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Physico-chemical foundations underpinning microarray and next-generation sequencing experiments

Harrison, Andrew; Binder, Hans; Buhot, Arnaud; Burden, Conrad J; Carlon, Enrico; Gibas, Cynthia; Gamble, Lara J; Halperin, Avraham; Hooyberghs, Jef; Kreil, David P; Levicky, Rastislav; Noble, Peter A; Ott, Albrecht; Pettitt, B Montgomery; Tautz, Diethard; Pozhitkov, Alexander E.

Description

Hybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next- generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids....[Show more]

dc.contributor.authorHarrison, Andrew
dc.contributor.authorBinder, Hans
dc.contributor.authorBuhot, Arnaud
dc.contributor.authorBurden, Conrad J
dc.contributor.authorCarlon, Enrico
dc.contributor.authorGibas, Cynthia
dc.contributor.authorGamble, Lara J
dc.contributor.authorHalperin, Avraham
dc.contributor.authorHooyberghs, Jef
dc.contributor.authorKreil, David P
dc.contributor.authorLevicky, Rastislav
dc.contributor.authorNoble, Peter A
dc.contributor.authorOtt, Albrecht
dc.contributor.authorPettitt, B Montgomery
dc.contributor.authorTautz, Diethard
dc.contributor.authorPozhitkov, Alexander E.
dc.date.accessioned2014-04-10T02:55:32Z
dc.date.available2014-04-10T02:55:32Z
dc.identifier.issn0305-1048
dc.identifier.urihttp://hdl.handle.net/1885/11556
dc.description.abstractHybridization of nucleic acids on solid surfaces is a key process involved in high-throughput technologies such as microarrays and, in some cases, next- generation sequencing (NGS). A physical understanding of the hybridization process helps to determine the accuracy of these technologies. The goal of a widespread research program is to develop reliable transformations between the raw signals reported by the technologies and individual molecular concentrations from an ensemble of nucleic acids. This research has inputs from many areas, from bioinfor- matics and biostatistics, to theoretical and experi- mental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present know- ledge and limitations of our physico-chemical understanding of high-throughput nucleic acid technologies. This meeting inspired us to write this summary, which provides an overview of the state-of-the-art approaches based on physico-chemical foundation to modeling of the nucleic acids hybridization process on solid surfaces. In addition, practical application of current knowledge is emphasized.
dc.format18 pages
dc.publisherOxford University Press
dc.rights© The Author(s) 2013.This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/3.0/), which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.
dc.sourceNucleic Acids Research 41.5 (2013): 2779–2796
dc.subjectphysico-chemical
dc.subjectmicroarray
dc.subjectnext-generation
dc.subjectsequencing
dc.titlePhysico-chemical foundations underpinning microarray and next-generation sequencing experiments
dc.typeJournal article
local.identifier.citationvolume41
dc.date.issued2013-01-09
local.identifier.absfor060102 - Bioinformatics
local.identifier.absfor010402 - Biostatistics
local.identifier.ariespublicationu4743872xPUB91
local.publisher.urlhttp://www.oxfordjournals.org/
local.type.statusPublished Version
local.contributor.affiliationHarrison, Andrew, University of Essex
local.contributor.affiliationBinder, Hans, University Leipzig
local.contributor.affiliationBuhot, Arnaud, CEA Grenoble
local.contributor.affiliationBurden, Conrad, College of Physical and Mathematical Sciences, ANU
local.contributor.affiliationCarlon, Enrico, Katholieke Universiteit Leuven
local.contributor.affiliationGibas, Cynthia, University of North Carolina at Charlotte
local.contributor.affiliationGamble, Lara J, University of Washington
local.contributor.affiliationHalperin, Avraham, University of Grenoble
local.contributor.affiliationHooyberghs, Jef, Flemish Institute for Technological Research
local.contributor.affiliationKreil, David P, University of Warwick
local.contributor.affiliationLevicky, Rastislav, Polytechnic Institute of New York University
local.contributor.affiliationNoble, Peter A, University of Washington
local.contributor.affiliationOtt, Albrecht, Universitaet des Saarlandes
local.contributor.affiliationPettitt, B Montgomery, The University of Texas Medical Branch
local.contributor.affiliationTautz, Diethard, Max-Planck Institut
local.contributor.affiliationPozhitkov, Alexander E, University of Washington
dc.relationhttp://purl.org/au-research/grants/arc/dp1094699
local.bibliographicCitation.issue5
local.bibliographicCitation.startpage2779
local.bibliographicCitation.lastpage2796
local.identifier.doi10.1093/nar/gks1358
local.identifier.doi10.1093/nar/gks1358
local.identifier.absseo970106 - Expanding Knowledge in the Biological Sciences
dc.date.updated2015-12-08T08:40:28Z
local.identifier.scopusID2-s2.0-84876354602
local.identifier.thomsonID000318062600008
CollectionsANU Research Publications

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