Laboratory of Bioinformatics and Systems Biology
1.Research area
The main research objects:
- Human genome/exome.
- Human cancer/normal transcriptomes.
- Bacterial genomes.
- Plant genomes/transcriptomes.
Laboratory of Bioinformatics and Systems Biology was established at the Center for Life Sciences, Nazarbayev University in 2015 on the basis of Department of Genomic and Personalized Medicine.
The mission of the Lab of Bioinformatics and Computational Systems Biology is development of Kazakhstani bioinformatics and systems biology by performing research, improving facility, establishing collaboration with the leading research groups as well as training of young researchers.
Main scientific researches of Laboratory focused on development of new approaches of ICA application for analysis and interpretation of tumor heterogeneity, on the study of gene expression and genomic variants in cancer/normal tissues, on analysis of whole genomes/exomes of Kazakh individuals and identification of Kazakh specific genomic variants with developing national genomic reference database, on the study of differential expression in plants in different states and parts, genome organization and genetic variants of drug-resistant M.tuberculosis strains circulating in Kazakhstan, on development of bioinformatics tools implementing a machine learning approaches as applied to DNA detection and amplification technologies as well as development of novel bioinformatics tools and databases.
The mission of the Lab of Bioinformatics and Computational Systems Biology is development of Kazakhstani bioinformatics and systems biology by performing research, improving facility, establishing collaboration with the leading research groups as well as training of young researchers.
Main scientific researches of Laboratory focused on development of new approaches of ICA application for analysis and interpretation of tumor heterogeneity, on the study of gene expression and genomic variants in cancer/normal tissues, on analysis of whole genomes/exomes of Kazakh individuals and identification of Kazakh specific genomic variants with developing national genomic reference database, on the study of differential expression in plants in different states and parts, genome organization and genetic variants of drug-resistant M.tuberculosis strains circulating in Kazakhstan, on development of bioinformatics tools implementing a machine learning approaches as applied to DNA detection and amplification technologies as well as development of novel bioinformatics tools and databases.
Laboratory of Bioinformatics and Systems Biology
was established at the Center for Life Sciences, Nazarbayev University in 2015 on the basis of Department of Genomic and Personalized Medicine.
The mission of the Lab of Bioinformatics and Computational Systems Biology is development of Kazakhstani bioinformatics and systems biology by performing research, improving facility, establishing collaboration with the leading research groups as well as training of young researchers.
Main scientific researches of Laboratory focused on development of new approaches of ICA application for analysis and interpretation of tumor heterogeneity, on the study of gene expression and genomic variants in cancer/normal tissues, on analysis of whole genomes/exomes of Kazakh individuals and identification of Kazakh specific genomic variants with developing national genomic reference database, on the study of differential expression in plants in different states and parts, genome organization and genetic variants of drug-resistant M.tuberculosis strains circulating in Kazakhstan, on development of bioinformatics tools implementing a machine learning approaches as applied to DNA detection and amplification technologies as well as development of novel bioinformatics tools and databases.
Our main research directions and research groups:
Laboratory carries out research in the following directions:- Bioinformatics analysis of high-throughput genomic data from the next-generation sequencing platforms (Illumina NovaSeq/HiSeq2000/MiSeq, Roche 454) and third generation sequencing platform (Oxford nanopore).
- Bioinformatics analysis and meta-analysis of tumor transcriptomes from high-throughput microarray platforms (Affymetrix/Illumina).
- Bioinformatics analysis of cancer transcriptome and gene expression data from next-generation sequencing platform Illumina NovaSeq/HiSeq2000 / MiSeq.
- Development of bioinformatics tools that implement machine learning approaches applied to DNA detection and amplification technologies for solving complex problems, including the development of PCR primers, probes and microarrays, as well as targeted sequencing.
- Development of new integrative bioinformatics approaches and methods for analysis of human whole transcriptomes and whole genomes.
- Development of bioinformatics facility, biological databases, bioinformatics methods for analysis of multidimensional biomedical data.
Analisis of data from high-throughput genomic platforms
- Statistical analysis of the data from high-throughput genomic platforms(next-generation sequencing, microarrays);
- Development and application of methodologies for meta-analysis;
- Application of mathematical methods for analysis of high-throughput data;
- Implementation, testing and adjustment different bioinformatics protocols and software for data analysis.
