Ansioluettelo

1. Docent (No. 325/114/2007), Department of Biosciences, Division of Genetics, University of Helsinki  

   Fields of Research:

   The major focus is on the evolution, RNA world, biology of retrotransposons and their applications as markers for biodiversity and breeding (our developed techniques: IRAP, REMAP, and iPBS amplification techniques), synthetic biology and comparative bioinformatics (programming with C#, Java, VB, VBA, and JavaScript), algorithms: string searching and complexity analysis, search of repeats, DNA alignment and assembly, and PCR primer design.

   Software development:
   
   GitHub 2023→  https://github.com/rkalendar/
   
   TotalRepeats 2024→  https://github.com/rkalendar/TotalRepeats

   virtualPCR 2024→ https://github.com/rkalendar/virtualPCR
   
   PCRpanel 2024→ https://github.com/rkalendar/PCRpanel

   FastPCR software 1998 →  is an integrated tools environment that provides comprehensive facilities for designing primers for most PCR applications; in silico (virtual) PCR primers or probe searching, comprehensive pairs and individual primers analysis tests are included. The program includes various bioinformatics tools for the analysis of sequences. Oligonucleotides design for assembly long sequence or polymerase chain assembly (PCA) - created to automate the design of oligodeoxynucleotides for the PCR-based construction of long DNA molecules (the desired gene sequence is segmented into short oligo sequences. The program includes various bioinformatics tools for patterns analysis of sequences with GC:(G-C)/(G+C), AT:(A-T)/(A+T), CG-AT:(S-W)/(S+W), purine-pyrimidine (R-Y)/(R+Y) skews, CG% content and the melting temperature and considers linguistic sequence complexity profiles.
   https://primerdigital.com/fastpcr.html http://primerdigital.com/tools/fastpcr.html

   JavaScript web tools for PCR, qPCR, LAMP, analyzing primers, setting up reactions, and repeats identification 2024 →
   PCR, qPCR primer design tool: The application is based on FastPCR software and provides professional facilities for designing primers for most PCR applications: standard, inverse, long-distance, real-time (TaqMan and MGB-probe assay design), and bisulfite PCR primer design.
   KASP primers assay design tool: Allele-Specific PCR (AS-PCR) - KASP™ (Kompetitive Allele Specific PCR) or PACE™ (PCR Allele Competitive Extension) or Allele-Specific Quantitative PCR (ASQ) based genotyping assay design for multiallelic discrimination of single nucleotide polymorphisms (SNPs) and insertions and deletions (Indels) at specific loci. The application is based on FastPCR software for genotyping assays design for SNP/InDel-specific KASP assay targeting primers (KASP Assay Mix) and the universal Master Mix.
   In silico PCR tool: Virtual (in silico) or electronic PCR (ePCR) primer or probe search against whole genome(s) or a list of chromosomes - prediction of likely PCR products and search for potential mismatches of the specified primers or probes. Search for multiple targets simultaneously within a specified range. In silico PCR primer searching is useful for the discovery of melting temperature target binding sites.
   Loop-mediated Isothermal Amplification (LAMP) primer design tool: The application is based on FastPCR software and provides professional facilities for designing primers for Loop-mediated Isothermal Amplification (LAMP) applications. LAMP uses 6, including 'loop' primers recognizing 8 distinct regions of target DNA for a particular amplification reaction. The LAMP Assay can also be used for bisulfite LAMP primer design.
   PrimerAnalyser: It comprehensively analyzes sequences with standard and mixed bases. The tool calculates the physical properties of the sequence, including length, CG content, melting temperature, molecular weight, extinction coefficient, optical density, sequence linguistic complexity, self-dimers detection. The melting temperature calculations are based on nearest-neighbor thermodynamic parameters for standard and degenerate oligonucleotides, including LNA modifications. It also provides a dilution and resuspension calculator for stocks.
   PrimersList: Analyzes different features of multiple primers simultaneously, including the melting temperature calculation for standard and degenerate oligonucleotides, GC content, sequence linguistic complexity, molecular weight, the extinction coefficient, and the optical density (OD); primers are analyzed for all secondary structures, including self-dimers and cross-dimers in primer pairs.
   TotalRepeats: Tool for de novo identification, masking and clustering of all repeated sequences at the genomic scale. This tool detects DNA sequences for interspersed repeats and low complexity DNA sequences (simple sequence repeats or microsatellites, telomers, and satellite sequences).
   PCR reaction setup calculator: PCR and LAMP (Loop-mediated Isothermal Amplification) reaction setup calculator.
   Universal dilution and mixing two solutions calculator: A dilution calculator is applicable for mixing two solutions with various concentrations (molar, %, or other), different pH levels, or the stock solution with a solvent like water.
   Oligo probe design for the Gator GeneSwift assay: Gator Bio’s GeneSwift Assay is a simple, fast, and reliable method for determining the titer. It streamlines a two-step procedure involving AAV lysis and genome hybridization within a single tube, which is succeeded by biolayer interferometry detection. https://primerdigital.com/tools/

