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Bioinformatics

 

Coordinator of the Network

Sampsa Hautaniemi / tel. +358 50 336 4765, e-mail sampsa.hautaniemi (at) helsinki.fi
Biomedicum Helsinki, University of Helsinki
Computational Systems Biology Laboratory

 

Due to advances in measurement technologies, such as microarrays, mass spectrometry, deep sequencing and large-scale screening, bioinformatics has become an integral part of biological and biomedical research. These technologies produce huge amounts of data on gene sequences, mutations, protein structures, human diseases and mouse phenotypes, and are typically collected into data banks.

 

Bioinformatics provides tools, such as in silico modeling and simulation, to translate multidimensional biological data into knowledge and medical benefits. Thus, the productivity of biomedical sciences and related industries is increasingly dependent on computational methodologies and software. Lack of such software or methodologies is seen as a bottleneck for cutting-edge research exploiting the high-quality Finnish biodata and novel measurement technologies. Therefore, the major objective of Bioinformatics Infrastructure network is to provide services for both bioscientists (e.g., data analysis, experimental design and software) and bioinformaticians (e.g., APIs to databases, technology transfer and technology platforms).

 

Technology platform services

Microarray analysis
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. Service providers [BCH, BCT, BCK]

 

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. Service providers [BCK]

 

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. Service providers [FIMM, BCT, BI]

 

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. See Genome-Wide Methods and Translational Technologies networks for experimental details. Service providers [FIMM]

 

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

 

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. Service providers [FIMM]

 

Protein structure analysis 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. Service providers [BCT, BI, BCO]

 

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. Service providers [BCO]

 

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. Service providers [BMT]

 

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. Service providers [BMT]

 

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

 

Proteomics data analysis. Mass-spectrometry data analysis. Service providers [BCH]

 

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. Service providers [BCO, BCH]

 

Bioinformatics helpdesk http://bioinformatics.biocenter.fi

Events Biocenter Finland Events

No upcoming events.

 

Technology platform service providers

Biocenter Kuopio (BCK)

Kuopio Bioinformatics Group
Garry Wong

 

Biocenter Oulu (BCO)

Biocenter Oulu Biocomputing and Bioinformatics
André Juffer

 

Biocentrum Helsinki (BCH)

Computational Systems Biology Laboratory
Sampsa Hautaniemi

 

BioCity Turku

Structural Bioinformatics Laboratory
Mark S. Johnson

in collaboration with Turku Bioinformatics Core (analysis of microarray and deep sequencing data)

 

FIMM

FIMM Technology Center / Bioinformatics
Imre Västrik

 

Institute of Biotechnology (BI)

Institute of Biotechnology Bioinformatics Group
Liisa Holm

 

BioMediTech (BMT)

Computational Biology Group

Matti Nykter