Division "Bioinformatics and genome evolution of microorganisms"

RDimitrov

Asc. Prof. Rumen Dimitrov
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NATIONAL CENTRE OF INFECTIOUS AND PARASITIC DISEASES

Domain of scientific research:

Evolurionary bioinformatics of microorganisms

Head of Division

"Bioinformatics and genome evolution of microorganisms"

departement of Microbiology

Plan of activities in 2019

Curriculum Vitae

PERSONAL INFORMATION
Name		DIMITROV, RUMEN ATANASOV
Address		National Center of Infectious and Parasitic Diseases (NCIPD), 26, Yanko Sakazov Blvd., Sofia 1504
E-mail		This email address is being protected from spambots. You need JavaScript enabled to view it., This email address is being protected from spambots. You need JavaScript enabled to view it.

Nationality		Bulgarian

Date of birth		01/07/1959 Sofia

WORK EXPERIENCE
Dates (from-to)		2018
Name and address of employer		National Center for Infectious and Parasitic Diseases (NCIPD), 26, Yanko Sakazov Blvd., Sofia 1504
Type of business or field of research		Scientific Research - Evolutionary Microbial Bioinformatics
Occupation		Associate Professor PhD, Head of Division: Bioinformatics and Genomic Evolution of Microbes, Department of Microbiology

Dates (from-to)		2004-2018
Name and address of employer		SOFIA UNIVERSITY, PHYSICAL FACULTY, DEPARTMENT OF THEORETICAL PHYSICS, BULGARIA JAMES BAUCHAR № 5, Sofia 1164, Bulgaria
Type of business or field of research		Bioinformatics, Computational Biology, Biophysics, Biological Evolution
Occupation		Physics, PhD
Main activities and responsibilities		Lectures, exercises and scientific activities

EDUCATION AND TRAINING
Dates (from-to)		2000-2004
Name and type of organization providing education and training		Rensselaer Polytechnic Institute, Troy, New York, USA
Principal subjects / occupational skills covered		Theoretical methods for calculating the statistical sum of RNA and DNA molecules
Title of qualification awarded		Post-doctoral position

Dates (from-to)		1995-2000
Name and type of organization providing education and training		Department of Biochemistry, Wageningen University and Research Center, Wageningen, The Netherlands
Principal subjects / occupational skills covered		Bioinformatics and computational biology
Title of qualification awarded		PhD
Level in national classification (if applicable)		PhD

Dates (from-to)		1990-1995
Name and type of organization providing education and training		Institute of Physics Belgrade, RAN, Pushchino, Moscow Oblast, Rosia
Principal subjects / occupational skills covered		Physics
Title of qualification awarded		Postgraduate qualification

Dates (from-to)		1985-1990
Name and type of organization providing education and training		Institute of Organic Chemistry, BAS, Sofia
Principal subjects / occupational skills covered		Electrostatic interactions in protein molecules
Title of qualification awarded		Specialist

Dates (from-to)		1980-1985
Name and type of organization providing education and training		SOFIA UNIVERSITY "KLIMENT OHRIDSKI"
Principal subjects / occupational skills covered		Physics with specialization "PHYSICS OF CONDENSED MATTER"
Title of qualification awarded		Master

PERSONAL SKILLS AND COMPETENCES
NATIVE LANGUAGE		BULGARIAN

OTHER LANGUAGES
		ENGLISH
Reading skills		Excellent
Writing skills		Excellent
Conversational skills		Excellent
		RUSSIAN
Reading skills		Excellent
Writing skills		Excellent
Conversational skills		Excellent

Bioinformatics and genome evolution of microorganisms

Our research focuses on understanding how natural selection, microbial demography and lifestyle have formed the patterns of microbial genomes biodiversity and how this can influence the emergence and development of virulent phenotypes of emerging microbial pathogens and their infectious potentials. Our goal is to identify the genes governing the origin of the infection and its transmission.

The scientific methods we apply have interdisciplinary character and overlap with directions such as molecular evolution, population genetics, molecular epidemiology, molecular genetics, microbial pathogen biology, mathematics, physics and computer information technology.

