Curriculum Vitae | Petar B. Petrov |
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Dear Visitor, My name is Petar, I was born in Sofia (Bulgaria) in 1982 and I have been living in Finland since 2005. I have a PhD in immunology and a MSc in biochemistry, both obtained from University of Oulu (Finland). My research projects have been in the fields of immunology, cell biology and protein evolution. I have done extensive work both in the wet lab and in silico. Apart from my mother tongue, I speak fluent English, I understand Russian pretty well, and I know some Finnish. At the moment I live in Oulu. Nice you stopped by! Best regards, Petar |
Degrees |
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PhD (2015)Immunology and cell biology - University of Oulu, Department of Medical Microbiology and Immunology; Oulu (Finland). Lymphocyte development group of Prof. Olli Vainio. Dissertation: Leukocyte protein Trojan, as a candidate for apoptotic regulatory role. D 1332 Acta Universitatis Ouluensis. D, Medica | |
MSc (2008)Biochemistry and Molecular Biology - University of Oulu, Department of Biochemistry; Oulu (Finland). Thesis done in the Department of Medical Microbiology and Immunology. Thesis: Trojan: a novel avian lymphocyte surface protein, involved in T-cell development | |
BSc (2004)Biotechnology - University of Perugia, Job Creation Oriented Biotechnology programme; Perugia (Italy). Thesis done in the Department of Microbiology, University of Turku (Finland) |
Work |
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Senior researcher (09.2021 - 03.2022), Researcher (05.2021-08.2021, part-time), Postdoc (08.2016 - 04.2021)
Researcher (01.2016 - 04.2016)PhD student (07.2008 - 12.2015)
Research assistant (02.2005 - 06.2008)Intern (2002; 2003; 2004) |
Competence |
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ResearchI have the experience to design, plan, carry out and optimise the experiments of my research, as well as interpret the data. I am capable of working individually and in a team. Through the years I have had the opportunity to work with people from different nationalities and institutions. I am strict in meeting deadlines such as project milestones, publication submissions/revisions and grant applications.WritingI am experienced in writing scientific texts and I have 5 papers as a first author (Petrov et al, 2010; 2015; 2017; 2019, 2022), with text written almost exclusively by me.FiguresI always aim to present data in a clear and logical way. I am particularly skilled in designing clear and visually appealing publication figures. Examples: Fig 1 (Petrov et al, 2015); Fig 3, Fig 4 (Petrov et al, 2019); Fig 3, Fig 5 (Petrov et al, 2022).PresentationsI have given presentations in a variety of conferences, seminars and other scientific meetings. |
Technical experience |
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Computational biologyI am proficient in BASH and I have been a Linux user since 2005. In my work, I have used BASH scripting, R (ggplot2, Phytools) and have briefly brushed upon C++, since I needed to prepare a patch for CAPS2 in order to extend its functionality and the verbosity of the results. Among the analyses I've done are:
Wet-labI have long years of experience in the wet-lab, using different techniques:
| OfficeI currently use WPS Office for text and presentations, while in the past I used OpenOffice.org and LibreOffice extensively. For spreadsheets, I still prefer Gnumeric, although lately I've been using also R/ggplot2.I use Inkscape for vector graphics and figures design in general. In addition, I use GIMP, mtPaint and Dia. I have used FIJI for image data quantification, GenomeTools to render graphically genomic coordinates from gff3 files, Pfam generator to render protein topology schematically from json format and Protter for polypeptide chain visualization. Finally, I use BlueFish for simple webpage design (like this one), while in the past I used Composer, part of the SeaMonkey suite. |
Papers |
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Petar B Petrov, Luqman O Awoniyi, Vid Šuštar, M Özge Balci & Pieta K Mattila.
AutoCoEv—A High-Throughput In Silico Pipeline for Predicting Inter-Protein Coevolution.
