Noise reduction methods for nucleic acid and macromolecule sequencing
Abstract
Methods, systems, and devices are disclosed for processing macromolecule sequencing data with substantial noise reduction. In one aspect, a method for reducing noise in a sequential measurement of a macromolecule comprising serial subunits includes cross-correlating multiple measured signals of a physical property of subunits of interest of the macromolecule, the multiple measured signals including the time data associated with the measurement of the signal, to remove or at least reduce signal noise that is not in the same frequency and in phase with the systematic signal contribution of the measured signals.
- Inventors:
- Issue Date:
- Research Org.:
- Los Alamos National Laboratory (LANL), Los Alamos, NM (United States)
- Sponsoring Org.:
- USDOE
- OSTI Identifier:
- 1440025
- Patent Number(s):
- 9965586
- Application Number:
- 14/664,738
- Assignee:
- The Regents of the University of California (Oakland, CA); Los Alamos National Laboratory (Los Alamos, NM)
- Patent Classifications (CPCs):
-
G - PHYSICS G16 - INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS G16B - BIOINFORMATICS, i.e. INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR GENETIC OR PROTEIN-RELATED DATA PROCESSING IN COMPUTATIONAL MOLECULAR BIOLOGY
- DOE Contract Number:
- AC52-06NA25396
- Resource Type:
- Patent
- Resource Relation:
- Patent File Date: 2015 Mar 20
- Country of Publication:
- United States
- Language:
- English
- Subject:
- 59 BASIC BIOLOGICAL SCIENCES
Citation Formats
Schuller, Ivan K., Di Ventra, Massimiliano, and Balatsky, Alexander. Noise reduction methods for nucleic acid and macromolecule sequencing. United States: N. p., 2018.
Web.
Schuller, Ivan K., Di Ventra, Massimiliano, & Balatsky, Alexander. Noise reduction methods for nucleic acid and macromolecule sequencing. United States.
Schuller, Ivan K., Di Ventra, Massimiliano, and Balatsky, Alexander. Tue .
"Noise reduction methods for nucleic acid and macromolecule sequencing". United States. https://www.osti.gov/servlets/purl/1440025.
@article{osti_1440025,
title = {Noise reduction methods for nucleic acid and macromolecule sequencing},
author = {Schuller, Ivan K. and Di Ventra, Massimiliano and Balatsky, Alexander},
abstractNote = {Methods, systems, and devices are disclosed for processing macromolecule sequencing data with substantial noise reduction. In one aspect, a method for reducing noise in a sequential measurement of a macromolecule comprising serial subunits includes cross-correlating multiple measured signals of a physical property of subunits of interest of the macromolecule, the multiple measured signals including the time data associated with the measurement of the signal, to remove or at least reduce signal noise that is not in the same frequency and in phase with the systematic signal contribution of the measured signals.},
doi = {},
journal = {},
number = ,
volume = ,
place = {United States},
year = {2018},
month = {5}
}
Works referenced in this record:
PEGylated Nanographene Oxide for Delivery of Water-Insoluble Cancer Drugs
journal, August 2008
- Liu, Zhuang; Robinson, Joshua T.; Sun, Xiaoming
- Journal of the American Chemical Society, Vol. 130, Issue 33, p. 10876-10877
Composites of Graphene with Large Aromatic Molecules
journal, August 2009
- Su, Qi; Pang, Shuping; Alijani, Vajiheh
- Advanced Materials, Vol. 21, Issue 31, p. 3191-3195
Conductance eigenchannels in nanocontacts
journal, December 1997
- Brandbyge, Mads; Sørensen, Mads R.; Jacobsen, Karsten W.
- Physical Review B, Vol. 56, Issue 23, p. 14956-14959
Application of DNA Hybridization Biosensor as a Screening Method for the Detection of Genetically Modified Food Components
journal, March 2008
- Tichoniuk, Mariusz; Ligaj, Marta; Filipiak, Marian
- Sensors, Vol. 8, Issue 4, p. 2118-2135
Unveiling Stability Criteria of DNA-Carbon Nanotubes Constructs by Scanning Tunneling Microscopy and Computational Modeling
journal, January 2011
- Kilina, Svetlana; Yarotski, Dzmitry A.; Talin, A. Alec
- Journal of Drug Delivery, Vol. 2011, p. 1-9
DNA Translocation through Graphene Nanopores
journal, August 2010
- Merchant, Christopher A.; Healy, Ken; Wanunu, Meni
- Nano Letters, Vol. 10, Issue 8, p. 2915-2921
Correlation dynamics and enhanced signals for the identification of serial biomolecules and DNA bases
journal, February 2014
- Ahmed, Towfiq; Haraldsen, Jason T.; Rehr, John J.
