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Browsing Laboratory of Bioinformatics and Systems Biology by Title

Browsing Laboratory of Bioinformatics and Systems Biology by Title

Now showing items 1-9 of 9

ANALYSIS OF BACTEROIDES FRAGILIS CLINICAL STRAINS ISOLATED IN KAZAKHSTAN

Zholdybayeva, Elena V.; Kozhahmetova, Saniya; Tarlykov, Pavel; Atavliyeva, Sabina; Mukhtarova, Kymbat; Syzdykov, Tleuli; Khasenov, Ruslan; Shevtsov, Alexsandr; Amirgazin, Asylulan; Daniyarov, Asset; Ramankulov, Yerlan (Microbiology Resource Announcements, 2021-02-04)

Our aim was to study the nucleotide sequences of 9 previously undescribed strains of B. fragilis collected from patients with intra-abdominal diseases at city hospitals in Nur-Sultan, Kazakhstan.
Assessing reproducibility of matrix factorization methods in independent transcriptomes

Cantini, Laura; Kairov, Ulykbek; de Reynies, Aurelien; Barillot, Emmanuel; Radvanyi, Francois; Zinovyev, Andrei (OXFORD UNIV PRESS, 2019)

Motivation Matrix factorization (MF) methods are widely used in order to reduce dimensionality of transcriptomic datasets to the action of few hidden factors (metagenes). MF algorithms have never been compared based on ...
IN SILICO ESTIMATION OF THE ABUNDANCE AND PHYLOGENETIC SIGNIFICANCE OF THE COMPOSITE OCT4-SOX2 BINDING MOTIFS WITHIN A WIDE RANGE OF SPECIES

Kulyyassov, Arman; Kalendar, Ruslan (MDPI, 2020-11-29)

High-throughput sequencing technologies have greatly accelerated the progress of genomics, transcriptomics, and metagenomics. Currently, a large amount of genomic data from various organisms is being generated, the volume ...
THE MAJOR SATELLITE DNA FAMILIES OF THE DIPLOID CHENOPODIUM ALBUM AGGREGATE SPECIES: ARGUMENTS FOR AND AGAINST THE “LIBRARY HYPOTHESIS”

Belyayev, Alexander; Jandova, Michaela; Josefiova, Jiřina; Kalendar, Ruslan; Mahelka, Va´clav; Manda´k, Bohumil; Krak, Karol (Public Library of Science, 2020-10-27)

Satellite DNA (satDNA) is one of the major fractions of the eukaryotic nuclear genome. Highly variable satDNA is involved in various genome functions, and a clear link between satellites and phenotypes exists in a wide ...
PALINDROMIC SEQUENCE-TARGETED (PST) PCR, VERSION 2: AN ADVANCED METHOD FOR HIGH-THROUGHPUT TARGETED GENE CHARACTERIZATION AND TRANSPOSON DISPLAY

Kalendar, Ruslan; Shustov, Alexandr V.; Schulman, Alan H. (Frontiers Media S.A., 2021-06-22)

Genome walking (GW), a strategy for capturing previously unsequenced DNA fragments that are in proximity to a known sequence tag, is currently predominantly based on PCR. Recently developed PCR-based methods allow for ...
RE-SEARCHER: GUI-BASED BIOINFORMATICS TOOL FOR SIMPLIFIED GENOMICS DATA MINING OF VCF FILES

Karabayev, Daniyar; Molkenov, Askhat; Yerulanuly, Kaiyrgali; Kabimoldayev, Ilyas; Daniyarov, Asset; Sharip, Aigul; Seisenova, Ainur; Zhumadilov, Zhaxybay; Kairov, Ulykbek (PeerJ Inc., 2021-05-03)

Background. High-throughput sequencing platforms generate a massive amount of high-dimensional genomic datasets that are available for analysis. Modern and user-friendly bioinformatics tools for analysis and interpretation ...
Transcriptional Programs Define Intratumoral Heterogeneity of Ewing Sarcoma at Single-Cell Resolution

Kairov, Ulykbek; Aynaud, Marie-Ming; Mirabeau, Olivier; Gruel, Nadege; Grossetête, Sandrine; Boeva, Valentina; Durand, Simon; Surdez, Didier; Zaïdi, Sakina; Gribkova, Svetlana; Fouché, Aziz; Raynal, Virginie; Tirode, Franck; Grünewald, Thomas G P; Bohec, Mylene; Baulande, Sylvain; Janoueix-Lerosey, Isabelle; Vert, Jean-Philippe; Barillot, Emmanuel (Cell Press, 2020-02-11)

EWSR1-FLI1, the chimeric oncogene specific for Ewing sarcoma (EwS), induces a cascade of signaling events leading to cell transformation. However, it remains elusive how genetically homogeneous EwS cells can drive the ...
WHOLE GENOME SEQUENCE DATA OF MYCOBACTERIUM TUBERCULOSIS XDR STRAIN, ISOLATED FROM PATIENT IN KAZAKHSTAN

Daniyarov, Asset; Molkenov, Askhat; Rakhimova, Saule; Akhmetova, Ainur; Nurkina, Zhannur; Yerezhepov, Dauren; Chingissova, Lyailya; Bismilda, Venera; Toxanbaeva, Bekzat; Akilzhanova, Ainur; Kozhamkulov, Ulan; Kairov, Ulykbek (Elsevier, 2020-12)

Drug-resistant tuberculosis (TB) is a major public health problem. Clinical Mycobacterium tuberculosis (MTB) isolate with Extensively drug-resistant tuberculosis (MTB-XDR) profile was subjected to whole-genome sequencing ...
WHOLE-GENOME SEQUENCING DATA OF KAZAKH INDIVIDUALS

Kairov, Ulykbek; Molkenov, Askhat; Rakhimova, Saule; Kozhamkulov, Ulan; Sharip, Aigul; Karabayev, Daniyar; Daniyarov, Asset; Lee, Joseph H.; Terwilliger, Joseph D.; Akilzhanova, Ainur; Zhumadilov, Zhaxybay (BioMed Central Ltd, 2021-02-04)

Objectives: Kazakhstan is a Central Asian crossroad of European and Asian populations situated along the way of the Great Silk Way. The territory of Kazakhstan has historically been inhabited by nomadic tribes and today ...