Meet the Group

Nelly Romani Vestman
Group Leader
DDS, MPH, PhD
Senior Counsult in Endodontics at the Region of Västerbotten, Sweden.
Assocoated researche at the Wallenberg Centre for Molecular Medicine, Umeå University, Umeå, Sweden.

Olena Rakhimova
Post Doc
Education and awards:

1988 - Diploma in Microbiology and Virology Odesa National University (Ukraine) with Honors
1990 - Internship “Design and maintenance of bacterial and fungi culture collection” in VKM (Collection of Microorganisms) - Pushchino Scientific Center for Biological Research of the Academy of Sciences USSR (Successor Russian Academy of Sciences);
1996 - Training Course “Computer in Microbiology”, Technical University of Wroclaw (Poland);
1999 - Fellowship grant for Young Scientists (Fellowship Reference No YSF99-08). Fellowship student, School of Biosciences, University of Westminster, London, GB. Project “Studies on the ability of Myxobacteria strains to accumulate heavy metals from wastewater” carried out in the laboratory of Dr Sharron McEldowney.

2001 - 3rd awards in INTAS Young Scientist Writing Competition (Grant Reference Number INTAS YS-WC-4);
2004 - 1-st degree Diploma for the Research Report on the VIII International medical Congress of Students and Young Scientists (Ukraine).
2004 - 1-st degree Diploma for the Research Report on the VIII International medical Congress of Students and Young Scientists (Ukraine).
2006 - Defense of PhD thesis in Microbiology: “Biological characteristics of Myxobacteria collected from the southern part of Ukraine”.

Olena is a life-learning person, who is constantly improving the level of her education. From 2007 till 2021-st she attended twelve educational courses at Umeå University, including Tumor biology, Electron Microscopy, Quantitative PCR and Biostatistics, Live Cell Imaging Microscopy, Experimental Statistics and Logic regression, Immunology at the advanced level, Basic Principles in Laboratory Animal Science, Fluorescence in situ Hybridization.
The fields of her scientific interests include Myxobacteria (unique group of predators in the world of prokaryote), Accumulation of the heavy metals from the wastewater, Preservations of bacterial strains and their use in biotechnology, Vaccination against bacteria including human pathogen Helicobacter pylori that recognized by WHO as a carcinogen, Oral microbiome and regeneration processes. In these fields, Olena has 25 scientific publications, participated in 26 scientific conferences with Poster or Oral presentations and has one declaration patent in Ukraine.

Technical skills:

Microbiology: Isolation, purification and characterization of bacterial and yeast strains by morphological, physiological, and biochemical methods. Design and maintenance of bacterial and fungi culture collection within the framework of the Ukrainian Collection of Microorganisms (UCM). Detecting antimicrobial resistance and minimum inhibitory concentration (MIC). Handling anaerobic bacteria.
Biochemistry: Protein analysis by Laemmli method and immunoblot detection. Radio Immuno Assay (RIA). Determination of protease activity by fluorescence-based assay.
Molecular Biology: Isolation of DNA from bacteria (including isolation from the formalin-fixed and paraffin-embedded eukaryotic tissue sections), PCR, Q-PCR, RT-PCR, DNA-sequencing. Transformation and selection of bacterial strains. Fluorescence in situ Hybridization. Cloning, Expression and Purification of recombinant proteins.
Immunological Methods: ELISA, Serum-titer determination, IF-microscopy.
Work with animals: Handling of transgenic mice. Immunizations and infection methods.
Work with cell lines: Continuous and primary cell cultures, including handling of stem cells.
Work with tissue samples: Fixation, storage, processing, embedding and sectioning followed by IHC and IF-microscopy analysis of samples.

She has experience in teaching as a full-time lecturer in Odessa national University (2001 - 2005) and every year participated in ERASMUS teaching courses from 2016 up till today with lectures and practical classes.

Hobby:
play piano and travel.

Valeria Zymovets
PhD Student
Education:
01.09.2020 -31.12.2021
Diploma M.Sc. (Hons) in Biotechnologies and Bioengineering in Odesa I.I. Mechnikov National University
Graduate thesis: «Development of a method for screening cytokines induction by apical papilla stem cells influenced by opportunistic bacteria»

01.09.2016 -30.06.2020
B.Sc. (Hons) in Biotechnologies in Odesa I.I. Mechnikov National University
Graduate thesis: Biotechnology for obtaining carotovoricins of Pectobacterium carotovorum for the development of biological products for plant protection

Publications:

Zymovets, V.; Razghonova, Y.; Rakhimova, O.; Aripaka, K.; Manoharan, L.; Kelk, P.; Landström, M.; Romani Vestman, N. Combined Transcriptomic and Protein Array Cytokine Profiling of Human Stem Cells from Dental Apical Papilla Modulated by Oral Bacteria. Int. J. Mol. Sci. 2022, 23, 5098. https://doi.org/10.3390/ijms23095098
Razghonova, Y.; Zymovets, V.; Wadelius, P.; Rakhimova, O.;Manoharan, L.; Brundin, M.; Kelk, P.;Romani Vestman, N. TranscriptomeAnalysis Reveals Modulation ofHuman Stem Cells from the Apical Papilla by Species Associated with Dental Root Canal Infection. Int. J. Mol. Sci. 2022, 23, 14420. https:// doi.org/10.3390/ijms232214420