At the bioinformatics level, this requires:

• application of modern methods for: sequencing of complete microbial genomes, genotyping, analysis of resistance mechanisms and virulence factors;

• analysis of the genomic architecture of microbial microorganisms;

• Analysis of the role played by genomic plasticity and the dynamics of genomic reorganizations in the emergence of new microbial pathogens at the microevolutionary and epidemiological level?

• What are the evolutionary mechanisms that model the processes of colonization of new hosts belonging to different phylogenetic units - species, genus, family, and others.

Our latest projects are focused on the genetics of macromolecular interactions. Using extensive research on genetic diversity in phylogenetic and population genetic frameworks, we analyse the impact of selection on genetic variability. We are currently developing a new approach for structurally related but highly divergent sequences to simultaneously align and fold DNA / RNA and proteins based on probability matching of their bases. A long-term goal is to understand the influence of mutational perturbations on molecular recognition mechanisms. These mechanisms are extremely important and underpin the dynamic transformation, folding and self-assembly of biological macromolecules in supramolecular complexes. It is also essential to involve the separate biological macromolecules and their supramolecular complexes in complex biological networks - genetic, signal, regulatory and metabolic. And most importantly, what is the effect of mutational perturbations on the phenotype of complex diseases.

	December 2018		In NCIPD was officially created and started functioning division "Bioinformatics and genome evolution of microorganisms" headed by Asc. Prof. Rumen Dimitrov

	November 2018		Participation in the INTERNATIONAL SCIENTIFIC CONFERENCE KLIMENT'S DAYS 8^th-9^th November 2018

	September 2018		European Molecular Biology Laboratory - EMBL certification

	November 2017		OpenAccess course "Bioinformatics for beginners" in SoftUni- Part 2 (in Bulgarian)

	September 2017		OpenAccess course "Bioinformatics for beginners" in SoftUni- Part 1 (in Bulgarian)

