Xiao CL - Search Results

1

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: xiao cl. Nat Commun. 2023 Jul 8;14(1):4054. doi: 10.1038/s41467-023-39784-9. Nat Commun. 2023. PMID: 37422489 Free PMC article.

2

MethSMRT: an integrative database for DNA N6-methyladenine and N4-methylcytosine generated by single-molecular real-time sequencing.

Ye P, Luan Y, Chen K, Liu Y, Xiao C, Xie Z. Ye P, et al. Nucleic Acids Res. 2017 Jan 4;45(D1):D85-D89. doi: 10.1093/nar/gkw950. Epub 2016 Oct 18. Nucleic Acids Res. 2017. PMID: 27924023 Free PMC article.

3

MECAT: fast mapping, error correction, and de novo assembly for single-molecule sequencing reads.

Xiao CL, Chen Y, Xie SQ, Chen KN, Wang Y, Han Y, Luo F, Xie Z. Xiao CL, et al. Nat Methods. 2017 Nov;14(11):1072-1074. doi: 10.1038/nmeth.4432. Epub 2017 Sep 18. Nat Methods. 2017. PMID: 28945707

4

N⁶-Methyladenine DNA Modification in the Human Genome.

Xiao CL, Zhu S, He M, Chen D, Zhang Q, Chen Y, Yu G, Liu J, Xie SQ, Luo F, Liang Z, Wang DP, Bo XC, Gu XF, Wang K, Yan GR. Xiao CL, et al. Mol Cell. 2018 Jul 19;71(2):306-318.e7. doi: 10.1016/j.molcel.2018.06.015. Epub 2018 Jul 12. Mol Cell. 2018. PMID: 30017583 Free article.

5

N6-Methyladenine DNA modification in Xanthomonas oryzae pv. oryzicola genome.

Xiao CL, Xie SQ, Xie QB, Liu ZY, Xing JF, Ji KK, Tao J, Dai LY, Luo F. Xiao CL, et al. Sci Rep. 2018 Nov 2;8(1):16272. doi: 10.1038/s41598-018-34559-5. Sci Rep. 2018. PMID: 30389999 Free PMC article.

6

DeepSignal: detecting DNA methylation state from Nanopore sequencing reads using deep-learning.

Ni P, Huang N, Zhang Z, Wang DP, Liang F, Miao Y, Xiao CL, Luo F, Wang J. Ni P, et al. Among authors: xiao cl. Bioinformatics. 2019 Nov 1;35(22):4586-4595. doi: 10.1093/bioinformatics/btz276. Bioinformatics. 2019. PMID: 30994904

7

Detection of DNA base modifications by deep recurrent neural network on Oxford Nanopore sequencing data.

Liu Q, Fang L, Yu G, Wang D, Xiao CL, Wang K. Liu Q, et al. Among authors: xiao cl. Nat Commun. 2019 Jun 4;10(1):2449. doi: 10.1038/s41467-019-10168-2. Nat Commun. 2019. PMID: 31164644 Free PMC article.

8

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: xiao cl. Nat Commun. 2021 Jan 4;12(1):60. doi: 10.1038/s41467-020-20236-7. Nat Commun. 2021. PMID: 33397900 Free PMC article.

9

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: xiao cl. Nat Commun. 2021 Oct 13;12(1):5976. doi: 10.1038/s41467-021-26278-9. Nat Commun. 2021. PMID: 34645826 Free PMC article.

10

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. 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.

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