CV

CAREER OBJECTIVE

My current goal is to use and develop efficient bioinformatics tools with the aim of unveiling new insights about challenging systems of major interest in biology/medicine.

WORK EXPERIENCE

March 2023 to now : Post-doctoral researcher in the group of Dr M. Miteva at CiTCoM UMR8038 CNRS - UPC, Inserm U1268 . Faculty of Pharmacy. University Paris Cité (France).

December 2019 - November 2021 : Post-doctoral scholarship in the group of  Dr L. Delemotte at  Science for Life Laboratory, Department of Applied Physics,  KTH Royal Institute of Technology (Stockholm, SWEDEN).

I'm investigating the gating mechanisms of HCN1 (Hyperpolarization-activated and Cyclic Nucleotide-gated channel 1), a voltage gated ion channel which controls the activity of pacemaker cells in the heart and the brain. I'm also contributing in studies of SARS-CoV-2 membrane/envelope proteins. Methods: MD simulations (GROMACS, Desmond) using most powerful supercomputing resources (Anton2, Folding@Home, Piz-Daint (PRACE), SNIC-Beskow (Sweden))

January 2017- November 2019 (3 years): Post-doctoral researcher supervised by Dr I. Callebaut and Dr F. Pietrucci at IMPMC-UMR7590 CNRS, Sorbonne University (Paris, FRANCE). My project was funded by the French association Vaincre La Mucoviscidose.

I was in charge of studying CFTR  anion channel whose mutations provoke cystic fibrosis, the most common inherited disease among Caucasians. In addition, I studied other membrane proteins either from the ABC family (ABCB4 transporter, involved in a severe rare biliary disease) or belonging to the MFS family (FPN1, involved in hemochromatosis type 4A). Methods: molecular dynamics and metadynamics simulations (NAMD, PLUMED) to identify the mechanisms that are affected in presence of mutations and/or modulators.

October 2013- January 2017 (3 years): PhD student supervised by Dr B. Hartmann et Dr C. Oguey at LBPA-UMR 8113 CNRS, University of Paris-Saclay and LPTM-UMR 8089 CNRS, University of Cergy-Pontoise.

Thesis title: The nucleosome dynamics and stability. I was investigating the effects of the histone tails & the DNA sequence on the DNA-protein interface and on the dynamics of the DNA within the nucleosome (with respect to free DNA). Methods: molecular dynamics simulations (NAMD, AMBER) and normal mode calculations (CHARMM) + development of VLDM, a geometrical approach to explore DNA-protein interface in solution.

January - June 2013 (6 months): Master M2 internship supervised by Dr B. Hartmann et Dr D. Perahia at LBPA – ENS of Cachan, UMR 8113 CNRS.

Internship title: Modelling study of the nucleosome core particle. I was in charge of carrying out molecular dynamics simulations and analyzing the DNA-protein interface in nucleosome.

April - June 2012 (3 months): Master M1 internship supervised by Prof. C. Etchebest and Dr M. Gueroult at INSERM, UMR-S 665.

Internship title: Structural modelling of rhesus membrane complex. I was in charge of building homology models (Modeller) of the rhesus complex proteins and studying the organization of the complex by performing a multimeric docking (ZDOCK).

2007-2009 (3 months by department): hospital clerkship as a medical student in different departments (endocrinology, gastroenterology, thoracic surgery, ophthalmology, internal medicine) at Avicenne hospital, Bobigny, France.

September 2007 (1 month): nursing internship in the Respiratory department at Avicenne hospital, Bobigny, FRANCE.

SCIENTIFIC EDUCATION

2013-2016 PhD in structural bioinformatics & molecular modeling (Nucleosome dynamics and stability)

Laboratories: LBPA, UMR8113 CNRS, University of Paris-Saclay – ENS of Cachan and LPTM, UMR8089 CNRS, University of Cergy-Pontoise, FRANCE.

