Publications

Minimizing reference bias with an imputed personalized reference
bioRxiv, January 1, 2026
Vaddadi K, Lin M, Majidian S, Mun T, Langmead B
OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data
Journal of Molecular Evolution, October 26, 2025
Yazdizadeh Kharrazi A, Altenhoff A, Romashchenko N, Dessimoz C, Majidian S
Movi Color: fast and accurate taxonomic classification with the move structure
Proceedings of the 16th ACM International Conference on Bioinformatics, Computational Biology, and Health Informatics (ACM-BCB), October 12, 2025
Tan S, Majidian S, Langmead B, Zakeri M
Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups
Journal of Molecular Evolution, September 30, 2025
Sarton-Lohéac G, Romashchenko N, Train C, Majidian S, Glover N
A roadmap for equitable reuse of public microbiome data
Nature Microbiology, September 26, 2025
Hug L, Hatzenpichler R, Moraru C, Soares A, Meyer F, Heyder A, The Data Reuse Consortium, Probst A
Logan: Planetary-Scale Genome Assembly Surveys Life’s Diversity
biorxiv preprint, September 1, 2025
Chikhi R … Majidian S … Babaian A
EvANI benchmarking workflow for evolutionary distance estimation
Briefings in Bioinformatics, June 12, 2025
Majidian S, Hwang S, Zakeri M, Langmead B
Inferring the Selective History of CNVs Using a Maximum Likelihood Model
Genome Biology and Evolution, March 18, 2025
Malekpour A, Kalirad A, Majidian S
Orthology inference at scale with FastOMA
Nature Methods, January 7, 2025
Majidian S, Nevers Y, Yazdizadeh Kharrazi A, Warwick Vesztrocy A, Pascarelli S, Moi D, Glover N, Altenhoff A, Dessimoz C
Quest for Orthologs in the era of Data Deluge and AI
Journal of Molecular Evolution, January 1, 2025
Majidian S, Hadziahmetovic A, Langschied F, Pascarelli S, Prieto-Baños S, Rojas-Vargas J, Braun E, Dessimoz C, Baniré Diallo A, Durand D, Fang G, Gabaldón T, Glover N, Liberles D, McWhite C, Sonnhammer E, Thomas P, Ouangraoua A, Julca I
New developments for the Quest for Orthologs benchmark service
NAR Genomics and Bioinformatics, December 11, 2024
Altenhoff A, ..., Majidian S, ..., Dessimoz C,Thomas P,Ebersberger I, Sonnhammer E
The GIAB genomic stratifications resource for human reference genomes
Nature Communications, October 19, 2024
Dwarshuis N, Kalra N, ..., Wagner J, Majidian S, Zook J
When less is more: sketching with minimizers in genomics
Genome Biololgy, October 14, 2024
Ndiaye M, Prieto-Baños S, Fitzgerald L, Yazdizadeh Kharrazi A, Oreshkov S, Dessimoz C, Sedlazeck F, Glover N, Majidian S
Quest for Orthologs in the Era of Biodiversity Genomics
, October 10, 2024
Langschied F, ..., Majidian S, ..., Gabaldón T, Sonnhammer E, Thomas P, Dessimoz C, Ebersberger I
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, January 5, 2024
Altenhoff A, Warwick Vesztrocy A, Bernard C, Train C, Nicheperovich A, Prieto Baños S, Julca I, Moi D, Nevers Y, Majidian S, Dessimoz C, Glover N
Genomic variant benchmark: if you cannot measure it, you cannot improve it
Genome Biology, October 5, 2023
Majidian S, Agustinho D, Chin CS, Sedlazeck F, Mahmoud M
Inference of phylogenetic trees directly from raw sequencing reads using Read2Tree
Nature Biotechnology, April 20, 2023
Dylus D, Altenhoff A, Majidian S, Sedlazeck F, Dessimoz C
Phylogenetic placement of whole genome duplications in yeasts through quantitative analysis of hierarchical orthologous groups
F1000 Research Preprint, April 12, 2023
Moix S,Glover N, Majidian S
Towards predicting essential proteins via federated SPARQL queries
SWAT4HCLS (The Semantic Web Applications and Tools for Healthcare and Life Science conference), February 13, 2023
Liakopoulous P, Banfalvi B, Wang X, Majidian S, Mendes de Farias T, Dessimoz C, Claudia Sima A
OMAMO: orthology-based alternative model organism selection
Bioinformatics, March 18, 2022
Nicheperovich A, Altenhoff A, Dessimoz C, Majidian S
Matrix Completion Using Graph Total Variation Based on Directed Laplacian Matrix
Springer Circuits Syst Signal Process, November 20, 2020
Ahmadi A, Majidian S, Kahaei MH
Matrix completion with weighted constraint for haplotype estimation
, October 12, 2020
Majidian S, Mohades M, Kahaei MH
PhaseME: Automatic rapid assessment of phasing quality and phasing improvement
GigaScience, July 24, 2020
Majidian S, Sedlazeck F
Responses of cucumber (Cucumis sativus L.) rhizosphere microbial community to some agronomic management practices
FEMS Microbiology Ecology, July 21, 2020
Ezazi R, Ahmadzadeh M, Majidian S, Stefani E, Pindo M, Donati C
cfCNV: an optimized pipeline for detecting copy number variations for cell free DNA data
European Journal of Human Genetics (57th ESHG), June 18, 2020
Palizban F, Majidian S
Transcriptomic data reveals the dynamics of terpenoids biosynthetic pathway of fenugreek
BMC Genomics, June 18, 2020
Lamei S., Beyraghdar A, Shojaeiyan A, Majidian S
Hap10: reconstructing accurate and long polyploid haplotypes using linked reads
BMC Bioinformatics, June 18, 2020
Majidian S, Kahaei MH, de Ridder D
, June 18, 2020
Majidian S, Kahaei MH, de Ridder D
Minimum error correction-based haplotype assembly: Considerations for long read data
PlOS One, June 12, 2020
Majidian S, Kahaei MH, de Ridder D
Anti-angiogenic effects of testis-specific gene antigen 10 on primary endothelial cells
Gene, June 5, 2020
Valipour E, ..., Majidian S, .., Modarressi MH
NGS based haplotype assembly using matrix completion
PlOS One, March 26, 2020
Majidian S, Kahaei MH
Haplotype Assembly Using Manifold Optimization and Error Correction Mechanism
IEEE Signal Processing Letters, April 11, 2019
Mohades MM, Majidian S, Kahaei MH