- Nanotechnology, Vol. 25, Issue 12, Article No. 125705
Real-Time DNA Sequencing from Single Polymerase Molecules
journal, January 2009
- Eid, John; Fehr, Adrian; Gray, Jeremy
- Science, Vol. 323, Issue 5910, p. 133-138
Angle-resolved photoemission study of the graphite intercalation compound : A key to graphene
journal, August 2009
- Grüneis, A.; Attaccalite, C.; Rubio, A.
- Physical Review B, Vol. 80, Issue 7, Article No. 075431
Formation and Self-Breaking Mechanism of Stable Atom-Sized Junctions
journal, January 2008
- Tsutsui, Makusu; Shoji, Kohei; Taniguchi, Masateru
- Nano Letters, Vol. 8, Issue 1, p. 345-349
A tale of three next generation sequencing platforms: comparison of Ion torrent, pacific biosciences and illumina MiSeq sequencers
journal, January 2012
- Quail, Michael; Smith, Miriam E.; Coupland, Paul
- BMC Genomics, Vol. 13, Article No. 341
Electronic Signature of DNA Nucleotides via Transverse Transport
journal, March 2005
- Zwolak, Michael; Di Ventra, Massimiliano
- Nano Letters, Vol. 5, Issue 3, p. 421-424
Improving sequencing by tunneling with multiplexing and cross-correlations
journal, April 2014
- Boynton, P.; Balatsky, A. V.; Schuller, I. K.
- Journal of Computational Electronics, Vol. 13, Issue 4, p. 794-800
Density-functional method for nonequilibrium electron transport
journal, March 2002
- Brandbyge, Mads; Mozos, José-Luis; Ordejón, Pablo
- Physical Review B, Vol. 65, Issue 16, Article No. 165401
Electronic Properties of DNA Base Molecules Adsorbed on a Metallic Surface
journal, October 2007
- Kilina, Svetlana; Tretiak, Sergei; Yarotski, Dzmitry A.
- The Journal of Physical Chemistry C, Vol. 111, Issue 39, p. 14541-14551
Single-Molecular AFM Probing of Specific DNA Sequencing Using RecA-Promoted Homologous Pairing and Strand Exchange
journal, March 2000
- Seong, Gi Hun; Niimi, Tomohisa; Yanagida, Yasuko
- Analytical Chemistry, Vol. 72, Issue 6, p. 1288-1293
Competing Interactions in DNA Assembly on Graphene
journal, April 2011
- Akca, Saliha; Foroughi, Ashkan; Frochtzwajg, Daniel
- PLoS ONE, Vol. 6, Issue 4, Article No. e18442
Measurement of the Elastic Properties and Intrinsic Strength of Monolayer Graphene
journal, July 2008
- Lee, C.; Wei, X.; Kysar, J. W.
- Science, Vol. 321, Issue 5887, p. 385-388
Hallmark of Perfect Graphene
journal, June 2004
- Duplock, Elizabeth J.; Scheffler, Matthias; Lindan, Philip J. D.
- Physical Review Letters, Vol. 92, Issue 22, Article No. 225502
Partial sequencing of a single DNA molecule with a scanning tunnelling microscope
journal, July 2009
- Tanaka, Hiroyuki; Kawai, Tomoji
- Nature Nanotechnology, Vol. 4, Issue 8, p. 518-522
The rise of graphene
book, August 2009
- Rodgers, Peter; Geim, A. K.; Novoselov, K. S.
- Nanoscience and Technology: A Collection of Reviews from Nature Journals, p. 11-19
Electronic Signatures of all Four DNA Nucleosides in a Tunneling Gap
journal, March 2010
- Chang, Shuai; Huang, Shuo; He, Jin
- Nano Letters, Vol. 10, Issue 3, p. 1070-1075
Role of thermal vibrations in molecular wire conduction
journal, December 2003
- Pecchia, A.; Gheorghe, M.; Di Carlo, A.
- Physical Review B, Vol. 68, Issue 23, Article No. 235321
The Sum of Log-Normal Probability Distributions in Scatter Transmission Systems
journal, January 1960
- Fenton, L.
