Beyond undergraduate FM-index

The original FM-index paper. Ferragina, P., & Manzini, G. (2000, November). Opportunistic data structures with applications. In Proceedings 41st annual symposium on foundations of computer science (pp. 390-398). IEEE.

An O(r)-space FM-index by storing RLEBWT. Mäkinen, V., & Navarro, G. (2004, August). Run-length FM-index. In Proc. DIMACS Workshop:“The Burrows-Wheeler Transform: Ten Years Later”(Aug. 2004) (pp. 17-19).

An O(r)-space “optimal-time” FM-index with efficient querying of runny permutations. Nishimoto, T., & Tabei, Y. (2020). Optimal-time queries on BWT-runs compressed indexes. arXiv preprint arXiv:2006.05104.

Space-efficient constrution of the BWT with prefix-free parsing. Boucher, C., Gagie, T., Kuhnle, A., Langmead, B., Manzini, G., & Mun, T. (2019). Prefix-free parsing for building big BWTs. Algorithms for Molecular Biology, 14(1), 13.

A review of generalization of the BWT to collection of strings. Cenzato, D., & Lipták, Z. (2024). A survey of BWT variants for string collections. Bioinformatics, 40(7), btae333.

Getting rid of $ in the BWT, for the sake of mathematical beauty. Mantaci, S., Restivo, A., Rosone, G., & Sciortino, M. (2007). An extension of the Burrows–Wheeler transform. Theoretical Computer Science, 387(3), 298-312.

Using the BWT to represent kmer sets, through masked-superstrings. Sladký, O., Veselý, P., & Břinda, K. (2026). FroM Superstring to Indexing: a space-efficient index for unconstrained k-mer sets using the Masked Burrows-Wheeler Transform (MBWT). Bioinformatics Advances, 6(1), vbaf290.

Using the BWT to represent kmer sets, through de Bruijn graphs. Alanko, J. N., Puglisi, S. J., & Vuohtoniemi, J. (2023). Small searchable κ-spectra via subset rank queries on the spectral burrows-wheeler transform. In SIAM Conference on Applied and Computational Discrete Algorithms (ACDA23) (pp. 225-236). Society for Industrial and Applied Mathematics.

Positional variant of the BWT for haplotypes queries. Durbin, R. (2014). Efficient haplotype matching and storage using the positional Burrows–Wheeler transform (PBWT). Bioinformatics, 30(9), 1266-1272.

Graph variant of the BWT for haplotypes queries. Novak, A. M., Garrison, E., & Paten, B. (2017). A graph extension of the positional Burrows–Wheeler transform and its applications. Algorithms for Molecular Biology, 12(1), 18.

A review of BWT for pangenomics. Baaijens, J. A., Bonizzoni, P., Boucher, C., Della Vedova, G., Pirola, Y., Rizzi, R., & Sirén, J. (2022). Computational graph pangenomics: a tutorial on data structures and their applications. Natural computing, 21(1), 81-108.