Laboratory of Bioinformatics and Systems Biology
1.Research area
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.
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.
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 main research objects:
- Human genome/exome.
- Human cancer/normal transcriptomes.
- Bacterial genomes.
- Plant genomes/transcriptomes.
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.
- Primers design and optimization of PCR pipelines and amplification.
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.
Our main computational facility
- 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.
Research Possibilities
- 1Bioinformatics analysis of human whole-genomes/exomes from high-throughput next-generation sequencing platforms (Illumina/Roche/SOLiD/IonTorrent)
- 2Bioinformatics analysis of human cancer transcriptomes from high-throughput genomic platforms (microarrays, NGS - Illumina/Affymetrix).
- 3Bioinformatics analysis of viral and bacterial genomes.
- 4Development of new bioinformatics methods and approaches and databases for analysis and visualization of multidimensional biomedical data from high-throughput genomic platforms.
- 5Training and internships for young Kazakhstani researchers as well as consulting in bioinformatics for different research centers from Kazakhstan.
- 6More than 100 bioinformatics methods , tools and pipelines have been implemented and installed
- 7Active 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.
h-index: 6
NU Researcher page: https://research.nu.edu.kz/en/persons/ulykbek-kairov
Google Scholar: https://scholar.google.com/citations?user=76JSOc4AAAAJ&hl=en
Research Interests
Bioinformatics, cancer biology, genomics, transcriptomics, systems biology.
h-index: 6
NU Researcher page: https://research.nu.edu.kz/en/persons/ulykbek-kairov
Google Scholar: https://scholar.google.com/citations?user=76JSOc4AAAAJ&hl=en
Lab's members
Ruslan Kalendar
Leading Researcher
PhD, Professor
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).
h-index: 33
NU Researcher page: https://research.nu.edu.kz/en/persons/ruslan-kalendar
Google Scholar: https://scholar.google.com/citations?user=zlwaLhQAAAAJ&hl=en
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).
h-index: 33
NU Researcher page: https://research.nu.edu.kz/en/persons/ruslan-kalendar
Google Scholar: https://scholar.google.com/citations?user=zlwaLhQAAAAJ&hl=en
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
h-index: 3
NU Researcher page: https://research.nu.edu.kz/en/persons/askhat-molkenov
Google Scholar: https://scholar.google.com/citations?user=Arr3KL8AAAAJ&hl=en
“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
h-index: 3
NU Researcher page: https://research.nu.edu.kz/en/persons/askhat-molkenov
Google Scholar: https://scholar.google.com/citations?user=Arr3KL8AAAAJ&hl=en
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
4.Publications
- Ulykbek Kairov, Amina Amanzhanova, Daniyar Karabayev, Saule Rakhimova, Akbota Aitkulova, Diana Samatkyzy, Ruslan Kalendar, Ulan Kozhamkulov, Askhat Molkenov, Aidana Gabdulkayum, Dos Sarbassov and Ainur Akilzhanova. A high scale SARS-CoV-2 profiling by its whole-genome sequencing using Oxford Nanopore Technology in Kazakhstan. Frontiers in Genetics 2022, WoS IF2021=4.772 Q1;
- Kairov U, Molkenov A, Sharip A, Rakhimova S, Seidualy M, Rhie A, Kozhamkulov U, Zhabagin M, Kim JI, Lee JH, Terwilliger JD, Seo JS, Zhumadilov Z, Akilzhanova A. Whole-Genome Sequencing and Genomic Variant Analysis of Kazakh Individuals. Frontiers in Genetics. 2022 Jul 11;13:902804. https://doi.org/10.3389/fgene.2022.902804, https://www.frontiersin.org/articles/10.3389/fgene.2022.906318/abstract, WoS IF2021=4.772 Q1;
- Captier N, Merlevede J, Molkenov A, Seisenova A, Zhubanchaliyev A, Nazarov PV, Barillot E, Kairov U, Zinovyev A: BIODICA: a computational environment for Independent Component Analysis. Bioinformatics 2022, btac204. https://doi:10.1093/bioinformatics/btac204 WoS IF2021=6.931 Q1 Scopus CiteScore2021=13.4 99th percentile SJR Q1 https://www.scopus.com/sourceid/17945
- Ainur Seisenova, Asset Daniyarov, Askhat Molkenov, Aigul Sharip, Andrei Zinovyev and Ulykbek Kairov. Meta-Analysis of Esophageal Cancer Transcriptomes Using Independent Component Analysis. Frontiers in Genetics 2021, https://doi.org/10.3389/fgene.2021.683632 , WoS IF2021=4.772 Q1;
- Daniyarov A, Molkenov A, Rakhimova S, Akhmetova A, Yerezhepov D, Chingissova L, Bismilda V, Toksanbayeva B, Rakisheva A, Akilzhanova A, Kozhamkulov U, Kairov U. Genomic Analysis of Multidrug-Resistant Mycobacterium tuberculosis Strains From Patients in Kazakhstan. Frontiers in Genetics 2021, https://doi.org/10.3389/fgene.2021.683515 , WoS IF2021=4.772 Q1;
