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Sonny T M Lee

@sonnytmlee.bsky.social
706 followers 569 following 20 posts

Associate Professor K-State - everything microbe. Getting a sneak peek into host-microbes interaction. Outside of the microbial world, I do cave diving, running

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Reposted by Sonny T M Lee
Microbiome @microbiomej.bsky.social · 17/08/2026
In #Microbiome Microbially derived glutathione from Eubacterium rectale alleviates oxidative stress and promotes intestinal epithelial recovery🦠 Read more➡️ doi.org/rjc8 #Microbes
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Tanner Richie @microberich.bsky.social · 18/08/2026
Final PhD chapter is PhDone!! ✨ Thrilled to see this out and a massive thank you to my incredible co-authors and mentor @sonnytmlee.bsky.social! Check it out below! #microbiome #microbialmetabolites #research #GutHealth #IBD
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Gang Fang @gangfang.bsky.social · 05/02/2026
New Preprint 📢 from our team 🔎 Critical assessment of #intratumor and #low #biomass #microbiome using #longread sequencing Some studies suggest bacteria 🦠 live inside tumors and influence cancer treatment. But there’s also been a major #debate: in these very​ low-microbe tissue samples, how much 1/
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Simon McArthur @drsimonmcarthur.bsky.social · 13/01/2026
Very pleased this is now published - led by Dr Emily Connell & @dvauzour.bsky.social, we show that a Mediterranean diet-inspired supplement can improve disease signs in an Alzheimer's mouse model, acting via the gut microbiota www.tandfonline.com/doi/full/10.... 🧪🧠 #gutbrainaxis #meddiet
tandfonline.com
A novel Mediterranean diet-inspired supplement reduces hippocampal amyloid deposits and microglial activation through the modulation of the microbiota gut-brain axis in 5xFAD mice
Alzheimer's disease (AD) is projected to increase in prevalence, heightening the need for strategies to alleviate its neuropathological burden. The bioactive constituents of a Mediterranean-style d...
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Karthik Anantharaman @karthik-a.bsky.social · 12/12/2025
Our paper "Ecosystem health shapes viral ecology in peatland soils" is out in Nature Microbiology! We show that peatland health strongly structures viral communities, shaping virus–host networks, and carbon and nutrient cycling. Please share. www.nature.com/articles/s41... #phagesky #Microsky
nature.com
Ecosystem health shapes viral ecology in peatland soils - Nature Microbiology
Metagenomics shows that viral diversity and community structure are shaped by geography and ecosystem health status, positioning viruses as unexpected players in peatland restoration.
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Michael Baym @baym.lol · 20/11/2025
Hot off the press! Our latest paper led by @fernpizza.bsky.social, understanding how plasmids evolve inside cells. These small, self-replicating DNA circles live inside bacteria and carry antibiotic resistance genes, but also compete with one another to replicate. 1/ www.science.org/doi/10.1126/...
science.org
Intracellular competition shapes plasmid population dynamics
From populations of multicellular organisms to selfish genetic elements, conflicts between levels of biological organization are central to evolution. Plasmids are extrachromosomal, self-replicating g...
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Jay Hinton @jayhinton.bsky.social · 30/10/2025
Proud to be part of this incredible multidisciplinary team uncovering why some people are NOT infected by Salmonella. This new Wellcome Trust @wellcometrust.bsky.social funding will allow us to uncover why some people naturally resist infection and colonisation by Salmonella Typhimurium.
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Chris Greening @greening.bsky.social · 24/10/2025
Why can our farts ignite? Time to find out (and quite a bit more) in our new paper in Nature Microbiology led by the amazing Dr Cait Welsh. Integrating atomic-to-ecosystem level insights. www.nature.com/articles/s41...
nature.com
A widespread hydrogenase supports fermentative growth of gut bacteria in healthy people - Nature Microbiology
A previously uncharacterized microbial enzyme is responsible for the production of molecular hydrogen in the gut, which drives the growth of other bacteria and has implications for human health.
