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Briefings in Bioinformatics|April 26, 2023
A survey on algorithms to characterize transcription factor binding sitesManuel Tognon, Rosalba Giugno, Luca PinelloBriefings in Bioinformatics|July 24, 2025
Benchmarking transcription factor binding site prediction models: a comparative analysis on synthetic and biological dataManuel Tognon, Alisa Kumbara, Andrea Betti, et al.Plos Computational Biology|September 27, 2021
GRAFIMO: Variant and haplotype aware motif scanning on pangenome graphsManuel Tognon, Vincenzo Bonnici, Erik Garrison, et al.Biorxiv : the Preprint Server for Biology|January 7, 2026
CRISPR-HAWK: Haplotype- and Variant-aware guide design toolkit for CRISPR-CasAlisa Kumbara, Manuel Tognon, Giulia Carone, et al.Medrxiv : the Preprint Server for Health Sciences|September 21, 2023
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantificationJayoung Ryu, Sam Barkal, Tian Yu, et al.Nature Genetics|December 15, 2022
Human genetic diversity alters off-target outcomes of therapeutic gene editingSamuele Cancellieri, Jing Zeng, Linda Yingqi Lin, et al.Nature Genetics|April 24, 2024
Joint genotypic and phenotypic outcome modeling improves base editing variant effect quantificationJayoung Ryu, Sam Barkal, Tian Yu, et al.Pageof 1