Greg Zynda

Greg Zynda

Bioinformatics Scientist

Emerging Technologies, Life Sciences Computing

512-232-5185
gzynda@tacc.utexas.edu


Greg Zynda is a part of the Emerging Technologies team within Life Sciences Computing, where he explores new tools and technologies to enable the broader scientific community. These technologies are then mapped onto the traditional HPC resources available through TACC and released with usability in mind.

Greg is a Ph.D. Candidate in Bioinformatics at Indiana University, where he started his career as a bioinformatics consultant and provided support for all next generation analyses. He joined the Life Sciences Computing group at TACC in 2014, performing research, software development, and user support. Greg also enjoys volunteering his time to teach students about science and computing either at TACC on tours or workshops, or in Austin at various educational events.


Areas of Research and Interest

  • Scalable bioinformatics algorithms and workflows
  • Repli-Seq, epigenetics, and genome assembly
  • Software containers for reproducible analysis
  • HPC Usability

Current Projects

  • DARPA - SD2E: Synergistic Discovery and Design Environment
  • IOS-1025830: Epigenome Dynamics During DNA Replication
  • NSF - CyVerse: Cyberinfrastructure for the Life Sciences
  • University of Texas Research Cyberinfrastructure (UTRC)

Selected Publications/Conferences

Concia, Lorenzo, Ashley M. Brooks, Emily Wheeler, Greg Zynda, Emily Elizabeth Wear, Chantal LeBlanc, Jawon Song et al. "Genome-Wide Analysis of the Arabidopsis thaliana Replication Timing Program." Plant physiology (2018): pp-01537.

Zynda, Gregory J., Jawon Song, Lorenzo Concia, Emily E. Wear, Linda Hanley-Bowdoin, William F. Thompson, and Matthew W. Vaughn. "Repliscan: a tool for classifying replication timing regions." BMC bioinformatics 18, no. 1 (2017): 362.

Song, Jawon, Greg Zynda, Samuel Beck, Nathan M. Springer, and Matthew W. Vaughn. "Bisulfite Sequence Analyses Using CyVerse Discovery Environment: From Mapping to DMRs." Current Protocols in Plant Biology(2016): 510-529.

Klijn, C., Durinck, S., Stawiski, E.W., Haverty, P.M., Jiang, Z., Liu, H., Degenhardt, J., Mayba, O., Gnad, F., Liu, J. and Pau, G., 2015. A comprehensive transcriptional portrait of human cancer cell lines. Nature biotechnology, 33(3), pp.306-312.

Li, Qing, Jonathan I. Gent, Greg Zynda, Jawon Song, Irina Makarevitch, Cory D. Hirsch, Candice N. Hirsch et al. "RNA-directed DNA methylation enforces boundaries between heterochromatin and euchromatin in the maize genome." Proceedings of the National Academy of Sciences 112, no. 47 (2015): 14728-14733.

Kilaru, Aruna, Xia Cao, Parker B. Dabbs, Ha-Jung Sung, Md Mahbubur Rahman, Nicholas Thrower, Greg Zynda et al. "Oil biosynthesis in a basal angiosperm: transcriptome analysis of Persea Americana mesocarp." BMC plant biology 15, no. 1 (2015): 203.

Li, Qing, Jawon Song, Patrick T. West, Greg Zynda, Steven R. Eichten, Matthew W. Vaughn, and Nathan M. Springer. "Examining the causes and consequences of context-specific differential DNA methylation in maize." Plant physiology (2015): pp-00052.

Zynda, Gregory, Niall Gaffney, Mehmet Dalkilic, and Matthew Vaughn. "Feature frequency profiles for automatic sample identification using PySpark." In Proceedings of the 5th Workshop on Python for High-Performance and Scientific Computing, p. 5. ACM, 2015.


Education

B.S., Mathematics and Computer Science
Rose-Hulman Institute of Technology

Ph.D. Candidate, Bioinformatics
Indiana University