Keywords: structural bioinformatics, molecular dynamics simulations, normal modes calculations, programming, protein-nucleic acids contacts.

Scholarship granted in the context of IDEX Paris Saclay project - IDI 2013

2011-2013 Master's degree ISDD (In Silico Drug Design)

Universities: University of Paris Diderot – Paris 7 and University of Strasbourg (chemoinformatics), FRANCE.

Keywords: drug design, chemoinformatics, biostatistics and data analysis, molecular modeling & dynamics, normal modes analysis, structural bioinformatics, programming, molecular docking & virtual screening, QSAR and pharmacophore.

2010-2011 Bachelor's degree of Biology (life sciences)

University: University of Paris13, FRANCE. Faculty of life sciences at Bobigny, FRANCE. Structure of Biomolecules specialty.

Keywords: molecular biology, bioorganic and bioinorganic chemistry, biological & biophysical methods, thermodynamics, maths, bioinformatics.

2007-2010 Medical studies

University: University of Paris 13. Faculty of medicine at Bobigny, FRANCE. In June 2007, I succeeded in passing the 1rst year entrance competition. Then, I stopped my medical studies during the 3 rd year in 2010.

Keywords: cellular and molecular biology, pharmacology, biochemistry, immunology, physiology and physiopathology, histology, anatomy and semiology.

SKILLS AND FOREIGN LANGUAGES

•  Structural Biology: knowledge regarding DNA , DNA-protein complexes, membrane transporters and ion channels structure and dynamics. Lipids and Ligands-membrane protein interactions.

• Proficient in Structural bioinformatics: Visualization (Pymol, VMD, Chimera), homology modelling (Modeller, Rosetta, Alphafold), standard and enhanced molecular dynamics (CHARMM, GROMACS, NAMD, AMBER, PLUMED, DESMOND), normal modes analysis (CHARMM, R:Bio3D), MD trajectory analysis (python: MDTraj, MDanalysis, ALLOPATH; R:Bio3D), protein & nucleic acids structural analysis (DNA: 3DNA, Curves + ; protein: VMD:tcl scripting, R & python scripting, geometrical approaches: VLDM, ).

• Usage of most powerful resources for MD calculations: Anton2 and Folding@Home and other facilities (France: CINES/GENCI and Sweden: BESKOW).

• Drug Design: Structure-Based: protein-ligand and protein-protein docking (AutoDock), virtual screening (Vina). A grounding in Ligand-Based: QSAR, Pharmacophore (MOE, Discovery Studio).

• A grounding in Biostatistics (bayesian) and machine learning methods (supervised: k-NN, SVM, Random Forest, Logistic Regression, Neural Network ; unsupervised: clustering, PCA) using R (caret, dplyr, rpart, randomForest, FactomineR ...) and python (NumPy, Scikit-Learn, TensorFlow, Pandas). 

• Evolutionary analysis: Multiple Sequence Alignment (mafft, hmmer), Clustering, Phylogenetic tree, Logos, Coevolution.

• Programming languages: bash, python, tcl, R, fortran, C/ C++ (basic knowledge), CUDA (basic knowledge).

• Web programming: html, css, Javascript, php (basic knowledge). A grounding in database: PostgreSQL, mysql (mariadb).

•  Office automation: Microsoft Office & OpenOffice & Google Docs. LaTeX (basic); O.S.: Windows, Mac and Unix/Linux.

• Languages: bilingual French/ Egyptian, advanced English.

SCIENTIFIC INTERESTS

Reviewer for IJMS / Briefings in Bioinformatics / Journal of Computational Biophysics and Chemistry / Journal of the Brazilian Chemical Society

2013-2019: member of the French society for biochemistry and molecular biology (SFBBM, FEBS).

2015-2019: member of the French Society for BioInformatics (SFBI).

2020-2021: member of Molecular Biophysics Stockholm (including gromacs developers)

List of publications : https://pubmed.ncbi.nlm.nih.gov/?term=elbahnsi