Bioinformatics

We are the Bioinformatics Unit at the Core Facility at the Faculty of Medicine and Health Sciences. At present, we are located at the Hus 462, Floor 10.

We offer several Bioinformatics analyses from Microarray to Next-Generation Sequencing to High-throughput Image Analysis, primarily with open-source software, like R, Python, etc. We also have licensed software for Whole Genome Sequencing analyses, such as Sentieon. We develop pipelines for data analysis, from RAW data to the functional genomics.

We can assist you in three ways

  • Support/consultancy: to advise on bioinformatics procedures, methods and resources.
  • Technical assistance: help with tools, database, making figures or other small bioinformatics tasks.
  • Research collaboration: requests that require an effort beyond technical assistance/consultancy will be set up as research collaboration.

Bioinformatics Unit’s mission at the Core Facility is to offer researchers support with bioinformatics analysis at any level. We firmly believe that the interface between bioinformatics and biology is the key-step towards success in our collaboration. For this reason, we are open to receive your projects for data analysis or development of computational pipelines of the project or maybe a small talk that you need for some statistical calculations.

Let us try to help with your projects and analysis.

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Services

  • Personal Bioinformatics team for project discussion, evaluation and analysis
  • PhD-level project manager to support the experiment and the data analysis
  • Quick turnaround time to analysis the sequencing data
  • Unlimited computing time based on the project planning
  • No one-size-fits-all analysis - develop new analytic tools for each project
  • Three-layered data protection with huge storage capacity

 

Analysis

Description

DNA sequencing analysis

  • Whole Genome Sequencing (WGS)
  • Whole Exome Sequencing (WES)

DNA sequencing analysis includes

  • Variant Calling
  • Variant Annotation
  • Copy Number Analysis
  • Genomic Rearrangements
  • Genomic assembly and refinement
  • Genome Annotation
  • Metagenomic Analysis

 

RNA sequencing analysis

  • Microarray Data Analysis
  • Allele-specific expression analysis
  • long non-coding RNA expression
  • alternate splicing
  • genetic variants
  • fusion genes
  • novel transcripts

 

  •  Epigenomic Data Analsysis
  • DNA methylation analysis
  • Illumina EPIC array analysis,
    both 450K and 850K array analysis
    from RAW data to functional genomics
  • BS-sequence analysis from the RAW data files
  • RRBS sequence analysis from the RAW data files

 

  • Project planning &
    Computational Pipeline Development
  • Detail discussion of the project before the experiment,
    during the experiment and also during the data analysis
  • Development of new pipelines with standard softwares
    and packages for each projects

 

  • Statistical Calculations
  • Downstream Analysis &
    Functional Genomics
  • Statistical calculations with R, SPSS, etc
  • Downstream analysis of the DEG/DMGs for functional and
    enriched biological pathway analysis using several
    open-source packages, including Gene Onlogy, KEGG, Reactome
    Panther, DAVID, Ontology, SPIA, pathfindR, etc

 

  •  Image Analysis
  • Image analysis through automated microscope, like IncuCyte,
    or MATLAB images analysis and also ImageJ

 


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Computational Resources

Computation

Description

 Computational Resources
  • 2 x 48 core Intel Xeon Gold Processors
  • 512 GiB of DDR4 RAM
  • Linux Kernel Distribution
 Storage Devices

More than 150TB data storage

  • RAID services
  • Please NOTE Data can only be stored
    maximum Three Months
 Data Security

Three-layered data encryption including -

  • Hard Disk Encryption,
  • Two-Factor Authentication, and
  • Unique login ID
 Softwares
  • Open-source softwares,
  • Licensed softwares

Projects are ordered via the Core Facility booking system iLab Show/Hide content

Clinical Genomics, Sweden Show/Hide content

We are also part of Clinical Genomics, Sweden, working with several bioinformaticians from seven other Universities in Sweden to develop and integrate new analytic computational pipelines for big data analysis. Please find more details here:

Clinical Genomics Homepage

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