Curriculum Vitae | Petar B. Petrov

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
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

Senior researcher (09.2021 - 03.2022), Researcher (05.2021-08.2021, part-time), Postdoc (08.2016 - 04.2021)

University of Turku, Institute of Biomedicine and MediCity Research Laboratories. Lymphocyte Cytoskeleton group of Docent Pieta Mattila. I was involved in several projects and had the leading role in two (bold):

AutoCoEv: a bioinformatics pipeline for the large-scale screening for coevolution between proteins. Paper published (Petrov et al., 2022). Script available at GitHub.

APEX2 proximity biotinylation reveals protein dynamics triggered by B cell receptor activation. Pre-print available at bioRxiv (Awoniyi et al., 2021).

Immunological and functional analysis of the membrane modulator MIM/MTSS1. Paper published (Sarapulov et al., 2020).

Antigen processing, vesicular transport and presentation in B cells. Paper published (Hernández-Pérez et al., 2020).

Evolutionary characterization of the conserved MIM/MTSS1 gene. Paper published (Petrov et al., 2019) and scripts developed for the study are available at GitHub.

Researcher (01.2016 - 04.2016)

University of Oulu, Department of Medical Microbiology and Immunology. Lymphocyte Development group of Prof. Olli Vainio. During this short period, I did finalising work on the last paper from my PhD studies.

PhD student (07.2008 - 12.2015)

University of Oulu, Department of Medical Microbiology and Immunology. Lymphocyte Development group of Prof. Olli Vainio. My PhD project studied a novel cell surface leukocyte protein called 'Trojan'. In this work, I showed that Trojan has an anti-apoptotic role, with a cytoplasmic signalling mechanism involving Ca++ mobilisation. I also described the novel gene family that Trojan belongs to and determined that it has been subjected to contrasting evolutionary constraints. The work was divided into three sub-projects, which produced three respective publications:

Characterisation of the novel, leukocyte protein 'Trojan' (Petrov et al., 2010).
Role of Trojan in apoptosis and its possible signalling mechanism (Petrov et al., 2017).
The evolutionary selection of the novel Trojan gene family (Petrov et al., 2015).

The papers are part of my Dissertation, titled 'Leukocyte protein Trojan, as a candidate for apoptotic regulatory role'.

Research assistant (02.2005 - 06.2008)

University of Oulu, Department of Medical Microbiology and Immunology. Lymphocyte Development group of Prof. Olli Vainio. I worked on lymphocytes development and part of my work was used for my MSc thesis, that was done in the same department. The title of my thesis was 'Trojan: a novel avian lymphocyte surface protein, involved in T-cell development' which later became my PhD project.

Intern (2002; 2003; 2004)

I did three internships for a total period of 11 months in University of Turku, Department of Microbiology.

Competence

Research

I 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.

Writing

I 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.

Figures

I 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).

Presentations

I have given presentations in a variety of conferences, seminars and other scientific meetings.

Technical experience

Computational biology

I 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:

Protein sequence characterisation, using EMBOSS/EMBASSY, Staden package, SA, as well as publicly available databases, such as SMART, ELM, PROSITE, NetPhos, NetGlyc and more. I have also performed protein modelling and structural analysis by Phyre2, CPHModels, Pcons.net, and UCSF Chimera.

I have done phylogenetic analyses by PhyML, and have used PAML/CodeML and HyPhy (SLAC, FUBAR, MEME) to test genes for evolutionary selection. I have also used CAPS2 and MISTIC to study intra- and inter- protein co-evolution.

I have experience with interrogating databases at Ensembl, NCBI or UCSC. I have also run blast locally and have used liftOver to extract genomic coordinates between species.

I have done gene modelling and prediction by GeneWise and GENSCAN. For publication figures, GenomeTools were used render graphically genomic coordinates from gff3 files. I have used Geneconv to determine gene conversion and have dated a gene duplication event by PAML/CodeML.

I have used the MeMe-suite for transcription factor binding sites (TFBS) motifs discovery, in an automated manner by custom scripts. Databases for TFBS matrices were HOCOMOCO and Jaspar.

Of course, I have done extensive multiple sequence alignments, using a variety of programs, among which are MAFFT, MUSCLE, PRANK, CLUSTAL-O/W and T-coffee. In addition, I have used PAL2NAL for creating codon MSA, and SIM/Lalnview to inspect pairwise alignments.

I am also interested in genomics/transcriptomics and I took three relevant courses: RNA-Seq Analysis (Babraham Bioinformatics, 29 Oct 2020), Long-read Transcriptomics (Edinburgh Genomics, 11-13 Nov 2020) and RNA-Seq Data Analysis (Edinburgh Genomics, 26-29 Apr 2021).

Wet-lab

I have long years of experience in the wet-lab, using different techniques:

I have worked with primary cells (lymphocytes from chicken and mouse), as well as, cell lines (chicken MDCC-CU T-cell lines, DT40, A20), including culturing, transfection and antibody production from hybridomas.

I am experienced in flow cytometry and have performed multiple-colour staining, CFSE proliferation assays, surface receptor internalisation assays, apoptosis assessment and calcium flux measurements. Instruments I have mainly used are FACSCalibur and Fortessa. Software for offline analysis I have mostly used is WEHI Weasel, FCSAlyzer and CellQuest (in the past).

I have background in biochemistry and have done immunoprecipitation (sepharose or magnetic beads coupled to protein A), SDS-PAGE, gel staining, western blotting and ELISA.

Among the molecular biology techniques that I have utilised are RNA isolation, (RT)-PCR, cloning inserts into vectors, bacteria transformation and plasmid isolation.

I also set up in Mattila lab the technique to measure cellular energetics by Agilent Seahorse.

Office

I 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

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

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

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

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

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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