Parameswaran S - Search Results

1

Fast nanopore sequencing data analysis with SLOW5.

Gamaarachchi H, Samarakoon H, Jenner SP, Ferguson JM, Amos TG, Hammond JM, Saadat H, Smith MA, Parameswaran S, Deveson IW. Gamaarachchi H, et al. Among authors: parameswaran s. Nat Biotechnol. 2022 Jul;40(7):1026-1029. doi: 10.1038/s41587-021-01147-4. Epub 2022 Jan 3. Nat Biotechnol. 2022. PMID: 34980914 Free PMC article.

2

Cache Friendly Optimisation of de Bruijn Graph Based Local Re-Assembly in Variant Calling.

Gamaarachchi H, Bayat A, Gaeta B, Parameswaran S. Gamaarachchi H, et al. Among authors: parameswaran s. IEEE/ACM Trans Comput Biol Bioinform. 2020 Jul-Aug;17(4):1125-1133. doi: 10.1109/TCBB.2018.2881975. Epub 2018 Nov 19. IEEE/ACM Trans Comput Biol Bioinform. 2020. PMID: 30452377

3

Featherweight long read alignment using partitioned reference indexes.

Gamaarachchi H, Parameswaran S, Smith MA. Gamaarachchi H, et al. Among authors: parameswaran s. Sci Rep. 2019 Mar 13;9(1):4318. doi: 10.1038/s41598-019-40739-8. Sci Rep. 2019. PMID: 30867495 Free PMC article.

4

GPU accelerated adaptive banded event alignment for rapid comparative nanopore signal analysis.

Gamaarachchi H, Lam CW, Jayatilaka G, Samarakoon H, Simpson JT, Smith MA, Parameswaran S. Gamaarachchi H, et al. Among authors: parameswaran s. BMC Bioinformatics. 2020 Aug 5;21(1):343. doi: 10.1186/s12859-020-03697-x. BMC Bioinformatics. 2020. PMID: 32758139 Free PMC article.

5

Flexible and efficient handling of nanopore sequencing signal data with slow5tools.

Samarakoon H, Ferguson JM, Jenner SP, Amos TG, Parameswaran S, Gamaarachchi H, Deveson IW. Samarakoon H, et al. Among authors: parameswaran s. Genome Biol. 2023 Apr 6;24(1):69. doi: 10.1186/s13059-023-02910-3. Genome Biol. 2023. PMID: 37024927 Free PMC article.

6

Efficient real-time selective genome sequencing on resource-constrained devices.

Shih PJ, Saadat H, Parameswaran S, Gamaarachchi H. Shih PJ, et al. Among authors: parameswaran s. Gigascience. 2022 Dec 28;12:giad046. doi: 10.1093/gigascience/giad046. Epub 2023 Jul 3. Gigascience. 2022. PMID: 37395631 Free PMC article.

7

Efficient end-to-end long-read sequence mapping using minimap2-fpga integrated with hardware accelerated chaining.

Liyanage K, Samarakoon H, Parameswaran S, Gamaarachchi H. Liyanage K, et al. Among authors: parameswaran s. Sci Rep. 2023 Nov 17;13(1):20174. doi: 10.1038/s41598-023-47354-8. Sci Rep. 2023. PMID: 37978244 Free PMC article.

8

Simulation of nanopore sequencing signal data with tunable parameters.

Gamaarachchi H, Ferguson J, Samarakoon H, Liyanage K, Parameswaran S, Deveson I. Gamaarachchi H, et al. Among authors: parameswaran s. Genome Res. 2024 May 1:gr.278730.123. doi: 10.1101/gr.278730.123. Online ahead of print. Genome Res. 2024. PMID: 38692839 Free article.

9

Improved VCF normalization for accurate VCF comparison.

Bayat A, Gaëta B, Ignjatovic A, Parameswaran S. Bayat A, et al. Among authors: parameswaran s. Bioinformatics. 2017 Apr 1;33(7):964-970. doi: 10.1093/bioinformatics/btw748. Bioinformatics. 2017. PMID: 27993787

10

Fast Short Read De-Novo Assembly Using Overlap-Layout-Consensus Approach.

Bayat A, Deshpande NP, Wilkins MR, Parameswaran S. Bayat A, et al. Among authors: parameswaran s. IEEE/ACM Trans Comput Biol Bioinform. 2020 Jan-Feb;17(1):334-338. doi: 10.1109/TCBB.2018.2875479. Epub 2018 Oct 11. IEEE/ACM Trans Comput Biol Bioinform. 2020. PMID: 30307874

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