Computational Systems Biology of Cancer
- Network and complex analysis of cancer signalling pathways;
- Development of maps and models of cancer signaling pathways using systems biology standards, programming languages, and software (SBML, SBGN, CellDesigner).
Computational Functional Genomics
- Functional annotation and analysis of validated lists of genes;
- Interpretation and functional characterization of genomic data;
- Visualization of multi-dimensional genomic data.
Applied Bioinformatics
- Development of databases and software;
- Application of cloud computing;
- Work with high-performance computing clusters;
- Storing and managing of genomic data.
High-performance bioinformatics cluster “Q-Symphony”: Hewlett-Packard Enterprise – Apollo (208 Cores x Intel Xeon, 3.26 TB RAM, 258 ТB RAID HDD, RedHat Linux) – max computing performance 7.5 TFlops: specifically designed architecture optimized for bioinformatics research and analysis of big genomics datasets (whole-genome/whole transcriptomes datasets and genomics bulk datasets with more than 100 samples simultaneously).
Small bioinformatics cluster Dell PowerEdge Cluster (64 x Cores AMD Opteron, 128 Gb RAM, 20 Tb RAID) – high-performance server capable to perform tasks on analysis of small sample size next-generation sequencing data (human whole-genome, whole-exomes, whole transcriptomes analysis, up to 10 samples simultaneously).
Server Dell T430 (2x Intel Xeon (12 Cores), 64 Gb RAM, 8 Tb RAID, Windows Server) – medium-performance server on Windows platform for developing Windows-based bioinformatics methods and Matlab codes application.
Server HP Z800 (2х Intel Xeon (16 Cores), 48 Gb RAM) – medium-performance server for performing bioinformatics analysis of viral and bacterial genomes.
Synology Storage System (50 Tb Raid) – archiving server for massive storage and biomedical data encryption.
Small bioinformatics cluster Dell PowerEdge Cluster (64 x Cores AMD Opteron, 128 Gb RAM, 20 Tb RAID) – high-performance server capable to perform tasks on analysis of small sample size next-generation sequencing data (human whole-genome, whole-exomes, whole transcriptomes analysis, up to 10 samples simultaneously).
Server Dell T430 (2x Intel Xeon (12 Cores), 64 Gb RAM, 8 Tb RAID, Windows Server) – medium-performance server on Windows platform for developing Windows-based bioinformatics methods and Matlab codes application.
Server HP Z800 (2х Intel Xeon (16 Cores), 48 Gb RAM) – medium-performance server for performing bioinformatics analysis of viral and bacterial genomes.
Synology Storage System (50 Tb Raid) – archiving server for massive storage and biomedical data encryption.
Bioinformatics analysis of human whole-genomes/exomes from high-throughput next-generation sequencing platforms (Illumina/Roche/SOLiD/IonTorrent)
Bioinformatics analysis of human cancer transcriptomes from high-throughput genomic platforms (microarrays, NGS - Illumina/Affymetrix).
Bioinformatics analysis of viral and bacterial genomes.
Development of new bioinformatics methods and approaches and databases for analysis and visualization of multidimensional biomedical data from high-throughput genomic platforms.
Training and internships for young Kazakhstani researchers as well as consulting in bioinformatics for different research centers from Kazakhstan.
More than 100 bioinformatics methods , tools and pipelines have been implemented and installed.
Active research collaboration with leading international bioinformatics groups and centers in the field of bioinformatics, genomics and systems biology;
Bioinformatics analysis of human cancer transcriptomes from high-throughput genomic platforms (microarrays, NGS - Illumina/Affymetrix).
Bioinformatics analysis of viral and bacterial genomes.
Development of new bioinformatics methods and approaches and databases for analysis and visualization of multidimensional biomedical data from high-throughput genomic platforms.
Training and internships for young Kazakhstani researchers as well as consulting in bioinformatics for different research centers from Kazakhstan.
More than 100 bioinformatics methods , tools and pipelines have been implemented and installed.
