Ali Sharifi Zarchi

Research Associate in Royan institute

Research Associate of Bioinformatics

 

Research interest(s):

  • Genetics
  • Algorithms
  • Next Generation Sequencing
  • Bioinformatics
  • Epigenetics
  • Data Mining
  • Transcriptomics
  • Data Structures

 

 Recent Papers:
  • Al-Husini N, Sharifi A, Mousavi SA, Chitsaz H, Ansari A., “Genomewide Analysis of Clp1 Function in Transcription in Budding Yeast.”, Scientific Reports, 7(1):6894, 2017.
  •  Karamzadeh R, Karimi-Jafari MH, Sharifi-Zarchi A, Chitsaz H, Salekdeh GH, Moosavi-Movahedi AA., “Machine Learning and Network Analysis of Molecular Dynamics Trajectories Reveal Two Chains of Red/Ox-specific Residue Interactions in Human Protein Disulfide Isomerase.” Scientific Reports, 7(1):3666, 2017.
  •  A. Sharifi-Zarchi, Hill, S. M., et al. “Inferring causal molecular networks: empirical assessment through a community-based effort.” Nature Methods, 1–13, 2016.
  •  A. Sharifi-Zarchi, M. Totonchi, K. Khaloughi, R. Karamzadeh, M.J. Araúzo- Bravo, H. Baharvand, R. Tusserkani, H. Pezeshk, H. Chitsaz, M. Sadeghi, “Increased Robustness of Early Embryogenesis through Collective Decision- Making by Key Transcription Factors”, BMC Systems Biology, 9:23, 2015.
  • S. Taleahmad, M. Mirzaei, L. Parker, S. Hassani, S. Mollamohammadi, A. Sharifi- Zarchi, P.A. Haynes, H. Baharvand & G. Hosseini Salekdeh, “Proteome Analysis of Ground State Pluripotency”, Nature Scientific Reports, 2015, 5, 17985.
  • H. Fonoudi, H. Ansari, S. Abbasalizadeh, M. Rezaei Larijani, S. Kiani, S. Hashemizadeh, A. Sharifi-Zarchi, A. Bosman, G.M. Blue, S. Pahlavan, M. Perry, Y. Orr, Y. Mayorchak, J. Vandenberg, M. Talkhabi, D.S. Winlaw, R.P. Harvey, N. Aghdami, and H. Baharvand. “A Universal and Robust Integrated Platform for the Scalable Production of Human Cardiomyocytes from Pluripotent Stem Cells”, Stem Cells Translational Medicine, 4:1-13, 2015.
  • F. Dorri, H. Mahini, A. Sharifi-Zarchi, M. Totonchi, R. Tusserkani, H. Pezeshk, M. Sadeghi, “Natural biased coin encoded in the genome determines cell strategy”, PLoS ONE 9(8), 2014.
  •  M. Gholami, A. Arbabi, A. Sharifi-Zarchi, H. Chitsaz and M. Sadeghi, “ARYANA: Aligning Reads by Yet Another Approach”, BMC-Bioinformatics, 15(Suppl 9):S12, 2014.
  •  S.-N. Hassani, M. Totonchi, A. Sharifi-Zarchi, S. Mollamohammadi, M. Pakzad, S. Moradi, A. Samadian, N. Masoudi, S. Mirshahvaladi, A. Farrokhi, B. Greber, M. J. Araúzo-Bravo, D. Sabour, M. Sadeghi, G. H. Salekdeh, H. Gourabi, H. R. Schöler, and H. Baharvand, “Inhibition of TGFβ Signaling Promotes Ground State Pluripotency.,” Stem Cell Reviews and Reports, vol 10, pp 16-30, 2014.
  • Y. Tahamtani, M. Azarnia, A. Farrokhi, A. Sharifi-Zarchi, N. Aghdami, and H. Baharvand, “Treatment of Human Embryonic Stem Cells with Different Combinations of Priming and Inducing Factors Toward Definitive Endoderm”, Stem Cells and Development, vol 22 (9), pp. 1419-1432, 2013.
  •  A. Safari, A. Sharifi, H. Pezeshk, P. Nickchi, S.A. Marashi, and C. Eslahchi, “A Multivariate Bayesian Model for Gene Networks”, Journal of Statistical Sciences, Vol. 6, No. 2, pp 187-200, 2012.
  • S. Akbari, O. Etesami, M. Mahmoody, H. Mahini and A. Sharifi-Zarchi, “Transversals in Long Rectangular Arrays”, Discrete Mathematics, 306:23, 2006.
  • B. Esfahbod, M. Ghodsi and A. Sharifi-Zarchi, “Common-Deadline Lazy Bureaucrat Scheduling Problems”, Springer Lecture Notes in Computer Science, V.2748, 2003.
  • Ali Sharifi-Zarchi, Mehdi Totonchi, Hossein Baharvand, Marcos J. Arauzo-Bravo, Ruzbeh Tusserkani4), Hamid Pezeshk, Mehdi Sadeghi, “Increased Stability of the Early Embryogenesis through Collective Decision-Making by the Key Transcription Factors”, Poster Presentation, Regeneration of Organs: Programming and Self Organization Symposium, RIKEN CDB, Japan, 2014
  • M. Gholami, A. Arbabi, A. Sharifi-Zarchi, H. Chitsaz and M. Sadeghi, “ARYANA: Aligning Reads by Yet Another Approach”, Oral Presentation in RECOM-Seq, Carnegie Mellon University, 2014
  • A. Sharifi-Zarchi, K. Adachi, M. Totonchi, H. Pezeshk, R.J. Taft, H.R. Schöler, H. Baharvand, M. Sadeghi and M.J. Araúzo-Bravo, “DNA Methylation Regulates Discrimination of Eukaryotic Promoters and Enhancers”, Oral Presentation, Royan international congress on stem cells, 2013
  • B. Esfahbod, M. Ghodsi and A. Sharifi-Zarchi, “Common-Deadline Lazy Bureaucrat Scheduling Problems”, Oral Presentation, Workshop of Algorithms and Data Structures (WADS) 2003
\