Publications and Submissions

For a complete list of my publications, please visit my Google Scholar

Selected Publications

• K. Vaddadi, M. Lin, S. Majidian, T. Mun, B. Langmead. Minimizing reference bias with an imputed personalized reference, Genome Research, 2026.
• S. Majidian, Y. Nevers, A. Yazdizadeh, A. Vesztrocy, S. Pascarelli, D. Moi, N. Glover, A. Altenhoff, C. Dessimoz. Orthology inference at scale with FastOMA. , Nature Methods, 2025. code, YouTube Talk.,
• S. Tan, S. Majidian, B Langmead, M. Zakeri. Movi Color: fast and accurate long-read classification with the move structure, The 16th ACM Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), 2025.
• R. Chikhi,... S. Majidian, ... A. Babaian. Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity, 2025.
• S. Majidian, A, Hadziahmetovic, ..., A. Ouangraoua, I. Julca. Quest for orthologs in the era of data deluge and AI. Journal of Molecular Evolution. 2025.
• 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. Majidian, M. Kahaei, D. de Ridder, Hap10: reconstructing accurate and long polyploid haplotypes using linked reads, BMC Bioinformatics, 2020, code.
• M. Mohades, S. Majidian, M. Kahaei, Haplotype assembly using manifold optimization and error correction mechanism, IEEE Signal Processing Letters, 2019, paper.

Invited talks and presentations

• Computational pangenomics for studying genome variation and evolution
  • University of Galway, Ireland. Oct. 2025.
  • University of Helsinki, Finland. Oct. 2025.
  • University College Dublin, Ireland. Oct. 2025.
  • Karolinska Institutet, Sweden. Oct. 2025.
  • VIB, Center for AI and Computational Biology, Belgium. July 2025.
• Computational comparative genomics in the era of BioGenome projects. Slides.,
  • SciLife Lab, Solna, Sweden. Apr. 2026.
  • The Zeavolution community. May. 2025.
  • Bioinformatics-Biostatistics Hub, Institut Pasteur, France. Mar. 2025.
  • Department of Systematic and Evolutionary Botany, University of Zurich, Switzerland. Nov. 2023.
• Scalable metagenomic classification in the era of long-read sequencing. Slam Talk. Johns Hopkins University, School of Medicine. USA. PDA Annual Conference May 2025.
• ANI, are you OK? Challenges for k-mer-based estimation of evolutionary distances. Pipeline, lightning talk, Biological Data Science 2024, Cold Spring Harbor Laboratory, 14 Nov 2024. US.
• Orthology inference at scale with FastOMA. YouTube Video., Slides.,
  • Workshop on Emerging Methods for Sequence Analysis . Pennsylvania State University, USA. Aug. 2024.
  • ISMB/ECCB 2023, Evolution and Comparative Genomics (EvolCompGen) COSI, Lyon, France. July 2023.
• Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree, Department of Microbiology, University of Lausanne. May 2023, Switzerland.
• 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.