Statistical inference for nanopore sequencing with a biased random walk model.

Kevin J Emmett, Jacob K Rosenstein, Jan-Willem van de Meent, Ken L Shepard, Chris H Wiggins

Abstract read

In one paragraph

Article in Biophysical journal, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it

0cells of the map it votes in

1citing papers in PubMed

–field-weighted citation impact

1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

1 citing paper in PubMed.

Wavelet Denoising of High-Bandwidth Nanopore and Ion-Channel Signals.Nano letters · 2019
Article

4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

5 authors.

Kevin J EmmettDepartment of Physics, Columbia University, New York, New York. Electronic address: kje@phys.columbia.edu.

Jacob K RosensteinSchool of Engineering, Brown University, Providence, Rhode Island.

Jan-Willem van de MeentDepartment of Statistics, Columbia University, New York, New York.

Ken L ShepardDepartment of Electrical Engineering, Columbia University, New York, New York.

Chris H WigginsDepartment of Applied Physics and Applied Math, Columbia University, New York, New York.

Funding

Nation Center: Multi-Scale Study- Cellular Networks(RMI)U54CA121852 · NCI · COLUMBIA UNIVERSITY HEALTH SCIENCES · PI CALIFANO, ANDREA · 2005 to 2015

$37.4M

Integrated, multiplexed high-frequency electronic analysis of DNA in nanoporesR01HG006879 · NHGRI · COLUMBIA UNIV NEW YORK MORNINGSIDE · PI SHEPARD, KENNETH L · 2012 to 2014

$1.4M

NCI NIH HHS U54 CA121852NCI NIH HHS U54-CA121852NHGRI NIH HHS R01 HG006879NHGRI NIH HHS R01-HG006879

6 · The paper itself

Abstract

Nanopore sequencing promises long read-lengths and single-molecule resolution, but the stochastic motion of the DNA molecule inside the pore is, as of this writing, a barrier to high accuracy reads. We develop a method of statistical inference that explicitly accounts for this error, and demonstrate that high accuracy (>99%) sequence inference is feasible even under highly diffusive motion by using a hidden Markov model to jointly analyze multiple stochastic reads. Using this model, we place bounds on achievable inference accuracy under a range of experimental parameters.

Indexed as

Models, StatisticalNanoporesDNASequence Analysis, DNADNA

Identifiers

PMID25902425

DOI10.1016/j.bpj.2015.03.013

PMCPMC4407257

What OpenQuestion holds

Textmetadata

Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.