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Dr. Marharyta (Margo) Petukh, joins the faculty as assistant professor of biology as the College launches its new computational biology program. Petukh comes to PC from the Joint Institute for Computational Sciences at the University of Tennessee. She has worked in the Department of Physics and Astronomy at Clemson University and with the faculty of Physics at Belarusian State University. She has earned several research awards at Clemson and has memberships with the American Chemical Society and Biophysical Society.

Education

Ph.D., Computational Biophysics, Clemson University, Clemson, SC
MS., Biophysics, Belarusian State University, Minsk, Belarus
BS., Physics, Belarusian State University, Minsk, Belarus

Research or Areas of Specialty

My research follows two main directions:

• Personalized medicine and drug discovery: Using computational (in-silico) approaches, I investigate how single amino acid substitutions in proteins alter their structure and function, potentially leading to disease. By understanding the specific phenotypic effects caused by these mutations, I aim to identify small molecules that can bind to the altered proteins and restore their normal function. These candidate compounds offer promising therapeutic solutions that can later be validated through experimental studies in vitro or in vivo.
• Developing new bioinformatics tools using Python language. I’m currently developing a novel graph-based algorithm called OrthoNet, which looks at the evolution of proteins and dynamically selects true orthologous sequences to generate cleaner evolutionary conservation profiles. This improves the accuracy of predicting whether specific mutations are likely to be disease-causing or neutral.

Recognitions

• Robert Freymeyer Award (2022), С����Ƶ, honor excellent scholars and researchers

Classes at PC

• CBIO 3370 “Bioinformatics Algorithms”
• BIOL 3360 “Bioinformatics”
• BIOL 2002 “Seminar in Biological Primary Literature”
• BIOL 1000 “Biology in the 21st century”
• BIOL 1150 “Biological concepts” (labs)

Organizations

• Membership
  • Protein Society (2024–Present)
  • International Society for Computational Biology (2020–Present)
• Reviewer
  • Journal of Biomolecular Structure & Dynamics
  • Journal of Computational Biology and Chemistry
  • PLOS Computational Biology
  • Journal of Biomedical Semantics
  • ACS Omega
  • The Journal of Physical Chemistry Letters
  • International Journal of Molecular Sciences
  • International Journal of Information Technology, Communications and Convergence

Certifications

• “Machine Learning with Python” – IBM Developer Skills Network (Coursera), issued March 3, 2025
• “Data Analysis in Python” – IBM Developer Skills Network (Coursera), issued January 26, 2025
• “Developing and Teaching an Online Course” – 2020 Summer Enrichment Session 1, issued July 5, 2020

Publications

Baker SM, Petukh M. Effect of pH on the Ability of N-Terminal Domain of Human NPC1 to Recognize, Bind, and Transfer Cholesterol. ACS Omega, 2020, 5(45), 29222–29230.

Gavira JA, Gumerov VM, Rico-Jiménez M, Petukh M, Upadhyay AA, Ortega A, Matilla MA, Zhulin IB, Krell T. How Bacterial Chemoreceptors Evolve Novel Ligand Specificities. mBio, 2020, 11(1).

Li C, Jia Z, Chakravorty A, Pahari S, Peng Y, Basu S, Koirala M, Panday SK, Petukh M, Li L, Alexov E. DelPhi Suite: New Developments and Review of Functionalities. Journal of Computational Chemistry, 2019, 40(28), 2502–2508.

Petukh M, Zhulin IB. Comparative study of the effect of disease-causing and benign mutations in position Q92 on cholesterol binding by the NPC1 N‐terminal domain. Proteins: Structure, Function, and Bioinformatics, 2018, 86(11), 1165–1175.

Adebali O, Petukh MG, Reznik AO, Tishkov AV, Upadhyay AA, Zhulin IB. Class III histidine kinases: a recently accessorized kinase domain in putative modulators of type IV pili-based motility. Journal of Bacteriology, 2017, JB-00218.

Getov I, Petukh M, Alexov E. SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach. International Journal of Molecular Sciences, 2016, 17(4), 512.

Petukh M, Li M, Alexov E. Statistical Investigation of Surface Bound Ions and Further Development of BION Server to Include pH and Salt Dependence. Journal of Computational Chemistry, 2015, 36(32), 2381–2393.

Petukh M, Li M, Alexov E. Predicting Binding Free Energy Change Caused by Point Mutations with Knowledge-Modified MM/PBSA Method. PLOS Computational Biology, 2015, 11(7): e1004276.

Petukh M, Kucukkal TG, Alexov E. On Human Disease‐Causing Amino Acid Variants: Statistical Study of Sequence and Structural Patterns. Human Mutation, 2015, 36, 524–534.

Kucukkal TG, Petukh M, Alexov E. Structural and Physico-Chemical Effects of Disease and Non-Disease nsSNPs on Proteins. Current Opinion in Structural Biology, 2015, pp. 18–24.

Petukh M, Alexov E. Ion Binding to Biological Macromolecules. Asian Journal of Physics, 2014, 23(5), 735.

Petukh M, Wu B, Stefl S, Smith N, Hyde-Volpe D, Wang L, Alexov E. Chronic Beryllium Disease: Revealing the Role of Beryllium Ion and Small Peptides Binding to HLA-DP2. PLOS One, 2014, 9:e111604.

Li M, Petukh M, Alexov E, Panchenko AR. Predicting the Impact of Missense Mutations on Protein–Protein Binding Affinity. Journal of Chemical Theory and Computation, 2014, 10, 1770–1780.

Kimmett T, Smith N, Witham S, Petukh M, Sarkar S, Alexov E. ProBLM Web Server: Protein and Membrane Placement and Orientation Package. Computational and Mathematical Methods in Medicine, 2014.

Campbell B, Petukh M, Alexov E, Li C. On the Electrostatic Properties of Homodimeric Proteins. Journal of Theoretical and Computational Chemistry, 2014.

Boccuto L, Aoki K, Flanagan-Steet H, Chen C-F, Fan X, Bartel F, Petukh M, Pittman A, Saul R, Chaubey A. A Mutation in a Ganglioside Biosynthetic Enzyme, ST3GAL5, Results in Salt & Pepper Syndrome, a Neurocutaneous Disorder with Altered Glycolipid and Glycoprotein Glycosylation. Human Molecular Genetics, 2014, 23, 418–433.

Petukh M, Kimmet T, Alexov E. BION Web Server: Predicting Non-Specifically Bound Surface Ions. Bioinformatics, 2013, 29, 805–806.

Zhang Z, Zheng Y, Petukh M, Pegg A, Ikeguchi Y, Alexov E. Enhancing Human Spermine Synthase Activity by Engineered Mutations. PLOS Computational Biology, 2013, 9:e1002924.

Zhang Z, Witham S, Petukh M, Moroy G, Miteva M, Ikeguchi Y, Alexov E. A Rational Free Energy-Based Approach to Understanding and Targeting Disease-Causing Missense Mutations. Journal of the American Medical Informatics Association, 2013, 20, 643–651.

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