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Mapping DNA replication with nanopore sequencing

https://doi.org/10.1101/426858
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What this work says

Outgoing claims: the papers this work cites, builds on, or argues with.

inferredcites →https://doi.org/10.1002/smtd.201800146openalex-snapshot
High‐Throughput Optical Mapping of Replicating DNA
inferredcites →https://doi.org/10.1006/jmbi.2000.3930openalex-snapshot
Replication fork density increases during DNA synthesis in X. laevis egg extracts11Edited by M. Yaniv
inferredcites →https://doi.org/10.1016/j.ymeth.2012.05.006openalex-snapshot
Visualising chromosomal replication sites and replicons in mammalian cells
inferredcites →https://doi.org/10.1038/27001openalex-snapshot
A Mec1- and Rad53-dependent checkpoint controls late-firing origins of DNA replication
inferredcites →https://doi.org/10.1038/27007openalex-snapshot
Regulation of DNA-replication origins during cell-cycle progression
inferredcites →https://doi.org/10.1038/282039a0openalex-snapshot
Isolation and characterisation of a yeast chromosomal replicator
inferredcites →https://doi.org/10.1038/nature01900openalex-snapshot
S-phase checkpoint proteins Tof1 and Mrc1 form a stable replication-pausing complex
inferredcites →https://doi.org/10.1038/ncb1358openalex-snapshot
Genomic mapping of single-stranded DNA in hydroxyurea-challenged yeasts identifies origins of replication
inferredcites →https://doi.org/10.1038/nmeth.4184openalex-snapshot
Detecting DNA cytosine methylation using nanopore sequencing
inferredcites →https://doi.org/10.1038/nmeth.4189openalex-snapshot
Mapping DNA methylation with high-throughput nanopore sequencing
inferredcites →https://doi.org/10.1038/nsmb.1932openalex-snapshot
Analysis of replication profiles reveals key role of RFC-Ctf18 in yeast replication stress response
inferredcites →https://doi.org/10.1046/j.1365-2443.2002.00559.xopenalex-snapshot
Mapping of early firing origins on a replication profile of budding yeast
inferredcites →https://doi.org/10.1083/jcb.140.6.1285openalex-snapshot
Replicon Clusters Are Stable Units of Chromosome Structure: Evidence That Nuclear Organization Contributes to the Efficient Activation and Propagation of S Phase in Human Cells
inferredcites →https://doi.org/10.1083/jcb.201407004openalex-snapshot
Peaks cloaked in the mist: The landscape of mammalian replication origins
inferredcites →https://doi.org/10.1093/bioinformatics/btp324openalex-snapshot
Fast and accurate short read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btp698openalex-snapshot
Fast and accurate long-read alignment with Burrows–Wheeler transform
inferredcites →https://doi.org/10.1093/bioinformatics/btu555openalex-snapshot
Poretools: a toolkit for analyzing nanopore sequence data
inferredcites →https://doi.org/10.1093/bioinformatics/btv046openalex-snapshot
Analysis of nanopore data using hidden Markov models
inferredcites →https://doi.org/10.1093/bioinformatics/btw569openalex-snapshot
Nanocall: an open source basecaller for Oxford Nanopore sequencing data
inferredcites →https://doi.org/10.1093/bioinformatics/bty841openalex-snapshot
BulkVis: a graphical viewer for Oxford nanopore bulk FAST5 files
inferredcites →https://doi.org/10.1093/gigascience/giy037openalex-snapshot
Chiron: translating nanopore raw signal directly into nucleotide sequence using deep learning
inferredcites →https://doi.org/10.1093/nar/29.7.1433openalex-snapshot
Monitoring S phase progression globally and locally using BrdU incorporation in TK+ yeast strains
inferredcites →https://doi.org/10.1093/nar/gkr982openalex-snapshot
Do replication forks control late origin firing in Saccharomyces cerevisiae?
inferredcites →https://doi.org/10.1093/nar/gng121openalex-snapshot
Reconstitution of an efficient thymidine salvage pathway in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1101/214841openalex-snapshot
Genome-Wide Identification of Early-Firing Human Replication Origins by Optical Replication Mapping
inferredcites →https://doi.org/10.1101/gad.12.18.2956openalex-snapshot
Recovery from DNA replicational stress is the essential function of the S-phase checkpoint pathway
inferredcites →https://doi.org/10.1101/gad.1784309openalex-snapshot
Genome-wide replication profiles indicate an expansive role for Rpd3L in regulating replication initiation timing or efficiency, and reveal genomic loci of Rpd3 function in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1109/icassp.2013.6638947openalex-snapshot
Speech recognition with deep recurrent neural networks
inferredcites →https://doi.org/10.1126/science.1064603openalex-snapshot
Visualization of DNA Replication on Individual Epstein-Barr Virus Episomes
inferredcites →https://doi.org/10.1145/1143844.1143891openalex-snapshot
Connectionist temporal classification
inferredcites →https://doi.org/10.1162/neco.1997.9.8.1735openalex-snapshot
Long Short-Term Memory
inferredcites →https://doi.org/10.1186/1471-2164-15-791openalex-snapshot
Different nucleosomal architectures at early and late replicating origins in Saccharomyces cerevisiae
inferredcites →https://doi.org/10.1371/journal.pone.0178751openalex-snapshot
DeepNano: Deep recurrent neural networks for base calling in MinION nanopore reads