Active research collaboration with leading international bioinformatics groups and centers in the field of bioinformatics, genomics and systems biology;
2.Lab team
Head of laboratory
Ulykbek Kairov
Head of the Laboratory of Bioinformatics and Systems Biology, Center for Life Sciences, National Laboratory Astana, Nazarbayev University, Astana, Kazakhstan
ulykbek.kairov@nu.edu.kz
ulykbek.kairov@nu.edu.kz
PhD, Committee for Control of Education and Science under the Ministry of Education and Science of the Republic of Kazakhstan (2012). Kazakh National University after Al-Farabi, Almaty, Kazakhstan / Department of Bioinformatics, Biostatistics, Epidemiology and Computational Systems Biology of Cancer, Institute Curie, Paris, France.
Research Interests
Bioinformatics, cancer biology, genomics, transcriptomics, systems biology.
Research Interests
Bioinformatics, cancer biology, genomics, transcriptomics, systems biology.
Lab's members
- Ruslan KalendarLeading Researcher
- Askhat MolkenovResearcher
- Asset DaniyarovJunior Researcher
- Aigul SharipAssistant Researcher
Ruslan Kalendar
Leading Researcher
Expert in the field of molecular biology and genetics, chemistry and bioinformatics.
The major focus of research interests is on the evolution, RNA world, biology of retrotransposons, their role in shaping the genome, and their applications as markers for biodiversity and breeding (developed techniques: PST-PCR, IRAP, REMAP and iPBS amplification techniques), genetics, synthetic biology, software development and bioinformatics (string searching and complexity analysis, search of repeats, DNA alignment and assembly, PCR primer design).
The major focus of research interests is on the evolution, RNA world, biology of retrotransposons, their role in shaping the genome, and their applications as markers for biodiversity and breeding (developed techniques: PST-PCR, IRAP, REMAP and iPBS amplification techniques), genetics, synthetic biology, software development and bioinformatics (string searching and complexity analysis, search of repeats, DNA alignment and assembly, PCR primer design).
Askhat Molkenov
Researcher
MSc Mathematical Biology, University of Dundee
“Application of mathematical approaches for analysis of next-generation sequencing data: Bayesian assessment” internship @ Department of Systems Biology, Harvard Medical School by Talap.
8th International Young Scientists School «Systems Biology and Bioinformatics» – SBB-2016 @ Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Federation.
“Bioinformatics analysis of whole genome and whole exome sequencing data” internship @ Genomic Medicine Institute, Seoul National University, Seoul, South Korea
Next-Generation Sequencing School @ Research Institute of Physical and Chemical
“Application of mathematical approaches for analysis of next-generation sequencing data: Bayesian assessment” internship @ Department of Systems Biology, Harvard Medical School by Talap.
8th International Young Scientists School «Systems Biology and Bioinformatics» – SBB-2016 @ Institute of Cytology and Genetics SB RAS, Novosibirsk, Russia Federation.
“Bioinformatics analysis of whole genome and whole exome sequencing data” internship @ Genomic Medicine Institute, Seoul National University, Seoul, South Korea
Next-Generation Sequencing School @ Research Institute of Physical and Chemical
Asset Daniyarov
Junior Researcher
MSc Biotechnology, L.N.Gumilyov Eurasian National University
“Epigenomic data analysis” @ Free University, Berlin, Germany.
“Bioinformatics and Molecular Genetics” @ Skolkovo Innovation Center, Moscow, Russia Federation.
Research interests
Bioinformatics, bacterial genome analysis, plant genomics, proteomics.
3.Research projects
2018-2020, PI of the project – Kairov Ulykbek.
2018-2020. PI of the project – Kairov Ulykbek.
2018-2020. PI of the PTF – Kushugulova Almagul.
2018-2020, PI of the project – Kozhakhmetov S.., BI analysis – LBSB.
Due dates
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4.Publications
List of selected publications of LBSB:
Current research collaborations:
Institute Curie, Paris, France.
Unit of bioinformatics and computational systems biology of cancer:
Zinovyev’s group of cancer systems biology
Seoul National University, Genomic Medicine Institute. Prof. Jong-Il Kim, Prof. Jeung-sun Seo.
Department of Biomedical Informatics, Harvard Medical School, USA. P. Kharchenko’s Laboratory for computational biology
Skolkovo Tech, Moscow, Russia. Bioinformatics lab: D. Alexeev, A. Tyakht.
