SBBD

Paper Registration

1

Select Book

2

Select Paper

3

Fill in paper information

4

Congratulations

Fill in your paper information

English Information

(*) To change the order drag the item to the new position.

Authors
# Name
1 Luísa Penze(l238001@dac.unicamp.br)
2 Lucas Oliveira(lucasperes@students.ic.unicamp.br)
3 Joao Meidanis(meidanis@unicamp.br)

(*) To change the order drag the item to the new position.

Reference
# Reference
1 Chen, Y., Wang, Y., Chen, W., Tan, Z., Song, Y., Human Genome Structural Variation Consortium, Chen, H., and Chong, Z. (2023). Gene Fusion Detection and Charac- terization in Long-Read Cancer Transcriptome Sequencing Data with FusionSeeker. Cancer Research, 83(1):28–33.
2 Davidson, N. (2021). Long read fusion simulation. https://figshare.com/ articles/dataset/Long_Read_Fusion_Simulation/14459007. Ac- cessed: 2024-08-10.
3 Davidson, N. M., Chen, Y., Sadras, T., Ryland, G. L., Blombery, P., Ekert, P. G., G¨ oke, J., and Oshlack, A. (2022). JAFFAL: detecting fusion genes with long-read transcriptome sequencing. Genome Biology, 23(1):10.
4 Denti, L., Khorsand, P., Bonizzoni, P., Hormozdiari, F., and Chikhi, R. (2023). SVDSS: structural variation discovery in hard-to-call genomic regions using sample-specific strings from accurate long reads. Nature Methods, 20(4):550–558.
5 Ferragina, P. and Manzini, G. (2000). Opportunistic data structures with applications. In Proceedings 41st Annual Symposium on Foundations of Computer Science, pages 390–398.
6 Karaoglanoglu, F., Chauve, C., and Hach, F. (2022). Genion, an accurate tool to detect gene fusion from long transcriptomics reads. BMC Genomics, 23(1):129.
7 Khorsand, P., Denti, L., Human Genome Structural Variant Consortium, Bonizzoni, P., Chikhi, R., and Hormozdiari, F. (2021). Comparative genome analysis using sample-specific string detection in accurate long reads. Bioinformatics Advances, 1(1):vbab005.
8 Li, H. (2012). Exploring single-sample SNP and INDEL calling with whole-genome de novo assembly. Bioinformatics, 28(14):1838–1844.
9 Li, H. (2024). BWT construction and search at the terabase scale. Bioinformatics, 40(12):btae717.
10 Liu, Q., Hu, Y., Stucky, A., Fang, L., Zhong, J. F., and Wang, K. (2020). LongGF: com- putational algorithm and software tool for fast and accurate detection of gene fusions by long-read transcriptome sequencing. BMC Genomics, 21(11):793.
11 Qin, Q., Popic, V., Wienand, K., Yu, H., White, E., Khorgade, A., Shin, A., Georgescu, C., Campbell, C. D., Dondi, A., Beerenwinkel, N., Vazquez, F., Al’Khafaji, A. M., and Haas, B. J. (2025). Accurate fusion transcript identification from long- and short-read isoform sequencing at bulk or single-cell resolution. Genome Research, 35(4):967– 986.
12 Wick, R. R. (2018). Badread: Simulation of error-prone long reads. https:// github.com/rrwick/Badread.