Meritförteckning

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

Fields of Research:

The major focus of 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, PCR primer design.

Software development:
Repeater2 2023→  [https://github.com/rkalendar/Repeater]

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 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]

Java web tools for PCR, in silico PCR, and oligonucleotide assembly and analyses 2008 → The tools provide comprehensive facilities for designing primers for most PCR applications. The in silico PCR primer or probe search includes comprehensive analyses of individual primers and primer pairs and is helpful for discovering target binding sites. The software can also be used for identifying simple sequence repeat (SSR) loci and for patterns analysis of sequences. It calculates the melting temperature for standard and degenerate oligonucleotides including LNA and other modifications and provides analyses for a set of primers with the prediction of oligonucleotide properties, self- and cross-dimer and G-quadruplexes detection, linguistic complexity, and provides a dilution and resuspension calculator for stocks. [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] 

Oligomer Web tools 2009-2012 "PrimerAnalyser" (comprehensive primer test, Tm calculation, PCR efficiency, dimers detection and dilution and resuspension calculator); ”in silico PCR” (in silico PCR primers and probes search - prediction of probable PCR products and search of potential mismatching location of the specified primer(s) or probe(s)); "PCR primers design" (designing any kind of PCR primers for standard, long distance, inverse, real-time PCR analysis). [http://www.oligomer.fi/en/analyysityokalut]

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.