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Paul Carini @uncultured.carinilab.com · 17/10/2025
New paper: Dried soil bacteria enter dormancy with "frozen" RNA & metabolite profiles—but water vapor alone can wake them up! #Microbiology #SoilScience #Dormancy #ClimateChange #MicroSky
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Jeremy Barr @jeremyjbarr.bsky.social · 15/10/2025
Very excited to share the latest work from our lab, which was published today in Nature! nature.com/articles/s41... PhD graduate and now post-doc Sofia Dahlman, along with co-senior author Sam Forster from The Hudson and other researchers from our lab and others.
nature.com
Isolation, engineering and ecology of temperate phages from the human gut - Nature
Human host-associated cellular products may act as induction agents for bacteriophages.
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Sarah McAnulty, Ph.D. @sarahmackattack.bsky.social · 13/10/2025
Good news: a grant I submitted got selected for an interview out of ~150 apps. Only 2 others got interviews! Bad news: @skypeascientist.bsky.social was not selected in the end 😞 I will keep trying. In the meantime, consider supporting our work with $5-10/month? givebutter.com/SupportSAS25
givebutter.com
Support Skype a Scientist!
By Skype a Scientist
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Elinne Becket, PhD @bielleogy.bsky.social · 03/10/2025
Becket Lab representing at @csucoast.bsky.social annual meeting! 💪
Selfie of 5 smiling women at the CSU Chancellor's Office board room
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EMBL Events @events.embl.org · 18/09/2025
☕🍏 Coffee break time at 'The human microbiome' symposium! #EESMicrobiome Microbes never sleep, but scientists definitely need their coffee 😅 A perfect chance to recharge, chat, and maybe spark the next big collaboration over a fresh cup ✨
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Katherine Aird @airdlab.bsky.social · 03/09/2025
Big day for multiple lab members who celebrated a promotion! Congrats to Apoorva Uboveja for promotion to Staff Scientist and Aidan Cole for starting as a postdoc! I am now a full professor too 🤓 Want to learn more about our science or join the lab? Visit Airdlab.com
airdlab.com
Aird Lab
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Sonny T M Lee @sonnytmlee.bsky.social · 01/09/2025
The weather held up for our lab shrimp boil. We gorged on delicious food, chatted leisurely over fire. I am fortunate to have these awesome trainees 🥹
Trainees eating shrimp boil Picking foodShrimp boilPreparing shrimp boil
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José Cerca @naturalselection.bsky.social · 19/08/2025
The 2025-26 Eco-Evo job list is out. Good luck to those applying! docs.google.com/spreadsheets...
docs.google.com
ecoevojobs.net 2025-26
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Geoff Zahn @geoffzahn.bsky.social · 20/03/2025
The Zahn lab is transitioning into the TIDAL Lab this Fall and moving to the Appl. Sci. Department at William & Mary. Would love to chat with students interested in doing a PhD at the nexus of microbial ecology and data science (starting 2026). RP please! gzahn.github.io
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TanentzapfLab @tanentzapflab.bsky.social · 13/08/2025
The goal of a PhD is not to learn some facts or read a few papers or learn a bunch of techniques. The goal of a PhD is to learn independence, problem solving, how to finish things you start, resilience, & gain the ability to adapt & think creatively. Learning these things is hard.
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Elinne Becket, PhD @bielleogy.bsky.social · 01/08/2025
At a symposium where I'm one of the only PUI faculty and I've just been playing therapist to super kind and well-meaning R1 faculty to get them to not 👏take👏mentee👏behavior👏personally👏. 1/n
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Matt Barber @biobarber.bsky.social · 01/08/2025
This week we said farewell to the amazing @caitlinkowa.bsky.social as she moves to start her new lab at Dartmouth. So grateful for all her leadership and mentoring the last few years. If you’re interested in all things skin microbes (especially fungi) check out her lab! I can’t recommend enough.
caitlinkowalski.com
HOME
Visit the post for more.
