Basic bioinformatics training, services as well as full-scale scientific collaborations
What services do we offer?
Our mission is to offer researchers support at all stages of bioinformatics analysis – from research idea, through execution to dissemination.
We offer a diverse set of services ranging from advice on experimental design, to grant costing calculations and final data analysis.
The Bioinformatics Core has experience working on multiple data types and we primarily operate on a fee for service model of data analysis but also offer full joint scientific collaborations and training.
A particular priority is to provide consultation, training and biologist-friendly solutions to researchers at the Department of Biomedicine in order to implement the use of OMICs and other large-scale data.
- Data analysis
A wide range of bioinformatics services are offered in the field of high-throughput analysis, sequence analysis and related areas. This includes data quality control, processing, and visualization. - Consultation
We advise on experimental design and provide general bioinformatical and statistical support in all parts of your project. - Training
From practice-oriented workshops about bioinformatics tools and databases to short lectures on various topics. - Research cooperation
If you are interested in more in-depth analysis and interpretation of your data, we also offer a full joint scientific cooperation. - Writing assistance
We assist in the preparation of grant proposals and manuscripts regarding bioinformatics sections and evaluations.
Who can use this service?
Scientists at Aarhus University as well as external academic and industrial partners.
Examples of services
- Consulting on experimental design, bioinformatics methods and computational tools.
- Data quality assessment, processing, analysis, visualization and interpretation
- Next Generation Sequence Analysis (e.g., bulk RNA-Seq, ChIP-Seq, DNA-Seq, scRNA-Seq)
- DNA analysis (e.g. functional annotation, gene set enrichment/association analysis)
- RNA Analysis (e.g. expression profiling, target prediction, splicing)
- Sequence analysis (e.g. variant detection, SNP annotation, transcription factor binding site enrichment)
- Preparation of data sets to submit in public repositories (e.g. GEO, SRA and PRIDE)
- Data mining of published datasets, correlation and integration of results
- Assistance with the preparation of manuscripts, presentations and grant proposals
- Workshops on bioinformatics topics to facilitate data access and analysis
Price
The Bioinformatics Core Facility provides 3 categories of services.
1. Fee for service costumer support/consultancy/data analysis:
| Internal AU HEALTH users: | DKK 550/hour |
| Other public institutions: | DKK 1100/hour |
| Private companies | DKK 1500/hour |
2. Scientific collaborations: Requests that require an effort beyond technical assistance/consultancy/analysis of individual data-sets will be set up as a research collaboration. Funding for collaborative research performed by core facility partners must be provided unless otherwise agreed – and will comprise a pre-agreed fixed cost of conducting the research. The result of joint research shall be published with joint authorship.
3. Workshop and lectures will be provided free of charge. Individual training sessions can be booked at a pre-agreed cost.
Initial project meeting is always for free and requests that can be solved within a few working hours are usually free of charge, provided that the core facility has resources available.
For scientific collaborations, we encourage users to include Bioinformatics Core staff as early as possible in the process – and preferably already in the preparation of grant proposals.
Example 1: Fee for service RNA-seq dataset analysis
- Project information meeting
- Transfer of raw data
- Quality assessment/trimming etc
- Sequence alignment
- Feature quantification
- Differential gene expression analysis
- Basic functional enrichment analysis
- Basic visualizations
- Project report
- Project report meeting
~15 hours for a project with <20 libraries
~DKK 8,250
Example 2: Scientific collaboration on genomic data mining
- Project information meeting
- Contribution to grant proposal
- Literature and data review
- Extraction of OMICs data from multiple sources
- Re-analysis of OMICs data from multiple sources
- Collective reporting of OMICs data incl. customized visualizations
- Contribution to interpretations
- Contribution to manuscripts
~60 hours distributed over multiple weeks.
~DKK 25,000
Booking
You are always free to come by for an initial discussion of your projects. We attempt to keep the core open every Monday 10.30-12.00.
However, we encourage you to call/write first and make an appointment.
Location
Bioinformatics Core Facility
Department of Biomedicine
The Skou Building 1116, room 456
Høegh-Guldbergsgade 10
8000 Aarhus C
Denmark
Publications and acknowledgements
Please acknowledge the Bioinformatics Core Facility, when publishing results obtained using our services, and please advise us about the publication by e-mailing us a link to the publication at per.q@biomed.au.dk.
