Systems Infection Biology facility

The Systems Infection Biology faciliy (CSIB) provides services for advanced bioinformatics analysis.

The Systems Infection Biology (CSIB) facility provides services for advanced bioinformatics analysis on transcriptomics, proteomics (targeted and untargeted), metabolomics (targeted and untargeted), microbiome (16s and metagenome), integrative multi-omics analysis including single cell analysis.

What we can provide

Based on our experiences in Systems Virology and infection-related translational research, we are always glad to discuss projects related to multi-omics system biology concerning study designing, analysis service for single omics and integrative multi-omics for a wide range of infectious diseases but not restricted to it.

What we do not do:

Generate a hypothesis or research question.


  • Single omic analysis of transcriptomics, proteomics, metabolomics, and microbiome and provide a report.
  • Generate publication-ready figures based on the hypothesis of the researcher or findings.
  • Provide training to the staff (with basic knowledge in R, Python).
  • Development of context-specific genome-scale metabolic modeling for different diseases.
  • Consultation for the project design.


Services provided by CSIB must be acknowledged in all scientific dissemination activities, such as publications, presentations, posters, etc., using the following statement:

”The authors acknowledge support from the Core Facility for Systems Infection Biology (CSIB), Department of Laboratory Medicine, Karolinska Institutet.”

User fees

User fees
Content KI internal Academia Corporate
Study designing and consultation 1500 SEK/hour 2000 SEK/hour -
Single omics analysis 800 SEK/hour 900 SEK/hour 1500 SEK/hour
Integrative omics analysis 1000 SEK/hour 1500 SEK/hour 3000 SEK/hour
Project setup cost (onetime) 3000 SEK 5000 SEK 8000 SEK
Training cost Based on the discussion Based on the discussion -

Booking and contact information


Phone number
08-524 836 80

Alfred Nobels Allé 8, 7th floor, Flemingsberg.

Responsible department

CSIB is located within the Systems Virology lab at the Division of Clinical Microbiology, Department of Laboratory Medicine, Karolinska Institutet, Campus Flemingsberg.

Key Publications

Multi-omics personalized network analyses highlight progressive disruption of central metabolism associated with COVID-19 severity.
Ambikan AT, Yang H, Krishnan S, Svensson Akusjärvi S, Gupta S, Lourda M, Sperk M, Arif M, Zhang C, Nordqvist H, Ponnan SM, Sönnerborg A, Treutiger CJ, O'Mahony L, Mardinoglu A, Benfeitas R, Neogi U
Cell Syst 2022 Aug;13(8):665-681.e4

A high-risk gut microbiota configuration associates with fatal hyperinflammatory immune and metabolic responses to SARS-CoV-2.
Albrich WC, Ghosh TS, Ahearn-Ford S, Mikaeloff F, Lunjani N, Forde B, Suh N, Kleger GR, Pietsch U, Frischknecht M, Garzoni C, Forlenza R, Horgan M, Sadlier C, Negro TR, Pugin J, Wozniak H, Cerny A, Neogi U, O'Toole PW, O'Mahony L
Gut Microbes 2022 ;14(1):2073131

Genome-scale metabolic models for natural and long-term drug-induced viral control in HIV infection.
Ambikan AT, Svensson-Akusjärvi S, Krishnan S, Sperk M, Nowak P, Vesterbacka J, Sönnerborg A, Benfeitas R, Neogi U
Life Sci Alliance 2022 Sep;5(9):

Multi-omics insights into host-viral response and pathogenesis in Crimean-Congo hemorrhagic fever viruses for novel therapeutic target.
Neogi U, Elaldi N, Appelberg S, Ambikan A, Kennedy E, Dowall S, Bagci BK, Gupta S, Rodriguez JE, Svensson-Akusjärvi S, Monteil V, Vegvari A, Benfeitas R, Banerjea A, Weber F, Hewson R, Mirazimi A
Elife 2022 Apr;11():

Content reviewer: