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Kiseok (Keith) Lee

@kiseokmicro.bsky.social
423 followers 627 following 52 posts

How can we understand & design robust community functions? Postdoc: UDel, Aditya Kunjapur lab PhD: UChicago, Seppe Kuehn lab Scholar: scholar.google.com/citations?user=&… Linkedin: www.linkedin.com/in/kiseokkeithlee

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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 17/09/2026
Excited to share our new preprint “The ecological context of enzymatic variation”! www.biorxiv.org/content/10.6... We use NarG nitrate reductase as a model system to connect enzyme sequence variation to ecological function.
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 12/09/2026
I feel very blessed and grateful to have visited Rutgers and given a seminar this week! Thanks to the Rutgers Department of Biochemistry and Microbiology for the warm welcome and invitation. The questions from students were stimulating, and conversations with faculty were extremely helpful.
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 03/09/2026
I'm excited to be giving a seminar at Rutgers on Sep 9th (Fermentation Club seminar series)! 📅 Wednesday, September 9 ⏰ 10:30-11:30 AM 📍 Institute for Food, Nutrition & Health, Room 205 (Rutgers University - New Brunswick) (in-person) If you’re around, let's chat!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 25/08/2026
<I am Recruiting!> The MEFE Lab (Microbiome Ecology & Functional Engineering) at Yonsei University, Seoul, Korea, will open March 2027. We'll start the recruitment process Sep-Oct 2026. Please share this post with anyone interested! Read the Join Us page carefully to apply! mefelab.github.io
mefelab.github.io
Microbiome Ecology & Functional Engineering Lab — Yonsei University
Microbiome Ecology & Functional Engineering Lab at Yonsei University, Department of Systems Biology (PI: Kiseok Lee).
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 22/08/2026
<Major career update> I will be starting as an assistant professor at Yonsei University, Seoul, Korea, Dept of Systems Biology, next March 2027. My lab will focus on understanding and designing robust microbiome functions! Sincerely grateful to all of my generous mentors. I will be recruiting soon!
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SeppeKuehnLab @seppekuehnlab.bsky.social · 29/06/2026
New paper out today in Nature Microbiology: "Epistatic interactions inform rational design of synthetic microbial communities for bioremediation." 🧵https://www.nature.com/articles/s41564-026-02386-4 @kiseokmicro.bsky.social @nitmb.bsky.social
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SeppeKuehnLab @seppekuehnlab.bsky.social · 05/03/2026
A new preprint with Matthew Schmitt, @kiseokmicro.bsky.social and Vincenzo Vitelli makes a huge step forward in learning functional groups of components in complex biological systems. It's dimension reduction that speaks to biological function. www.biorxiv.org/content/10.6...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 04/03/2026
I think this paper will be a game-changer for studying microbiome function. Matthew Schmitt and I found that a simple neural network, when trained on paired sequencing and functional data, can infer functional group structure directly from data. Pls read our preprint! www.biorxiv.org/content/10.6...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 07/11/2025
Wow wow wow. As soon as I saw this paper, I dropped everything I was doing and read it. Brilliant simple model and experiment to validate synergistic effect of toxin & private nutrient for strain displacement. My research directions greatly impacted. Amazing work Erik and the Foster lab!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 11/10/2025
It was eye opening to listen to Sara Molinari (University of Maryland)'s fascinating talk on engineering protein secretion to create cell aggregates/living materials. Asked so many questions and learned so much! @saramol.bsky.social
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 09/10/2025
Ohio State microbiology department is hiring assistant professor of Microbiome science (due Nov 6). It's an amazing department please apply!! (I would apply if I had more pubs haha...) jobs.sciencecareers.org/job/675478/a...
