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!
Addressing uncertainty in genome-scale metabolic model reconstruction and analysis, @GenomeBiology https://t.co/dbNpN7Co26 by @d_b_bernstein, @SnorreSulheim, @AlmaasLab
Every day, we learn more and more about how microbes interact with each other and with their hosts.
How can we ensure we’re making the most out of this growing wealth of data?
1/12
We are looking for a postdoc who ❤️phages & is passionate about uncovering host-phage specificity determinants by generating >200K phage-bacteria interactions, 1000’s of HT genetic assays & powerful machine learning algorithms. Work will be in my lab & @AdamArkinLab plz reach out
Another great contribution to improving annotation and understanding metabolism of microbes by my long term collaborator Morgan Price! https://t.co/GMvPQ8367W
Hey All,
We have a great postdoctoral position to apply the awesome power of the one of the most powerful supercomputers on earth to build data-driven and mechanistic approaches to model large metagenomic compendia. https://t.co/VB9VQTQjta
Are two coenzymes better than one? Find out what selective pressures might have driven the usage of multiple redundant coenzymes in modern metabolism in our latest paper, published today in @PNASNews! 1/2
https://t.co/2gAu2k179O
We also compiled a broad set of resources that researchers with varying levels of computational/experimental expertise can use to get started with using models for microbiome studies:
https://t.co/aw0LjnpGg3
Our comprehensive guide to #COMETS (Computation Of Microbial Ecosystems in Time and Space) is out at @NatureProtocols. Read at https://t.co/B56rp7DRXA. We hope you will find it useful for #modeling the dynamics of #metabolism in microbial communities. #dFBA#microbiomes. 1/6
Analyzing reaction networks in artificial string chemistries (e.g. ab+aa->abaa) helps understand the evolution of metabolism. @devmoy1 w @d_b_bernstein & @alanrpacheco, developed a toolbox (https://t.co/fQ46nhUbdC) to do #FBA of string chemistries @JMolEvo https://t.co/LBYlwbqwOj
Inspiring and important read on the sources of uncertainty in metabolic modeling by David Bernstein et al from the Segre lab @dsegre https://t.co/yDv7vcRGO9
We know that the resources available to a microbial community play a big role in shaping its structure and function.
So if we wanted to design a community with specific properties, could we find a combination of nutrients that would get us there? (1/5)
https://t.co/PzcJ7aHew5
How does resource diversity shape microbial communities?
In our new paper, @MelisaLKO, @dsegre, and I identify key factors that define this relationship and quantify how communities challenge expectations of growth and diversity in complex environments.
https://t.co/qL4xqIIvFr
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!
https://t.co/lmBV9eFXRd
Genome-scale metabolic models (GEMs) aim to capture a representation of the entirety of metabolic functions of a cell. We review their major sources of uncertainty and survey existing approaches developed for representing and addressing them. @segrelab
https://t.co/MuwvdfOqgO
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!
Announcing the latest preprint from my PhD work! Here, we show how specific microbial community behaviors can be identified via rational environmental modification. 1/3 https://t.co/eYlC0PssVs
Today's #FFF: researcher's using #KBase have been quantifying metabolic networks between microbes in the human oral microbiome.
Check it out here: https://t.co/KYohr9JRKG.