Publications and Submissions

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Seven first-author and five senior-author publications.

Publications and Submissions

S. Majidian, Y. Nevers, A. Yazdizadeh, A. Vesztrocy, S. Pascarelli, D. Moi, N. Glover, A. Altenhoff, C. Dessimoz. Orthology inference at scale with FastOMA. , Accepted, Nature Methods, 2024. code.
N. Dwarshuis, N. Kalra, ..., J. Wagner, S. Majidian*, J. Zook*. The GIAB genomic stratifications resource for human reference genomes. , Nature Communications, 2024.
D. Dylus , A. Altenhoff , S. Majidian , F. Sedlazeck, C. Dessimoz, Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree, Nature Biotechnology. 2024. code.
M. Ndiaye, S. Banos, L. Fitzgerald, A. Yazdizadeh, S. Oreshkov, C. Dessimoz, F. Sedlazeck, N. Glover, S. Majidian. When less is more: applications of minimizers in genomics, Genome Biology. 2024.
S. Lamei, A. Beyraghdar, A. Shojaeiyan, S. Majidian. Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek. , BMC Genomics, 2024.
A. Altenhoff, A.W Vesztrocy,C. Bernard, C. Train, A. Nicheperovich, S. PrietoBanos, I. Julca, D. Moi,Y. Nevers, S. Majidian, C. Christophe Dessimoz & N. Glover, 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. Web browser.
F. Langschied, .., S. Majidian, .., I. Ebersberger Quest for Orthologs in the Era of Biodiversity Genomics. , Genome Biology and Evolultion, 2024.
S. Majidian, D. Paiva Agustinho, F. Sedlazeck, M. Mahmoud, Genomic variant benchmark: if you cannot measure it, you cannot improve it. Genome Biology. 2023.
The Quest for Orthologs Benchmark Service in 2024. Under review in NARGB.
Inferring the selective history of CNVs using a maximum likelihood model. , Under review in GBE.
Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups. . F1000 preprint.
P. Liakopoulous, B. Banfalvi, X. Wang, S. Majidian, T. Farias, C. Dessimoz and A. Claudia-Sima. Towards predicting essential proteins via federated SPARQL queries, Code, Conference proceedings, The Semantic Web Applications and Tools for Healthcare and Life Science conference (SWAT4HCLS), Basel, Switzerland 2023.
A. Nicheperovich, A. Altenhoff, C. Dessimoz, S. Majidian*, OMAMO: orthology-based alternative model organism selection, Bioinformatics, 2022, code, web service.
S. Majidian., M. Mohades, M. Kahaei, Matrix completion with weighted constraint for haplotype estimation, Digital Signal Processing, 2021.
S. Majidian, F. Sedlazeck, PhaseME: Automatic rapid assessment of phasing quality and phasing improvement, GigaScience, 2020, code.
S. Majidian, M. Kahaei, D. de Ridder, Hap10: reconstructing accurate and long polyploid haplotypes using linked reads, BMC Bioinformatics, 2020, code.
S. Majidian, M. Kahaei, D. de Ridder, Minimum error correction-based haplotype assembly: considerations for long read data, PLOS one, 2020, code.
M. Mohades, S. Majidian, M. Kahaei, Haplotype assembly using manifold optimization and error correction mechanism, IEEE Signal Processing Letters, 2019, paper.
S. Majidian, M. Kahaei, NGS based haplotype assembly using matrix completion, PLOS one, 2019, code.
R. Ezazi, M. ..., S. Majidian, E. Stefani, M. Pindo, C. Donati, Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices, FEMS Microbiology Ecology, 2021.
E. Valipour, ..., S. Majidian, F. Motevaseli, M. Modarressi, Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells, Gene Elsevier, 2020.
A. Ahmadi, S. Majidian*, M. Kahaei*, Matrix completion using graph total variation based on directed laplacian matrix, Circuits, Systems, and Signal Processing Springer, 2021.
K. Walker, ..., S. Majidian, ..., Fritz J Sedlazeck, Ben Busby, The third international hackathon for applying insights into large-scale genomic composition to use cases in a wide range of organisms, F1000Research, 2022. code.

Invited talks and presentations

Computational Comparative Genomics in the era of BioGenome projects, Slides., University of Zurich. 23 Nov 2023, Switzerland.

Orthology inference at scale with FastOMA, YouTube Video., Slides., International Conference on Intelligent Systems for Molecular Biology. 23-27 July 2023. France.

BIOQA: toward a representative benchmark dataset of biological questions/answers involving orthology, gene expression, and complementary omics data., Slides., 21st European Conference on Computational Biology. Quest For Orthologs session. 12-21 September 2022. Spain.

A fast pipeline for species tree inference using placement in Hierarchical Orthologous Groups, Slides., Biodiversity Genomics 2021, a virtual conference organised by Wellcome Trust Genome Campus. Aug. 2021.

PhaseRE: Identifying recombination location per sample using long reads, Poster., BC2 Basel Computational Biology Conference, Switzerland. Sep. 2021.

Towards pathway-specific model organism with orthology relationships. PDF of presentation., International Conference on Genetics and Human Genomics, Iran. Dec. 2021.

Haplotype assembly using rank minimization. The 7th Conference on Bioinformatics, Iran, Jan. 2018.

Haplotype estimation for NGS data using polynomial optimization. The 10th Biotechnology Congress, Iran, Aug. 2017.