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Bioinformatics Training

 

Hi, I am Ramy and I currently work as a Research Associate at the University of Cambridge (CSCI, UK). Propelled by my passion for science (biology in particular), I completed a PhD in Genomics and Bioinformatic in 2016. My project focused on the immune response to infection and its interaction with inflammation. During this time, I was also involved in processing clinical data obtained from thousands of patients being admitted for infection in intensive care. I performed a GWAS (genome wide association studies) in order to highlight genomic markers correlating with a sepsis or a septic shock condition. I joined the Cambridge Stem Cell Institute (Cambridge University) as a PostDoc in Dr Brian Hendrich's lab, during which my research interests evolved. I am now focused on investigating the role of chromatin remodellers in gene expression regulation and transcription. My idea is to better understand how a gene regulatory network (GRN) is established and maintained, and what are the key actors that rules this process. Working in Dr. Brian Hendrich team has been and is still a great opportunity for me to study this fascinating process as well as developing my bioinformatic skills to a high level. In my role as bioinformatician, I have analysed a wide range of data sets, including: ChIP-seq, CUT&RUN, CUT&TAG, bulk RNA-seq and single cell RNA-seq. As the only dry-lab member of the team, I have contributed actively to developing solution based ideas for the team. I have also taught my team mates the fundamentals of bioinformatic techniques (from the theory to practical).

Biography

Education

  • Aix-Marseille University

    PhD, Bioinformatique 2012 - 2016


  • Aix-Marseille University

    Master of Bioinformatic, Biostructural Chemistry and Genomic, Science des gènes / génomique 2011 - 2012

    • Grade: moyenne = 15.21 - Mention = Bien

      • Lauréat du concours de l'Ecole Doctorale des Sciences de la Vie et de la Santé Marseille (EDSVS).


  • Aix-Marseille University

    Master 2 (M2), Science des gènes / génomique 2010 - 2012

Publications

Key publications: 

 

Enhancer-promoter interactions are reconfigured through the formation of long-range multiway hubs as mouse ES cells exit pluripotency

  • March 2024
  • Molecular Cell 84(8)
  • 84(8)

DOI:10.1016/j.molcel.2024.02.015


The Nucleosome Remodelling and Deacetylation complex coordinates the transcriptional response to lineage commitment in pluripotent cells

  • December 2023
  • Biology Open 13(1)
  • 13(1)

DOI:10.1242/bio.060101


Differential regulation of lineage commitment in human and mouse primed pluripotent stem cells by the Nucleosome Remodelling and Deacetylation Complex

  • June 2020
  • Stem Cell Research 46(56–72):101867
  • 46(56–72):101867

DOI:10.1016/j.scr.2020.101867


Live-cell 3D single-molecule tracking reveals how NuRD modulates enhancer dynamics

  • April 2020

DOI:10.1101/2020.04.03.003178


Interplay between trauma and Pseudomonas entomophila infection in flies: A central role of the JNK pathway and of CrebA

  • November 2017
  • Scientific Reports 7(1)
  • 7(1)

DOI:10.1038/s41598-017-14969-7


Vorinostat and Mithramycin A in combination therapy as an interesting strategy for the treatment of Sézary T lymphoma: a transcriptomic approach

  • October 2017
  • Archives of Dermatological Research 309(10)
  • 309(10)

DOI:10.1007/s00403-017-1761-0

Teaching and Supervisions

Teaching: 

 

2024/2025:

  • Bulk RNA-seq analysis - Trainer
Ramy Ragheb

Contact Details

Email address: 
Cambridge Stem Cell Institute
Jeffrey Cheah Biomedical Centre
Puddicombe Way
Cambridge Biomedical Campus
CB2 0AW