Bioinformatics Center, Kyoto University, Japan.
Prof. K. Minoru, Prof. Ogata.
University of Southern California, USA. Yerbol Kurmangaliyev.
Tel-Aviv University, Israel. Prof. N. Shomron
School of Science and Technology, School of Engineering, NU. Prof.Schoenbach, Dr. A. Zollanvari.
- Christian Guelly, Zhannur Abilova, Omirbek Nuralinov, Katrin Panzitt, Ainur Akhmetova, Saule Rakhimova, Ulan Kozhamkulov, Ulykbek Kairov, Askhat Molkenov, Ainur Seisenova, Slave Trajanoski, Gulzhaina Abildinova (Rashbayeva), Galina Kaussova, Christian Windpassinger, Joseph H. Lee, Zhaxybay Zhumadilov, Makhabbat Bekbossynova and Ainur Akilzhanova. Patients with coronary heart disease, dilated cardiomyopathy and idiopathic ventricular tachycardia share overlapping patterns of pathogenic variation in cardiac risk genes // PeerJ, 2021, https://doi.org/10.7717/peerj.10711.
- Ulykbek Kairov, Askhat Molkenov, Saule Rakhimova, Ulan Kozhamkulov, Aigul Sharip, Daniyar Karabayev, Asset Daniyarov, Joseph H.Lee, Joseph D.Terwilliger, Ainur Akilzhanova and Zhaxybay Zhumadilov. Whole-genome sequencing data of Kazakh individuals // BMC Research Notes, 2021, under publication.
- Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Nurkina Z, Yerezhepov D, Chingissova L, Bismilda V, Toxanbaeva B, Akilzhanova A, Kozhamkulov U, Kairov U. Whole genome sequence data of Mycobacterium tuberculosis XDR strain, isolated from patient in Kazakhstan // Data Brief, 2020 Oct 17, doi:10.1016/j.dib.2020.106416.
- M-M Aynaud, O Mirabeau, N Gruel, S Grossetête, V Boeva, S Durand, D Surdez, O Saulnier, S Zaïdi, S Gribkova, U Kairov, V Raynal, F Tirode, TGP Grünewald, M Bohec, S Baulande, I Janoueix-Lerosey, J-P Vert, E Barillot, O Delattre, A Zinovyev. Transcriptional programs define intratumoral heterogeneity of Ewing sarcoma at single cell resolution // Cell reports, 2020, doi: 10.1016/j.celrep.2020.01.049.
- Nicolas Sompairac, Petr Nazarov, Urszula Czerwinska, Laura Cantini, Askhat Molkenov, Zhaxybay Zhumadilov, Emmanuel Barillot, Francois Radvanyi, Alexander Gorban, Ulykbek Kairov and Andrei Zinovyev. Independent component analysis for unraveling complexity of cancer omics datasets // International Journal of Molecular Science, 2019, 20(18), 4414; https://doi.org/10.3390/ijms20184414
- Cantini L, Kairov U, de Reyniès A, Barillot E, Radvanyi F, Zinovyev A. Assessing reproducibility of matrix factorization methods in independent transcriptomes // Bioinformatics, 2019 Apr 2, doi: 10.1093/bioinformatics/btz225.
- Askhat Molkenov, Altyn Zhelambayeva, Akbar Yermekov, Saule Mussurova, Aliya Sarkytbayeva, Yerbol Kalykhbergenov, Zhaxybay Zhumadilov, Ulykbek Kairov. Transcriptomic Databases // Reference Module in Life Sciences. Chapter in Encyclopedia of Bioinformatics and Computational Biology, Elsevier press, June 2018, https://doi.org/10.1016/B978-0-12-809633-8.20208-2.
- Czerwinska U., Kairov U., Cantini L., Barillot E., Zinovyev A. Application of Independent Component Analysis to Tumor Transcriptomes Reveals Specific and Reproducible Immune-Related Signals // Chapter in Book Latent Variable Analysis and Signal Separation. Lecture Notes in Computer Science, vol. 10891. 2018, Springer, doi.org/10.1007/978-3-319-93764-9_46.
