Contact information

Contact person:
Matti Nykter

Email:
matti.nykter (at) uta.fi

Links

Systems Biology Unit,
Sampsa Hautaniemi

Kuopio Bioinformatics Group,
Jussi Paananen

Biocenter Oulu Biocomputing and Bioinformatics Core Facilities,
André Juffer

Structural Bioinformatics Laboratory,
Mark S. Johnson

FIMM Tecnology Center / Bioinformatics,
Matti Kankainen

Institute of Biotechnology Bioinformatics Group,
Liisa Holm

IBT Bioinformatics Group,
Matti Nykter



Services

If you are not using an e-mail program, you can send a contact request to the bioinformatics-helpdesk(at)helsinki.fi address with the service title as the subject of the message.

Microarray analysis moksiskaan pic
1) experimental design, 2) preprocessing, 3) computational/statistical analysis, 4) annotation (Gene Ontology/pathway/protein-protein interaction analysis, utilization of specialized databases), 5) reporting and visualization, 6) data submission to public repositories.

Genotype (SNP, CNV) data management, hosting and analysis
Data archiving and access services as well as association analysis, i.e. finding gene variants associated with phenotypes of interest.

DNA-sequence archiving and analysis with focus on next-gen sequencing
1) alignment of sequence reads, 2) visualization, 3) DNA-Seq and SNP scoring, 4) RNA-Seq: gene, transcript, exon and miRNA quantification, identification of aberrant/spliced transcripts, 5) binding sites in the genome (ChIP-Seq), 6) DNA modifications (Methyl-Seq), 7) genome sequence assembly and automated annotation 8) archiving of sequence reads, 9) web access to archives.

High throughput and high-content screening data
management normalization, QC and analysis service for HT and high-content screening, from microplate-based HTS to next-generation uHTS cell microarrays.

image analysis pic

Microscopy image analysis
recognition and quantification of features of interest (e.g. cell count, protein localization) from both static and video images.

Server hotel and hosting
for bioinformatics data and application development, testing and utilization for users with large amounts of data, but who do not want to manage their own servers and databases. It offers local national copies of relevant international resources (e.g. Ensembl) for heavy computational use. This service is offered in coordination with CSC.

Protein structure analysis services:
1) prediction of protein 3D structure from sequence, 2) identification of structurally similar proteins, 3) prediction of sequence-structure-function relationships, 4) modeling and visualization platform for users, analysis of domains in primary sequences, homology and annotation, 5) Software and databases via consortia coordinated by CSC.

In silico modeling and simulation
including 1) Characterization of enzyme mechanisms by quantum mechanics/molecular mechanics (QM/MM) methodologies, 2) Analysis of thermodynamic, dynamical and structural properties of proteins and other biomolecules using molecular dynamics, free energy calculations, acid dissociation constant predictions (electrostatics), protein modeling techniques, ligand-docking methodologies, and so forth, 3) Computational platform for users to run small to medium sized simulation projects themselves.

Pathogenicity of genetic variants analysis
includes wide array of bioinformatics tools (currently 40+ programs and analyses) ranging from gene and genome level to RNA and protein, including structure, function, tolerance, stability, aggregation propensity, disorder tendency, sequence conservations, interactions, structural predictions and simulations etc.

Immunology and immunodeficiency knowledge bases for 1) genes and proteins essential for immune system including their modifications, variations, interactions and evolution, 2) genetic variations responsible for primary immunodeficiences with wide array of additional information, 3) resources for general and detailed knowledge about immunodeficiencies, expert system for immunodeficiency diagnosis and some 130 mutation databases, majority of which are for immunodeficiencies.

Data integration and assorted analysis, 1) identification of domains, 2) retrieval of known interactors, 3) optimization of mRNA sequence for protein production purposes.

Proteomics data analysis
Mass-spectrometry data analysis.

Bioinformatics software development and Anduril
Professional programming support. Development and maintenance of Anduril framework and inclusion of novel methods to Anduril for easy assembly of analysis pipelines. These activities are executed with CSC.