DNA gif Publikacii

RA Dimitrov, D. Gouliamova. Genetic and phenotypic cut-off values for species and genera discrimination of the kazachstania clade. Comptes rendus de l’Académie Bulgare des Sciences, in press.
D. Gouliamova, RA Dimitrov. Kazachstania chrysolinae and kazachstania bozae two new yeast species of the genus kazachstania. transfer of four kazachstania species to grigorovia gen. nov. as new combinations. Comptes rendus de l’Académie Bulgare des Sciences, in press.
D. Gouliamova, RA Dimitrov, M. Stoilova-Dasheva. New species Priceomyces Vitoshaensis isolated from Pterostichus melas (Carabidae, Coleoptera). In book: Microbiology for a better health and industry-70 years the Stephan Angeloff Institute of Microbiology. (Editors: H. Najdenski, M. Angelova, L. Kabaivanova, N. Kostadinova, J. Miteva-Staleva), 2017, Sofia, ISBN 978-954-92882-2-3.
P.W. Crous, M.J. Wingfield, T.I. Burgess, A.J. Carnegie, G.E.St.J. Hardy, D. Smith, B.A. Summerell, J.F. Cano-Lira, J. Guarro, J. Houbraken, L. Lombard, M.P. Martín, M. Sandoval-Denis, A.V. Alexandrova, C.W. Barnes, I.G. Baseia, J.D.P. Bezerra, V. Guarnaccia, T.W. May, M. Hernández-Restrepo, A.M. Stchigel, A.N. Miller, M.E. Ordoñez, V.P. Abreu, T. Accioly, C. Agnello, A. Agustin Colmán, C.C. Albuquerque, D.S. Alfredo, P. Alvarado, G.R. Araújo-Magalhães, S. Arauzo, T. Atkinson, A. Barili, R.W. Barreto, J.L. Bezerra, T.S. Cabral, F. Camello Rodríguez, R.H.S.F. Cruz, P.P. Daniëls, B.D.B. da Silva, D.A.C. de Almeida, A.A. de Carvalho Júnior, C.A. Decock, L. Delgat, S. Denman, R.A. Dimitrov, J. Edwards, A.G. Fedosova, R.J. Ferreira, A.L. Firmino, J.A. Flores, D. García, J. Gené, A. Giraldo, J.S. Góis, A.A.M. Gomes, C.M. Gonçalves, D.E. Gouliamova, M. Groenewald, B.V. Guéorguiev, M. Guevara-Suarez, L.F.P. Gusmão, K. Hosaka, Hubk. Fungal Planet description sheets: 625–715. Persoonia, 2017, 39, 270-464.
P.W. Crous, M.J. Wingfield, D.M. Richardson,, J.J. Le Roux, D. Strasberg, J. Edwards, F. Roets, V. Hubka, P.W.J. Taylor, M. Heykoop, M.P. Martín, G. Moreno, D.A. Sutton, N.P. Wiederhold, C.W. Barnes, J.R. Carlavilla, J. Gené, A. Giraldo, V. Guarnaccia, J. Guarro, M. Hernández-Restrepo, M. Kolařík, J.L. Manjón,, I.G.Pascoe, E.S. Popov, M. Sandoval-Denis, J.H.C. Woudenberg,, K. Acharya, A.V. Alexandrova, P. Alvarado, R.N. Barbosa,, I.G. Baseia, R.A. Blanchette, T. Boekhout, T.I Burgess, J.F. Cano-Lira, A. Čmoková, R.A. Dimitrov, M.Yu. Dyakov, M. Dueñas, A.K. Dutta, F. Esteve- Raventós, A.G. Fedosova, J. Fournier, P. Gamboa, D.E. Gouliamova, T. Grebenc, M. Groenewald, B. Hanse,, G.E.St.J. Hardy, B.W. Held, Ž. Jurjević, T. Kaewgrajang, K.P.D. Latha, L. Lombard, J.J. Luangsa-ard, P. Lysková, N. Mallátová, P. Manimohan, A.N. Miller, M. Mirabolfathy, O.V. Morozova, Obodai, N.T. Oliveira, M.E. Ordóñez, E.S.Otto, S. Paloi, S.W. Peterson, C. Phosri, J. Roux, W.A. Salazar, A. Sánchez, G.A. Sarria, H.-D. Shin, B.D.B Silva, G.A. Silva, M.Th. Smith, C.M. Souza-Motta, A.M. Stchigel, M.M. Stoilova-Disheva, M.A. Sulzbacher, M.T. Telleria, C. Toapanta, J.M. Traba, N. Valenzuela-Lopez, R. Watling, J.Z. Groenewald. Fungal Planet description sheets: 400–468. Persoonia, 36, National Herbarium of the Netherlands, 2016, ISSN:0031-5850, 316-458.
Dilnora E. Gouliamova, Roumen A. Dimitrov, Maudy Th. Smith, Marizeth Groenеwald, Margarita M. Stoilova-Disheva, Borislav V. Guéorguiev, Teun Boekhout. DNA barcoding revealed Nematodospora valgi genus nova species nova and Candida cetonia species nova in the Lodderomyces clade. Fungal Biology, 2015, doi:10.1016/j.funbio.2015.05.008