- IEEE Transactions on Communications, Vol. 8, Issue 1, p. 57-67
Formation of Pt-induced Ge atomic nanowires on Pt/Ge(001): A density functional theory study
journal, June 2008
- Vanpoucke, Danny E. P.; Brocks, Geert
- Physical Review B, Vol. 77, Issue 24, Article No. 241308
Fast DNA Sequencing via Transverse Electronic Transport
journal, April 2006
- Lagerqvist, Johan; Zwolak, Michael; Di Ventra, Massimiliano
- Nano Letters, Vol. 6, Issue 4, p. 779-782
Electrical Detection of Single Methylcytosines in a DNA Oligomer
journal, June 2011
- Tsutsui, Makusu; Matsubara, Kazuki; Ohshiro, Takahito
- Journal of the American Chemical Society, Vol. 133, Issue 23, p. 9124-9128
DNA Translocation through Graphene Nanopores
journal, August 2010
- Schneider, Grégory F.; Kowalczyk, Stefan W.; Calado, Victor E.
- Nano Letters, Vol. 10, Issue 8, p. 3163-3167
Single-Molecule Electrical Random Resequencing of DNA and RNA
journal, July 2012
- Ohshiro, Takahito; Matsubara, Kazuki; Tsutsui, Makusu
- Scientific Reports, Vol. 2, Article No. 501
Towards writing the encyclopaedia of life: an introduction to DNA barcoding
journal, October 2005
- Savolainen, V.; Cowan, R. S.; Vogler, A. P.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 360, Issue 1462, p. 1805-1811
Dynamics of water in confined space (porous alumina): QENS study
journal, August 2001
- Mitra, S.; Mukhopadhyay, R.; Tsukushi, I.
- Journal of Physics: Condensed Matter, Vol. 13, Issue 37, p. 8455-8465
Approaching ballistic transport in suspended graphene
journal, July 2008
- Du, Xu; Skachko, Ivan; Barker, Anthony
- Nature Nanotechnology, Vol. 3, Issue 8, p. 491-495
Colloquium: Physical approaches to DNA sequencing and detection
journal, January 2008
- Zwolak, Michael; Di Ventra, Massimiliano
- Reviews of Modern Physics, Vol. 80, Issue 1, p. 141-165
Identifying single nucleotides by tunnelling current
journal, March 2010
- Tsutsui, Makusu; Taniguchi, Masateru; Yokota, Kazumichi
- Nature Nanotechnology, Vol. 5, Issue 4, p. 286-290
Fast DNA sequencing with a graphene-based nanochannel device
journal, February 2011
- Min, Seung Kyu; Kim, Woo Youn; Cho, Yeonchoo
- Nature Nanotechnology, Vol. 6, Issue 3, p. 162-165
Self-interaction correction to density-functional approximations for many-electron systems
journal, May 1981
- Perdew, J. P.; Zunger, Alex
- Physical Review B, Vol. 23, Issue 10, p. 5048-5079
A decade’s perspective on DNA sequencing technology
journal, February 2011
- Mardis, Elaine R.
- Nature, Vol. 470, Issue 7333, p. 198-203
Soft self-consistent pseudopotentials in a generalized eigenvalue formalism
journal, April 1990
- Vanderbilt, David
- Physical Review B, Vol. 41, Issue 11, p. 7892-7895
Rapid Sequencing of Individual DNA Molecules in Graphene Nanogaps
journal, February 2010
- Postma, Henk W. Ch.
- Nano Letters, Vol. 10, Issue 2, p. 420-425
Electronic Fingerprints of DNA Bases on Graphene
journal, January 2012
- Ahmed, Towfiq; Kilina, Svetlana; Das, Tanmoy
- Nano Letters, Vol. 12, Issue 2, p. 927-931
Theoretical Calculations of Dissociative Adsorption of on an Ir(111) Surface
journal, January 2001
- Henkelman, Graeme; Jónsson, Hannes
- Physical Review Letters, Vol. 86, Issue 4, p. 664-667
Detection of Nucleic Acids with Graphene Nanopores: Ab Initio Characterization of a Novel Sequencing Device
journal, September 2010
- Nelson, Tammie; Zhang, Bo; Prezhdo, Oleg V.
- Nano Letters, Vol. 10, Issue 9, p. 3237-3242
Efficient iterative schemes for ab initio total-energy calculations using a plane-wave basis set
journal, October 1996
- Kresse, G.; Furthmüller, J.
- Physical Review B, Vol. 54, Issue 16, p. 11169-11186
Visualization of detailed structures within DNA
journal, August 2003
- Tanaka, Hiroyuki; Kawai, Tomoji
- Surface Science, Vol. 539, Issue 1-3, p. L531-L536
Identifying single bases in a DNA oligomer with electron tunnelling
journal, November 2010
- Huang, Shuo; He, Jin; Chang, Shuai
- Nature Nanotechnology, Vol. 5, Issue 12, p. 868-873
The electronic properties of graphene
journal, January 2009
- Castro Neto, A. H.; Guinea, F.; Peres, N. M. R.