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SeppeKuehnLab @seppekuehnlab.bsky.social · 16/09/2025
Great new paper from Kyle Crocker -- a talented postdoc in the group who is ** on the job market now ** !! @kylecrocker.bsky.social bsky.app/profile/kyle...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 30/08/2025
It was one of the most interactive departmental seminar I've given. Thank you @xinsun-putiger.bsky.social for hosting this seminar in the beautiful campus of Penn, Department of Biology! Astounded by a full room of people studying soil, marine ecology, plant biology, and earth/environmental science.
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SeppeKuehnLab @seppekuehnlab.bsky.social · 17/07/2025
New paper in @nature.com! With @kiseokmicro.bsky.social , Siqi Liu, Kyle Crocker, Jojo Wang, Mikhail Tikhonov & Madhav Mani — a massive dataset and simple model reveal a few conserved regimes that capture how soil microbiome metabolism responds to perturbations. www.nature.com/articles/s41...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 16/07/2025
News article covering our story/research here from Matt Wood! biologicalsciences.uchicago.edu/news/soil-mi...
biologicalsciences.uchicago.edu
Simple rules govern soil microbiome responses to environmental change
Research from UChicago shows how environmental changes lead to predictable responses in soil microbiome metabolism.
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 16/07/2025
Published in Nature today! Here, we sought to systematically ask how natural community's metabolism changes with the environment. A simple consumer-resource model can predict N-cycle metabolism (nitrate use) and, more importantly, the mechanism behind its change. www.nature.com/articles/s41...
nature.com
Functional regimes define soil microbiome response to environmental change - Nature
Experimental perturbation of soil pH leads to a generalizable model of the soil microcosm comprising three functional regimes with distinct mechanisms linking environmental change to metabolite dynami...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 05/07/2025
Woohoo!! Starting Gordon Research Seminar (Microbial population biology) at Andover, NH. Thank you GRC GRS organizers!! @mikeblazanin.bsky.social @lcatherines.bsky.social
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 04/07/2025
Let's connect soon at GRC / GRS Microbial Population Biology!!! I have a very late night talk on Saturday around 9pm in the GRS hahaha...!! I am super excited to (re)connect with old/new friends/colleagues! So many talks I am looking forward to 😀 #grc2025 #microbialpopulationbiology
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 15/06/2025
<End of the PhD chapter> Graduation happened last week! So grateful for all the relationships I nurtured at uchicago. I will miss this place! Thank you Cathy for hooding me! Also, I am very excited to start postdoc tomorrow in Aditya Kunjapur @kunjapur.bsky.social lab in University of Delaware!
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Jesse McNichol @jcmcnch.bsky.social · 26/05/2025
So happy to see this paper finally out! A fun project with collaborators Emily Zakem, @jlw-ecoevo.bsky.social and Yubin Raut!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 27/05/2025
Congrats on this work being published Harish!!
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Alex Chase 🧬🌋🌊 @microbomics.bsky.social · 20/05/2025
When is microbial cross-feeding evolutionarily stable? www.biorxiv.org/content/10.1...
biorxiv.org
When is microbial cross-feeding evolutionarily stable?
Cross-feeding, a phenomenon in which organisms share metabolites, is frequently observed in microbial communities across the natural world. One of the most common forms is waste-product cross-feeding,...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 17/05/2025
Thank you everyone for coming to my PhD defense today in person and on zoom. Really can't thank everyone enough. Special thanks to Seppe Kuehn @seppekuehnlab.bsky.social and Madhav Mani for supporting me throughout the PhD journey. Thanks Hyunkyung for the beautiful cake resembling the soil!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 02/05/2025
Congratulations for this work seeing the light after many years of hard incredible work!! Go go Forti (Mandy) et al. and Aditya (soon to be postdoc advisor). Commensalism engineered with non-standard amino acid: www.nature.com/articles/s41...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 25/04/2025
Such a great conference! @recombconf.bsky.social RECOMB-Microbiome. Learned so much and asked a lot! Was able to catch up with many colleagues/professors and met amazing people doing great science!!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 11/04/2025
Caltech is such a research paradise! The resource, the people... just in awe. Thanks for hosting me Hannah!! Made so many amazing scientist friends/colleagues!!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 08/04/2025
<Shameless seminar self-promotion> I'll be giving a talk at Caltech in the Geoclub Seminar Series (www.gps.caltech.edu/news-and-eve...) this Thursday (4/10 4pm, Buwalda Rm). Join us if you are interested in hearing about the functional response of the soil microbiome to environmental perturbations!
