Bioinformatics group
TalTech priority area
Research classification (Frascati)
Head of the research group
Research group member
Doctoral students
Keyword
Overview
Bioinformatics and computational methods inbiology allow analysis of large scale data andmodeling of biological phenomena by combiningthe biosciences, statistics, applied mathematics,physics and computer science. Using these methods, it is possible to discover new knowledge onhow the biological systems function at differentlevels, ranging from single genes and cells towhole organisms and their interactions.The group is currently leading research effortsin the following topics: (1) computational genomics and data integration in the life sciences atgenome scale; (2) Identification of genomic factors affecting wood formation with a genomicsapproach.
Related projects
TalTech development program 2016–2022,code 2014-2020.4.01.16-0032
Related department
- Almeida, B. L. B., Bahrudeen, M. N. M., Chauhan, V., Dash, S., Kandavalli, V., Häkkinen, A., Lloyd-Price, J., Cristina, P. S. D., Baptista, I. S. C., Smolander, O.-P. [et al] The transcription factor network of E. coli steers global responses to shifts in RNAP concentration // Nucleic acids research (2022) vol. 50, 12, p. 6801-6819.
https://doi.org/10.1093/nar/gkac540 - Smolander, O.-P., Blande, D., Ahola, V., Rastas, P., Tanskanen, J., Kammonen, J. I, Oostra, V., Pellegrini, L., Ikonen, S., Dallas, T. et al. Improved chromosome-level genome assembly of the Glanville fritillary butterfly (Melitaea cinxia) integrating Pacific Biosciences long reads and a high-density linkage map // GigaScience (2022) vol. 11, art. giab097.
https://doi.org/10.1093/gigascience/giab097 - Roos, K., Rooda, I., Keif, R.-S., Liivrand, M., Smolander, O.-P., Salumets, A., Velthut-Meikas, A. Single-cell RNA-seq analysis and cell-cluster deconvolution of the human preovulatory follicular fluid cells provide insights into the pathophysiology of ovarian hyporesponse // Frontiers in Endocrinology (2022) vol. 13, art. 945347.
https://doi.org/10.3389/fendo.2022.945347 - Sanka, I., Bartkova, S., Pata, P., Smolander, O.P., Scheler, O. Investigation of different free image analysis software for high-throughput droplet detection // ACS omega (2021) Vol. 6, 35, p. 22625-22634 : ill.
https://doi.org/10.1021/acsomega.1c02664 - Teppo, J., Vaikkinen, A., Stratoulias, V., Smolander, O.-P. et al. Molecular profile of the rat peri-infarct region four days after stroke : Study with MANF // Experimental neurology (2020) vol. 329, art. 113288, 19 p. : ill.
https://doi.org/10.1016/j.expneurol.2020.113288 - Alonso-Serra, J., Shi, X., Peaucelle, A., Smolander, O.-P. et al. ELIMÄKI Locus is required for vertical proprioceptive response in birch trees // Current biology : CB (2020) vol. 30, 4, p. 589-599.
https://doi.org/10.1016/j.cub.2019.12.016 - Sõmera, M., Fargette D., Hébrard, E., Sarmiento, C., ICTV Report Consortium ICTV Virus Taxonomy Profile : Solemoviridae 2021 // Journal of General Virology (2021) vol. 102, 12, art. 001707.
https://doi.org/10.1099/jgv.0.001707 - Scheler, O., Makuch, K., Debski, P. R., Smolander, O.-P. et al. Droplet-based digital antibiotic susceptibility screen reveals singlecell clonal heteroresistance in an isogenic bacterial population // Scientific reports (2020) vol. 10, 1, art. 3282, 8 p. : ill.
https://doi.org/10.1038/s41598-020-60381-z - Rump, A., Risti, R., Kristal M.-L., Reut, J., Syritski, V., Lõokene, A., Rüütel Boudinot, S. Dual ELISA using SARS-CoV-2 N protein produced in E. coli and CHO cells reveals epitope masking by N-glycosylation // Biochemical and biophysical research communications (2021) vol. 534, p. 457−460.
https://doi.org/10.1016/j.bbrc.2020.11.060 - Sõmera, M., Kvarnheden, A., Desbiez, C., Gantsovski, M., Truve, E. et al. Sixty years after the first description : genome sequence and biological characterization of European wheat striate mosaic virus infecting cereal crops // Phytopathology (2020) vol. 110, 1, p. 68-79.
https://doi.org/10.1094/PHYTO-07-19-0258-FI - Rooda, I., Hasan, M.M., Roos, K., Viil, J., Smolander, Velthut-Meikas, A. et al. Cellular, extracellular and extracellular vesicular miRNA profiles of pre-ovulatory follicles indicate signaling disturbances in polycystic ovaries // International journal of molecular sciences (2020) vol. 21, 24, art. 9550, 23 p. : ill.
