Author of "Biophysical metabolic modeling of complex bacterial colony morphology" https://nitter.cf/t.co/cAo35BXE0p
Joined November 2011
- Tweets1.3K
- Following632
- Followers215
- Likes164
Ilija Dukovski retweeted
Recently, there's been complaints on low-quality AI reviews at conferences and journals. What if we put the frontier LMs into an agent harness?
With the right setup, on 82 Nature-family papers, 45 expert scientists judged that AI reviewers outperform the best human reviewer!
🤗 huggingface.co/papers/2605.2…
Ilija Dukovski retweeted
How do bacteria organize? 🦠 @BU_Tweets researchers reveal in @CellPressNews that colony shape, metabolism & nutrients drive growth, diversity & striking rings. Learn more: spr.ly/6012AGQbj
Ilija Dukovski retweeted
How we can approach space travel & co-create sustainable, ethical human colonies on Mars?
Join the discussion at "Space Travel with Earth Wisdom," our symposium featuring researchers at the intersection of #space science, #ecology, #sustainability & #ML
tinyurl.com/2bshaftt
Ilija Dukovski retweeted
BREAKING NEWS
The Royal Swedish Academy of Sciences has decided to award the 2023 #NobelPrize in Physics to Pierre Agostini, Ferenc Krausz and Anne L’Huillier “for experimental methods that generate attosecond pulses of light for the study of electron dynamics in matter.”
Ilija Dukovski retweeted
A eukaryotic-like ubiquitination machinery in bacteria! Beautiful structures from the Corbett lab.
This machinery defends bacteria against phage infection by targeting phage structural proteins and interfering with virion assembly
I'm thrilled to share the latest work from my lab, showing that a bacterial anti-phage immune system encodes a ubiquitination pathway strikingly similar to our own! biorxiv.org/content/10.1101/… (1/12)
Ilija Dukovski retweeted
Very happy to announce that my tool for reconstructing genome-scale metabolic models is now public on GitHub and installable via pip. It's especially relevant for models that will take part in microbiome simulations: github.com/rcolpo/pgp_recons… #SysBio
Ilija Dukovski retweeted
More thoughts on the demise of disruptive science.
Take Fred Sanger, 2x Nobel Prize winner. Sydney Brenner wrote about him in an obituary that multiple times in Fred's career, he went 10+ years without publishing as he was working on 'disruptive' science.
science.org/doi/full/10.1126…
Ilija Dukovski retweeted
This piece brought to mind so many conversations in our lab and in class about the importance of null expectations in biological theory, and the need to be critical about these and where they come from. I thoroughly enjoyed the read.
journals.uchicago.edu/doi/10…
Ilija Dukovski retweeted
An excellent read by @a_m_mastroianni on why grant funding is broken.
TL;DR: hacking, bad proxies, rewarding of conventional success, and paternalism
experimentalhistory.substack…
Ilija Dukovski retweeted
#NewNProt Using COMETS (Computation Of Microbial Ecosystems in Time and Space) to generate simulations of multiple microbial species in molecularly complex and spatially structured environments go.nature.com/3mOa0N4 #microbialcommunities #computational #modeling
Ilija Dukovski retweeted
Great to see the new version of COMETS published. It was really fun getting to collaborate with this team. @idouk, @metaboli3am, @JeremyMChacon, and Mike Quintin did some heavy lifting with lots of support from Korolev lab, @asanchez_lab, and @segrelab.
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
Ilija Dukovski retweeted
#COMETS was made possible by funding from @doescience. Development of specific functionalities was enabled also by grants from @NIH, @NSF, @HFSP and others. 6/6
Ilija Dukovski retweeted
We hope #COMETS will continue to grow as a collaborative tool with new biological modules and capabilities. Check @RunCOMETS for updates, gitter.im/segrelab/comets for feedback, questions and discussions, and let us know if you want to contribute! 5/6
Ilija Dukovski retweeted
#COMETS enables computer simulations of multiple species interacting with the environment and each other through competition/exchange of metabolites. This is dictated by resource allocation in organisms, as a function of metabolic stoichiometry encoded in their genomes. 3/6
Ilija Dukovski retweeted
This is collective work in @asanchez_lab, @HarcombeLab, Korolev lab, @segrelab. Thanks @idouk @metaboli3am @JeremyMChacon and Mike Quintin for leading the way, @jccvila @SnorreSulheim @alanrpacheco @d_b_bernstein for crucial contributions, and @real_riehl for early code. 2/6
Ilija Dukovski 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
Ilija Dukovski retweeted
Thank you to @idouk from @BU_Tweets who kicked off #metabolic modeling week!
Check out :
- his next paper on @RunCOMETS arxiv.org/abs/2009.01734
- his research with @dsegre (@segrelab) on understanding the flow of #molecules and #energy in #microbiomes
bit.ly/3mal07t
Ilija Dukovski retweeted
Thanks @katjmcalpine for highlighting @NatureComms #SyntheticEcology work by @alanrpacheco with @MelisaLKO bit.ly/3wo9s3W @BU_Tweets @BuMicrobiome