gps.caltech.edu
GPS Event Calendar
From the Caltech Division of Geological and Planetary Sciences
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 05/04/2025
My good friend Dr. Myeonghwan Kim et al. figured out the molecular mechanism of how lipid nanoparticle encapsulated mRNA uptake happens in the cellular level! Today in Science! www.science.org/doi/10.1126/...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 03/04/2025
So great to be breathing the same air with the great minds in the same room! Simons foundation NITMB annual meeting in NY!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 31/03/2025
Seppe's thread!!
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SeppeKuehnLab @seppekuehnlab.bsky.social · 26/03/2025
Another preprint! Microbiomes are often structured in guilds, or groups of taxa that use similar resources - wastewater, fermentation, human gut. How do these guilds respond to environmental fluctuations? Can we learn these guilds from time series in the wild?
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 29/03/2025
Excited to share our new paper!🎉 We (the amazing Mahmoud Yousef et al.) learn the functional landscape from designing synthetic communities🧫 to degrade plastic-derived pollutant BPA in soils. As we increase BPA concentration, epistatic effects dominate! www.biorxiv.org/content/10.1...
biorxiv.org
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Paul Carini @uncultured.carinilab.com · 29/03/2025
In our latest blog post we discuss why "Shadow Mentors" are important in careers. I've been fortunate to have many—too many to list here. Check it out below and please share with someone who might find it useful. uncultured.carinilab.com/p/beyond-off...
uncultured.carinilab.com
Beyond Official Advisors: The Power of Shadow Mentors
Build a Cabinet of "Shadow Mentors"
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 27/03/2025
It was amazing to connect with Dr. Otto Cordero again! His talk at UChicago was intellectually very satisfying!! I knew Xiaoyu's great coarse-graining work but Dr. Stefany Moreno Gamez's work on the molecular mechanism of niche partitioning was super stimulating...!! Thanks Otto!
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Jay T Lennon @jaytlennon.bsky.social · 27/03/2025
How can we leverage microbes to address the climate crisis? The @asm.org & IUMS Scientific Advisory Group introduces a new framework in Nature for assessing microbial solutions, focusing on economic returns, safety and societal impact. Read more @nature.com: www.nature.com/articles/d41...
nature.com
Microbes can capture carbon and degrade plastic — why aren’t we using them more?
Interventions involving bacteria or fungi could help to sequester greenhouse gases, create more sustainable products and clean up pollution — in ways that are economically viable and safe.
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Dr. Aaron Thierry @thierryaaron.bsky.social · 27/03/2025
"We notably predict that Madrid’s climate in 2050 will resemble Marrakech’s climate today, Stockholm will resemble Budapest, London to Barcelona, Moscow to Sofia, Seattle to San Francisco, Tokyo to Changsha" By 2050! journals.plos.org/plosone/arti...
journals.plos.org
Understanding climate change from a global analysis of city analogues
Combating climate change requires unified action across all sectors of society. However, this collective action is precluded by the ‘consensus gap’ between scientific knowledge and public opinion. Her...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 19/03/2025
If you are interested in environmental microbiology and the intersection of ecology and physiology, join this wonderful group of scientists in Karna Gowda lab at Ohio State University!! I guarantee great mentorship and fascinating science!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 18/03/2025
Happy to be reunited with Professor Yong-Hwan Lee (SNU) at his RR Nelson memorial lecture at Penn State! He is a living history with ~40 years of ground-breaking forward/reverse genetics and bioinformatics on rice blast. He had a profound influence on me.
