Yu YW - Search Results

1

On Minimizers and Convolutional Filters: Theoretical Connections and Applications to Genome Analysis.

Yu YW. Yu YW. J Comput Biol. 2024 May;31(5):381-395. doi: 10.1089/cmb.2024.0483. Epub 2024 Apr 30. J Comput Biol. 2024. PMID: 38687333

2

flopp: Extremely Fast Long-Read Polyploid Haplotype Phasing by Uniform Tree Partitioning.

Shaw J, Yu YW. Shaw J, et al. Among authors: yu yw. J Comput Biol. 2022 Feb;29(2):195-211. doi: 10.1089/cmb.2021.0436. Epub 2022 Jan 17. J Comput Biol. 2022. PMID: 35041529 Free PMC article.

3

Joker de Bruijn: Covering k-Mers Using Joker Characters.

Orenstein Y, Yu YW, Berger B. Orenstein Y, et al. Among authors: yu yw. J Comput Biol. 2018 Nov;25(11):1171-1178. doi: 10.1089/cmb.2018.0032. Epub 2018 Aug 17. J Comput Biol. 2018. PMID: 30117747 Free PMC article.

4

Image-centric compression of protein structures improves space savings.

Staniscia L, Yu YW. Staniscia L, et al. Among authors: yu yw. BMC Bioinformatics. 2023 Nov 21;24(1):437. doi: 10.1186/s12859-023-05570-z. BMC Bioinformatics. 2023. PMID: 37990290 Free PMC article.

5

Mora: abundance aware metagenomic read re-assignment for disentangling similar strains.

Zheng A, Shaw J, Yu YW. Zheng A, et al. Among authors: yu yw. BMC Bioinformatics. 2024 Apr 23;25(1):161. doi: 10.1186/s12859-024-05768-9. BMC Bioinformatics. 2024. PMID: 38649836 Free PMC article.

6

Theory of local k-mer selection with applications to long-read alignment.

Shaw J, Yu YW. Shaw J, et al. Among authors: yu yw. Bioinformatics. 2022 Oct 14;38(20):4659-4669. doi: 10.1093/bioinformatics/btab790. Bioinformatics. 2022. PMID: 36124869 Free PMC article.

7

Fast and robust metagenomic sequence comparison through sparse chaining with skani.

Shaw J, Yu YW. Shaw J, et al. Among authors: yu yw. Nat Methods. 2023 Nov;20(11):1661-1665. doi: 10.1038/s41592-023-02018-3. Epub 2023 Sep 21. Nat Methods. 2023. PMID: 37735570 Free PMC article.

8

Proving sequence aligners can guarantee accuracy in almost O(m log n) time through an average-case analysis of the seed-chain-extend heuristic.

Shaw J, Yu YW. Shaw J, et al. Among authors: yu yw. Genome Res. 2023 Jul;33(7):1175-1187. doi: 10.1101/gr.277637.122. Epub 2023 Mar 29. Genome Res. 2023. PMID: 36990779 Free PMC article.

9

Levenshtein Distance, Sequence Comparison and Biological Database Search.

Berger B, Waterman MS, Yu YW. Berger B, et al. Among authors: yu yw. IEEE Trans Inf Theory. 2021 Jun;67(6):3287-3294. doi: 10.1109/tit.2020.2996543. Epub 2020 May 21. IEEE Trans Inf Theory. 2021. PMID: 34257466 Free PMC article.

10

HyperMinHash: MinHash in LogLog space.

Yu YW, Weber GM. Yu YW, et al. IEEE Trans Knowl Data Eng. 2022 Jan;34(1):328-339. doi: 10.1109/tkde.2020.2981311. Epub 2020 Mar 17. IEEE Trans Knowl Data Eng. 2022. PMID: 38288326 Free PMC article.

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