Thanks for the applications
Our open doctoral student and postdoc positions closed over the weekend, and in total we had 110 applications, although some persons applied to more than one of the positions, bringing the total number of applicants down a bit. Still, this will be a lot of work for me. I will prioritize the postdoc position, as this had the fewest applications. So if you applied to one of the two PhD student positions, please give it some time.
A quick skimming of the applications shows that we have had extraordinary high quality of applications overall, although some of the applicants will be a bit too wet-lab oriented for these specific positions.
Thanks a lot for your interest in the lab’s work! I appreciate all of your efforts!
We’re hiring 2 PhD students and a postdoc
As I wrote a few days ago, I have now started my new position at Chalmers SysBio. This position is funded by the SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS), which also funds PhD and postdoc positions. We are now announcing two doctoral student projects and one postdoc project within the DDLS program in my lab.
Common to all projects is that they will the use of large-scale data-driven approaches (including machine learning and (meta)genomic sequence analysis), high-throughput molecular methods and established theories developed for macro-organism ecology to understand biological phenomena. We are for all three positions looking for people with a background in bioinformatics, computational biology or programming. In all three cases, there will be at least some degree of analysis and interpretation of large-scale data from ongoing and future experiments and studies performed by the group and our collaborators. The positions are all part of the SciLifeLab national research school on data-driven life science, which the students and postdoc will be expected to actively participate in.
The postdoc and one of the doctoral students are expected to be involved in a project aiming to uncover interactions between the bacteria in microbiomes that are important for community stability and resilience to being colonized by pathogens. This project also seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. The project tasks may include things like predicting genes involved in pathogenicity and other interactions from sequencing data, and performing large-scale screening for such genes in microbiomes.
The second doctoral student is expected to work in a project dealing with understanding and limiting the spread of antibiotic resistance through the environment, identifying genes involved in antibiotic resistance, defining the conditions that select for antibiotic resistance in different settings, and developing approaches for monitoring for antibiotic resistance in the environment. Specifically, the tasks involved in this project may be things like identifying risk environments for AMR, define potential novel antibiotic resistance genes, and building a platform for AMR monitoring data.
For all these three positions, there is some room for adapting the specific tasks of the projects to the background and requests of the recruited persons!
We are very excited to see your applications and to jointly build the next generation of data driven life scientist! Read more about the positions here.
My first day at Chalmers
Today was a big day, as it was my first ‘real’ working day at SysBio at Chalmers University of Technology. (Quotation marks as I have had access to an office at SysBio for a few weeks, and also because I spend the afternoon on meetings at Sahlgrenska.) Regardless, this marks the start of a transition period where the lab will be moving more and more of our routines to Chalmers, which will culminate when the lab-dependent persons will move into our new labs after the summer.
We also welcomed our Erasmus intern Manuela Seehauser to the lab today, as well as Marius Surleac who is visiting us for a few weeks from Romania.
Finally, we have announced new positions related to my new Chalmers-funding. More on those soon. Speaking of jobs, if you’re interested in doing a bioinformatics postdoc with me and Joakim Larsson you have two more days to apply for that position!
Open postdoc position
Together with Joakim Larsson‘s lab, we now have an open two-year postdoc position in bioinformatics on antibiotic resistance and biocide resistance. The development of antibiotic resistance has been driven by use of antibiotics, but antibacterial biocides also have the potential to select for antibiotic resistance. However, knowledge of which genes that contribute to biocide resistance and could be associated with antibiotic resistance is sparse. To some extent, such genes are documented in the BacMet database which we have developed, but this collection of resistance genes is only scratching the surface of all biocide resistance that exists among bacteria in the environment.
We are now looking for a postdoctoral fellow to continue the important work on bioinformatic analysis of biocide and antibiotic resistance to answer the question whether increasing biocide resistance would be a threat to human health. The postdoc will be working with the development of the BacMet database to make it more targeted towards biocidal substances and products in addition to resistance genes. The tasks include bioinformatic sequence analysis, literature studies and database and web programming. The work will also include investigations of the prevalence of the identified resistance genes in genomes and metagenomes.
The recruited person will work closely with both my group and the group of Prof. Joakim Larsson, and will participate in the JPIAMR-funded BIOCIDE project. You can apply to the postdoc position at the University of Gothenburg application portal: https://web103.reachmee.com/ext/I005/1035/job?site=7&lang=UK&validator=9b89bead79bb7258ad55c8d75228e5b7&job_id=25122
The deadline is May 4, 2022. Come work with us on this exciting topic in the intersect between two great research environments (if I may say it myself!) We look forward to your application!
