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
Nodes
Services
Recent user publications

Contact details

Platform Chair

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

Nodes

Node/Host UniversityNode PI
Medical Bioinformatics Centre, UTU
Laura Elo
laura.elo@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, single-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

Csader S, Ismaiah MJ, Kuningas T, Heinäniemi M, Suhonen J, Männistö V, Pentikäinen H, Savonen K, Tauriainen MM, Galano JM, Lee JC, Rintamäki R, Karisola P, El-Nezami H, Schwab U. Twelve Weeks of High-Intensity Interval Training Alters Adipose Tissue Gene Expression but Not Oxylipin Levels in People with Non-Alcoholic Fatty Liver Disease. Int J Mol Sci. 2023 May 9;24(10):8509. doi: 10.3390/ijms24108509. PMID: 37239856; PMCID: PMC10218057.

Dufva O, Gandolfi S, Huuhtanen J, Dashevsky O, Duàn H, Saeed K, Klievink J, Nygren P, Bouhlal J, Lahtela J, Näätänen A, Ghimire BR, Hannunen T, Ellonen P, Lähteenmäki H, Rumm P, Theodoropoulos J, Laajala E, Härkönen J, Pölönen P, Heinäniemi M, Hollmén M, Yamano S, Shirasaki R, Barbie DA, Roth JA, Romee R, Sheffer M, Lähdesmäki H, Lee DA, De Matos Simoes R, Kankainen M, Mitsiades CS, Mustjoki S. Single-cell functional genomics reveals determinants of sensitivity and resistance to natural killer cells in blood cancers. Immunity. 2023 Dec 12;56(12):2816-2835.e13. doi: 10.1016/j.immuni.2023.11.008. PMID: 38091953

Ohnuma T, Tsujii J, Kataoka C, Yoshimoto T, Takeshita D, Lampela O, Juffer AH, Suginta W, Fukamizo T. Periplasmic chitooligosaccharide-binding protein requires a three-domain organization for substrate translocation. Sci Rep. 2023 Nov 23;13(1):20558. doi: 10.1038/s41598-023-47253-y. PMID: 37996461; PMCID: PMC10667598.

Peuhu E, Jacquemet G, Scheele CLGJ, Isomursu A, Laisne MC, Koskinen LM, Paatero I, Thol K, Georgiadou M, Guzmán C, Koskinen S, Laiho A, Elo LL, Boström P, Hartiala P, van Rheenen J, Ivaska J. MYO10-filopodia support basement membranes at pre-invasive tumor boundaries. Dev Cell. 2022 Oct 24;57(20):2350-2364.e7. doi: 10.1016/j.devcel.2022.09.016. PMID: 36283390.

Saralahti AK, Harjula SE, Rantapero T, Uusi-Mäkelä MIE, Kaasinen M, Junno M, Piippo H, Nykter M, Lohi O, Rounioja S, Parikka M, Rämet M. Characterization of the innate immune response to Streptococcus pneumoniae infection in zebrafish. PLoS Genet. 2023 Jan 9;19(1):e1010586. doi: 10.1371/journal.pgen.1010586. PMID: 36622851; PMCID: PMC9858863.

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. 2022 Nov 14;13(1):6953. doi: 10.1038/s41467-022-34539-4. PMID: 36376313; PMCID: PMC9663514.

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