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PLOS Biology @plosbiology.org · 23/07/2025
How are bacterial transport machineries regulated by external cues? @brochadolab.bsky.social &co identify environmental chemicals that regulate #transporter transcription, identifying the TF Rob as a key modulator of #EffluxPump expression in #Ecoli #AMR @plosbiology.org 🧪 plos.io/46pUM9Q
Left: Compound-promoter interaction network. Fifty-three significant compound-promoter interactions are shown as edges in a Sankey diagram connecting the compounds (left, source nodes) to the promoters (right, target nodes). Edge thickness represents mean Z-scores (n = 8), while node size represents the total number of interactions. Right: Proposed model for the molecular mechanism of caffeine-ciprofloxacin antagonism. Caffeine triggers expression of MicF small RNA in a Rob-dependent manner, which then binds to the 5′-UTR of ompF mRNA to inhibit and decrease OmpF protein levels. This ultimately prevents ciprofloxacin from entering the cell, resulting in caffeine-ciprofloxacin antagonism
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Dr. Sue Ishaq @drsueishaq.bsky.social · 08/07/2025
The Summit on Microbiome Stewardship is happening this week!!! Program details and free registration can be found here.  Please note, the webinars and the workshop each require registration to help us manage attendance. Who should attend? Students, and professionals from any discipline, are…
sueishaqlab.org
The Summit on Microbiome Stewardship is happening this week!!!
Program details and free registration can be found here.  Please note, the webinars and the workshop each require registration to help us manage attendance. Who should attend? Students, and professionals from any discipline, are encouraged to attend! The summit is highly interdisciplinary and we welcome diverse perspectives: research presentation and workshop activities represent microbiome, ethics, health, food systems, ecology, and environmental sciences, and more!
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Rafal Mostowy @rafalmostowy.bsky.social · 26/06/2025
What determines who a phage can infect? We tackled this question for temperate phages of Klebsiella — a bacterial pathogen — using a genome-wide association study (GWAS) and a massive protein testing effort. 👇 A thread!
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Roland Hatzenpichler @environmicrobio.bsky.social · 24/06/2025
Manuscript/resource alert #microsky 🦠 My lab offers the community a collection of 30 E. coli (CloneFISH) cultures, each carrying a plasmid for the heterologous expression of a (near) full-length 16S rRNA gene from one of 30 lineages of archaea, including 19 yet uncultured ones.
List of 30 CloneFISH cultures available for free (requester is asked to pay shipping fees).
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Elinne Becket, PhD @bielleogy.bsky.social · 12/06/2025
I think it's important to be able to say: I'm keeping it together but I'm not ok. I can manage, I can laugh, I can live and appreciate life, but I'm not ok. Feelings don't need to be simple.
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James Gurney @jamesgurney.bsky.social · 10/06/2025
Big day for the Gurney lab, first paper from the lab is now published. @sczerwinski.bsky.social led this work and answered a simple question does phage steering work when other bacteria are around? Tldr: yes! journals.asm.org/doi/epub/10....
journals.asm.org
Phage steering in the presence of a competing bacterial pathogen
You have to enable JavaScript in your browser's settings in order to use the eReader.
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Daan Speth @daanspeth.bsky.social · 10/06/2025
I'm happy to announce the latest release of the GlobDB, available at globdb.org. The GlobDB is a database of "species dereplicated" microbial genomes, and as of release 226 contains twice the number of species-representative genomes (306,260) than the latest GTDB release.
globdb.org
home | GlobDB
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Ran Blekhman @blekhman.bsky.social · 05/06/2025
📣 Happy to share our review on host-microbiome genomics! We synthesize the growing field exploring interactions between human genetics and the microbiome, building a roadmap for mapping the dialogue between our genes and microbes Out now in Nature Reviews Genetics👇 www.nature.com/articles/s41...
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A. Murat Eren (Meren) @merenbey.bsky.social · 05/06/2025
We have a new 3-year postdoc position in our group at the @hifmb.de to study plasmids and plasmids systems of the marine environment to survey their utility in microbial responses to environmental change. Please see the official job ad here, and spread the word: jobs.awi.de/Vacancies/20...
jobs.awi.de
PostDoc in ecology and evolution of plasmids in polar waters at HIFMB (f/d/m)
Layout AWI HIPP extern, englisch
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Nagissa Mahmoudi @nagissa.bsky.social · 03/06/2025
Officially TENURED! 🥳 Grateful to those who supported me along the way – colleagues, collaborators, mentors, students, postdocs and friends. It takes a village and I’m lucky to have mine.
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Willem van Schaik @wvschaik.bsky.social · 02/06/2025
For those that missed it this morning, our paper describing Noodlococcus (and what it has taught us about the evolution and taxonomy of Kocuria rhizophila) is now on BioRxiv www.biorxiv.org/content/10.1...
