Medlock Lab

Do you like the #microbiome? Do you like metabolic models? If yes to EITHER of these questions, share your perspective on the use of metabolic modeling in the microbiome field! forms.gle/TXeVsQyxQsejAJ…

It's happening! runcomets.org

Very excited to have this review out! We cover major sources of uncertainty in genome-scale metabolic modeling and approaches developed for addressing this uncertainty. We hope this review will serve as a roadmap for those interested in further developing methods in this area!

Second, 3rd year @UVABME undergraduate Sam Park earned a Harrison award for his proposal on using genome-scale metabolic modeling and machine learning to study host-microbiome interactions in inflammatory bowel disease. Go Sam!

Much exciting news to share today! First, @MariaMurach has joined the lab for her @uva_bims PhD in Biochemistry & Molecular Genetics. We can’t wait for the exciting computational and experimental advances Maria will bring to microbiome research!

Introducing the BioMe plate! This modified 96-well microplate enables the observation of microbes interacting across a porous membrane. Very happy to have the paper from my graduate work with @segrelab co-led by Charles Jo (who also made this awesome GIF) out on BioRxiv now!

We are looking for a post-bac researcher! Primary responsibilities will be metabolomics data analysis and in vitro culture of anaerobic bacteria. Partial support through @UVA_TUMI to help with collaborative microbiome research. Pls RT! @UVABME uva.wd1.myworkdayjobs.com/UVAJobs/job/Ch…

We are recruiting PhD students! Come study gut systems biology with us - experimental & computational opportunities in probiotic design, genome-scale metabolic modeling, metabolomics, & more. Apply through @UVABME by Dec 15th! DM for details, pls RT engineering.virginia.edu/departments/bi…

excited to share our latest preprint! Cryptosporidium, a protozoan parasite, causes overt diarrhea or subclinical infection, but both types of infection in infants are associated with growth stunting. so what is different between these outcomes? why do some kids get diarrhea?1/3

@jtyurkovich, @me_beber, @dr_drae, @papinsysbio, and I performed a community-wide survey to follow up on a panel on standards in metabolic modeling (at the 2018 @COBRAcon2020). Results & recommendations here: embopress.org/doi/10.15252/m… (1/2)

Awesome preprint from @oveoyas @CSB_ETHZ describing an intuitive method for identifying "minimal pathways" in constraint-based metabolic models. We need more methods like this that are both algorithmically compact and computationally efficient!