Person:
Szalay, Tamas

Profile Picture

Email Address

AA Acceptance Date

Birth Date

Research Projects

Organizational Units

Job Title

Last Name

Szalay

First Name

Tamas

Name

Szalay, Tamas
Author's Publications: search.filters.isAuthorOfPublication.82ab9baa-d82c-41e6-9140-b21b3e4d1070

Search Results

Now showing 1 - 4 of 4
  • Thumbnail Image
    Publication
    Thermal Motion of DNA in an MspA Pore
    (Elsevier BV, 2015) Lu, Bo; Fleming, Stephen Jordan; Szalay, Tamas; Golovchenko, Jene
  • Thumbnail Image
    Publication
    De novo sequencing and variant calling with nanopores using PoreSeq
    (Nature Publishing Group, 2015) Szalay, Tamas; Golovchenko, Jene
    The single-molecule accuracy of nanopore sequencing has been an area of rapid academic and commercial advancement, but remains challenging for the de novo analysis of genomes. We introduce here a novel algorithm for the error correction of nanopore data, utilizing statistical models of the physical system in order to obtain high accuracy de novo sequences at a range of coverage depths. We demonstrate the technique by sequencing M13 bacteriophage DNA to 99% accuracy at moderate coverage as well as its use in an assembly pipeline by sequencing E. coli and DNA at a range of coverages. We also show the algorithm’s ability to accurately classify sequence variants at far lower coverage than existing methods.
  • Thumbnail Image
    Publication
    Electrical pulse fabrication of graphene nanopores in electrolyte solution
    (AIP Publishing, 2015) Kuan, Aaron; Lu, Bo; Xie, Ping; Szalay, Tamas; Golovchenko, Jene
    Nanopores in graphenemembranes can potentially offer unprecedented spatial resolution for single molecule sensing, but their fabrication has thus far been difficult, poorly scalable, and prone to contamination. We demonstrate an in-situfabrication method that nucleates and controllably enlarges nanopores in electrolyte solution by applying ultra-short, high-voltage pulses across the graphenemembrane. This method can be used to rapidly produce graphenenanopores with subnanometer size accuracy in an apparatus free of nanoscale beams or tips.
  • No Thumbnail Available
    Publication
    Improved Analysis of Nanopore Sequence Data and Scanning Nanopore Techniques
    (2016-05-10) Szalay, Tamas; Golovchenko, Jene A.; Manoharan, Vinothan N.; Burns, Michael M.; Protopapas, Pavlos
    The field of nanopore research has been driven by the need to inexpensively and rapidly sequence DNA. In order to help realize this goal, this thesis describes the PoreSeq algorithm that identifies and corrects errors in real-world nanopore sequencing data and improves the accuracy of \textit{de novo} genome assembly with increasing coverage depth. The approach relies on modeling the possible sources of uncertainty that occur as DNA advances through the nanopore and then using this model to find the sequence that best explains multiple reads of the same region of DNA. PoreSeq increases nanopore sequencing read accuracy of M13 bacteriophage DNA from 85\% to 99\% at 100X coverage. We also use the algorithm to assemble \textit{E. coli} with 30X coverage and the $\lambda$ genome at a range of coverages from 3X to 50X. Additionally, we classify sequence variants at an order of magnitude lower coverage than is possible with existing methods. This thesis also reports preliminary progress towards controlling the motion of DNA using two nanopores instead of one. The speed at which the DNA travels through the nanopore needs to be carefully controlled to facilitate the detection of individual bases. A second nanopore in close proximity to the first could be used to slow or stop the motion of the DNA in order to enable a more accurate readout. The fabrication process for a new pyramidal nanopore geometry was developed in order to facilitate the positioning of the nanopores. This thesis demonstrates that two of them can be placed close enough to interact with a single molecule of DNA, which is a prerequisite for being able to use the driving force of the pores to exert fine control over the motion of the DNA. Another strategy for reading the DNA is to trap it completely with one pore and to move the second nanopore instead. To that end, this thesis also shows that a single strand of immobilized DNA can be captured in a scanning nanopore and examined for a full hour, with data from many scans at many different voltages obtained in order to detect a bound protein placed partway along the molecule.