#25 · Genomics
Single-molecule mapping of replication forks, DNA conformations and abasic sites
The common thread is sequencing-based mapping of DNA features at molecular resolution, with computational inference applied to raw or labelled reads. ForkML combines a machine learning method for nanopore reads with multipulse BrdU labelling to map replication forks at single-molecule, kilobase resolution across the human genome. A second preprint detects alternative DNA conformations from Oxford Nanopore long reads after permanganate probing, using logistic regression, random forest, XGBoost and 1D CNN models on raw current data. DEPACE-seq, a published method, maps abasic sites at single-nucleotide resolution and characterises dynamic, long-lived AP landscapes in mammalian genomes. What is new is the shift toward per-molecule and per-nucleotide readouts of replication, DNA structure and lesion states in genomic DNA.
Published papers
DEPACE-seq enables high-fidelity, single-nucleotide-resolution mapping of abasic sites and characterization of dynamic and long-lived AP landscapes in mammalian genomes.
High-fidelity single-nucleotide-resolution mapping of abasic (AP) sites in mammalian genomes remains technically challenging due to low abundance and high backg
Preprints
High-resolution single-molecule replication profiling of the human genome
ForkML, an ML method for nanopore reads, with multipulse BrdU labelling maps replication forks at single-molecule, kilobase resolution across the genome.
Direct detection of alternative DNA conformations with long-read sequencing and machine learning approaches
Uses Oxford Nanopore long-read sequencing with permanganate probing and ML models (logistic regression, random forest, XGBoost, 1D CNN) on raw current data to…
Topic history
| Date | Rank |
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| #25 | |
| #32 | |
| #29 |