A multi panel figure showing a bright yellow colony, shaped like a bowl of noodles, on an agar plate. Purple Gram-stain. The bottom images are scanning electron micrographs, showing the cells to be coccoid.
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Joe Zackular @joeyzacks.bsky.social · 23/05/2025
Incredibly honored to be selected as a @bwfund.bsky.social Investigator in the Pathogenesis of Infectious Disease. Thank you to @bwfund.bsky.social for supporting our work - I am thrilled to join this amazing community! And special thank you to my AMAZING team (past & present) for getting us here!
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Dr. Sue Ishaq @drsueishaq.bsky.social · 11/05/2025
Congratulations to Dr. Lola Holcomb and Dr. Tolu Alaba!!!!
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Sonny T M Lee @sonnytmlee.bsky.social · 15/04/2025
Check out @brookevogt.bsky.social new preprint #MicroSky
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bioRxiv Microbiology @biorxiv-microbiol.bsky.social · 13/04/2025
Plant host identity drives Andropogon gerardii rhizobiome assembly strategies under increasing abiotic stress www.biorxiv.org/content/10.1101/202…
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Thiago Carvalho @cyrilpedia.bsky.social · 11/04/2025
Can't get much more "pseudo" than this: 'An additional emerging semantic issue is the use of the term “pseudo-germfree mice” when referring to antibiotic-treated mice.' link.springer.com/article/10.1...
link.springer.com
A blueprint for contemporary studies of microbiomes - Microbiome
This editorial piece co-authored by the Senior Editors at Microbiome aims to highlight current challenges in the field of environmental and host-associated microbiome research. We also take the opport...
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Hallie Wiechman @halliewiechman.bsky.social · 02/04/2025
Check out our paper here! www.nature.com/articles/s41... We hope our highly resolved soil-associated MAGs will be useful to the scientific community! #soil #microbiome
nature.com
Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient - Scientific Data
Scientific Data - Recovery of 679 metagenome-assembled genomes from different soil depths along a precipitation gradient
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Christoph Kaleta @kaletalab.bsky.social · 26/03/2025
1/12 Thrilled to share our latest paper on host-microbiome-interactions in aging out in Nature Microbiology @naturemicrobiol.bsky.social, great work led by Lena Best @sci-witch.bsky.social with the Frahm lab within the ITN SmartAge. @crc1182.bsky.social @uni-kiel.de www.nature.com/articles/s41...
nature.com
Metabolic modelling reveals the aging-associated decline of host–microbiome metabolic interactions in mice - Nature Microbiology
A multi-omics approach reveals host–microbiome interactions in aging in mice.
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Daniel Garrido-Sanz @dgarrs.bsky.social · 26/03/2025
🚀 Exciting news! Our latest research is out in Nature Microbiology! 🌾 "Seed-borne bacteria drive rhizosphere microbiome assembly via niche partitioning and facilitation." Seed-inherited bacteria are the architects of #wheat #microbiome assembly! 🌱🦠 @naturemicrobiol.bsky.social rdcu.be/efagM
rdcu.be
Seed-borne bacteria drive wheat rhizosphere microbiome assembly via niche partitioning and facilitation
Nature Microbiology - A sequential propagation strategy shows how the microbes initially on seeds are key to building complex, reproducible and heritable plant microbiomes.
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Tanner Richie @microberich.bsky.social · 25/03/2025
Very excited to join this fantastic group! 🧫🦠🧪 #microbiome #openaccess
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Tiago Peixoto @tiago.skewed.de · 05/02/2025
Bumping this again! IT:U is a great place to work. Groups are very well equipped, the culture is perfect for interdisciplinary research! You also get the opportunity help shape a brand new university. Deadline is Feb 28, 2025. Get in touch if you want to learn more.
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Michael Brockhurst @brockhurstlab.bsky.social · 06/02/2025
☎️ Calling #MEvoSky ☎️ 2x 5-year research associate / research assistant positions in experimental evolution ERC-funded project: How do mobile genetic elements and defence systems shape bacterial genome evolution? Join the friendly and exciting @mermanchester.bsky.social community in Manchester!
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Dr. Lauren E. Fuess @laurenfuess.bsky.social · 03/01/2025
Alright yesterday I did the division plugs for #sicb2025, today I’ll be plugging the talks and posters from our lab! First up is me!, presenting some prelim data from our long term coral monitoring in Belize. I’ll be chatting about mechanisms of multi-stressor resistance! Int Salon 8, 1/4, 3:15 pm!
