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Yannis Ntekas

@ntekasi.bsky.social
83 followers 200 following 21 posts

Spatial Biology x Microbiome | Postdoc at Xavier lab @mskcancercenter.bsky.social

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MSKEducation @mskeducation.bsky.social · 16/09/2026
Closing out the MSK Postdoc Slam is Ioannis Ntekas ( @ntekasi.bsky.social ) from the Xavier Lab. Yannis maps the hidden world of the gut microbiome 🦠, uncovering how microbes interact with our bodies in health and disease and how these relationships can be steered toward better health.
Postdoc Slam
September 16, 2026
Ioannis Ntekas, PhD
Xavier Lab/ Computational and Systems Biology
A map for the microbiome
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Yannis Ntekas @ntekasi.bsky.social · 16/09/2026
@mskcancercenter.bsky.social friends join us for this year’s Postdoc Slam competition. And stick around till the end… I’ve heard there is some interesting talks coming up later 👀
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Reposted by Yannis Ntekas
MSKEducation @mskeducation.bsky.social · 16/09/2026
🎉 The MSK Postdoc Slam is extra special this year as we celebrate the 20th Anniversary of the Zuckerman Research Center! @mskcancercenter.bsky.social, join us today at 4 PM for a showcase of postdoc research, creativity, and discovery. Let’s celebrate science and 20 years of impact together! 🎤✨
2026 MSK Postdoc Slam & 20th Anniversary
Celebration of the Zuckerman Research Center
Wednesday, September 16 | 4:00 p.m. | ZRC Auditorium
4:20 p.m. Presentations:
Marton Kovacs, PhD
Maciejowski Lab/ Molecular Biology
Some like it HOT: Turning immunologically cold tumors hot
Elena Lin, PhD
Diehl Lab/ Immunology
All aboard the G(ut) train: How our microbes and immune
system work together to keep us healthy
Charles Ng, MD, PhD
Thompson Lab/ Cancer Biology and Genetics
Getting T cells fit to fight cancer
Zoe Louise Walt, PhD
Scott Lab/ Exercise Oncology Services
The surprising importance of exercise in cancer care
Elio Issa, MD
Tabar Lab/ Neurosurgery
One for all, none for one: Predicting tumor follow-up
Yao Yu, MD, PhD
Hohl Lab/ Immuno-Oncology
CNS Aspergillosis: A hidden complication in cancer
immunotherapy
Marc Hilmi, MD, PhD
Iacobuzio-Donahue Lab/ Center for Pancreatic Cancer Research
The super-killers locked out by fibroblasts
Carlin Liao, PhD
Nadeem Lab/ Medical Physics
Stomaching risk
Helen Grimsley, PhD
Powell Lab/ Radiation Oncology; Molecular Biology
Destroy cancer's final lifeline
Ioannis Ntekas, PhD
Xavier Lab/ Computational and Systems Biology
A map for the microbiome
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Reposted by Yannis Ntekas
bioRxiv Genomics @biorxiv-genomic.bsky.social · 12/09/2026
RNA-aware tissue preservation workflows for high-quality spatial transcriptomics www.biorxiv.org/content/10.64898/20…
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Yannis Ntekas @ntekasi.bsky.social · 14/05/2026
We made it to the front of @natmicrobiol.nature.com 🤯 In this case, judging by the cover is encouraged Spatial transcriptomics maps host–gut microbiome biogeography at high resolution
rdcu.be
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution
Nature Microbiology - Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with...
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Marlis Denk-Lobnig @marlis.bsky.social · 10/05/2026
Interested in teaching your kids or students about bacteria and how they interact to collectively respond to antibiotics? The @sj4k.bsky.social worked with us to adapt our recent paper into an article to help teens think about social interactions in bacterial communities:
sciencejournalforkids.org
How do bacteria protect each other from antibiotics? - Science Journal for Kids and Teens
Researchers show how bacteria living close together form patterns, share protection, and respond to antibiotics in surprising ways.
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Yannis Ntekas @ntekasi.bsky.social · 10/04/2026
Thank you for highlighting our work!
