Publications by Arnaud Amzallag

Bending modes of DNA directly addressed by cryo-electron microscopy of DNA minicircles

John Maddocks, Davide Demurtas, Andrzej Stasiak, Jacques Dubochet, Arnaud Amzallag

We use cryo-electron microscopy (cryo-EM) to study the 3D shapes of 94-bp-long DNA minicircles and address the question of whether cyclization of such short DNA molecules necessitates the formation of sharp, localized kinks in DNA or whether the necessary ...

Oxford University Press2009

Probabilistic base calling of Solexa sequencing data

Felix Naef, Jacques Rougemont, Christian Iseli, Arnaud Amzallag, Ioannis Xenarios

BACKGROUND: Solexa/Illumina short-read ultra-high throughput DNA sequencing technology produces millions of short tags (up to 36 bases) by parallel sequencing-by-synthesis of DNA colonies. The processing and statistical analysis of such high-throughput dat ...

BioMed Central2008

Effects of base-pair sequence, nicks and gaps on DNA minicircle shapes : analysis and experiment

Arnaud Amzallag

DNA is a long polymer with the form of a double helix of about two nanometers diameter (2.10-9 meters). It is composed of nucleotides whose sequence carries the information of heredity. The four possible nucleotides have slightly different geometries, and ...

EPFL2008

3D Reconstruction and Comparison of Shapes of DNA Minicircles Observed by Cryo-Electron Microscopy

Michaël Unser, Andrzej Stasiak, Arnaud Amzallag, Mathews Jacob

We use cryo-electron microscopy to compare 3D shapes of 158 bp long DNA minicircles that differ only in the sequence within an 18 bp block containing either a TATA box or a catabolite activator protein binding site. We present a sorting algorithm that corr ...

The Author(s)2006