International Journal of Molecular Sciences (2022) Luqman O Awoniyi, Marika Runsala, Vid Šuštar, Sara Hernández-Pérez, Alexey V Sarapulov, Petar B Petrov & Pieta K Mattila. Novel players and large-scale protein dynamics of BCR activation revealed by APEX2 proximity labelling of lipid rafts. bioRxiv Alexey V Sarapulov, Petar Petrov, Sara Hernández-Pérez, Vid Šuštar, Elina Kuokkanen, Marika Vainio, Lena Cords, Marco Fritzsche, Yolanda R Carrasco & Pieta K Mattila. Missing-In-Metastasis / Metastasis Suppressor 1 regulates B cell receptor signaling, B cell metabolic potential and T cell-independent immune responses. Frontiers Immunology (2020) Sara Hernández-Pérez, Marika Vainio, Elina Kuokkanen, Vid Šuštar, Petar Petrov, Sofia Forstén, Vilma Paavola, Johanna Rajala, Luqman O. Awoniyi, Alexey V Sarapulov, Helena Vihinen, Eija Jokitalo, Andreas Bruckbauer & Pieta K Mattila. B cells rapidly target antigen and surface-derived MHCII into peripheral degradative compartments. Journal of Cell Science (2019) Petar Petrov, Alexey V Sarapulov, Lel Eöry, Cristina Scielzo, Lydia Scarfò, Jacqueline Smith, David W Burt & Pieta K Mattila. Computational analysis of the evolutionarily conserved Missing In Metastasis/Metastasis Suppressor 1 gene predicts novel interactions, regulatory regions and transcriptional control. Scientific Reports (2019) Petar Petrov, Riikka Syrjänen, Tatsuya Uchida & Olli Vainio. Leucocyte protein Trojan, a possible regulator of apoptosis. APMIS (2017) Petar Petrov, Riikka Syrjänen, Jacqueline Smith, M Weronika Gutowska, Tatsuya Uchida, Olli Vainio, David W Burt. Characterization of the Avian Trojan Gene Family Reveals Contrasting Evolutionary Constraints. PLOS ONE (2015) Riikka Syrjänen, Petar Petrov, Virpi Glumoff, Shentong Fang, Petri Salven, Eeva-Riitta Savolainen, Olli Vainio & Tatsuya Uchida. TIM-family molecules in embryonic hematopoiesis: Fetal liver TIM-4lo cells have myeloid potential. Experimental Hematology (2014) Petar Petrov, Maki Motobu, Jussi Salmi, Tatsuya Uchida & Olli Vainio. Novel leukocyte protein, Trojan, differentially expressed during thymocyte development. Molecular Immunology (2010) |
Presentations and posters |
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AutoCoEv: overview.
Presented on an internal group meeting (2021) presentation.
Leukocyte protein Trojan, as a candidate for apoptotic regulatory role. Presented on the 43rd Annual Meeting of the Scandinavian Society for Immunology; Turku, Finland, May (2016) presentation. Trojan, a possible regulator of apoptosis, belongs to a novel protein family. Shown on the 4th European Congress of Immunology, Vienna, Austria, Sep (2015) poster. Trojan, a possible regulator of apoptosis, belongs to a novel protein family. Shown on the 12th Science Day at Faculty of Medicine; Oulu, Finland, Feb (2015) poster. Characterisation of Trojan: a novel leukocyte protein. Presented on the European Congress of Immunology; Glasgow, Scotland, Sep (2012) poster. Common γ-chain cytokine receptors. Presented on a journal club meeting of the Department of Medical Microbiology and Immunology; University of Oulu, Finland, Nov (2011) presentation. Calcium signalling Presented on an internal group meeting of the Department of Medical Microbiology and Immunology; Oulu, Finland, Jan (2011) presentation. |
Teaching |
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I was tutor of junior students: two summer interns and a medical student doing his syventävät.
I have participated in teaching planning, group sessions with students, essays evaluations and laboratory exercises. Also, I have occasionally substituted a lecturer.
I am always glad to help others in the lab with protocols, equipment or scientific software.
During my PhD studies, I was member of the FACS core facility at University of Oulu. In addition to the flow cytometers maintenance, I helped researchers with the machines operation, acquisition software and offline analysis programs, such as WEHI Weasel. |
Grants |
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2017 Collaboration visit: the Roslin Institute, Scotland (by University of Turku Foundation: 1800 €) 2016 Conference travel: 43rd Meeting of the Scandinavian Society for Immunology; Turku, Finland (by SSI: 250 €) 2015 Conference travel: 4th European Congress of Immunology.; Vienna, Austria (by SSI: 500 €) 2014 Conference travel: 42nd Meeting of the Scandinavian Society for Immunology; Reykjavík, Iceland (by SSI 1000 €) 2012 Conference travel: 3rd European Congress of Immunology in Glasgow, Scotland (by SSI 500 €) 2011 Personal grant: one year financing (by Finnish Cultural Foundation 21,000 €) 2010 Course: Methods for Massively Parallel Sequencing; Uppsala, Sweden (by University of Uppsala 500 €) |
Hobbies |
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I have been a Linux user since 2005. For over 15 years, my distribution of choice was Slackware. A year ago,
I migrated to CRUX; the reasons are described in my humble blog.
I contributed to an open source project, called SlackBuilds.org -- a ports-like repository for Slackware Linux. I joined in 2011 and for version 14.2, I was among the top 10 maintainers, responsible for 150 entries. The majority of my scripts build scientific software that I use or have used for my work. There are some office programs and, well, a couple of small games, too... :) My recent updates can be viewed here. For CRUX, I maintain my own repository of ports at my personal GitHub page. There, I also have a few other mini-projects, such as FASTA colouring for my favourite text editor, Xfce 4.12 for Slackware 15.0, and more. As mentioned above, I have a small blog, called Slackalaxy, where I collect all Linux-related tutorials, tips and tricks that I have found useful. There, you can find the full list of what I maintain at SBo, as well as, a page dedicated to Slackware for biologists. |
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