The BF Bioinformatics Platform offers top-level expertise for the analysis of various omics and imaging data and data integration. In addition, the Platform provides support for bioinformatics tools and data management, as well as training and consultation. The support is accessible nationwide. New data analysis pipelines and workflows are established when new technologies are taken in use among the BF technology platforms. Additionally, the BF Bioinformatics Platform provides scientific IT support for researchers and other BF Platforms that need local expertise in their data management, storage and computing. These operations are organized in collaboration with CSC and ELIXIR.

The BF Bioinformatics Platform provides high-level data analysis support according to available resources, covering different areas of bioinformatics, including:

  • Genomics
  • Transcriptomics
  • Epigenomics
  • Proteomics
  • Metabolomics
  • Spatial omics
  • Structural bioinformatics
In silico modeling and simulation of biological systems


Contact details


Platform Chair


Laura Elo
laura.elo@utu.fi
University of Turku


Platform Coordinator


Asta Laiho
asta.laiho@utu.fi
University of Turku


Nodes


Node/Host UniversityNode PI
Medical Bioinformatics Centre, UTU
Asta Laiho
asta.laiho@utu.fi
Bioinformatics Facility, TAU
Matti Nykter
matti.nykter@tuni.fi
Structural Bioinformatics Laboratory, ÅAU
Jukka Lehtonen
jukka.lehtonen@abo.fi
Helsinki Bioinformatics, UH
Website under development
Esa Pitkänen
esa.pitkanen@helsinki.fi
Biocenter Oulu Biocomputing, UO
André H. Juffer
andre.juffer@oulu.fi
Bioinformatics Center, UEF
Virpi Ahola
virpi.ahola@uef.fi
CSC-ELIXIR
#1 , #2
Tommi Nyrönen
tommi.nyronen@csc.fi

UEF: University of Eastern Finland; UH: University of Helsinki; UO: University of Oulu;
UTU: University of Turku; TAU: Tampere University; ÅAU: Åbo Akademi University



Services


All nodes provide general bioinformatics consultation. Nodes also provide basic and advanced data analysis support, training, and support for accessing computational tools, infrastructure, and data storage resources. Special data analysis expertise areas:


Node 1 (UTU):


proteomics, epigenomics, singl- cell omics, clinical applications

Node 2 (UTA):


spatial omics

Node 3 (ÅAU):


structure-based analysis of protein function and evolution

Node 4 (UH):


genomics, single-cell omics, multi-omics, ecology and evolution

Node 5 (UO):


in silico modeling and simulation of biological systems

Node 6 (UEF):


genomics, single-cell omics, multi-omics, metabolomics

Recent user publications


Laukkanen S, Veloso A, Yan C, Oksa L, Alpert EJ, Do D, Hyvärinen N, McCarthy K, Adhikari A, Yang Q, Iyer S, Garcia SP, Pello A, Ruokoranta T, Moisio S, Adhikari S, Yoder JA, Gallagher K, Whelton L, Allen JR, Jin AH, Loontiens S, Heinäniemi M, Kelliher M, Heckman CA, Lohi O, Langenau DM. Therapeutic targeting of LCK tyrosine kinase and mTOR signaling in T-cell acute lymphoblastic leukemia. Blood 140(17):1891-1906, 2022. doi: 10.1182/blood.2021015106.

Lehtiniemi T, Bourgery M, Ma L, Ahmedani A, Mäkelä M, Asteljoki J, Olotu O, Laasanen S, Zhang FP, Tan K, Chousal JN, Burow D, Koskinen S, Laiho A, Elo LL, Chalmel F, Wilkinson MF, Kotaja N. SMG6 localizes to the chromatoid body and shapes the male germ cell transcriptome to drive spermatogenesis. Nucleic Acids Res 50(20):11470-11491, 2022. doi: 10.1093/nar/gkac900.

Vaparanta K, Jokilammi A, Tamirat M, Merilahti JAM, Salokas K, Varjosalo M, Ivaska J, Johnson MS, Elenius K. An extracellular receptor tyrosine kinase motif orchestrating intracellular STAT activation. Nat Commun  13(1):6953, 2022. doi: 10.1038/sg41467-022-34539-4.


Ianevski A, Lahtela J, Javarappa KK, Sergeev P, Ghimire BR, Gautam P, Vähä-Koskela M, Turunen L, Linnavirta N, Kuusanmäki H, Kontro M, Porkka K, Heckman CA, Mattila P, Wennerberg K, Giri AK, Aittokallio T. Patient-tailored design for selective co-inhibition of leukemic cell subpopulations. Sci Adv 7(8):eabe4038, 2021. doi: 10.1126/sciadv.abe4038.


Mokkala K, Paulin N, Houttu N, Koivuniemi E, Pellonperä O, Khan S, Pietilä S, Tertti K, Elo LL, Laitinen K. Metagenomics analysis of gut microbiota in response to diet intervention and gestational diabetes in overweight and obese women: a randomised, double-blind, placebo-controlled clinical trial. Gut 70(2):309-318, 2021. doi: 10.1136/gutjnl-2020-321643.



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