Crous PW, Wingfield MJ, Guarro J, Hernández-Restrepo M, Sutton DA, Acharya K, Barber PA, Boekhout T, Dimitrov RA, Dueñas M, Dutta AK, Gené J, Gouliamova DE, Groenewald M, Lombard L, Morozova OV, Sarkar J, Smith MT, Stchigel AM, Wiederhold NP, Alexandrova AV, Antelmi I, Armengol J, Barnes I, Cano-Lira JF, Castañeda Ruiz RF, Contu M, Courtecuisse PR, da Silveira AL, Decock CA, de Goes A, Edathodu J, Ercole E, Firmino AC, Fourie A, Fournier J, Furtado EL, Geering AD, Gershenzon J, Giraldo A, Gramaje D, Hammerbacher A, He XL, Haryadi D, Khemmuk W, Kovalenko AE, Krawczynski R, Laich F, Lechat C, Lopes UP, Madrid H, Malysheva EF, Marín-Felix Y, Martín MP, Mostert L, Nigro F, Pereira OL, Picillo B, Pinho DB, Popov ES, Rodas Peláez CA, Rooney-Latham S, Sandoval-Denis M, Shivas RG, Silva V, Stoilova-Disheva MM, Telleria MT, Ullah C, Unsicker SB, van der Merwe NA, Vizzini A, Wagner HG, Wong PT, Wood AR, Groenewald JZ. Fungal Planet description sheets: 320-370. Persoonia, 2015,34:167-266. doi: 10.3767/003158515X688433.
Dimitrov R. A., Gouliamova D. E. Biological sequence comparison, molecular evolution and phylogenetics. Biotech. & Biotech. Equip., First published online DOI: 10.5504/50YR-
TIMB. 2011, 209-217.
Gouliamova D. E., Dimitrov R. A., Stoilova-Disheva M. M. DNA-barcoding of yeasts from selected Bulgarian food products. Biotech. & Biotech. Equip., First published on line DOI:10.5504/50 YRTIMB. 2011, 32-34.
Gouliamova D. E., Stoilova-Disheva M. M, Dimitrov R. A., Gushterova A. Preliminary characterization of yeasts and actinomycetes isolated from mammalian feces. Biotech. & Biotech. Equip., First published on line DOI: 10.5504/50YRTIMB. 2011, 26:1-4.
Dimitrov R. A., Gouliamova D. E. New method for sequence alignment based on proba-bilities of nucleotide correspondences. Biotech. & Biotech. Equip., First published online DOI:10.5504/50YRTIMB.2011, 218-223.
Gouliamova D. E., Dimitrov R., Petrova P., Stoyancheva G. and Petrov K. Genomic approaches to yeast taxonomy. Biotech. & Biotech. Equip., 23/2009/SE, 519-523.
Dimitrov R. A., Gouliamova D. E. Bioinformatic education perspective and challenges. Biotech. & Biotech. Equip., 23/2009/SE, 40-42.
Petrova P., Gouliamova D. E., Petrov K., Stoyancheva G., Dimitrov R. Starch-degrading activities of Bulgarian yeast isolates. Biotech. & Biotech. Equip., 23/2009/SE, 651-654.
RA Dimitrov, M Zuker. Prediction of hybridization and melting for double-stranded nucleic acids. Biophysical Journal, 2004, 87 (1), 215-226.
SI Dimitrov, RA Dimitrov, BG Tenchov. Effect of ionic strength on the chromatin conformational transitions. A differential scanning calorimetry study. International Journal of Biological Macromolecules, 1988, 10 (3), 149-152.
R Dimitrov. microRNA Gene Finding and Target Prediction - Basic Principles and Challenges. MOJ Proteomics & Bioinformatics, 2014, 1 (4), 24
RA Dimitrov. A new formalism for calculation of the partition function of single stranded nucleic acids. Bulg. J. Phys. 2005, 32, 220–235
Gouliamova D. E., Dimitrov R. A., Stoilova-Disheva M. M., Boekhout T. DNA barcoding analysis of yeasts from selected Bulgarian Ecosystems. New Trends In Microbiology. 2012, p. 205-216. (ISBN 978-954-92882-1-6).
RA Dimitrov, RR Crichton. Self-consistent field approach to protein structure and stability. i. ph dependence of electrostatic contribution. Self-consistent field approach to protein structure and stability, Proteins: Structure, Function and Genetics, 1997, 4:576-596.
Paul R Gooley, Max A Keniry, Roumen A Dimitrov, Danny E Marsh, David W Keizer, Kenwyn R Gayler, Bruce R Grant. The NMR solution structure and characterization of pH dependent chemical shifts of the β-elicitin, cryptogein. Journal of Biomolecular NMR, 1998, 12: 523–534.
RA Dimitrov. Self-consistent field approach to protein structure and stability. Published by: Grafisch Service Centrum, Nude 40, Wageningen, The Netherlands, 1999, ISBN:90-5485-986-5
Finkelstein A.V., Dimitrov R.A., Badretdinov A.Ya, Reva B. A.. Prediction of 3D Structures of Globular Proteins Based on Self-Consistent Molecular Field Theory. Protein Structure by Distance Analysis, 1994, 145-157