https://doi.org/10.3390/ijms21249550 - Rump, A., Smolander, O-P., Rüütel-Boudinot, S. et al. Evolutionary origin of the P2X7 C-ter region : capture of an ancient ballast domain by a P2X4-Like gene in ancient jawed vertebrates // Frontiers in immunology (2020) vol. 11, art. 113, 15 p. : ill.
https://doi.org/10.3389/fimmu.2020.00113 - Guarino, F., Cicatelli, A., Castiglione, S., Agius, D. R., Orhun, G. E., Fragkostefanakis, S., Leclercq, J., Dobranszki, J., Sõmera, M., Sarmiento, C., et al. An epigenetic alphabet of crop adaptation to climate change : review article // Frontiers in Genetics (2022) vol. 13, art. 818727.
https://doi.org/10.3389/fgene.2022.818727 - Sõmera, M., Massart, S., Tamisier, L., Sooväli, P., Sathees, K., Kvarnheden, A. A survey using high-throughput sequencing suggests that the diversity of cereal and barley yellow dwarf viruses is underestimated // Frontiers in microbiology (2021) Vol. 12, art. 673218.
https://doi.org/10.3389/fmicb.2021.673218 - Rooda, I., Kaselt, B., Liivrand, M., Smolander, O.-P., Salumets, A., Velthut-Meikas, A. Hsa-mir-548 family expression in human reproductive tissues // BMC Genomic Data (2021) Vol. 22, Issue 1, Art. 40.
https://doi.org/10.1186/s12863-021-00997-w - Sarmiento, C., Sõmera, M., Truve, E. Solemoviruses (Solemoviridae) // Encyclopedia of Virology, 4th edition. Oxford : Academic Press, 2021. p. 712-718.
https://www.elsevier.com/books/encyclopedia-of-virology/bamford/978-0-12-814515-9 - Sanka, I., Bartkova, S., Pata, P, Smolander, O.-P., Scheler, O. High-throughput pipeline for polydisperse droplet analysis // MicroTAS 2021 - 25th International Conference on Miniaturized Systems for Chemistry and Life Sciences. : Chemical and Biological Microsystems Society, 2021. p. 563-564.
https://microtas2021.org/program/MicroTAS2021_Program.pdf - Sõmera, M., Truve, E., Sooväli, P. First report of wheat dwarf virus in winter wheat in Estonia // Plant disease (2019) vol. 103, 7, p. 1797.
https://doi.org/10.1094/PDIS-11-18-2059-PDN - Deptula, P., Loivamaa, I., Smolander, O.-P. et al. Red-brown pigmentation of acidipropionibacterium jensenii is tied to haemolytic activity and cyl-Like gene cluster // Microorganisms (2019) vol. 7, 11, p. 15 p. : ill.
https://doi.org/10.3390/microorganisms7110512 - Kammonen, J. I., Smolander, O.-P., Paulin, L. et al. gapFinisher : a reliable gap filling pipeline for SSPACE-LongRead scaffolder output // PLoS ONE (2019) vol. 14, 9, art. e0216885, 21 p. : ill.
https://doi.org/10.1371/journal.pone.0216885 - Teras, M., Viisileht, E., Pahtma-Hall, M., Rump, A., Paalme, V., Pata, P., Pata, I., Langevin, C., Boudinot Ruutel, S. Porcine circovirus type 2 ORF3 protein induces apoptosis in melanoma cells // BMC cancer (2018) Vol. 18, Issue 1, art. 1237, 12 p. : ill.
https://doi.org/10.1186/s12885-018-5090-2 - Paalme, V., Rump, A., Mädo, K., Teras, M., Truumees, B., Aitai, H., Ratas, K., Teras, J., Rüütel Boudinot, S. et al. Human peripheral blood eosinophils express high levels of the purinergic receptor P2X4 // Frontiers in immunology (2019) vol. 10, art. 2074, 15 p. : ill.
https://doi.org/10.3389/fimmu.2019.02074 - Mäkinen, M., Kuuskeri, J., Laine, P., Smolander, O-P. et al. Genome description of Phlebia radiata 79 with comparative genomics analysis on lignocellulose decomposition machinery of phlebioid fungi // BMC genomics (2019) vol. 20, 1, art. 430, 22 p. : ill.
https://doi.org/10.1186/s12864-019-5817-8 - Rajendran, J., Purhonen, J., Tegelberg, S., Smolander, O-P. et al. Alternative oxidase‐mediated respiration prevents lethal mitochondrial cardiomyopathy // EMBO Molecular Medicine (2019) vol. 11, 1, art. e9456, 19 p. : ill.
https://doi.org/10.15252/emmm.201809456 - Mätlik, K., Anttila, J.A., Kuan-Yin, T., Arumäe, U. et al. Poststroke delivery of MANF promotes functional recovery in rats // Science advances (2018) vol. 4, 5, art. eaap8957 ; 8 p. : ill.
https://doi.org/10.1126/sciadv.aap8957 - Pentinmikko, N., Iqbal, S., Mana, M., Smolander, O.-P. et al. Notum produced by Paneth cells attenuates regeneration of aged intestinal epithelium // Nature (2019) 571, p. 398–402, [12] p. : ill.
