Continuous base identification for single-molecule nanopore DNA sequencing.

By James Clarke, Hai‐Chen Wu, Lakmal Jayasinghe, Alpesh Patel, Stuart J. Reid, H. Bayley. Nature Nanotechnology, 2009

1,736 citations recorded by the source corpus.

Subfields: Biomedical Engineering, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/5c8c84ac39a3a1d63e96b2f1b540792c32bb5c07

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Citations in the corpus

Utilization of next-generation sequencing platforms in plant genomics and genetic variant discovery (2010, methodology): “2008) for the real-time detection of DNA bases (Clarke et al. 2009).”
Next generation sequencing technology: Advances and applications. (2014, methodology): “, using the natural pore forming protein alphahemolysin [19] or manufactured solid state pores [20,21].”
Nanotechnology for Early Cancer Detection (2010, background): “Various studies have been conducted on nanopores for sensing biomolecules including DNA [131-133], proteins [134,135], ions [136,137], and drug molecules [138].”
RATT: Rapid Annotation Transfer Tool (2011, background): “Second generation technologies are drastically reducing the cost of DNA sequencing, while dramatically increasing throughput (1), a trend that is likely to continue (2).”
Mapping single molecule sequencing reads using basic local alignment with successive refinement (BLASR): application and theory (2012, methodology): “Other SMS methods have been proposed using detection of cleaved bases that pass through a protein nanopore [25], and identifying bases that have translocated through a nanopore fabricated in a graphene membrane [27].”
High‐throughput DNA sequencing – concepts and limitations (2010, methodology): “[18], Oxford Nanopore’s BASE technology [14] and, recently, IBM’s proposal of silicon-based nanopores [78].”
Nanopore-based Fourth-generation DNA Sequencing Technology (2015, background): “demonstrated that a-HL with a covalently-attached adapter molecule can be used to continuously identify unlabeled single nucleotides (dAMP, dCMP, dGMP, and dTMP) through nanopore-based resistive current measurements [59].”
Third generation sequencing: technology and its potential impact on evolutionary biodiversity research (2016, background): “Negatively charged DNA can be forced by this gradient to pass the nanopore and each nucleotide passing the pore characteristically decreases the amplitude of the ion current, which can be detected by a sensor (Branton et al., 2008; Clarke et al., 2009).”
LUMPY: a probabilistic framework for structural variant discovery (2012, methodology): “The read-pair module maps the output of a paired-end sequence alignment algorithm such as NOVOALIGN (C Hercus, unpublished) [8] or BWA [9], the split-read module maps the output of a split-read sequence alignment algorithm (for example, YAHA [10], BWA-SW [11], or BWA-MEM [5]), and the generic…”
Haplotype-based variant detection from short-read sequencing (2012, methodology): “We then describe our implementation of this framework in a haplotype-based variant detector, FreeBayes.”
Annotating non-coding regions of the genome (2010, background): “Although second-generation platforms sacrifice read length to reduce cost and increase coverage, some third-generation platforms promise to generate very long reads that would span repetitive regions and make assembly much easie”