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You can find out here the main topics of my research. I think that synthetic and systems biology promise to develop novel approaches for analysis of complex gene expression control networks and engineering living cells with many practical applications to the pharmaceutical industry and nanobiotechnology. I employ various computational and experimental methods of molecular modeling in order to develop novel analytical and therapeutical approaches. The research in my laboratory is all about making innovations that have both theoretical and practical impacts on science and technology (see our research on LinkedIn). For instance, recently we have filed two patent applications in the field of drug development. Our research was noticed and commented in journals such as Nature Biotechnology, Nature Methods, ACS Synthetic Biology, and RSC Chemistry World.

Our recent paper is an editors' choice of the American Chemical Society! grant:DN13/14/20.12.2017

Our research and experience was discussed in an interview given to the magazin of Bulgarian Science by Prof. Robert Penchovsky, broadcasted on 04/21/2022. You can listen to it below in Bulgarian only.

Our research funded by grant DN13/14/20.12.2017 was presented on the main webpage of Sofia University (see the image below).

Our research was discussed in an interview given to the Bulgarian National Radio (BNR) by Prof. Robert Penchovsky, broadcasted on 3/24/2022. You can listen to it below in Bulgarian only.

Recently, the research in the Robert Penchovsky laboratory was supported by a grant DN13/14/20.12.2017, completed with 20 publications with IF of 84 points and Q1-4 of 274 points, entitled "Design and experimental validation of chimeric antisense oligonucleotides as antibacterial agents", featured on the website of Sofia University (see the image above) and is currently supported by a grant KP-06-H31/18/13.12.2019 entitled "Engineering functional nucleic acids for synthetic control of gene expression in prokaryotes and eukaryotes" awarded by the Bulgarian National Science Fund (BNSF). You can see a presentation of the results of the first half of the project DN13/14/20.12.2017 on the video below (in Bulgarian only).

Video 1. Robert presents the results of the first half of the project DN13/14/20.12.2017 (in Bulgarian).

Our research is acknowledged in several News and Views papers, including publications in Nature Biotechnology, Nature Methods, and others (see the publication page). Our research was praised by Prof. Dr. Draga Toncheva, the national consultant on Medical genetics, in an interview given to the Bulgarian National Radio (BNR) on 09/09/2017. You can listen to it below in Bulgarian only.

My research was acknowledged by an award from the Bulgarian national contest for scientific excellence for researchers of all areas over 35 years old organized by the Union of the Scientists in Bulgaria. My research was awarded for scientific excellence achieved in the fields of synthetic biology, bioinformatics and molecular evolution. The ceremony was held in the aula of Sofia University on November 2nd, 2015 (see the photo below).

Robert is receiving an award from the Bulgarian national contest for scientific excellence

The research in Robert Penchovsky's laboratory was supported by 17 different grants, including grant:DDVU02/5/2010, entitled "Design and applications of RNA biosensors in vitro and in vivo" awarded by the Bulgarian National Science Fund. This grant was very successfully completed with 9 research publications with a common impact factor of 34 for only 42 400 EUR in July 2014.

Synthetic cellular circuitries

Two of my Ph.D. students, Georgi and Antoniya, working in the lab.

Bravo Antoniya, a doctoral student of main - the first prize winner in the national contest "Young and Energetic Scientists" in Ph.D. category, 2021 at the ceremony with Mariya Gabriel, European Commissioner for Innovation, Research, Culture, Education and Youth.

Our highly respectable rector Prof. Anastas Gerdzhikov together with my doctoral student Georgi Miloshev, the winner of the prize "doctoral student of the year 2022" of Sofia University, in the Aula of the SU, after the ceremony, May 26, 2022. Georgi works on several research projects, including DN13/14/20.12.2017, KP-06-H31/18/13.12.2019, and KP-06-M33/5/18.12.2019 awarded by the BNSF (for more information click here).

Here you can see a poster of awarded best research project RD-22-838/2020 of Dr.Martina Traykovska (see the image below) with supervisor Prof. Robert Penchovsky by the Bulgarian Ministry of Education and Science for young scientists in biology, Sofia Science Festival, May 15-16, 2021 (for more information click here).

The members of Penchovsky laboratory Dr. Katya Popova, Dr. Nikolet Pavlova, Dr. Martina Traykovska, and Dr. Lozena Otcheva (from left to right-hand) in front of their 2nd place award winning posters at 14th Congress of Microbiologists in Bulgaria with International Participation, October 10-13, 2018 (see the image below -for more information click here).

Note that I am doing not only research but also biotech consulting for various institutions in the scientific areas mentioned below. Inquiries on biotech consulting are very welcome. We have all essential pieces of equipment in my laboratory of Synthetic Biology (see the images below).

Essential pieces of equipment in my laboratory of Synthetic Biology
tools tools

We have established a newly equipped laboratory of Molecular Genetics and Genomics completely funded with a donation by the “Petar Mandjoukov“ Foundation. We are very thankful to all people from the “Petar Mandjoukov“ Foundation and particularly to Mr. Petar Mandjoukov for his great generosity and vision to support our teaching and research activities (see the image below).

Robert in the new lab.

Dr. Dimitrina Miteva played a pivotal role in the establishment of the newly equipped laboratory of Molecular Genetics and Genomics, which was completely funded with a donation by the “Petar Mandjoukov“ Foundation (see the image below).

Dimitrina in the new lab.

Robert's research keywords: ribozymes, riboswitches, bioinformatics, biosensors, microfluidics, DNA/RNA computing, RNA synthetic biology, and rational drug design.

In synthetic biology, my research is developing novel universal strategies for exogenous control of gene expression, re-programming the cell fate, and anticancer therapies. I am engineering complex gene expression control networks (our plasmid pRS414ge - sequence) that apply allosteric ribozymes, called designer riboswitches. The riboswitches function as Boolean logic gates both in vitro and in vivo by sensing the presence of predefined oligonucleotides (short DNAs and RNAs). All designer riboswitches are obtained by on novel and efficient computational procedure that is subject to a pending patent application. This engineering approach has a significant scientific impact not only on synthetic biology but also will have many useful applications to the pharmaceutical and biotech industries.

  Pipeting Robot     Parallel Computing     RNA Autoradiographies     E. coli Bacterium     Plasmid DNA  
tools tools tools tools tools

In computational biology, I have applied a novel strategy for computational high-throughput screening of key RNAs or proteins with known 3D-structures for drug discovery. The approach employs highly parallel computing platforms and can rapidly test millions of chemical compounds significantly reducing the resources spent for drug lead discovery.


In RNA biology - riboswitches, I have been experimentally verifying the putative function of non-coding RNAs. In addition, I have been involved in developing high-throughput screening arrays for antibacterial drug discovery using RNA targets.

In microfluidics, I have designed fully programmable and automated microfluidic chips for parallel biochemical analytical arrays under isothermal conditions. For this aim, I have developed novel chemical procedures for    nucleic acids and protein immobilization and DNA selection.

In biosensor engineering and nanobio- technology, I have built biosensors using my designer riboswitches for molecular diagnostics and computing. Such biosensors function as nanodevices that sense the presence of predefined molecular signals and execute complex logical circuits. The integration of those biosensors with microflow reactors is a very promising approach with my analytical applications to nanobiotechnology.

In bioinformatics, we have designed 15 essential and very useful bioinformatics applets, bioinformatics database and programs for computational design of allosteric ribozymes (see the application page).

In drug development, we have designed and tested many ASO-based drug candidates. You can see an interview on this subject with Dr. Martina Traykovska (see the image above) here (in Bulgarian only).