title: Physico-chemical foundations underpinning microarray and next-generation sequencing experiments.
abstract: 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. This research has inputs from many areas, from bioinformatics and biostatistics, to theoretical and experimental biochemistry and biophysics, to computer simulations. A group of leading researchers met in Ploen Germany in 2011 to discuss present knowledge 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.
authors: University of Essex-Mathematical Sciences, Colchester CO4 3SQ, Essex, United Kingdom.
authors: Andrew
authors: A
authors: Harrison
authors: Hans
authors: H
authors: Binder
authors: Arnaud
authors: A
authors: Buhot
authors: Conrad J
authors: CJ
authors: Burden
authors: Enrico
authors: E
authors: Carlon
authors: Cynthia
authors: C
authors: Gibas
authors: Lara J
authors: LJ
authors: Gamble
authors: Avraham
authors: A
authors: Halperin
authors: Jef
authors: J
authors: Hooyberghs
authors: David P
authors: DP
authors: Kreil
authors: Rastislav
authors: R
authors: Levicky
authors: Peter A
authors: PA
authors: Noble
authors: Albrecht
authors: A
authors: Ott
authors: B Montgomery
authors: BM
authors: Pettitt
authors: Diethard
authors: D
authors: Tautz
authors: Alexander E
authors: AE
authors: Pozhitkov
mesh_terms: D000465:Algorithms; D016477:Artifacts; D020029:Base Pairing; D002138:Calibration; D004247:DNA / Q000737:chemistry / Q000235:genetics; D015342:DNA Probes / Q000737:chemistry / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing; D006801:Humans; D007091:Image Processing, Computer-Assisted; D008954:Models, Biological; D009693:Nucleic Acid Hybridization / Q000379:methods; D020411:Oligonucleotide Array Sequence Analysis; D013499:Surface Properties; D013816:Thermodynamics
chemical_list: D015342:DNA Probes; D004247:DNA