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TAIGA Lunch Pitch Johan Henriksson/Laura Carroll

Wed
20
Sep
Time Wednesday 20 September, 2023 at 12:00 - 13:00
Place MIT.A.216 Seminar room.

Come and listen to new project ideas and hopefully find new collaborators in the first round of TAIGAs pitch events. This time the pitches are organized by the TAIGA focus area AI for Health and Medicine.  

Register here to secure your lunch or drop in bringing your own food.

 

Single cell analysis - a tool for the clinic?

Single cell analysis is rapidly dropping in cost, to the point where it soon will be viable for clinical diagnosis - especially with a new system just purchased in Umeå. We believe it can be a great fit with e.g. fine needle autopsies (FNA), as we can extract a huge amount of information and improve robustness as compared to bulk analysis methods (i.e. qPCR etc). I will present a case where we can computationally dissect telomere length and other markers, and we are interested in clinical applications which can maximize the potential of this technology.

Johan Henriksson, PhD, Group Leader, Dept. Molecular Biology / Molecular Infection Medicine Sweden (MIMS)

 

Novel Microbial Secondary Metabolite Discovery with GECCO

Biosynthetic gene clusters (BGCs) are enticing targets for (meta)genomic mining efforts, as they may be responsible for the production of novel, specialized metabolites with potential uses in medicine and industry (e.g., novel antimicrobials, anticancer agents) or roles in human health (e.g., novel toxins, carcinogens, pathogen virulence factors). Here, I describe GECCO (GEne Cluster prediction with COnditional random fields; https://gecco.embl.de), a high-precision, scalable method for identifying novel BGCs in (meta)genomic data using conditional random fields (CRFs). Based on an extensive evaluation of de novo BGC prediction, GECCO is both more accurate and faster than other state-of-the-art machine learning approaches (domain-level AUPR=0.89). When applied to (i) a set of >300k genomes and metagenomes derived from human gut-associated microbes, and (ii) all publicly available, high-quality prokaryotic isolate genomes (>1 million genomes), GECCO identifies over 600k and nearly 3 million BGCs, respectively, including BGCs enriched in microbiome-mediated disease states (e.g., colorectal cancer). Overall, GECCO provides unprecedented insight into microbial biosynthetic potential; however, future experiments are needed to validate the most promising candidate BGCs (e.g., putative novel antimicrobials, toxins, carcinogens) in vitro and/or in vivo.

Looking for experimental microbiologists, molecular biologists, and (bio)chemists interested in working with BGCs and/or secondary metabolites.

Laura Carroll, Assistant Professor

Event type: Seminar
Speaker
Johan Henriksson
Research fellow
Read about Johan Henriksson
Speaker
Laura Carroll
Assistant professor, other position
Read about Laura Carroll
Contact
Annakarin Resoluth
Read about Annakarin Resoluth