Laboratory for Sequencing and Mathematical Modeling of the Transcriptome

The main project of the laboratory is the development of the system for the diagnostics of rare Mendelian disorders with a usage of the massive parallel sequencing technologies

Laboratory of sequencing and mathematical modelling of the transcriptome was established in MIPT in 2011 and is now part of the MIPT Life Sciences Center. Since 2013 the main project of the laboratory has become the development of the system for the diagnostics of rare Mendelian disorders with a usage of the massive parallel sequencing technologies. The work is being carried out under the State Contract of the Ministry of Industry and Trade of the Russian Federation No. 13411.1008799.13.086 for the performance of research and development work “The development of technology and production organization of the analysis system of genetic diseases with the use of massively parallel sequencing”. 

The diagnosis system of rare genetic diseases with the use of next-generation sequencing (NGS), developed in the laboratory, is designed to diagnose over 60 diseases by detecting at least 1500 of the known mutations in 60 genes. Nowadays, as a result of the joint work of medical genetics, molecular biologists and bioinformatics, the socially significant monogenic hereditary diseases caused by single-nucleotide substitutions, short insertions and deletions were selected, the database of the mutations associated with the most common hereditary diseases was created, and the algorithms for the analysis of DNA sequences were implemented. The primer panel for targeted amplification of genes associated with 60 hereditary diseases (about 450 pairs of primers) was developed and partially tested. The research work on the creation of the forecating system of the effect of mutations on the structural and functional properties of proteins encoded by the genes, in which mutations cause rare diseases, was carried out. 

The system of genetic diseases analysis, the first system in Russia, focused on the screening of the carriers of genetic defects associated with hereditary diseases was created in the laboratory. Such systems only begin to develop abroad.

Current Projects 
  • The development of the analysis system of hereditary respiratory diseases based on the next-generation sequencing 
  • The development of the analysis system of hereditary oncological diseases based on the next-generation sequencing 
  • The development of the software package that allows forecasting the effect of mutations on the structural and functional protein properties.

Sergey Kovalenko

Head of laboratory

Education

Associate professor

PhD in biology

Professional experience
Sergey Petrovich Kovalenko — the head of the laboratory, Candidate of Biological Sciences, Assistant Professor. The author of over 50 publications in the field of genetic engineering and molecular genetics of cancer, the founder of the Russian company "BioLink" focused on the development and use of genodiagnostic systems in oncology. The scientific director of Bioron Diagnostics GmbH Company (Ludwigshafen,Germany).
Academic Interests

Kamil Khafizov

Researcher

Professional experience
Kamil Khafizov — research scientist, Ph.D., Head of Bioinformatics Group, author of over 15 publications in top international scientisic magazines, has ~10 years years of working experience in the leading research institutes in Europe and the United States, an expert in the field of molecular modeling and simulations of protein structures and analysis of biological data, the co-author of the popular bioinformatics product AlignMe for the analysis of the protein homology, the co-author of dozens protein structures (PDB).
Academic Interests

Artem Kasianov

Researcher

Professional experience
Artem Sergeyevich Kasianov — research scientist, Candidate of Physical and Mathemetical Sciences, the author of 4 publications in top international scientisic magazines, the specialist in the development of new methods for the analysis of data obtained with the help of modern sequencing technologies.
Academic Interests

Olga Glazova

Junior researcher

Professional experience
Olga Vladimirovna Glazova — junior research scientist, the specialist of the next-generation sequencing, she developed and put into practice a system for the analysis of genetic cardiovascular diseases.
Academic Interests

Lev Petrenko

Senior researcher

Education
PhD in biology

Alina Matsvai

Laboratory assistant

Education
Undergraduate student

Inna Kichatova

Laboratory assistant

Education

Kichatova holds a degree in medical biophysics from Volgograd State Medical University.

She also has a diploma of a laboratory geneticist from the Russian Medical Academy of Postgraduate Education.

Maxim Ivanov

Technician

Education
MIPT student

2013

Journal of Structural and Functional Genomics

Crystal structure of human Karyopherin β2 bound to the PY-NLS of Saccharomyces cerevisiae Nab2

Soniat M, Khafizov K

Moscow Institute of Physics and Technology

PLoS ONE

Alignment of helical membrane protein sequences using AlignMe

Stamm M, Staritzbichler R, Khafizov K, Forrest LR

Moscow Institute of Physics and Technology

The Breast

BRCA1 gene mutations frequency estimation by allele-specific real-time PCR of pooled genomic DNA samples

M. S. Anisimenko, D. V. Mitrofanov, O. B. Chasovnikova, M. I. Voevoda, S.P. Kovalenko

Moscow Institute of Physics and Technology

2014

Molecular Vision

Gene regulation by PAX6: Structural-functional correlations of missense mutants and transcriptional control of Trpm3/miR-204

Q. Xie, D. Ung, K. Khafizov, A. Fiser, A. Cvekl

Moscow Institute of Physics and Technology

Proceedings of the National Academy of Sciences

Trends in structural coverage of the protein universe and the impact of the Protein Structure Initiative

K. Khafizov, C. Madrid-Aliste , S.C. Almo , A. Fiser

Moscow Institute of Physics and Technology

Nucleic Acids Research

AlignMe – a Membrane Protein Sequence Alignment Web Server

M. Stamm, R. Staritzbichler, K. Khafizov, L.R. Forrest

Moscow Institute of Physics and Technology

Melanoma Research

Allele-specific RealTime PCR assay for sensitive detection of BRAF V600E mutation in melanoma samples

Shamanin V.A., Pisareva E.E., Gutkina N.I., Lyubchenko L.N., Schneider-Stock R., Kovalenko S.P.

Moscow Institute of Physics and Technology

Institute of Molecular Biology and Biophysics

Institute of Medical Genetics

Research Institute of Pulmonology

Russian Cancer Research Center

Bioron Diagnostics GmbH Company