Department of Plant Physiology & Molecular Biology, University of Plovdiv originate since the High Pedagogical Institute is established in 1961 as a branch of knowledge Plant Physiology in Department of Botany. In 1974, Plant Physiology is established as different branch of knowledge with head Prof. George Kimenov and five lecturers more. The first young assistants and post-graduates are approved in 1989–1990. Since 1989, head of department is Prof. Ivan Minkov.  At the same time in the department is established a new branch of knowledge – Molecular Biology, as educational and scientific research, later on and Genetic Engineering with head Associate Professor Stefan Dukyandjiev. Laboratory of Genetic Engineering and Plant Biotechnologies are built. In the department are incoming gradually new young lecturers and PhD students. The number of the disciplines is increasing. In 1995, the department is renamed as "Department of Plant Physiology and Molecular Biology'. Since 2015, head of department is Prof. Valentina Toneva

In 2000 as a result of hard work by the department and the rectorship, in the Faculty of Biology starts new bachelor degree of education - Molecular Biology. It is the most popular and desired discipline at the moment. The major disciplines studied in our department are Molecular Biology, Molecular Genetics, Molecular Virology, Molecular Evolution, Genetic Engineering, Biological Membranes, Bioinformatics and Molecular Ecology.Later in 2004 is introduced one more bachelor degree – Bioinformatics.The department has played a major role for its approvment.There are two Master degrees at the department – Bioinformatics and Molecular Biotechnologies.

At the moment, the staff of department includes 25 members – 10 are lecturers, 3 experts, 6 PhD students and 6 scientific workers and specialists, appointed at international and national scientific programs.

In the department are developing the following scientific branches of knowledge: "Molecular principles of abiotic tress and programmed cell death", "Interaction between viroids and high plants", "Bioinformatical research of viroids", "Regulation of human oncogenes by miRNA", "Role of the mobile genetic elements and miRNA for the evolution", "Insecticide delta-endo toxins and transgenic plants, resistant to insects", "Plant vaccine against hepatitis B", "Bioinformatical approaches for researching of miRNA", "Molecular Phytopathology of Orobanche sp.", "Research of some new transcriptional factors in Arabidopsis sp.", "Epigenesis and DNA methylation".

In 2003 on the basis of department, in University of Plovdiv is established Genomics Research Center which is taking participation in several international projects.In a result of scientific work, in the last 6-7 years many scientific articles with impact factor in common 120 are published, repeatedly quoted in authoritative international scientific journals.

Since 1994 until now, the department has taken participation in many scientific and educational projects with fund amount 1 000 000 EUR. In the last 3-4 years the department has involved in seven projects under Sixth Framework Programme (FP6), in a result University of Plovdiv "Paisii Hilendarski" has been awarded as best performed regional FP6 University.

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