   Thermo Fisher Scientific Inc. Web tools for PCR and qPCR 2005-2009, 2011 http://www.thermoscientificbio.com/webtools/

   Horizon Discovery Ltd. https://horizondiscovery.com/en/ordering-and-calculation-tools

   Mapping 1995-1998 The multipoint genetic linkage program (MS-DOS) https://primerdigital.com/soft/mapping.zip

   Trees 1993-1999 Phylogeny software (MS-DOS) https://primerdigital.com/soft/tree.zip

    

   Teaching and short projects supervising visitors and students:

   1. Alex Baumel, Population, Species and Evolution Lab., UMR CNRS 6553, University of Rennes 1. Campus Scientifique de Beaulieu, Rennes Cedex, France;
   2. Turkki Eeva-Marja, Institute of Biotechnology, University of Helsinki, Finland;
   3. Elisenda Ramallo Flaquer, Institut de Biologia Molecular de Barcelona – CSIC, c/Jordi Girona 18-26, 08034 Barcelona, Spain;
   4. Kristiina Antonius-Klemola, MTT, Plant Production Research, 31600 Jokioinen, Finland;
   5. Maria Pilar Valles Brau, Estacion Experimental Aula Dei, Av. Montanana 1005, 50059 Zaragoza, Spain;
   6. Angelika Zuk, Biological Institute of Latvian University, Plant genetic laboratory, Miera 3, Salaspils, rigas raj. 2169, Latvia;
   7. Marco Vukich, Universita di Pisa, Dipartimento di biologia delle piante agrarie, Italy;
   8. Kaisa Kajala, Queens' College, CB3 9ET, Cambridge, United Kingdom;
   9. Alena Gajdosova, Institute of Plant Genetics and Biotechnology, Slovak Academy of Sciences, Akademicka 2, P.O.B. 39A, 95007 Nitra, Slovak Republic;
   10. Petr Smykal, AGRITEC Plant Research Ltd., Plant Biotechnology Department, Zemedelska 2520/16, Sumperk, Czech Republic;
   11. Babak Abdollahi Mandoulakani, Department of Agronomy and Plant Breeding, Faculty of Agriculture, Tehran University, Karaj, Iran;
   12. Svetlana V. Boronnikova, the Faculty of Biology, Perm State University, Bukireva str., 15 Perm, Russia;
   13. Andrej Benjak, Dipl.Ing, Institute of Horticulture and Viticulture, Department of Applied Plant Sciences and Plant Biotechnology, University of Natural Resources and Applied Life Sciences, Peter Jordan Strasse 82, A-1190 Vienna, Austria;
   14. Ahmed Mansour Mohamed Mansour, Genetics Department, Faculty of Agriculture, Zagazig University, Sharkia Governorate, Egypt;
   15. Gabor Gyulai, Szent Istvan University, Godollo, H-2103, Institute of Genetics and Biotechnology, Hungary;
   16. Mary Jayne Manrique, Philippine Nuclear Research Institute, Philippines;
   17. Maria Goldshmidt, Institute of Evolution, Haifa, Israel;
   18. Roman Lunins, Biological Institute of Latvian University, Plant genetic laboratory, Miera 3, Salaspils, rigas raj. 2169, Latvia;
   19. Doungous Oumar, J.P.J. Biotechnology Laboratory, Institute of Agricultural Research for Development (IRAD), IRAD Ekona Regional Research Centre, PMB 25, BUEA, Cameroon;
   20. Natali Paramonova, Biological Institute of Latvian University, Plant genetic laboratory, Miera 3, Salaspils, rigas raj. 2169, Latvia;
   21. Lita Lapina, Institute of Biology, University of Latvia, Miera Str. 3, Salaspils, LV-2169, Latvia;
   22. Andrej Trebichalský, Slovak University of Agriculture in Nitra, Slovakia;
   23. Krzysztof Stawujak, Plant Breeding and Seed Science, the University of Agriculture in Krakow, Poland;
   24. Tatiana Zachepilo, Pavlov Institute of Physiology of the Russian Academy of Sciences, Laboratory of Genetics of Higher Nervous Activity, Saint-Petersburg, Russia;
       
   25. Vasilis Papasotiropoulos, Technological Educational Institute of Messolonghi, Greece;
   26. Marwa Mahmoud Ghonaim, Agriculture Research Center, Cairo, Egypt;
   27. Asmaa Abdel-Ghany, Agriculture Research Center, Cairo, Egypt;
   28. Viktor Tokan, Masaryk University, Faculty of Science, Czech Republic;
   29. Violetta Kotseruba, Komarov Botanical Institute RAS, Saint-Petersburg, Russia;
   30. Ivan Vogel, Institute of Biophysics, Brno Czech Republic.