about

Everything you wanted to know (and more!) about the CompMicroLab @ UmU 🤓

Welcome to our group website!


🤓 Who we are

We're a group of bioinformaticians and computational biologists interested in developing and utilizing bioinformatic approaches to monitor and combat the spread of bacterial pathogens...basically, we develop computational methods to make sense of trillions of bacterial A's, C's, G's, and T's! 🤓 🦠 🧬 💻 🧫 🔬 🧪

🧬 To learn more about us, check out our team page.

🧬 Interested in joining our group? All open and upcoming positions are posted on our jobs page.


💻 What we do

(Meta)genomic sequencing is playing an increasingly pivotal role in clinical and public health microbiology. As such, the amount of publicly available (meta)genomic data derived from microbes--including pathogens--is growing rapidly. As a computational microbiology group, we develop and utilize bioinformatic approaches, which can leverage these massive data sets to improve pathogen surveillance, source tracking, outbreak detection, and risk evaluation efforts.

Specifically, we develop and deploy

  • phylodynamic models, which can be used to track the evolution and transmission of zoonotic pathogens between animal reservoirs and the human population
  • machine learning approaches, which can be used to identify microbial genomic determinants associated with phenotypes of clinical and industrial importance (e.g., host disease states, antimicrobial resistance phenotypes)
  • multi-omics methods, which can be used to predict pathogen virulence potential

We are also passionate about bridging the gap between experimental and computational microbiologists by making (meta)genomic data analysis methods accessible and approachable to all through teaching and outreach.

🧬 To learn more about our research, check out our current and ongoing projects, as well as our recent publications.

🧬 To learn more about the tools we develop and maintain, check out our software page.

🧬 To view our teaching, extension, and outreach materials, check out our teaching page.


🇸🇪 Where we're located

Our research group is located in the Department of Clinical Microbiology at Umeå University in beautiful Umeå, Sweden.

Umeå at sunset.


🔬 Our philosophy

😎 Good vibes, better science!

It started out as an ironic group motto (with an ironic group logo to match!), but it truly captures the lab atmosphere that we try to cultivate. Specifically:

🌍 We believe that bioinformatics is for everyone.

We believe that bioinformatics is for everyone, and we strive to maintain a positive, diverse, safe, and inclusive research environment, where all scientists can learn and grow. We believe that anyone can become a bioinformatician, and we approach our teaching and mentoring duties with a "growth mindset", in which intelligence and ability are viewed as attributes that can be developed over time, rather than static characteristics inherent to an individual.

🧪 We do good science.

We conduct high-quality research with integrity and honesty. We are defined by these values, not by the number of publications we produce, or the impact factors of the journals we publish in. We are curious, rigorous, and critical-thinking scientists, and our research outputs reflect that. We develop and maintain open-source software that is freely available to the public, and we strive to adhere to FAIR/Open Science principles to the greatest extent possible.

🤗 We emphasize collaboration, NOT competition.

We maintain a highly collaborative group environment, in which group members are encouraged to work together, ask questions, and help each other freely. We make sure to acknowledge the contributions of others, and we give credit where credit is due. We celebrate each other’s successes, and we approach mistakes or failures as teachable moments and learning experiences. We recognize that group members contribute to the group in different ways, and we value ALL contributions equally...not just the scientific ones!

🏠 We advocate for a healthy work-life balance.

We believe that the best science happens when researchers feel supported and valued, with the ability to maintain a healthy work-life balance. We respect individuals' free time, including weekends and vacations, and we adhere to flexible work schedules, provided each researcher is (i) trying their best, (ii) making progress with their project(s) each week, and (iii) actively communicating/engaging with the group. We value progress and research outcomes over time spent in the office/lab.

🏆 We recognize that success looks different for each researcher.

We believe that there is no single, set definition of "success" that can be applied to all researchers. There are many possible career paths a bioinformatician can take, including careers outside of academia, and we encourage our group members to pursue what makes them happy. "Successes" can take many forms (e.g., publishing a paper, landing an internship, learning a new type of data analysis method, writing a grant, teaching a workshop or course, engaging in extension/outreach, developing a software tutorial, presenting at a conference, publishing a popular science piece). As a result, we provide all group members with personalized mentorship and support, and we celebrate and value all successes and accomplishments equally.


🤝 Our affiliations

As a computational microbiology group engaged in highly interdisciplinary and collaborative research, we're grateful to be a part of:




The Department of Clinical Microbiology at Umeå University

Umeå University

Our research group is housed in the Department of Clinical Microbiology at Umeå University, which is part of Norrlands universitetssjukhus (University Hospital of Umeå), the major hospital of northern Sweden.




The SciLifeLab and Wallenberg National Program for Data-Driven Life Science (DDLS)

SciLifeLab

The SciLifeLab and Wallenberg National DDLS program is a 12-year, 3.1 billion SEK initiative aimed at recruiting and training the next generation of data-driven life scientists.




The Laboratory for Molecular Infection Medicine Sweden (MIMS)

MIMS

MIMS is a member of the Nordic EMBL Partnership for Molecular Medicine, which is dedicated to the growing field of life sciences that investigates the molecular basis of disease and explores molecularly and genetically based treatments.




The Umeå Centre for Microbial Research (UCMR)

UCMR

UCMR is a National Linnaeus Center of Excellence at Umeå University that promotes interdisciplinary cutting-edge microbial and translational research.




The Integrated Science Lab (IceLab) at Umeå University

IceLab

IceLab is an interdisciplinary hub, which aims to bring researchers with wide-ranging backgrounds, questions and ways of thinking together, with the goal of breaking down the traditional boundaries between different scientific disciplines.


🙏 Our funding

We're extremely grateful for the generous funding and support that we have received over the years from:

Knut och Alice Wallenbergs Stiftelse

Knut och Alice Wallenbergs Stiftelse




The Swedish Research Council (Vetenskapsrådet)

Swedish Research Council




SciLifeLab

SciLifeLab




The International Association for Food Protection (IAFP)

IAFP




The U.S. National Science Foundation (NSF)

NSF




Umeå University

Umeå University