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Reposted by Yannis Ntekas
Hao Yin @haoyin.bsky.social · 26/03/2026
Spatial Gut-Microbiome MegaTranscriptomics Use in situ polyadenylation on #Visium #StereoSeq to enhance host & bacterial RNA recovery (⏫99-fold) Fresh-frozen🐭GI Non-coding RNAs enriched to gut wall Microorganisms enriched at CRC tumor boundary #NatMicrobiol 2026 www.nature.com/articles/s41...
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Reposted by Yannis Ntekas
Nature Microbiology @natmicrobiol.nature.com · 06/03/2026
Out Now! Spatial transcriptomics maps host–gut microbiome biogeography at high resolution #MicroSky
go.nature.com
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution
Nature Microbiology, Published online: 06 March 2026; doi:10.1038/s41564-026-02286-7Bulk polyadenylation improves the capture of microbial RNA, enabling host–microorganism interactions to be visualized at a high resolution when combined with commercially available spatial transcriptomics platforms.
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Yannis Ntekas @ntekasi.bsky.social · 09/03/2026
Thank you! 🙏Happy to discuss more if you have any questions.
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Yannis Ntekas @ntekasi.bsky.social · 09/03/2026
Thank you Joram! 🙏 Great question. Tissue is rapidly collected and frozen within minutes, which should preserve the RNA content in the lumen, including that of anaerobes. We also see strong agreement between our method and bulk metatranscriptomics from adjacent tissue in the large intestine.
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Yannis Ntekas @ntekasi.bsky.social · 07/03/2026
Thanks again to all collaborators in the De Vlaminck and Brito labs that haven't yet migrated to bluesky
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Yannis Ntekas @ntekasi.bsky.social · 07/03/2026
Our method adds to the toolbox that allows the community to rethink host–microbiome interactions by measuring microbiome spatial structure and host responses directly in tissue. Also an awesome weekend read 😉 Feel free to reach out if you’d like to try it or discuss more.
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Yannis Ntekas @ntekasi.bsky.social · 07/03/2026
We combine spatial RNA-seq with enzymatic in situ polyadenylation to greatly improve bacterial RNA capture in intestinal tissue, generating high-res maps of microbiome biogeography and host–microbiome interactions. A deeper-dive in our preprint thread: bsky.app/profile/ntek...
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Yannis Ntekas @ntekasi.bsky.social · 07/03/2026
Our work with Lena Takayasu and @dwmckellar.bsky.social in Iwijn De Vlaminck's lab is now out in @natmicrobiol.nature.com ! 🎉 Spatial transcriptomics maps host–gut microbiome biogeography at high resolution rdcu.be/e7i7o
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Waggoner Lab @labwaggoner.bsky.social · 06/03/2026
Spatial transcriptomics maps host–gut microbiome biogeography at high resolution www.nature.com/articles/s41... @natmicrobiol.nature.com @dwmckellar.bsky.social @ntekasi.bsky.social
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Ran Blekhman @blekhman.bsky.social · 19/11/2025
I wrote about the recent autism-microbiome paper, why I think it's the most important microbiome paper this year, and what it says about the field open.substack.com/pub/blekhman...
open.substack.com
The Autism-Microbiome Hypothesis Is Falling Apart
Why this new review paper should be required reading for every microbiome researcher
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Harris Wang @harriswang.bsky.social · 17/11/2025
Introducing Foli-seq in @natbiotech.nature.com today. Foli-seq can be used to measure gut-derived RNA from fecal matter (signals of immune, secretory & epithelial cells). We used this to map gut inflammation, drug response, and host-microbe interactions. 💩🧬💊🦠 www.nature.com/articles/s41...
nature.com
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology
Profiling host RNA shed in feces reveals disease states in the gut.
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Reposted by Yannis Ntekas
Sean Gibbons 🦠💩 @gibbological.bsky.social · 18/11/2025
Another banger from the @harriswang.bsky.social Lab this month! “Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut” www.nature.com/articles/s41...
nature.com
Fecal exfoliome sequencing captures immune dynamics of the healthy and inflamed gut - Nature Biotechnology
Profiling host RNA shed in feces reveals disease states in the gut.
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Reposted by Yannis Ntekas
Carolyn Bertozzi @carolynbertozzi.bskyverified.social · 11/03/2025
Exciting discovery by Svensson lab and collaborators @stanfordmedicine.bsky.social, computational discovery of 2500 new bioactive peptides, including 12-mer named BRP that reduces food intake leading to weight loss w/o nausea in mice! www.nature.com/articles/s41...
nature.com
Prohormone cleavage prediction uncovers a non-incretin anti-obesity peptide - Nature
Computational drug discovery is used to identify a 12-mer peptide derived from BRINP2 with potent anti-obesity effects that are independent of leptin, glucagon-like peptide 1 receptor and melanocortin...
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Reposted by Yannis Ntekas
Itai Yanai @itaiyanai.bsky.social · 23/02/2025
Contributions from: Jeffrey Moffitt, @drmingyaoli.bsky.social, Qing Nie, Kazumasa Kanemaru, Sarah Teichmann, Daniel Dar, @ltkagohara.bsky.social, Shalev Itzkovitz, Roser Vento-Tormo, @fertiglab.bsky.social, @fabiantheis.bsky.social
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Yannis Ntekas @ntekasi.bsky.social · 14/12/2024
Mitosis?
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bioRxivpreprint @biorxivpreprint.bsky.social · 04/12/2024
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues www.biorxiv.org/content/10.1101/202…
biorxiv.org
Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues https://www.biorxiv.org/content/10.1101/2024.12.03.626516v1
The Tabula Sapiens is a reference human cell atlas containing single cell transcriptomic data from m
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Reposted by Yannis Ntekas
Tim Straub @timothystraub.com · 21/11/2024
New research from the Xavier lab at Broad reveals the gut's adaptability and immune-driven control in specific regions. A spatial map of the mouse intestines highlights its resilience to perturbations like inflammation, with implications for understanding diet, food allergies, and IBD in humans 🧬🦠
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Yannis Ntekas @ntekasi.bsky.social · 20/11/2024
Thank you Micha! 🙏
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
We believe our approach marks a paradigm shift in microbiome science, integrating spatial context to uncover how the host interacts with the microbiome at relevant scales. Reach out if you want to try it yourselves
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Finally, we explore a vignette of host-microbe interaction in a tumor-bearing tissue section, revealing microbial invasion into the host, possibly because misplaced mucus-producing cells leave the tissue unprotected, enabling generalized host-microbe interaction.
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
What excites me most: the achieved micron resolution lets us measure colony sizes for individual taxa, potentially linking them to their in vivo growth rates. The cherry on top? We can identify colocalizing taxa and capture not just rRNA but also microbial genes!
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Regarding the host, we retrieve both coding and non-coding signatures along the crypt-villus axis. We observe high and diverse expression at villus tips, high % unspliced molecules near crypts, and high non-coding RNA percentages closer to the gut wall
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Combining in situ polyadenylation with the StereoSeq platform, we reconstruct detailed maps of both cell types and microbial taxa at micron resolution, unlocking unprecedented insights into host-microbe interaction
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Using Visium with in situ polyadenylation we explore microbial niches across the transverse and longitudinal axes of the GI
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
We first tested whether in situ polyadenylation enhances recovery of microbiome-derived RNA at low spatial resolution. Applying our method across murine gut sections, we observed up to a 100-fold enrichment in microbial RNA while preserving host gene expression.
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Building on previous work from @dwmckellar.bsky.social , we combine a single enzymatic step of in situ polyadenylation with commercial spatial transcriptomics platforms—Visium and StereoSeq—to map host gene expression and microbiome in mouse gut tissue sections
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Previous methods to map the interface, like imaging-based HiPR-FISH from our lab and sequencing-based with modified arrays like those developed by the Vickovic and Giacomello labs, capture target microbes but limit unbiased discovery or produce low-resolution maps. Here we address these challenges.
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Yannis Ntekas @ntekasi.bsky.social · 19/11/2024
Spatial structure shapes the host-microbiome interactome. Our new method to map the host-microbiome interface at high-resolution, now on bioRxiv! Co-led with Lena Takayasu & @dwmckellar.bsky.social collab between the De Vlaminck and Brito labs doi.org/10.1101/2024... A thread⬇️
doi.org
High Resolution Spatial Mapping of Microbiome-Host Interactions via in situ Polyadenylation and Spatial RNA Sequencing
Inter–microbial and host–microbial interactions are thought to be critical for the functioning of the gut microbiome, but few tools are available to measure these interactions. Here, we report a metho...
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