Sina Majidian

I finished my PhD in 2020 at Iran University of Science and Technology where I was working on mathematical analysis of the haplotype assembly problem. I spent one year as a guest researcher in the Bioinformatics group of Wageningen University working on polyploid haplotype estimation using 10X Genomics linked-read data. I have joined Prof. Dessimoz’s lab at the University of Lausanne (UNIL) as a Postdoctoral Fellow to develop algorithms for orthology inference since May 2021.


Research interests

  • Comparative genomics
  • Genetic variations
  • Haplotype assembly
  • Data and Signal processing

Publications and submissions

Haplotype assembly

  1. Matrix completion with weighted constraint for haplotype estimation. Digital Signal Processing, 2021, paper, code.

  2. PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. GigaScience, 2020, paper, code

  3. Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. BMC Bioinformatics, 2020, paper, code.

  4. Minimum error correction-based haplotype assembly: considerations for long read data. PLOS one, 2020, paper, code.

  5. Haplotype assembly using manifold optimization and error correction mechanism. IEEE Signal Processing Letters, 2019, paper.

  6. NGS based haplotype assembly using matrix completion. PLOS one, 2019, paper, code.

    Applied Bioinformatics

  7. Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells. Gene, 2020, paper.

  8. Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices. FEMS Microbiology Ecology, 2021, paper.

  9. Bioinformatics evaluation of SPATA19 gene expression in different parts of brain. Research in Molecular Medicine, 2021, paper.

  10. Overexpression of TSGA10 in HeLa cells downregulates miR-183 level; TSGA10 defeats miR-183/HIF1A network. Submitted.

  11. The critical role of RHOXF1 transcription factor in the stress response expression of TSGA10 by a transcriptional regulation network in testis and cancer tissues. Submitted.

    Signal and data processing

  12. Matrix completion using graph total variation based on directed laplacian matrix. Circuits, Systems, and Signal Processing, 2021, paper.

  13. Haplotype estimation using low-rank matrix factorization in presence of outliers, 2021, Journal of Iranian Association of Electrical and Electronics Engineers, abstract.

  14. Haplotype Estimation Using Polynomial Optimization Relaxation, Tabriz Journal of Electrical Engineering (TJEE), abstract.

  15. Direction of arrival (DOA) estimation using kronecker subspace. Signal and Data Processing, 2018, abstract.

  16. Direction of arrival (DOA) estimation using Khatri-Rao subspace. 2017. Journal of Iranian Association of Electrical and Electronics Engineers. abstract.


Conferences

  1. PhaseRE: Identifying recombination location per sample using long reads, Accepted as Poster presentation, Basel Computational Biology Conference BC2, September 2021

  2. Detection of biomarker miRNAs and their functions by co-expression network analysis in gastric cancer. Poster presentation, The second international congress on biomedicine, Iran, December 2018.

  3. Haplotype assembly using rank minimization. Selected talk, The seventh conference on bioinformatics, Iran, January 2018.

  4. Haplotype assembly using matrix completion. Invited talk, International workshop in signal processing (IWSP), Iran, May 2018.

  5. Haplotype estimation for NGS data using polynomial optimization. Poster presentation, The tenth biotechnology congress, Iran, August 2017.


Education

  • (2015 – 2020) Doctor of Philosophy in Electrical Engineering, Iran University of Science & Technology, Dissertation: Haplotype assembly for next generation sequencing data using matrix completion, GPA: 3.75.

  • (2013 - 2015) Master of Science in Electrical Engineering, Iran University of Science & Technology, GPA: 3.22.

  • (2008 - 2013) Bachelor of Science in Electrical Engineering, Shahid Beheshti University.


Teaching experience

  • Guest lecturer. Bioinformatics (postgraduate course), Tehran University of Medical Sciences, 2020.
  • Workshop Instructor. Gene expression analysis using R, Tehran University of Medical Sciences, 2019.
  • Workshop Instructor. R programming, Tehran University of Medical Sciences, 2018.
  • Lecturer. Microwave 1, wireless communication (undergrad courses), Sadra Institute, 2017.
  • Lecturer. Mathematics 1 (undergrad course), Nahavand Institute, 2016.
  • Teaching Assistant. Convex optimization, stochastic process, digital signal processing (postgraduate courses). Iran University of Science & Technology, 2016.
  • Teaching Assistant. Physics 1, physics lab, circuits lab (undergrad courses), Shahid Beheshti university, 2013.

Awards, honours and funds

  • Ranked in the top 2% among 20,000+ electrical engineering applicants in nation-wide M.Sc. University entrance exam.
  • Ranked in the top 0.5% among 350,000+ participants in Iranian national university entrance exam for mathematics and Physics.
  • Co-supervising Master thesis. Creating an Ensemble Method Combining Haplotype Estimates. Wageningen University, The Netherlands. 2019.
  • Co-supervising summer intern. Orthology guided model organism selection. University College London. 2021.
  • Mentoring several undergraduate and graduate students for defining and conducting their projects.
  • Review Editor of the journal of Frontiers in Systems Biology journal, Integrative Genetics and Genomics section.
  • Peer review service for IET systems biology journal.
  • Tuition fee waiver by the Ministry of Science for undergraduate students, Shahid Beheshti University.
  • University research grant of the Ministry of Science (€8160).
  • Proposal submission for The Marie-Skłodowska Curie Postdoctoral Fellowship Individual fellowships- MSCA IF, scored 79.8%.

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