I started my journey in bioinformatics in 2015 when I wanted to choose the subject of my PhD thesis which was situated in the intersection of data science and genetics. Using in-depth mathematical concepts, I developed algorithms to assemble haplotypes from high-throughput DNA sequencing data. Working as an exchange PhD student in the plant department of Wageningen University, provided me the opportunity to develop a novel method and software for reconstructing the least fragmented haplotypes of polyploid species using 10X Genomics linked-read data. I have joined Prof. Dessimoz’s lab at the University of Lausanne as a Postdoctoral Fellow to develop algorithms for orthology inference since May 2021.
OMA orthology in 2024: improved prokaryote coverage, ancestral and extant GO enrichment, a revamped synteny viewer and more in the OMA Ecosystem. Nucleic Acids Research. 2024. paper .Web browser.
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Nature Biotechnology, 2023. paper. Software.
OMAMO: orthology-based alternative model organism selection. Bioinformatics, 2022, paper, code, web service.
Genetic variations & Haplotype assembly
When less is more: applications of minimizers in Genomics. 2023.
The GIAB genomic stratifications resource for human reference genomes. bioRxiv, 2023. preprint. resource.
Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biology, 2023. paper.
Matrix completion with weighted constraint for haplotype estimation. Digital Signal Processing, 2021, paper, code.
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement. GigaScience, 2020, paper, code
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads. BMC Bioinformatics, 2020, paper, code.
Minimum error correction-based haplotype assembly: considerations for long read data. PLOS one, 2020, paper, code.
Haplotype assembly using manifold optimization and error correction mechanism. IEEE Signal Processing Letters, 2019, paper.
NGS based haplotype assembly using matrix completion. PLOS one, 2019, paper, code.
Applied Bioinformatics
Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek. preprint. 2023.
Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells. Gene, 2020, paper.
Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices. FEMS Microbiology Ecology, 2021, paper.
Overexpression of TSGA10 in HeLa cells downregulates miR-183 level; TSGA10 defeats miR-183/HIF1A network. Submitted.
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
Matrix completion using graph total variation based on directed laplacian matrix. Circuits, Systems, and Signal Processing, 2021, paper.
Orthology inference at scale with FastOMA. ISMB/ECCB 2023.
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree. Invited talk. Department of Microbiology, University of Lausanne. May 2023.
BIOQA: toward a representative benchmark dataset of biological questions/answers involving orthology, gene expression, and complementary omics data. Oral presentation. ECCB-QFO. 2022.
A fast pipeline for species tree inference using placement in Hierarchical Orthologous Groups, Invited Talk, Biodiversity Genomics, Aug. 2021, Sanger website, slides.
Towards pathway-specific model organism with orthology relationships. Invited Talk. International Conference on Genetics and Human Genomics, Dec. 2021. slides.
PhaseRE: Identifying recombination location per sample using long reads, Accepted as Poster presentation, Basel Computational Biology Conference BC2, Sep. 2021, slides.
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.
Haplotype assembly using rank minimization. Selected talk, The seventh conference on bioinformatics, Iran, January 2018.
Haplotype assembly using matrix completion. Invited talk, International workshop in signal processing (IWSP), Iran, May 2018.
Haplotype estimation for NGS data using polynomial optimization. Poster presentation, The tenth biotechnology congress, Iran, August 2017.