- Reviews of Modern Physics, Vol. 81, Issue 1, p. 109-162
The problems and promise of DNA barcodes for species diagnosis of primate biomaterials
journal, October 2005
- Lorenz, J. G.; Jackson, W. E.; Beck, J. C.
- Philosophical Transactions of the Royal Society B: Biological Sciences, Vol. 360, Issue 1462, p. 1869-1877
Conventional Methods versus 16S Ribosomal DNA Sequencing for Identification of Nontuberculous Mycobacteria: Cost Analysis
journal, March 2003
- Cook, V. J.; Turenne, C. Y.; Wolfe, J.
- Journal of Clinical Microbiology, Vol. 41, Issue 3, p. 1010-1015
Graphite: a mimic for DNA and other biomolecules in scanning tunneling microscope studies
journal, February 1991
- Clemmer, C.; Beebe, T.
- Science, Vol. 251, Issue 4994, p. 640-642
Enhanced DNA Sequencing Performance Through Edge-Hydrogenation of Graphene Electrodes
journal, May 2011
- He, Yuhui; Scheicher, Ralph H.; Grigoriev, Anton
- Advanced Functional Materials, Vol. 21, Issue 14, p. 2674-2679
DNA sequencing with chain-terminating inhibitors
journal, December 1977
- Sanger, F.; Nicklen, S.; Coulson, A. R.
- Proceedings of the National Academy of Sciences, Vol. 74, Issue 12
The rise of graphene
journal, March 2007
- Geim, A. K.; Novoselov, K. S.
- Nature Materials, Vol. 6, Issue 3, p. 183-191
Noise reduction methods for nucleic acid and macromolecule sequencing
patent, May 2018
- Schuller, Ivan K.; Di Ventra, Massimiliano; Balatsky, Alexander
- US Patent Document 9,965,586
Many-body interactions in quasi-freestanding graphene
journal, June 2011
- Siegel, D. A.; Park, C.-H.; Hwang, C.
- Proceedings of the National Academy of Sciences, Vol. 108, Issue 28, p. 11365-11369
The potential and challenges of nanopore sequencing
book, August 2009
- Rodgers, Peter; Branton, Daniel; Deamer, David W
- Nanoscience and Technology: A Collection of Reviews from Nature Journals, p. 261-268
Graphene as a subnanometre trans-electrode membrane
journal, August 2010
- Garaj, S.; Hubbard, W.; Reina, A.
- Nature, Vol. 467, Issue 7312, p. 190-193
Controlling DNA Translocation through Gate Modulation of Nanopore Wall Surface Charges
journal, June 2011
- He, Yuhui; Tsutsui, Makusu; Fan, Chun
- ACS Nano, Vol. 5, Issue 7, p. 5509-5518
Scanning Tunneling Microscopy of DNA-Wrapped Carbon Nanotubes
journal, January 2009
- Yarotski, Dzmitry A.; Kilina, Svetlana V.; Talin, A. Alec
- Nano Letters, Vol. 9, Issue 1, p. 12-17
Electric Field Effect in Atomically Thin Carbon Films
journal, October 2004
- Novoselov, K. S.
- Science, Vol. 306, Issue 5696, p. 666-669
Probing Single-Stranded DNA Conformational Flexibility Using Fluorescence Spectroscopy
journal, April 2004
- Murphy, M. C.; Rasnik, Ivan; Cheng, Wei
- Biophysical Journal, Vol. 86, Issue 4, p. 2530-2537
Effect of Noise on DNA Sequencing via Transverse Electronic Transport
journal, October 2009
- Krems, Matt; Zwolak, Michael; Pershin, Yuriy V.
- Biophysical Journal, Vol. 97, Issue 7, p. 1990-1996
Scalable molecular dynamics with NAMD
journal, January 2005
- Phillips, James C.; Braun, Rosemary; Wang, Wei
- Journal of Computational Chemistry, Vol. 26, Issue 16, p. 1781-1802
Benchmark database of accurate (MP2 and CCSD(T) complete basis set limit) interaction energies of small model complexes, DNA base pairs, and amino acid pairs
journal, January 2006
- Jurečka, Petr; Šponer, Jiří; Černý, Jiří
- Physical Chemistry Chemical Physics, Vol. 8, Issue 17, p. 1985-1993