Postdoc at UC Berkeley @AdamArkinLab. PhD from Boston U @segrelab. Alum of @uvmcems. Systems biology, microbial communities, and metabolic networks.
Joined July 2016
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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 bit.ly/2ZqZhx4 by @d_b_bernstein, @SnorreSulheim, @AlmaasLab
David Bernstein retweeted
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
David Bernstein retweeted
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
David Bernstein retweeted
Another great contribution to improving annotation and understanding metabolism of microbes by my long term collaborator Morgan Price! journals.plos.org/plosgeneti…
David Bernstein retweeted
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. m.rfer.us/LBLmYL4pG
David Bernstein retweeted
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
pnas.org/doi/10.1073/pnas.21…
David Bernstein retweeted
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:
journals.asm.org/doi/10.1128…
David Bernstein retweeted
Check out the results of our survey & publication in @mSystemsJ:
Enhancing Microbiome Research through Genome-Scale Metabolic Modeling journals.asm.org/doi/10.1128…
@symbiosisnana @d_b_bernstein @Mbiggs86153124 @MicroMindy @beagj @MeiyappanL @alanrpacheco @SnorreSulheim @medlockgreg
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/TXeVsQyxQsejAJX76
David Bernstein retweeted
Our comprehensive guide to #COMETS (Computation Of Microbial Ecosystems in Time and Space) is out at @NatureProtocols. Read at rdcu.be/czjo9. We hope you will find it useful for #modeling the dynamics of #metabolism in microbial communities. #dFBA #microbiomes. 1/6
David Bernstein retweeted
My first paper on grad school work has just been published; ironically it has almost nothing to do with my thesis project link.springer.com/article/10…
David Bernstein retweeted
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 (git.io/Jc9mL) to do #FBA of string chemistries @JMolEvo bit.ly/36hm4yR
David Bernstein retweeted
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)
royalsocietypublishing.org/d…
David Bernstein retweeted
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.
nature.com/articles/s41467-0…
David Bernstein retweeted
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/TXeVsQyxQsejAJX76
David Bernstein retweeted
It's happening! runcomets.org
David Bernstein retweeted
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
genomebiology.biomedcentral.…
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!
A co-culture microplate for real-time measurement of microbial interactions biorxiv.org/cgi/content/shor… #bioRxiv
David Bernstein retweeted
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 doi.org/10.1101/2020.11.25.3…
David Bernstein retweeted
Today's #FFF: researcher's using #KBase have been quantifying metabolic networks between microbes in the human oral microbiome.
Check it out here: ow.ly/dmpM50vse9p.
Really excited to have my first paper from grad school published in @elife! The nicely formatted version is now out! A computational analysis of human oral microbiome organism’s biosynthetic capabilities doi.org/10.7554/eLife.39733