- SORLA is required for insulin-induced expansion of the adipocyte precursor pool in visceral fat
Vanessa Schmidt, Carla Horváth, Hua Dong, Matthias Blüher, Per Qvist, Christian Wolfrum, and Thomas Willnow Journal of Cell Biology, 2021. DOI: 10.1083/jcb.202006058 - Enhanced Production of Mesencephalic Dopaminergic Neurons from Lineage-Restricted Human Undifferentiated Stem Cells
Muyesier Maimaitili, Muwan Chen, Fabia Febbraro, Noëmie Mermet-Joret, Johanne Lauritsen, Ekin Ucuncu, Ida Hyllen Klæstrup, Per Qvist, Sadegh Nabavi, Marina Romero-Ramos and Mark Denham. Nature Communications. DOI: 10.1038/s41467-023-43471-0 - Sorting receptor SORCS2 facilitates a protective stress response in pancreatic islets
Oleksandra Kalnytska, Per Qvist, Séverine Kunz, Thomas Conrad, Thomas E. Willnow and Vanessa Schmidt. iScience. DOI: 10.1016/j.isci.2023.108725 - Sortilin Inhibition Protects Neurons From Degeneration in the Diabetic Retina
Thomas Stax Jakobsen, Jakob Appel Østergaard, Mads Kjolby, Elisa Lund Birch, Toke Bek, Anders Nykjær, Thomas J Corydon and Anne Louise Askou. Retina, 2023. DOI: 10.1167/iovs.64.7.8 - SorCS2 binds progranulin and regulates motor axon outgrowth
Thomasen P, Salasova A, Login H, Beel S, Tranbjerg-Jensen J, Qvist P, Ovesen PL, Nolte S, Nejsum LN, Chao MV, Van Damme P, Kjaer-Sorensen, Oxvig C, Nykjær A. Cell Reports. DOI: 10.1016/j.celrep.2023.113333 - High-Dose Vitamin D Supplementation Significantly Affecs the Placental Transcriptome
Vestergaard AL, Andersen MK, Olesen RV, Bor P, Larsen A. Nutrients. DOI: 10.1101/2023.02.08.527602 - Itaconate enhances oncolytic virotherapy by multitarget inhibition of antiviral and inflammatory pathways
Kurmasheva N, Said A, Wong B, Kress A, Liu Z, Wang C, Carter-Timofte M, Holm E, van der Horst D, Hoang H, Twayana K, Ottosen R, Svenningsen E, Begnini F, Kiib A, Weiss H, di Carlo D, Muscolini M, Higgins M, Kinderman P, van der Heijden, Tong T, Ozsvar A, Hou WH, Schack V, Holm C, van Montfoort N, Zheng Y, Ruzek M, Kalucka J, de la Vega L, Elgaher W, Korshoej A, Lin R, Hiscott J, Poulsen T, O'Neill L, Diallo JS, FArin H, Alain T, Olagnier D. Nature Communications 2024. DOI: 10.1038/s41467-024-48422-x
Activities
Upcoming and past events
- 4th Danish Single-Cell Symposium: Technology towards Cell Biology and Medicine
Poster presentation
May 2024 - GeoMx data analysis workshop at MOMA
Presentation
April 2024 - Workshop - Hands on basic bioinformatics
Teitur Trophics.
March 2024 - PhD Course - Single cell and spatial OMICS (advanced Course)
PhD course in single cell and spatial OMICS offered by AU HEALTH PhD school. Read more about the course here.
November 2023 - Workshop - Hands on basic bioinformatics
Paludan lab thematic day.
August 2023 - AU HEALTH - Interdisciplinary Research Meeting
Presentation of the Bioinformatics Core Facility. Find slides from the meeting here.
May 2023 - PhD Course - Single cell and spatial OMICS (Basic Course)
PhD course in single cell and spatial OMICS offered by AU HEALTH PhD school. Read more about the course here.
May 2023 and 2024 - Meet-and-Greet - Introduction to the Bioinformatics Core Facility
Paludan lab. Find slides from the seminar here.
February 2023 - Workshop - Analysis of bulk RNA-sequencing data using Galaxy and UCloud
A physical workshop with the subject of analyzing bulk RNA-sequencing data. The participants will be presented to the computational workflow of analyzing bulk RNA-sequencing data including file formats, file information, data processing, result generation, and interpretation. The workshop will include a live analysis and description for participants to do their work themself - without the need of coding experience. Find slides from the workshop here.
19th January 2023 - Seminar - Introduction to the Bioinformatics Core Facility and its use in single cell analyses
OMICs focus group meeting 3. Find slides from the seminar here.
October 2022