SICB app screenshot for the talk: “Long-term sampling provides powerful insight regarding mechanisms of coral resilience”. It is on Sat, Jan 4 from 3:15-3:30 in International Salon 8
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Dan Sprockett @danielsprockett.bsky.social · 03/01/2025
More cool strain-level findings from @mattolm.bsky.social -- kind of unbelievable that this hadn't been done yet! "Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut" www.nature.com/articles/s41...
nature.com
Metagenomic immunoglobulin sequencing reveals IgA coating of microbial strains in the healthy human gut - Nature Microbiology
Metagenomic immunoglobulin sequencing (MIg-seq) uncovered patterns of IgA antibody binding of bacterial strains in the healthy human gut microbiome.
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Karthik Anantharaman @karthik-a.bsky.social · 03/01/2025
New paper alert: Our 20-year study of viral ecology and evolution reveals viral roles in microbial dynamics, phage genome evolution over time, and key interactions with hosts. A big thank you to our awesome collaborators @quendi.bsky.social @archaeal.bsky.social www.nature.com/articles/s41...
nature.com
Unravelling viral ecology and evolution over 20 years in a freshwater lake - Nature Microbiology
A long-term metagenomic time series reveals how viruses impact diversity, ecological dynamics and evolution of freshwater microbiomes.
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Brett Baker @archaeal.bsky.social · 03/01/2025
After 24 years of work, I’m thrilled to announce the TYMEFLIES dataset, which comprises metagenomes from Lake Mendota (Madison, WI), collected roughly every 10 days (471 samples) for 20 years! @quendi.bsky.social @robinrohwer.bsky.social rdcu.be/d5put A thread…
rdcu.be
Two decades of bacterial ecology and evolution in a freshwater lake
Nature Microbiology - A 471-metagenome time series from Lake Mendota in Wisconsin, USA, reveals seasonal and decadal shifts in bacterial functional and ecological dynamics, especially in response...
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Prof Francine Marques @fzmarques.bsky.social · 23/12/2024
Our latest paper was published today in Gut Microbes We used a cool new method called metaproteomics to quantify all proteins in a human faecal sample (>22K proteins!) and identify risk of CVD Congratulations to the 1st author, PhD student Chaoran Yang www.tandfonline.com/doi/full/10....
tandfonline.com
Faecal metaproteomics analysis reveals a high cardiovascular risk profile across healthy individuals and heart failure patients
The gut microbiota is a crucial link between diet and cardiovascular disease (CVD). Using fecal metaproteomics, a method that concurrently captures human gut and microbiome proteins, we determined ...
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Contagion® @contagionlive.bsky.social · 18/12/2024
The final part of our conversation with Dr. @joeyzacks.bsky.social discussed the challenges of community-acquired #Cdifficile. #IDsky #MEDsky Listen here for deeper insights on this complicated infection and hope for it's possible #mRNAvaccine: www.contagionlive.com/view/while-h...
contagionlive.com
While Hospital-Acquired C difficile Cases Have Decreased, Community-Acquired Cases Have Risen
Contagion® is a fully integrated news resource for practitioners and specialists to assist with the identification, diagnosis, treatment, and prevention of infectious diseases.
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Sean Gibbons 🦠💩 @gibbological.bsky.social · 18/12/2024
For the first time on Bluesky, it's the lab's 2024 research roundup 🤠🔬🦠 It's been a year of high highs & low lows. I'll stay focused on the positive in this thread, except to mention that we lost a dear colleague at @isbscience.org this year, Ilya Shmulevich: isbscience.org/news/2024/06... 🧵...
isbscience.org
‘A Life Like No Other:’ Remembering Beloved ISB Professor Ilya Shmulevich
The Institute for Systems Biology community mourns the loss of Professor Ilya Shmulevich, PhD, who died on April 13, 2024.
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A. Murat Eren (Meren) @merenbey.bsky.social · 16/12/2024
We are very happy to announce a free-to-attend #anvio workshop and ECR symposium in Oldenburg to discuss integrated microbial 'omics and learn applications of anvi'o. More information and application link (application deadline is Jan 10): anvio.org/workshops/20... Please apply and/or circulate 😇
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