Research Profile

I am a Research Scientist II, working in the Molecular Diagnostics Laboratory of the National Institute for Infectious Diseases “Matei Balș” and in the Research Institute of University of Bucharest. My bioinformatic scientific expertise covers: Bacterial (ESKAPE pathogens, Bacillus cereus, Bacillus anthracis), fungal (Candida auris, Candida tropicalis, Nacaseomyces glabratus) and viral (SARS-CoV-2, Influenza, Monkey Pox, HIV, HTLV, HCV, HBV, Measles) WGS sequencing bioinformatics analysis methods (QC, de novo assembly, reference mapping, MLST prediction, antimicrobial resistance predictions, mobile genetic elements (MGE) predictions, phylogenies, pangenome analysis, functional analysis, variant analysis); 16S & Shotgun Metagenomics sequencing analysis; Developing original methods and computational scripts & analysis pipelines (AWK, bash, Python, R); Structural bioinformatics methods (Sequence bioinformatics predictions, Protein Homology Modelling (Remote, Ab initio), DNA modelling, RNA modelling, N-Glycans modelling, Protein/DNA Molecular Dynamics simulations, Molecular Docking, Drug Design); Interactomics; Phylogenetic analysis; Biostatistics; Molecular Biology and Biophysics wet lab techniques.

During my PhD, I developed and implemented special biomolecular modeling and simulation techniques, adjusted to study interactions and protein-induced effects on nucleic acids in vital biological processes such as: somatic (or V(D)J) recombination, decatenation checkpoint, mRNA degradation; processes which are among the cutting-edge research topics.

After my PhD I have optimised & automatised sequencing analysis pipelines. Lately, together with my student, we developed a bioinformatic workflow (e.g. PeGAS) for bacterial WGS sequencing analysis, that covers all from QC, de novo assembly, MLST, antibiotic resistance and virulence factor predictions, to annotating genomes and pangenome analysis in one go. This tool is intended to help researchers with limited bioinformatics skills, to be able to analyse their own sequencing data. We also developed a new Python tool that analyses the relationships between the antibiotic resistance genes and mobile genetic elements for instance. We plan to offer comprehensive WGS analysis pipelines, as there is a notable scarcity of such workflows. The few existing ones are typically not user-friendly and lack adequate descriptions.

My expertise is reflected in 27 scientific papers (10 of which as first author) and 1 international book chapter (as main author). My scientific papers have been published in some of the following journals: Nature, Nucleic Acids Research, Antimicrobial Resistance and Infection Control, Frontiers in Microbiology, Scientific Reports, JBC, Heliyon, PloS ONE, FEBS Journal, International Journal of Molecular Sciences, Journal of Clinical Medicine, Antibiotics, Life, etc.

I have a cumulative Impact Factor of 161.22 and cumulative AIS of 55.63 (of which 14.16 from first authorship papers). 92% of my papers are in Q1/Q2 quartiles. My Hirsch index according to Web of Science = 11, Google Scholar = 13.

In 2020 I won a one-year research fellowship for young researchers, awarded by the Research Institute of University of Bucharest (ICUB). In 2021 I won a Postdoctoral project funded by UEFISCDI. I have also actively participated in 14 national and international research projects.

I have participated with oral and poster presentations in over 40 scientific conferences (international and national) of which I won several awards and participation scholarships.

On November 2019, I have been appointed to hold a Structural Bioinformatics course in Tours, France, for master students in the ERASMUS – International MSc Infectious Disease and One Health program.

In 2022 and 2023, I had exchange visits at the Centre for Antibiotic Resistance Research at University of Gothenburg – CARe (Key person: Professor Joakim Larsson) and at the Chalmers University of Technology (Key person: Assistant Professor Johan Bengtsson-Palme), Sweden; the collaboration with the Swedish groups is ongoing.

Starting with 2022, I collaborate with Dr. Kgaugelo E Lekota, Senior Lecturer in Microbiology from the School of Biological Sciences, North-West University(NWU), South Africa, on Bacillus (Bacillus anthracis, Bacillus cereus, Bacillus thuringiensis) WGS sequencing studies.

Since 2022 I am teaching the LINUX, Biostatistics and Nucleic Acids courses at the MSc Professional Medical Bioinformatics program, at the University of Bucharest, Romania.

On June 26-29th, 2023, I have been accepted and participated to the „How to design and deliver pathogen genomics training for health and research professionals” course organised by Wellcome Connecting Science & Centre for Genomic Pathogen Surveillance at Wellcome Genome Campus, Hinxton, Cambridge, UK.

On October 23-24th, 2023, I held the “Hands-on Pathogen genomics course – from sequence analysis to impact on public health” workshop together with Monica Abrudan (CGPS, University of Oxford, UK) at ”Babeș-Bolyai” University, Cluj Napoca, Romania.

On January 30th – February 1st, 2024, I was invited as a participant to the “GenEpi-BioTrain - topical training: Bioinformaticians’ roles and responsibilities in WGS-based MRSA, CRE and Clostridioides difficile surveillance and outbreak investigation” course organized by ECDC & Statens Serum Institut, in Copenhagen, Denmark.

I am currently Operational Contact Point for ECDC on AMR, SARS-CoV-2 and Influenza.