From squiggle to basepair: computational approaches for improving nanopore sequencing read accuracy

FJ Rang, WP Kloosterman, J de Ridder - Genome biology, 2018 - Springer
Nanopore sequencing is a rapidly maturing technology delivering long reads in real time on
a portable instrument at low cost. Not surprisingly, the community has rapidly taken up this …

Beyond assembly: the increasing flexibility of single-molecule sequencing technology

PW Hook, W Timp - Nature Reviews Genetics, 2023 - nature.com
The maturation of high-throughput short-read sequencing technology over the past two
decades has shaped the way genomes are studied. Recently, single-molecule, long-read …

Reading the primary structure of a protein with 0.07 nm3 resolution using a subnanometre-diameter pore

E Kennedy, Z Dong, C Tennant, G Timp - Nature nanotechnology, 2016 - nature.com
The primary structure of a protein consists of a sequence of amino acids and is a key factor
in determining how a protein folds and functions. However, conventional methods for …

Nanopore sequencing detects structural variants in cancer

AL Norris, RE Workman, Y Fan… - Cancer biology & …, 2016 - Taylor & Francis
Despite advances in sequencing, structural variants (SVs) remain difficult to reliably detect
due to the short read length (< 300 bp) of 2nd generation sequencing. Not only do the reads …

Emerging tools for studying single entity electrochemistry

Y Wang, X Shan, N Tao - Faraday discussions, 2016 - pubs.rsc.org
Electrochemistry studies charge transfer and related processes at various microscopic
structures (atomic steps, islands, pits and kinks on electrodes), and mesoscopic materials …

Single-molecule protein identification by sub-nanopore sensors

M Kolmogorov, E Kennedy, Z Dong… - PLoS computational …, 2017 - journals.plos.org
Recent advances in top-down mass spectrometry enabled identification of intact proteins,
but this technology still faces challenges. For example, top-down mass spectrometry suffers …

Biological computation and computational biology: survey, challenges, and discussion

Z Chelly Dagdia, P Avdeyev, MS Bayzid - Artificial Intelligence Review, 2021 - Springer
Biological computation involves the design and development of computational techniques
inspired by natural biota. On the other hand, computational biology involves the …

Analyte sequencing with nanopores

J Gundlach, IM Derrington, MD Collins - US Patent 9,588,079, 2017 - Google Patents
Provided herein are methods and systems pertaining to sequencing units of analytes using
nanopores. In general, arresting constructs are used to modify an analyte such that the …

A scalable discrete-time integrated CMOS readout array for nanopore based DNA sequencing

Y Dawji, M Habibi, E Ghafar-Zadeh… - IEEE Access, 2021 - ieeexplore.ieee.org
This paper introduces a high-speed mixed-signal readout array in 130-nm CMOS for the
amplification and digitization of picoampere-range signals. Its design is inspired by the …

Amino acid discrimination in a nanopore and the feasibility of sequencing peptides with a tandem cell and exopeptidase

G Sampath - Rsc Advances, 2015 - pubs.rsc.org
In polymer sequencing with a nanopore multiple discriminators may be used to distinguish
among more monomers than usual. This leads to a proposal to sequence peptides using a …