http://dx.doi.org/10.1038/s41586-019-1383-0 - Bartkova, S., Vendelin, M., Sanka, I., Pata, P., Scheler, O. Droplet image analysis with user-friendly freeware CellProfiler // Analytical methods (2020) vol. 12, 17, p. 2287-2294 : ill.
https://doi.org/10.1039/D0AY00031K - Teras, M., Rump, A., Paalme, V., Rüütel Boudinot, S. Porcine Circovirus Type 2 ORF3 protein induces apoptoses in melanoma cells // 5th European Congress of Immunology : abstract book. Vienna : ECI, 2018. p. 221.
https://www.eci2018.org/fileadmin/user_upload/documents/ECI_2018_Abstract_Book_web_21082018.pdf - Sõmera, M., Massart, S., Tamisier, L., Sooväli, P., Sathees, K., Kvarnheden, A. Corrigendum: A survey using high-throughput sequencing suggests that the diversity of cereal and barley yellow dwarf viruses is underestimated (Front. Microbiol., (2021), 12, (673218), 10.3389/fmicb.2021.673218) // Frontiers in microbiology (2021) vol. 12, art. 772637, 2 p.
https://doi.org/10.3389/fmicb.2021.772637 - Azizi, T., Carvalho De Araujo, L., Cetecioglu, Z., Clancy, A. J., Feger, M. L., Liran, O., O’Byrne, C., Sanka, I., Scheler, O., Sedlakova-Kadukova, J., Ziv, C., De Biase, D., Lund, P. A. A COST Action on microbial responses to low pH : developing links and sharing resources across the academic-industrial divide // New biotechnology (2022) vol. 72, p. 64-70.
https://doi.org/10.1016/j.nbt.2022.09.002 - Sustek-Sánchez, F., Rognli, O.A., Rostoks, N., Sõmera, M., Jaškūnė, K., Kovi, M.R., Statkevičiūtė, G., Sarmiento, C. Improving abiotic stress tolerance of forage grasses - prospects of using genome editing // Frontiers in plant science (2023) vol. 14, art. 1127532.
https://doi.org/10.3389/fpls.2023.1127532 - Kasprzak, M. M., Sady, M., Kruk, J., Bartkova, S., Sanka, I., Scheler, O., Jamroz, E., Berski, W., Onacik-Guer, S. et al. Replacement of milk fat by rapeseed oil stabilised emulsion in commercial yogurt // PeerJ (2023) vol. 11, art. e16441.
https://doi.org/10.7717/peerj.16441 - Frei, M., Sarmiento, C., Kärblane, K., Niehl, A., Sõmera, M. Sequencing and biological characterization of historical cynosurus mottle virus isolates from Germany // Archives of virology (2023) vol. 168, 10, art. 265.
https://doi.org/10.1007/s00705-023-05893-5 - Sõmera, M., Sooväli, P. First report of Cocksfoot mottle virus infecting wheat in Estonia // New disease reports (2023) vol. 48, 1, art. e12206.
https://doi.org/10.1002/ndr2.12206 - Oja, T., Sooväli, P., Sõmera, M. Characterization of the complete genome of oat sterile dwarf virus : a fijivirus occurring in the temperate climate zone of Europe // Archives of virology (2023) vol. 168, 10, art. 259.
https://doi.org/10.1007/s00705-023-05890-8 - Rump, A., Ratas, K., Lepasepp, T. K., Suurväli, J., Smolander, O‐P., Gross‐Paju, K., Toomsoo, T., Kanellopoulos, J., Rüütel Boudinot, S. Sex‐dependent expression levels of VAV1 and P2X7 in PBMC of Multiple Sclerosis patients // Scandinavian journal of immunology (2023) vol. 98, 2, art. e13283, 15 p. : ill.
https://doi.org/10.1111/sji.13283 - Rollin, J., Bester, R., Brostaux, Y., Caglayan, K., De Jonghe, K., Eichmeier, A., Foucart, Y., Haegeman, A., Koloniuk, I., Kominek,, P., Maree, H., Onder, S., Posada Cespedes, S., Roumi, V., Šafarova, D., Schumpp, O., Ulubas Serce, C., Sõmera, M., Tamisier, L., Vainio, E., van der Vlugt, R. A., Massart, S. Detection of single nucleotide polymorphisms in virus genomes assembled from high-throughput sequencing data: large-scale performance testing of sequence analysis strategies // PeerJ (2023) vol. 11, art. e15816.
https://doi.org/10.7717/peerj.15816 - Sanka, I., Bartkova, S., Pata, P., Ernits, M., Meinberg, Monika M., Agu, N., Aruoja, V., Smolander, O-P., Scheler, O. User-friendly analysis of droplet array images // Analytica chimica acta (2023) vol. 1272, art. 341397.
https://doi.org/10.1016/j.aca.2023.341397