Michelle Jonika

Genetics PhD Student · Blackmon Lab · Department of Biology · Texas A&M University
Michelle19@tamu.edu
Current CV

Evolutionary biologist using big data, bioinformatics, machine learning, and genomics to answer broad evolutionary questions. Check out some of my research projects below!

Next month I will be competing in the TAMU datathon, a part of the 2020 Major League Hacking schedule!


Education & Experience

PhD in Genetics

Texas A&M University, College Station, TX

Studying the evolution of microsatellites in insects and the pseudoautosomal region in mammals. Advised by: Heath Blackmon

August 2018 - Present

Bachelor of Science in Forensic and Investigative Science (Minor: Genetics)

Texas A&M University, College Station, TX

Undergraduate Thesis: Genes as Markers of Sex for Forensic Entomology Advised by: Aaron M. Tarone

August 2014-May 2018

Research

Microsatellite Evolution

Microsatellites are short, repetitive DNA sequences that can rapidly expand and contract due to slippage during DNA replication. These repeat sequences have important impacts on transcription, genome structure, and disease. Despite their importance, relatively little is known about the evolutionary dynamics of these short sequences across long evolutionary periods. To address this gap in our knowledge we have developed new software to facilitate the analyses of large genomic datasets and have used it to characterize microsatellite content across all sequenced insect genomes (304 species). Using this dataset, we have determined the impact of sequence assembly methods and genome quality on the inference of microsatellite content. We have also built a phylogeny for species in our dataset and explored the influence of a variety of organismal traits on the tempo and mode of microsatellite evolution across one of the most speciose clades on the planet.

Mammalian Pseudoautosomal Region

I am studying the pseudo-autosomal region (PAR) of sex chromosomes. The PAR is the part of the X and Y chromosome that is the same and must pair during meiosis in males. When this pairing process fails, the result is offspring with Turner or Klinefelter syndromes. Though modern sequencing technology has given us the ability to sequence the genomes of over 300 mammals, there are only nine genomes that have defined the size of this pairing region of the sex chromosomes.I am taking a machine learning approach to look at the evolution of the size of PAR regions across the mammalian tree of life.


Publications

Check out my Google Scholar page

2019

Michelle M Jonika, Carl E Hjelmen, Ashleigh M Faris, Alex S McGuane, Aaron M Tarone. Genes as Markers of Sex for Forensic Entomology. Journal of Forensic Science – Under Peer Review

Johnathan Lo, Michelle M Jonika, Heath Blackmon. 2019. micRocounter: Microsatellite Characterization in Genome Assemblies. G3: Genes | Genomes | Genetics – In Press [PDF]

Riddhi D Perkins, Julio Rincones Gamboa, Michelle M Jonika, Johnathan Lo, Amy Shum, Richard H Adams, Heath Blackmon. 2019. A Database of Amphibian Karyotypes. Chromosome Res – In Press [PDF]

Michelle M Jonika, Ashleigh M Faris, Carl E Hjelmen, Aaron M Tarone. 2019. Transcriptional Markers of Sex Determination for Forensic Entomology. Proceedings of the American Academy of Forensic Sciences. 2019 25 813 [PDF]

Guard, Blake, J. Honneffer, A. Jergens, M. Jonika, L. Toresson, Y. Lawrence, C. Webb, S. Hill, J. Lidbury, J. Steiner, J. Suchodolski. 2018. Longitudinal Assessment of Microbial Dysbiosis and Fecal Bile Acids Concentrations in Dogs with Chronic Inflammatory Enteropathy. J Vet Intern Med. 2018 33:1295-1305.[PDF]

2018

AB Blake, BC Guard, JB Honneffer, MM Jonika, J Chaitman, JA Lidbury, JM Steiner and JS Suchodolski. 2018. Altered Fecal Fatty Acid, Sterol and Bile Acid Metabolism in Dogs with Acute Diarrhea. J Vet Intern Med. 2018 32:2248.[PDF]

Jonika, M. M., A. M. Tarone. 2018. Genes as Markers of Sex for Forensic Entomology. Undergraduate Thesis, Texas A&University, College Station, Texas.

2017

BC Guard, MM Jonika, JB Honneffer, JA Lidbury, JM Steiner, AE Jergens, and JS Suchodolski. 2017. Longitudinal Characterization of the Fecal Metabolome in Dogs with Inflammatory Bowel Disease. J Vet Intern Med. 2017 31:1289. [PDF]

BC Guard, MM Jonika, JB Honneffer, JA Lidbury, JM Steiner, and JS Suchodolski. 2017. Development and Analytical Validation of an Assay for the Quantification of Fecal Bile Acids. J Vet Intern Med. 2017 31:1289. [PDF]

BC Guard, JB Honneffer, MM Jonika, JA Lidbury, JM Steiner, AE Jergens, and JS Suchodolski. 2017. Longitudinal Characterization of Dysbiosis and Unconjugated Bile Acid Profiles in the Feces of Dogs with Inflammatory Bowel Disease. Gastroenterology 152.5 (2017): S992. [PDF]


Skills

Programming Languages & Tools
Workflow
  • Beginner knowledge in Machine Learning, Deep Learning, TensorFlow and PyTorch
  • Intermediate knowledge in Python and Unix
  • Advanced knowledge in R
  • Advanced knowledge in Statistics
  • Advanced knowledge in Genomics
  • Advanced knowledge in Molecular Genetics
  • Expert in Research
  • Expert in Critical Thinking and Problem Solving

Awards & Certifications