Lab

Computational Biology Research Center

About the lab

Computational Biology Research Center

Featured projects (4)

Featured research (2)

As a consequence of COVID-19 crisis, CBRC has been moved to as online weekly seminar event starting in Autumn 2020. This series of seminars is run by prominent bioinformatics professors from other universities, research centers, and Ph.D. students in undergraduate degrees. These webinars are open to members of the University and to the general public. This event is free but requires Registration. The meeting will be held virtually over Adobe Connect. The meeting link can be found at http://bioinformatics.aut.ac.ir/seminars/. Wednesdays, 18:30 – 19:30
Cell cycle phase is a decisive factor in determining the repair pathway of DNA double-strand breaks (DSBs) by non-homologous end joining (NHEJ) or homologous recombination (HR). Recent experimental studies revealed that 53BP1 and BRCA1 are the key mediators of the DNA damage response (DDR) with antagonizing roles in choosing the appropriate DSB repair pathway in G1, S, and G2 phases. Here, we present a stochastic model of biochemical kinetics involved in detecting and repairing DNA DSBs induced by ionizing radiation during the cell cycle progression. A three-dimensional stochastic process is defined to monitor the cell cycle phase and DSBs repair at times after irradiation. To estimate the model parameters, a Metropolis Monte Carlo method is applied to perform maximum likelihood estimation utilizing the kinetics of γ-H2AX and RAD51 foci formation in G1, S, and G2 phases. The recruitment of DSB repair proteins is verified by comparing our model predictions with the corresponding experimental data on human cells after exposure to X and γ-radiation. Furthermore, the interaction between 53BP1 and BRCA1 is simulated for G1 and S/G2 phases determining the competition between NHEJ and HR pathways in repairing induced DSBs throughout the cell cycle. In accordance with recent biological data, the numerical results demonstrate that the maximum proportion of HR occurs in S phase cells and the high level of NHEJ takes place in G1 and G2 phases. Moreover, the stochastic realizations of the total yield of simple and complex DSBs ligation are compared for G1 and S/G2 damaged cells. Finally, the proposed stochastic model is validated when DSBs induced by different particle radiation such as iron, silicon, oxygen, proton, and carbon.

Lab head

Fatemeh Zare-Mirakabad
Department
  • Department of Mathematics and Computer Science

Members (10)

Farzaneh Salari
  • Amirkabir University of Technology
Zahra Ghorbanali
  • Amirkabir University of Technology
Mohadeseh Lotfi
  • Amirkabir University of Technology
Fazeleh Sadat Mohseni-Salehi
  • Amirkabir University of Technology
Amin Rahmani
  • Amirkabir University of Technology
Nafis Banirazi
  • Universitat Politècnica de Catalunya
Milad Besharati
  • Amirkabir University of Technology
Mina Shaigan
  • RWTH Aachen University
Farzaneh Salari
Farzaneh Salari
  • Not confirmed yet
Bahram Mohammadpour Esfahani
Bahram Mohammadpour Esfahani
  • Not confirmed yet
Behnoosh Ashrafi
Behnoosh Ashrafi
  • Not confirmed yet