American University of Beirut

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

BRD4 bimodal binding at promoters and drug-induced displacement at Pol II pause sites associates with I-BET sensitivity.
Khoueiry P, Ward Gahlawat A, Petretich M, Michon AM, Simola D, Lam E, Furlong EE, Benes V, Dawson MA, Prinjha RK, Drewes G, Grandi P. 
Epigenetics & chromatin, 2019

Deep targeted sequencing analysis of hot spot mutations in non-small cell lung cancer patients from the Middle Eastern population.
Khoueiry P, Fakhri G, Akel R, El Assaad M, Mahfouz R, Khuri F, Chami H, Petersen J, Viet S, Davies G, Kadara H, Tfayli A. 
Journal of thoracic disease, 2019

The role of chromatin accessibility in cis-regulatory evolution.
Peng PC, Khoueiry P, Girardot C, Reddington JP, Garfield DA, Furlong EEM, Sinha S.
Genome biology and evolution, 2019

Discovery of New Fusion Transcripts in a Cohort of Pediatric Solid Cancers at Relapse and Relevance for Personalized Medicine.
Dupain C, Harttrampf AC, Boursin Y, Lebeurrier M, Rondof W, Robert-Siegwald G, Khoueiry P, Geoerger B, Massaad-Massade L. 
Molecular therapy : the journal of the American Society of Gene Therapy​, 2019

Uncoupling evolutionary changes in DNA sequence, transcription factor occupancy and enhancer activity.
Khoueiry P, Girardot C, Ciglar L, Peng PC, Gustafson EH, 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
Current biology : CB​, 2016​

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