Author

Fadel Berakdar

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Biology Disciplines

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Bioinformatics· 1

Signature Assays, Organisms & Methods

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Assay:bulk RNA-seq· 1 Approach:deep learning· 1 Organism:human· 1 Approach:transformer / foundation model· 1 Research Focus:variant calling· 1

Frequent Co-Authors

Mehrzad SamadiiD· 1 shared Pankaj VatsiD· 1 shared Thomas D. WuiD· 1 shared Tong Zhu· 1 shared

Activity by Year

2026-2026 · peak 1/yr

Co-Author Collaboration Network

4 top collaborators · 6 mutual co-author links

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1 shared paperBioinformatics

Mehrzad SamadiORCID

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1 paper

Recent·Most cited

DeepSAP: Improved RNA-Seq Alignment by Integrating Transcriptome Guidance with Transformer-Based Splice Junction Scoring

Fadel Berakdar, Thomas D. Wu, Tong Zhu, Mehrzad Samadi, Pankaj Vats

DeepSAP improves RNA-seq alignment by combining transcriptome-guided alignment with a transformer-based model for splice junction scoring, achieving the highest F1 score on simulated datasets.

Genome biology · May 9, 2026Peer-reviewedBioinformatics