Pierre Khoueiry Lab

​​​​​​​​​​​​​​​​​​​​​​​​​​​​​Link to Dr. Khoueiry​'s​ FMIS Profile

​​​​​​Research Area

Gene regulatory mechanisms in development and disease

Research Interests

Regulatory regions bind transcription factors and activate or repress their target genes. The main focus of my group is to understand principles of transcriptional regulation in development and disease including cancer. Mainly, we study the dynamics of regulatory regions activity to get insights into the mechanisms that lead to developmental defects and disease progression. We combine computational (Bioinformatics) and experimental approaches, to contrast information between healthy and disease states. We use evolutionary information (comparative genomics) to gain better insights on functional regulatory elements.

Research Projects

  • DNA regulatory regions dynamics during cancer progression
  • Mechanisms conferring robustness to transcriptional regulatory programs
  • Development of computational pipelines and methods for Next Generation Sequencing data analysis
  • Assessment of the mutational landscape using whole exome sequencing

Selected Publications

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity
Khoueiry P, Girardot C, Ciglar L, Peng P, Gustafson H, Sinha S, Furlong EE.
Elife. 2017

Shadow enhancers are pervasive features of developmental regulatory networks
Cannavò E, Khoueiry P, Garfield DA, Geeleher P, Zichner T, Gustafson EH, Ciglar L, Korbel JO, Furlong EE.
Elife. 2017

A pipeline for the systematic identification of non-redundant full-length cDNAs for polymorphic and evolutionary divergent genomes: application to the ascidian Ciona intestinalis
Gilchrist M, Sobral D, Khoueiry P, Daian F, Laporte B, Patrushev I, Matsumoto J, Hastings K, Satou Y, Lemaire P, Rothbächer U
Dev Biol. 2015 May 27

Biggest challenges in bioinformatics.
Fuller J C, Khoueiry P, Dinkel H, Forslund K, Stamatakis A, Barry J, Budd A, Soldatos T G, Linssen K, Rajpu A M
Dev Biol. 2015 May 27

A cis-regulatory signature in ascidians and flies, independent of transcription factor binding sites.
Khoueiry P, Rothbächer U, Ohtsuka Y, Daian F, Frangulian E, Roure A, Dubchak I, Lemaire P.
Curr Biol. 2010 May 11

The ANISEED database: digital representation, formalization, and elucidation of a chordate developmental program.
Tassy O, Dauga D, Daian F, Sobral D, Robin F, Khoueiry P, Salgado D, Fox V, Caillol D, Schiappa R, Laporte B, Rios A, Luxardi G, Kusakabe T, Joly JS, Darras S, Christiaen L, Contensin M, Auger H, Lamy C, Hudson C, Rothbächer U, Gilchrist MJ, Makabe KW, Hotta K, Fujiwara S, Satoh N, Satou Y, Lemaire P.
Genome Res. 2010 Oct

Similar regulatory logic in Ciona intestinalis for two Wnt pathway modulators, ROR and SFRP-1/5.
Auger H, Lamy C, Haeussler M, Khoueiry P​, Lemaire P, Joly JS.
Genome Res. 2010 Oct