Author

Hassan Nikaein

Sharif University of Technology

Listed by name: these papers carry no ORCID for this author, so different people with the same name may be mixed together.

Biology Disciplines

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Bioinformatics· 2

Signature Assays, Organisms & Methods

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Research Focus:benchmarking· 2 Approach:statistical model· 2 Research Focus:variant calling· 2 Assay:DNA methylation· 1 Organism:E. coli· 1 Organism:human· 1 Assay:long-read sequencing· 1 Research Focus:sequence-to-function modeling· 1

Frequent Co-Authors

Ali Sharifi‐ZarchiiD· 2 shared Afsoon AfzaliD· 1 shared Farzane Rasti· 1 shared Govindarajan Kunde‐RamamoorthyiD· 1 shared Hamidreza Chitsaz· 1 shared Saeedeh Ezzati· 1 shared

Activity by Year

2022-2025 · peak 1/yr

Co-Author Collaboration Network

6 top collaborators · 15 mutual co-author links

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2 shared papersBioinformatics

Ali Sharifi‐ZarchiORCID

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Author profile →

2 papers

Recent·Most cited

ARYANA-BS: Context-Aware Alignment of Bisulfite-Sequencing Reads

Hassan Nikaein, Ali Sharifi‐Zarchi, Afsoon Afzal, Saeedeh Ezzati, Farzane Rasti, Hamidreza Chitsaz, Govindarajan Kunde‐Ramamoorthy

ARYANA-BS improves bisulfite sequencing read alignment by considering DNA methylation patterns, achieving high accuracy and efficiency.

BMC Bioinformatics · Jul 21, 2025Peer-reviewedBioinformatics

Alignment of Single-Molecule Sequencing Reads by Enhancing the Accuracy and Efficiency of Locality-Sensitive Hashing

Hassan Nikaein, Ali Sharifi‐Zarchi

The paper improves the accuracy and efficiency of MinHash for aligning single-molecule sequencing reads by using a single hash function and allowing one sequencing error in seed sequences, outperforming existing aligners on E. coli and human genomes.

bioRxiv · May 15, 2022 · PreprintBioinformatics