Open PhD position
We are hiring a PhD student to work with interactions between the bacteria in human and environmental microbiomes that are important for community stability and resilience to being colonized by unwanted bacteria (including pathogens). The project seeks to unearth which environmental and genetic factors that are important determinants of bacterial invasiveness and community stability. You can read more at our Open Positions page.
We are looking for a candidate with experience with both bioinformatics and experimental microbiology. Previous experience with microbial communities is a plus, but not a must, as is work with human cell lines.
The project is fully funded by a grant from the Swedish Research Council and the position is planned for 4.5 years, with 4 years of research and course work and half a year of teaching.
If you feel that you are the right person for this position, you can apply here. We look forward to your application! The deadline for applications is October 21.
Open postdoc position
We are hiring a postdoc to work with environmental monitoring of antimicrobial resistance. The project is part of the EMBARK program and will consider different aspects of establishing a baseline for background antibiotic resistance in the environment, standardization of monitoring protocols and development of methods to detect emerging resistance threats. The project will involve work with environmental sampling, DNA extractions, bacterial culturing and generation of large-scale DNA sequence data. In terms of bioinformatic analyses, the project will encompass analysis of next-generation sequence data, genome-resolved metagenomics, short-read assembly and network analysis.
We look for a skilled bioinformatician, preferably with experience of experimental laboratory work. If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is January 3.
Quick update on the PhD position
I just wanted to very quickly brief applicants to the recently announced PhD position in the lab. We got 71 applications in total, most of which I consider relevant for the position. The bottom line is that this will take a few days to go through, but we are working on it, and will get in touch with the top candidates when we are done. I would, however, already like to thank everyone who applied – it’s amazing that you want to spend your time doing research that I find exiting!
Open PhD position
We are hiring a PhD student to work with effects of antibiotics on microbial communities! The project will use large-scale techniques to investigate how sub-inhibitory concentrations of antibiotics affect microbial communities. Specifically, the project will examine how the ability for bacteria to colonize and invade established microbial communities is impacted by antibiotics. The project will also explore how antibiotics influence the interactions between different species in bacterial communities and if this may change their ability to withstand invasions. The goal is to identify the genes and mechanisms that contribute to change and stability in microbial communities.
A cool thing about this position is that it is fairly adaptable to the eventual candidate, and the project can be somewhat tailored to suit the profile of the PhD student. This means that we’re looking for someone who is either a bioinformatician or an experimentalist (or both). Previous experience with microbial communities is a plus, but not a must.
If you feel that you are the right person for this position, you can apply here. More information is also available here. We look forward to your application! The deadline for applications is December 9.
New employment – same work
Today, I started my new position at the University of Gothenburg as a non-tenured assistant professor (forskarassistent)*. In essence, this means that I have a position funded by my own grant until the end of 2020, although I will be on a leave-of-absence while doing my PostDoc with Jo Handelsman in Wisconsin. Speaking of which, I will be leaving to the US on Thursday next week for a month of setting things up at her lab (and also going to the EDAR4 conference in Lansing). I will return to Sweden in mid-September and leave for the US for real early next year.
In terms of actual work, this change of position will not mean very much at the moment. I will continue to do the same things for some time, and I will remain closely associated with Joakim Larsson’s lab at the Dept. of Infectious Diseases. And luckily, I will retain my lovely roommates for at least the time being. In the long run, however, this means that I will shift my research focus slightly, away from antibiotic resistance risk management towards interactions in microbial communities (still related to antibiotics though). Exciting times ahead!
* For some reason, the university administration refuses to call this position assistant professor in English at this time, instead referring to the position as “Postdoctoral research fellow”. I guess that it might be bloody annoying explaining that this is not the same as “postdoctoral researcher” and virtually everywhere else would be called “(non-tenured) assistant professor”, but then on the other hand, who cares about titles anyway?
Looking for a super-interesting job in bioinformatics?
If you’re looking for super-interesting jobs within bioinformatics, you don’t need to look any further. Instead, you should apply for a position at 1928 Diagnostics here in Gothenburg and join them in the fight against antibiotic resistant bacteria. The position is in the development team and the deadline for application is December 19. All the details can be found here.