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Signal-based optical map alignment.

Akdel M, van de Geest H, Schijlen E, van Rijswijck IMH, Smid EJ, Sanchez-Perez G, de Ridder D. Akdel M, et al. PLoS One. 2021 Sep 30;16(9):e0253102. doi: 10.1371/journal.pone.0253102. eCollection 2021. PLoS One. 2021. PMID: 34591846 Free PMC article.

Geometricus represents protein structures as shape-mers derived from moment invariants.

Durairaj J, Akdel M, de Ridder D, van Dijk ADJ. Durairaj J, et al. Among authors: akdel m. Bioinformatics. 2020 Dec 30;36(Suppl_2):i718-i725. doi: 10.1093/bioinformatics/btaa839. Bioinformatics. 2020. PMID: 33381814

PanTools: representation, storage and exploration of pan-genomic data.

Sheikhizadeh S, Schranz ME, Akdel M, de Ridder D, Smit S. Sheikhizadeh S, et al. Among authors: akdel m. Bioinformatics. 2016 Sep 1;32(17):i487-i493. doi: 10.1093/bioinformatics/btw455. Bioinformatics. 2016. PMID: 27587666

Caretta - A multiple protein structure alignment and feature extraction suite.

Akdel M, Durairaj J, de Ridder D, van Dijk ADJ. Akdel M, et al. Comput Struct Biotechnol J. 2020 Apr 6;18:981-992. doi: 10.1016/j.csbj.2020.03.011. eCollection 2020. Comput Struct Biotechnol J. 2020. PMID: 32368333 Free PMC article.

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