- Daniyar Karabayev, Askhat Molkenov, Kaiyrgali Yerulanuly, Ilyas Kabimoldayev, Asset Daniyarov, Aigul Sharip, Ainur Seisenova, Zhaxybay Zhumadilov, Ulykbek Kairov. re-Searcher: GUI-based bioinformatics tool for simplified genomics data mining of VCF files. PeerJ 2021, e11333. doi: 10.7717/peerj.11333 https://pubmed.ncbi.nlm.nih.gov/33987016/ WoS IF2021=3.061 Q2; Scopus CiteScore2021=4.7 83th percentile SJR Q1 https://www.scopus.com/sourceid/21100239256
- Guelly C, Abilova Z, Nuralinov O, Panzitt K, Akhmetova A, Rakhimova S, Kozhamkulov U, Kairov U, Molkenov A, Seisenova A, Trajanoski S, Abildinova Rashbayeva G, Kaussova G, Windpassinger C, Lee JH, Zhumadilov Z, Bekbossynova M, Akilzhanova A. Patients with coronary heart disease, dilated cardiomyopathy and idiopathic ventricular tachycardia share overlapping patterns of pathogenic variation in cardiac risk genes. PeerJ 2021, e11333. https://pubmed.ncbi.nlm.nih.gov/33552729/ , https://doi.org/10.7717/peerj.10711 , WoS IF2021=3.061 Q2; Scopus CiteScore2021=4.7 83th percentile SJR Q1
- Kalendar R, Shustov AV, Akhmetollaev IA, Kairov U 2022. Designing allele-specific competitive-extension PCR-based assays for high-throughput genotyping and gene characterization. Frontiers Molecular Biosciences, 9:773956. DOI: 10.3389/fmolb.2022.773956 https://pubmed.ncbi.nlm.nih.gov/35300118/ WoS IF 2021 =6.113 Q1; Scopus CiteScore 2021 =3.5 SCR Q1 63th percentile https://www.scopus.com/sourceid/21100843667
- Kalendar R, Baidyussen A, Serikbay D, Zotova L, Khassanova G, Kuzbakova M, Kurishbayev A, Jatayev S, Hu Y-G, Schramm C, Anderson PA, Jenkins CLD, Soole KL, Shavrukov Y 2022. Modified ‘Allele-specific qPCR’ method for SNP genotyping based on FRET. Frontiers in Plant Science, 12: 747886. DOI: 10.3389/fpls.2021.747886 https://pubmed.ncbi.nlm.nih.gov/35082803/ WoS IF 2020 =5.753 Q1; Scopus CiteScore 2021 =8.2 SCR Q1 95th percentile https://www.scopus.com/sourceid/21100313905
- Kalendar R, Khassenov B, Ramankulov Y, Samuilova O, Ivanov KI 2017. FastPCR: an in silico tool for fast primer and probe design and advanced sequence analysis. Genomics, 109: 312-319. DOI:10.1016/j.ygeno.2017.05.005 https://pubmed.ncbi.nlm.nih.gov/28502701/ WoS IF 2021 =4.31 Q2; Scopus CiteScore 2021 =5.4 58th percentile SJR Q2 https://www.scopus.com/sourceid/22215
- Kalendar R, Shustov AV, Seppänen MM, Schulman AH, Stoddard FL 2019. Palindromic sequence-targeted (PST) PCR: a rapid and efficient method for high-throughput gene characterization and genome walking. Scientific Reports, 9: 17707. DOI:10.1038/s41598-019-54168-0 https://pubmed.ncbi.nlm.nih.gov/31776407/ WoS IF 2021 =4.996 Q2; Scopus CiteScore 2021 =6.9 91th percentile SJR Q1 https://www.scopus.com/sourceid/22215
- Kairov U, Molkenov A, Rakhimova S, Kozhamkulov U, Sharip A, Karabayev D, Daniyarov A, J HL, J DT, Akilzhanova A, Zhumadilov Z: Whole-genome sequencing data of Kazakh individuals. BMC Research Notes 2021, 14(1):45. DOI:10.1186/s13104-021-05464-4 https://pubmed.ncbi.nlm.nih.gov/33541395/ Scopus CiteScore 2021 =3.5 48th percentile SJR Q2 https://www.scopus.com/sourceid/19600166028
- Kalendar R, Raskina O, Belyayev A, Schulman AH 2020. Long tandem arrays of Cassandra retroelements and their role in genome dynamics in plants. International Journal of Molecular Sciences, 21(8): 2931. DOI:10.3390/ijms21082931 https://www.mdpi.com/1422-0067/21/8/2931 WoS IF 2001 =6ю208 Q1; Scopus CiteScore 2021 =6.9 85rd percentile SJR Q1 https://www.scopus.com/sourceid/25879
- Kalendar R, Shustov AV, Schulman AH 2021. Palindromic sequence-targeted (PST) PCR, version 2: an advanced method for high-throughput targeted gene characterization and transposon display. Frontiers in Plant Science, 12: 691940. DOI:10.3389/fpls.2021.691940 https://pubmed.ncbi.nlm.nih.gov/34239528/ WoS IF 2020 =5.753 Q1; Scopus CiteScore 2020 =8.2 SCR Q1 95th percentile https://www.scopus.com/sourceid/21100313905
5.Collaborations
Institute Curie, Paris, France. Unit of bioinformatics and computational systems biology of cancer: Emmanuel Barillot and Andrei Zinovyev
Center for Biomedical Informatics, Harvard Medical School, USA.
Peter Kharchenko’s Laboratory for computational biology
Institute of Physical-Chemical Medicine, Moscow, Russia. Bioinformatics lab: Dmitriy Alexeev, Alexandr Tyakht.
Seoul National University, Genomic Medicine Institute.
Prof. Jong-Il Kim, Prof. Jeung-sun Seo.
Columbia University, USA. Prof.Joseph H.Lee.
University of California, USA. Dr. Yerbol Kurmangaliyev.
Al-Farabi Kazakh National University, Kazakhstan. Prof.Boguspayev and Prof.Bissenbayev
6.Life in the Lab