Publications by Alina Isakova | EPFL Graph Search

SMiLE-seq identifies binding motifs of single and dimeric transcription factors

Didier Trono, Giovanna Ambrosini, Bart Deplancke, Philipp Bucher, Romain Fernand Pietro Groux, Riccardo Dainese, Daniel Alpern, Michaël Imbeault, Alina Isakova, Pernille Yde Rainer

Resolving the DNA-binding specificities of transcription factors (TFs) is of critical value for understanding gene regulation. Here, we present a novel, semiautomated protein-DNA interaction characterization technology, selective microfluidics-based ligand ...

Nature Publishing Group2017

Microfluidic device and method for isolation of nucleic acids

Bart Deplancke, Alina Isakova

The present invention concerns a microfluidic device for mechanically induced trapping of molecular interactions comprising at least a first unit cell and a second unit cell, each unit cell comprising - a membrane chamber comprising a membrane, - a flow ch ...

2016

Quantification of Cooperativity in Heterodimer-DNA Binding Improves the Accuracy of Binding Specificity Models

Vassily Hatzimanikatis, Bart Deplancke, Alina Isakova, Yves Berset

Many transcription factors (TFs) have the ability to cooperate on DNA elements as heterodimers. Despite the significance of TF heterodimerization for gene regulation, a quantitative understanding of cooperativity between various TF dimer partners and its i ...

American Society for Biochemistry and Molecular Biology2016

Dissecting the DNA binding principles of transcription factor monomers and heterodimers

Alina Isakova

EPFL2014

A yeast one-hybrid and microfluidics-based pipeline to map mammalian gene regulatory networks

Bart Deplancke, Alina Isakova, Sebastian Martin Waszak, Jovan Simicevic, Sunil Kumar Raghav, Antonina Iagovitina, Carine Delattre-Gubelmann, Jean-Daniel Feuz

The comprehensive mapping of gene promoters and enhancers has significantly improved our understanding of how the mammalian regulatory genome is organized. An important challenge is to elucidate how these regulatory elements contribute to gene expression b ...

Nature / European Molecular Biology Organization2013

Topology and dynamics of the zebrafish segmentation clock core circuit

Bart Deplancke, Andrew Charles Oates, Sebastian Maerkl, Daniele Soroldoni, Alina Isakova

During vertebrate embryogenesis, the rhythmic and sequential segmentation of the body axis is regulated by an oscillating genetic network termed the segmentation clock. We describe a new dynamic model for the core pace-making circuit of the zebrafish segme ...

2012

Automated protein-DNA interaction screening of Drosophila regulatory elements

Bart Deplancke, Andreas Massouras, Alina Isakova, Julien Bryois, Antonina Iagovitina, Jean-Daniel Feuz

Drosophila melanogaster has one of the best characterized metazoan genomes in terms of functionally annotated regulatory elements. To explore how these elements contribute to gene regulation, we need convenient tools to identify the proteins that bind to t ...

2011