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Bioinformatics (Oxford, England)|August 13, 2025
NanoFilter: Enhancing Phasing Performance by Utilizing Highly Consistent INDELs and SNVs in Nanopore SequencingShanming Chen, Fan Nie, Jianxin WangGigascience|June 17, 2025
PISAD: reference-free intraspecies sample anomalies detection tool based on k-mer countingZhantian Xu, Fan Nie, Jianxin WangBioinformatics (Oxford, England)|November 27, 2024
Phasing nanopore genome assembly by integrating heterozygous variations and Hi-C dataJun Zhang, Fan Nie, Feng Luo, et al.IEEE/ACM Transactions on Computational Biology and Bioinformatics|November 19, 2020
SACall: A Neural Network Basecaller for Oxford Nanopore Sequencing Data Based on Self-Attention MechanismNeng Huang, Fan Nie, Peng Ni, et al.Bioinformatics (Oxford, England)|May 11, 2021
NeuralPolish: a novel Nanopore polishing method based on alignment matrix construction and orthogonal Bi-GRU NetworksNeng Huang, Fan Nie, Peng Ni, et al.Briefings in Bioinformatics|October 7, 2021
BlockPolish: accurate polishing of long-read assembly via block divide-and-conquerNeng Huang, Fan Nie, Peng Ni, et al.Bioinformatics (Oxford, England)|August 17, 2022
Fec: a fast error correction method based on two-rounds overlapping and cachingJun Zhang, Fan Nie, Neng Huang, et al.Bioinformatics (Oxford, England)|December 22, 2022
NanoSNP: a progressive and haplotype-aware SNP caller on low-coverage nanopore sequencing dataNeng Huang, Minghua Xu, Fan Nie, et al.Nature Communications|April 5, 2024
De novo diploid genome assembly using long noisy readsFan Nie, Peng Ni, Neng Huang, et al.Nature Communications|October 14, 2021
Genome-wide detection of cytosine methylations in plant from Nanopore data using deep learningPeng Ni, Neng Huang, Fan Nie, et al.Pageof 107