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Avi Flamholz @flamholz.bsky.social · 18/03/2025
Glad this paper is out. The review was quite an adventure.
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 14/03/2025
<Shameless seminar promotion at Ohio State> Please join us at the QMicro seminar, where I will delve into soil microbial ecology and how metabolic functions change in varying environments! - When: Tuesday, March 18, 2025, 3:00 PM EST - Where: Pomerene Hall, Rm 150, Ohio State University
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Xin Sun @xinsun-putiger.bsky.social · 07/03/2025
First post: 🦠🌊Denitrification is the main nitrogen loss process, but how do microbes performing different steps coexist? We outline the rules governing this coexistence and explain why some denitrifiers are more abundant than others in the ocean. Check it out here: www.pnas.org/doi/10.1073/...
pnas.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Shinichi Nakagawa @itchyshin.bsky.social · 04/03/2025
Postdocs interested in meta-science and want to work in Canada - our Centre for Open Science & Synthesis in Ecology and Evolution will be happy to host you! (U of Alberta has one of the best Computer Science Dept) - apply.sloan.org/prog/call_fo... Please DM me or email me if you are interested
apply.sloan.org
Call for submissions: Metascience and AI postdoctoral fellowship -
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Pamela Ferretti @pamferretti.bsky.social · 26/02/2025
Last week @richabdill.com and @samanthagraham.bsky.social's paper was featured on the cover of Cell! The cover, portraying microbes on shelves shaped like a world map, was possible thanks to the amazing team of illustrators at SciStories ✏️🦠
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 23/02/2025
Detecting food DNA in the stool metagenomics!
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 23/02/2025
The annual microbiome symposium TMC2025 will be on April 11th at UChicago 9am-5pm. We had so many new faculty hires at UChicago studying microbiome in the last 3 years that this is an exciting place to be in! Certainly a frontier in the field. Typo in image: Alice Cheng.
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 22/02/2025
A recent pretty comprehensive primer on metagenomics analysis! www.nature.com/articles/s43...
nature.com
Analysis of metagenomic data - Nature Reviews Methods Primers
Metagenomics describes the analysis of genetic information in a microbial community to provide taxonomic or functional information on the constituent microorganisms. This Primer describes suitable sam...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 13/02/2025
Coach Nick Sirianni's quote feels quite relevant to science and research: "You can't be great without the greatness of others (collaborators and intellectual discussion partners)."
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Pete Chuckran @pchuckran.bsky.social · 13/01/2025
Wetting dry soil rapidly stimulates microbial activity and has important consequences for biogeochemical cycling. In our paper out today, we show that part of that response can be explained by how bacterial genomes are written (i.e. codon usage, nucleotide freq., genome size) doi.org/10.1073/pnas...
doi.org
PNAS
Proceedings of the National Academy of Sciences (PNAS), a peer reviewed journal of the National Academy of Sciences (NAS) - an authoritative source of high-impact, original research that broadly spans...
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 09/02/2025
I registered for the RECOMB-microbiome conference in Korea in April 24th! It will be a blast where the focus is in microbiome data analysis. Looking forward to the keynote from @hutlab.bsky.social . DM me if you are going too! Let's meet and chat!! @recombconf.bsky.social recomb.org/recomb2025/r...
recomb.org
RECOMB 2025 | RECOMB Microbiome
RECOMB 2025 - Yonsei University, Seoul
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Kiseok (Keith) Lee @kiseokmicro.bsky.social · 07/02/2025
Using engineered Lactobacillus to deliver appetite regulating hormones through the nose to bypass BBB! www.cell.com/cell/fulltex...
cell.com
Engineered commensals for targeted nose-to-brain drug delivery
Shen et al. investigate the use of Lactobacillus plantarum, a commensal bacterial strain, as a chassis for targeting the olfactory mucosa to facilitate precise nose-to-brain delivery of therapeutic mo...
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