Conferences:

Zymovets V., Schmidt A., Rakhimova O., Grellier C., Landström M., Singer B. B., Romani Vestman N. (2022, September 11-14). Monoclonal antibodies against Fusobacterium spp. of oral origin: A prospective biotherapeutic strategy in regenerative endodontic treatment. 30th International CEA Symposium, Essen, Germany.
Zymovets V. O., Slobodyan V. O., Murinska N. A. Characteristics of phages isolates of phytopathogens causing the fire blight disease (2019, April 23-24). Science student conference “English in touch with science”, Odesa, Ukraine.
Zymovets V. O., Kotlyarova L. B., Zhuminska G. I. Characteristics of bacterial isolates from willows with symptoms of “Witches broom” disease. (2020, April 23-24). 76 conference of ONU I. I. Mechnikov, Odesa, Ukraine.
Lukina A.,  Zhunko I., Zhuminska G., Murinska N., Zymovets V., Slobodnyan V., Zaletska N. The secretion of siderophores by some strains of Pantoea agglomerans (2018, June 20-23). Materials of young scientists international conference "Modern problems of microbiology and biotechnology”, Odesa, Ukraine.

Certificates:

Certificate of Attendance, NBIS workshop “Introduction to Bioinformatics using NGS data” – 6-10^th February, 2023; Total 40 hours of lectures and computer exercises.
Certificate of Attendance NMMP Summer School in Transcriptomics During Development and Cancer – 27-30th June, 2022.
Certificate for an online course, Johns Hopkins University “Introduction to Genomic Technologies” – June 19, 2022
ESCMID Postgraduate Education Course, Online Attendance Certificate Personalised phage therapy: basic principles of monitoring and treatment – 7-10th June, 2022.
Course certificate for participation in practical part of FISH (Fluorescence in Situ Hybridization) course - November 2020.
Participation and completion of 5 Days of Stem Cells virtual events (by Thermo Fisher Scientific) – October 2020.
Participation in Nordic meeting on Development, Stem cells and regeneration – October 14th -15th, 2020; total of 14 hours of presentations.
Attendance the virtual workshop “Incucyte Live-Cell Analysis System” – November 11th, 2020

I am a bioinformatics researcher with expertise in cancer genomics and transcriptomics, protein/peptide therapeutics, and machine learning. Skilled in Python, R, bash/shell scripting, and tools like GEO, TCGA, cBioportal, STRING, Cytoscape and Weka. I have experience developing bioinformatics pipelines and working with HPC for efficient data processing. Also, I am currently expanding my skill set by working on amplicon sequencing data analysis for microbial community profiling.

EDUCATION

PhD Bioinformatics, 2014-2020

Pondicherry University, Puducherry, India

M.Phil. Bioinformatics,  2013-2014

Vels University, Chennai, India

MSc. Bioinformatics, 2009-2011

University of Madras, Chennai, India

BSc. Microbiology, 2006-2009

University of Madras, Chennai, India

WORK EXPERIENCE

Research Associate, April 2023 – February 2025

Computational Biology, Bioinformatics & Crosstalk Lab, ACTREC – Tata Memorial Centre, Navi Mumbai, Maharashtra, India

Research Associate, October 2020 – September 2022
Department of Computational Biology, Indraprastha Institute of Information Technology, Delhi, India

Medical Coder, 2011-2013

Ajuba Solutions Pvt. Ltd., Chennai, Tamil Nadu, India

AWARDS AND ACHIEVEMENTS

DBT-Research Associate, October 2020 - September 2022

Department of Biotechnology, Govt.. of India

Senior Research Fellow-Direct, May 2018 - April 2020

Council of Scientific & Industrial Research, Govt. of India

I have authored 27 publications, including original research articles, reviews, and book chapters in top-tier international peer-reviewed journals from renowned publishers such as Elsevier, Wiley, Oxford University Press, PLOS One and Springer. My work has received over 577 citations to date. I have served as a peer reviewer for several prestigious journals, including Scientific Reports, BMC journals, and Springer publications. I have co-mentored multiple research projects across various academic levels and collaborated extensively with clinicians to support interdisciplinary research. I have presented my research through oral and poster presentations at several national and international conferences. Additionally, I received a Certificate of Appreciation for delivering sessions in a virtual workshop on “Data Science and Machine Learning in Biology.” One of my review articles, “Computational Resources in Healthcare,” has been featured in Biotech Express Magazine, titled  “New Developments Led by Prof. Gajendra Raghava, IIIT-D in Computational Biology”.