Welcome To
Avican Lab
About Us
Bacterial infections are linked to high human morbidity and death rates and antibiotic-resistant bacteria are becoming a more widespread concern. Aside from their virulence strategies, diverse bacterial pathogens are extremely capable of adapting to stressful host environments. They sense and respond to stressors by re-programming their transcriptome with complex regulatory networks for maintenance of infection. Therefore, bacterial stress responses can be potential targets for novel antimicrobial strategies. We aim to retrieve novel knowledge of bacterial tissue adaptation mechanisms and identify bacterial gene products which can be used as potential antimicrobial targets in combatting bacterial infections.
Our Research
RNA Atlas for Human
Bacterial Pathogens
An interactive RNA atlas for global expression profiles of 32 different bacterial pathogens under 11 infection-relevant stress conditions
Single Cell
Transcriptomics
Developing a novel bacterial scRNA-seq method by using SPCs
Prosthetic Joint
Infection
Identifying bacterial determinants that can be targeted for developing new antimicrobials
Teaching Activities
Facilities
µNiSCH (µNordic Single Cell Hub) is a cutting-edge infrastructure dedicated to advancing single cell biology at Umeå University. Our facility focuses on consolidating and expanding research in this dynamic field. We are also at the forefront of developing innovative molecular tools for single cell transcriptomics and genomics, with a special emphasis on microbial studies.
Web Servers
Our experimental systems biology approach produces large transcriptomics and genomics data (currently), both from laboratory settings and directly from infected human specimens. We have revealed and analysed gene expression of 32 human pathogens exposed to 11 infection-relevant conditions and collected all data in a searchable database, PATHOgenex constituting an excellent source for applications of systems biology approaches.
Co-PATHOgenex, an interactive and user-friendly web application that enables users to construct networks from gene co-expressions using custom-defined thresholds. The incorporated search functions and visualizations within the tool simplify the usage and facilitate the interpretation of the analysis output. Co-PATHOgenex also includes stress stimulons for various bacterial species, which can help identify gene products not previously associated with a particular stress condition.
News
May 25, 2024
Courses
AI applications in infection biology co-organized by Kemal Avican
We attended the "AI Applications in Infection Biology" course organised by NDPIA.
June 12, 2024
Conference
IceLab Stress Response Kickoff
We had an amazing time at the kick-off held by IceLab on June 10-11, where researchers shared exciting insights into complex systems and proposed new research directions in understanding stress responses in living systems.
September 26, 2025
Team News
Teaching Kids Biology
We were excited to once again present our 3D “build-a-bacterium” experience at this year’s Science Night (ForskarFredag), inspiring kids to explore biology in a fun and interactive way!
September 28, 2024
Team News
Researchers' Friday at Curiosum
Want to see and build your bacteria in 3D? Members of our research group met with young people whose explored how to build a bacterium in 3D virtual reality at the largest science festival of Sweden.
