Nie F - Search Results

1

NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing data.

Huang N, Xu M, Nie F, Ni P, Xiao CL, Luo F, Wang J. Huang N, et al. Among authors: nie f. Bioinformatics. 2023 Jan 1;39(1):btac824. doi: 10.1093/bioinformatics/btac824. Bioinformatics. 2023. PMID: 36548365 Free PMC article.

2

SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention Mechanism.

Huang N, Nie F, Ni P, Luo F, Wang J. Huang N, et al. Among authors: nie f. IEEE/ACM Trans Comput Biol Bioinform. 2022 Jan-Feb;19(1):614-623. doi: 10.1109/TCBB.2020.3039244. Epub 2022 Feb 3. IEEE/ACM Trans Comput Biol Bioinform. 2022. PMID: 33211664

3

Efficient assembly of nanopore reads via highly accurate and intact error correction.

Chen Y, Nie F, Xie SQ, Zheng YF, Dai Q, Bray T, Wang YX, Xing JF, Huang ZJ, Wang DP, He LJ, Luo F, Wang JX, Liu YZ, Xiao CL. Chen Y, et al. Among authors: nie f. Nat Commun. 2021 Jan 4;12(1):60. doi: 10.1038/s41467-020-20236-7. Nat Commun. 2021. PMID: 33397900 Free PMC article.

4

NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU Networks.

Huang N, Nie F, Ni P, Luo F, Gao X, Wang J. Huang N, et al. Among authors: nie f. Bioinformatics. 2021 Oct 11;37(19):3120-3127. doi: 10.1093/bioinformatics/btab354. Bioinformatics. 2021. PMID: 33973998

5

BlockPolish: accurate polishing of long-read assembly via block divide-and-conquer.

Huang N, Nie F, Ni P, Gao X, Luo F, Wang J. Huang N, et al. Among authors: nie f. Brief Bioinform. 2022 Jan 17;23(1):bbab405. doi: 10.1093/bib/bbab405. Brief Bioinform. 2022. PMID: 34619757

6

Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learning.

Ni P, Huang N, Nie F, Zhang J, Zhang Z, Wu B, Bai L, Liu W, Xiao CL, Luo F, Wang J. Ni P, et al. Among authors: nie f. Nat Commun. 2021 Oct 13;12(1):5976. doi: 10.1038/s41467-021-26278-9. Nat Commun. 2021. PMID: 34645826 Free PMC article.

7

Fec: a fast error correction method based on two-rounds overlapping and caching.

Zhang J, Nie F, Huang N, Ni P, Luo F, Wang J. Zhang J, et al. Among authors: nie f. Bioinformatics. 2022 Sep 30;38(19):4629-4632. doi: 10.1093/bioinformatics/btac565. Bioinformatics. 2022. PMID: 35977383

8

Semi-automated assembly of high-quality diploid human reference genomes.

Jarvis ED, Formenti G, Rhie A, Guarracino A, Yang C, Wood J, Tracey A, Thibaud-Nissen F, Vollger MR, Porubsky D, Cheng H, Asri M, Logsdon GA, Carnevali P, Chaisson MJP, Chin CS, Cody S, Collins J, Ebert P, Escalona M, Fedrigo O, Fulton RS, Fulton LL, Garg S, Gerton JL, Ghurye J, Granat A, Green RE, Harvey W, Hasenfeld P, Hastie A, Haukness M, Jaeger EB, Jain M, Kirsche M, Kolmogorov M, Korbel JO, Koren S, Korlach J, Lee J, Li D, Lindsay T, Lucas J, Luo F, Marschall T, Mitchell MW, McDaniel J, Nie F, Olsen HE, Olson ND, Pesout T, Potapova T, Puiu D, Regier A, Ruan J, Salzberg SL, Sanders AD, Schatz MC, Schmitt A, Schneider VA, Selvaraj S, Shafin K, Shumate A, Stitziel NO, Stober C, Torrance J, Wagner J, Wang J, Wenger A, Xiao C, Zimin AV, Zhang G, Wang T, Li H, Garrison E, Haussler D, Hall I, Zook JM, Eichler EE, Phillippy AM, Paten B, Howe K, Miga KH; Human Pangenome Reference Consortium. Jarvis ED, et al. Among authors: nie f. Nature. 2022 Nov;611(7936):519-531. doi: 10.1038/s41586-022-05325-5. Epub 2022 Oct 19. Nature. 2022. PMID: 36261518 Free PMC article.

9

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing.

Ni P, Nie F, Zhong Z, Xu J, Huang N, Zhang J, Zhao H, Zou Y, Huang Y, Li J, Xiao CL, Luo F, Wang J. Ni P, et al. Among authors: nie f. Nat Commun. 2023 Jul 8;14(1):4054. doi: 10.1038/s41467-023-39784-9. Nat Commun. 2023. PMID: 37422489 Free PMC article.

10

De novo diploid genome assembly using long noisy reads.

Nie F, Ni P, Huang N, Zhang J, Wang Z, Xiao C, Luo F, Wang J. Nie F, et al. Nat Commun. 2024 Apr 5;15(1):2964. doi: 10.1038/s41467-024-47349-7. Nat Commun. 2024. PMID: 38580638 Free PMC article.

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