What points at this work

Incoming claims: where this work appears in other papers’ reference lists and arguments.

inferred← citeshttps://doi.org/10.1007/s10577-019-09624-yopenalex-snapshot
Genomic methods for measuring DNA replication dynamics
inferred← citeshttps://doi.org/10.1016/j.biocel.2020.105799openalex-snapshot
Long-read sequencing to understand genome biology and cell function
inferred← citeshttps://doi.org/10.1016/j.ceb.2019.03.003openalex-snapshot
Metazoan DNA replication origins
inferred← citeshttps://doi.org/10.1016/j.tig.2021.11.003openalex-snapshot
A blood drop through the pore: nanopore sequencing in hematology
inferred← citeshttps://doi.org/10.1038/s10038-019-0679-0openalex-snapshot
Recent advances in the detection of base modifications using the Nanopore sequencer
inferred← citeshttps://doi.org/10.1038/s41587-021-01108-xopenalex-snapshot
Nanopore sequencing technology, bioinformatics and applications
inferred← citeshttps://doi.org/10.1042/ebc20190027openalex-snapshot
Latest techniques to study DNA methylation
inferred← citeshttps://doi.org/10.1093/nar/gkad1022openalex-snapshot
Single molecule MATAC-seq reveals key determinants of DNA replication origin efficiency
inferred← citeshttps://doi.org/10.1186/s13059-020-02013-3openalex-snapshot
FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing
inferred← citeshttps://doi.org/10.1186/s13059-020-1935-5openalex-snapshot
Opportunities and challenges in long-read sequencing data analysis
inferred← citeshttps://doi.org/10.1186/s13072-024-00558-2openalex-snapshot
Shedding light on DNA methylation and its clinical implications: the impact of long-read-based nanopore technology
inferred← citeshttps://doi.org/10.3389/fcell.2021.699771openalex-snapshot
Single-Molecule Techniques to Study Chromatin
inferred← citeshttps://doi.org/10.3390/genes10020094openalex-snapshot
On the Interplay of the DNA Replication Program and the Intra-S Phase Checkpoint Pathway
inferred← citeshttps://doi.org/10.3410/f.738031761.793583813openalex-snapshot
Faculty Opinions recommendation of FORK-seq: replication landscape of the Saccharomyces cerevisiae genome by nanopore sequencing.
inferred← citeshttps://doi.org/10.70675/7133a1b8z5ce3z455dzb04dz2dc272ec5a44openalex-snapshot
Genome-Wide Mapping of Human DNA Replication by Optical Replication Mapping Supports a Stochastic Model of Eukaryotic Replication
inferred← citeshttps://doi.org/10.70675/f5a44dd5za4ecz4b2dza1e7z4faae2e6dbc4openalex-snapshot
Quantitative analysis of the regulation of the DNA replication program by the intra-S phase checkpoint in Xenopus embryos
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