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Nat Commun July 2023 PMID 37422489

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

Peng Ni, Fan Nie, Zeyu Zhong, Jinrui Xu, Neng Huang, Jun Zhang, Haochen Zhao, You Zou, Yuanfeng Huang, Jinchen Li, Chuan-Le Xiao, Feng Luo, Jianxin Wang

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22
Peak: 15 in Mar 2022
across 2 sources since Mar 2022

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Mar 2022 – Oct 2023

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AI synopsis

What people are saying

Several discussions celebrate the innovative aspects of combining deep learning with PacBio sequencing, citing increased accuracy and robustness, as well as potential for broader applications in methylation detection. The tone is generally positive and future-focused, emphasizing the research's importance and potential impact on genomics advancements.

AgreementModerate agreement

Most discussions express support or approval of the publication, emphasizing the usefulness of new tools and methods.

InterestHigh interest

The discussions show high interest, with many posts highlighting the potential of the sequencing techniques and deep-learning approaches.

EngagementModerate engagement

Posts demonstrate active engagement by referencing specific methods, tools, and their implications, such as mention of high accuracy and robustness.

ImpactModerate impact

While not all posts are equally detailed, there is a recognition that this research could significantly influence future genomic studies.

Abstract in brief

  • Long single-molecular sequencing technologies like PacBio CCS and nanopore sequencing are effective for detecting DNA 5-methylcytosine (5mCpG) in repetitive genomic areas, but current PacBio methods lack accuracy.
  • A new deep-learning method called ccsmeth improves the detection of 5mCpGs with PacBio CCS, achieving high accuracy (0.90) and excellent correlation (>0.90) with traditional bisulfite sequencing.
  • Additionally, a Nextflow pipeline, ccsmethphase, enables haplotype-aware methylation detection and has been tested on sequencing a Chinese family trio, showcasing its robustness and accuracy.
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Javier Santoyo
@jsantoyo · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #LongRead #HiFi @PacBio #Sequencing https://t.co/wsV9HLHFHj @biorxivpreprint

Mar 1, 2022 · 13 likes · 4 shares · 6,107 followers View post →
bioRxiv
@biorxivpreprint · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI1bfc #bioRxiv

Mar 1, 2022 · 5 likes · 4 shares · 136,955 followers View post →
Eduardo Eyras
@EduEyras · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/k8seNtMsHF

Mar 11, 2022 · 2 likes · 2,363 followers View post →
bioRxiv Bioinfo
@biorxiv_bioinfo · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/y4kn3Pf253 #biorxiv_bioinfo

Mar 1, 2022 · 1 like · 18,072 followers View post →
GenomeMining
@MiningGenome · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/5LmLtlefAB High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing https://t.co/hLLBozbNmP #Genomics

Feb 18, 2023 · 1 like · 1,268 followers View post →
Qian Cheng
@sgqcheng · X

New Bioinformatics tools using #deeplearning: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing ⁦@NatureComms⁩ #BiotechNatureComms #PacBio #longreadsequencing #5mCpGs https://t.co/q7avo8pccL

Jul 9, 2023 · 1 like · 601 followers View post →

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Qian Cheng
@sgqcheng · X

New Bioinformatics tools using #deeplearning: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing ⁦@NatureComms⁩ #BiotechNatureComms #PacBio #longreadsequencing #5mCpGs https://t.co/q7avo8pccL

Jul 9, 2023 · 1 like · 601 followers View post →
Nanopore_research
@Nanoporepapers_ · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing Follow us :) https://t.co/nzJQgDedDe

Jul 9, 2023 · 100 followers View post →
Long-read metagenomics-Papers
@LR_metagenomics · X

PacBio: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/lxEVaPZJv3

Jul 9, 2023 · 1 like · 368 followers View post →
Long-read metagenomics-Papers
@LR_metagenomics · X

nanopore: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XLOJC3nZ87

Jul 9, 2023 · 368 followers View post →
GenomeMining
@MiningGenome · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/5LmLtlefAB High contiguity de novo genome sequence assembly of Trifoliate yam (Dioscorea dumetorum) using long read sequencing https://t.co/hLLBozbNmP #Genomics

Feb 18, 2023 · 1 like · 1,268 followers View post →
bioRxivbot
@BiorxivB · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/gencty4Sv6

Feb 17, 2023 · 21 followers View post →
Eduardo Eyras
@EduEyras · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/k8seNtMsHF

Mar 11, 2022 · 2 likes · 2,363 followers View post →
Jon Seddon
@JonSeddon2 · X

RT @biorxivpreprint: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI…

Mar 2, 2022 · 4 shares · 210 followers View post →
Emanuel ebioman@genomic.social
@ebioman · X

RT @jsantoyo: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #…

Mar 2, 2022 · 4 shares · 219 followers View post →
felix
@felixlee0608 · X

RT @jsantoyo: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #…

Mar 2, 2022 · 4 shares · 28 followers View post →
Helio Rocha
@_elioRocha · X

#bioRxiv DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing #bioinfo https://t.co/vHuK9zNERn

Mar 2, 2022 · 609 followers View post →
k a y l e e
@Kaylee__Mueller · X

RT @jsantoyo: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #…

Mar 1, 2022 · 4 shares · 2,577 followers View post →
Taco Jesse
@TJesse62 · X

RT @jsantoyo: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #…

Mar 1, 2022 · 4 shares · 1,730 followers View post →
Javier Santoyo
@jsantoyo · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing. #5mC #MethylationPhasing #LongRead #HiFi @PacBio #Sequencing https://t.co/wsV9HLHFHj @biorxivpreprint

Mar 1, 2022 · 13 likes · 4 shares · 6,107 followers View post →
Niki Newell
@NikiNewell7 · X

RT @biorxivpreprint: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI…

Mar 1, 2022 · 4 shares · 223 followers View post →
Jennifer Malsom
@J_Malsom · X

RT @biorxivpreprint: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI…

Mar 1, 2022 · 4 shares · 750 followers View post →
CompBiolPapers
@CompBiolPapers · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing [NEW RESULTS] https://t.co/LpUPeSLQRX

Mar 1, 2022 · 1,780 followers View post →
k a y l e e
@Kaylee__Mueller · X

RT @biorxivpreprint: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI…

Mar 1, 2022 · 4 shares · 2,577 followers View post →
Long-read metagenomics-Papers
@LR_metagenomics · X

nanopore: DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/3nv0Bteqoq

Mar 1, 2022 · 368 followers View post →
bioRxiv Bioinfo
@biorxiv_bioinfo · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/y4kn3Pf253 #biorxiv_bioinfo

Mar 1, 2022 · 1 like · 18,072 followers View post →
bioRxiv
@biorxivpreprint · X

DNA 5-methylcytosine detection and methylation phasing using PacBio circular consensus sequencing https://t.co/XYbxVI1bfc #bioRxiv

Mar 1, 2022 · 5 likes · 4 shares · 136,955 followers View post →