequencing technologies has revolutionized the field of genomics, allowing us to study structural and functional variations within the genome to base pair level. These technologies can also be used to probe the associated epigenome, where DNA-binding proteins alter the structural integrity of the genome, restricting or enabling localized gene expression in a heritable fashion. By using assays that identify the binding location of these proteins, so called 'epigenetic marks' can be used to discover and correlate molecular functions and phenotypes being studied. As such 'epigenetic marks' are inherently plastic in their nature, being easily perturbed by environmental stimuli, they are a compelling and important area of study in the context of human development and diseases. One of the most commonly studied epigenetic marks is DNA methylation: attachment of the methyl group to cytosines in CpG dinucleotides - an occurrence where two cytosine nucleotides are immediately followed by two guanine nucleotides in tandem. This modification can directly block the binding of regulatory proteins to that specific location thus effectively 'silencing' transcriptional activities. There are roughly 2.8 million such CpG loci in a human genome, making it an excellent target for performing a genome-wide methylation assay using sequencing technologies.

Original languageEnglish (US)
Title of host publicationACM International Conference Proceeding Series
DOIs
StatePublished - 2013
EventConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013 - San Diego, CA, United States
Duration: Jul 22 2013Jul 25 2013

Other

OtherConference on Extreme Science and Engineering Discovery Environment, XSEDE 2013
CountryUnited States
CitySan Diego, CA
Period7/22/137/25/13

Fingerprint

Genes
Nucleotides
Assays
Proteins
Methylation
Structural integrity
Gene expression
DNA
Plastics

Keywords

  • Bioinformatics
  • Computational biology
  • DNA
  • Epigenomics
  • Gateway
  • Grid computing
  • High performance computing
  • Parallel computing

ASJC Scopus subject areas

  • Human-Computer Interaction
  • Computer Networks and Communications
  • Computer Vision and Pattern Recognition
  • Software

Cite this

Rhee, D., Hargitai, J., Brent Calder, R., Broin, P. Ó., Shieh, K., & Golden, A. (2013). Spring through the gateway - Deploying genomic workflows with XSEDE. In ACM International Conference Proceeding Series [30] https://doi.org/10.1145/2484762.2484812

Spring through the gateway - Deploying genomic workflows with XSEDE. / Rhee, David; Hargitai, Joseph; Brent Calder, R.; Broin, Pilib Ó; Shieh, Kevin; Golden, Aaron.

ACM International Conference Proceeding Series. 2013. 30.

Research output: Chapter in Book/Report/Conference proceedingConference contribution

Rhee, D, Hargitai, J, Brent Calder, R, Broin, PÓ, Shieh, K & Golden, A 2013, Spring through the gateway - Deploying genomic workflows with XSEDE. in ACM International Conference Proceeding Series., 30, Conference on Extreme Science and Engineering Discovery Environment, XSEDE 2013, San Diego, CA, United States, 7/22/13. https://doi.org/10.1145/2484762.2484812
Rhee D, Hargitai J, Brent Calder R, Broin PÓ, Shieh K, Golden A. Spring through the gateway - Deploying genomic workflows with XSEDE. In ACM International Conference Proceeding Series. 2013. 30 https://doi.org/10.1145/2484762.2484812
Rhee, David ; Hargitai, Joseph ; Brent Calder, R. ; Broin, Pilib Ó ; Shieh, Kevin ; Golden, Aaron. / Spring through the gateway - Deploying genomic workflows with XSEDE. ACM International Conference Proceeding Series. 2013.
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