- Ulykbek Kairov, Laura Cantini, Alessandro Greco, Askhat Molkenov, Urszula Czerwinska, Emmanuel Barillot, Andrei Zinovyev. Determining the optimal number of reproducible independent components for transcriptomic data analysis. BMC Genomics. 2017, Sep 11;18(1):712. doi: 10.1186/s12864-017-4112-9.
- Saliev T, Begimbetova D, Baiskhanova D, Abetov D, Kairov U, Gilman CP, Matkarimov B, Tachibana K. Apoptotic and genotoxic effects of low-intensity ultrasound on healthy and leukemic human peripheral mononuclear blood cells. // Journal of Medical Ultrasonics, 2017 Jul 8. doi: 10.1007/s10396-017-0805-6.
- Kozhamkulov U.A., Kairov U.E., Yerezhepov D.A., Akhmetova A.Zh., Molkenov A.B., Akilzhanova A.R. Whole-genome sequencing of clinical mycobacterium tuberculosis isolates with different drug sensitivity profiles // Eurasian Journal of Applied Biotechnology, 2016. Issue 2, P. 20-29.
- Saule Е. Rakhimova, Ulykbek E. Kairov, Dauren A. Yerezhepov, Askhat B. Molkenov, Madina R. Zhalbinova, Aliya T. Abilmazhinova, Yuri V. Zhukov, Marat Kh. Omarov, Ainur R. Akilzhanova. RNA-sequencing of squamous esophageal cancer: from collection of the biomaterial until sequencing on hiseq2000 // Science and Healthcare. 2016, Vol.5, P.53-63.
- Ainur Akilzhanovа, Ulan Kozhamkulov, Ulykbek Kairov, Saule Rakhimova, Ainur Akhmetova, Dauren Yerezhepov, Askhat Molkenov, Zhannur Abilova, Zhaxybay Zhumadilov. Determination of genetic variants associated with hypertension, obesity and diabetes in kazakh population to study interaction of genetic variants and metabolome // Science and Healthcare. 2016, Vol.5, P.30-42.
- Kozhakhmetov SS, Kushugulova AR, Saduakhasova SA, Shakhabayeva GS, Khassenbekova ZR, Molkenov AB3, Kairov UE, Issayeva RB, Nurgozhin TS, Zhumadilov ZS. Draft Genome Sequence of Lactobacillus rhamnosus CLS17. Genome Announcements. 2015 May 14; 3(3). e00478-15. doi: 10.1128/genomeA.00478-15.
- Kairov Ulykbek, Ulan Kozhamkulov, Askhat Molkenov, Saule Rakhimova, Ayken Askapuli, Maxat Zhabagin, Ainur Akhmetova, Dauren Yerezhepov, Zhannur Abilova, Aliya Abilmazhinova, Venera Bismilda, Leila Chingisova, Zhaxybay Zhumadilov, Ainur Akilzhanova.. Draft Genome Sequences of Two Clinical Isolates of Mycobacterium tuberculosis from Sputum of Kazakh Patients. Genome Announcements. 2015 May 14; 3(3). e00466-15. doi: 10.1128/genomeA.00466-15.
- Dmitriev, U.Kairov, T.Robert, A.Barat, V.Lazar, G.Garnac, Y.Vassetzky. Cancer-related genes in the transcription signature of facioscapulohumeral dystrophy myoblasts and myotubes // Journal of Cellular and Molecular Medicine.2014 Feb;18(2):208-17
Current research collaborations:
Institute Curie, Paris, France.
Unit of bioinformatics and computational systems biology of cancer:
Zinovyev’s group of cancer systems biology
Seoul National University, Genomic Medicine Institute. Prof. Jong-Il Kim, Prof. Jeung-sun Seo.
Department of Biomedical Informatics, Harvard Medical School, USA. P. Kharchenko’s Laboratory for computational biology
Skolkovo Tech, Moscow, Russia. Bioinformatics lab: D. Alexeev, A. Tyakht.
Bioinformatics Center, Kyoto University, Japan.
Prof. K. Minoru, Prof. Ogata.
University of Southern California, USA. Yerbol Kurmangaliyev.
Tel-Aviv University, Israel. Prof. N. Shomron
School of Science and Technology, School of Engineering, NU. Prof.Schoenbach, Dr. A. Zollanvari.
5.Life in the Lab