Jose Clemente
@clemelab.bsky.social
Mount Sinai | Microbiome | Genetics & Genomics | Immunology
Reposted by Jose Clemente
📢 SIGN & SHARE THE PETITION! 📢
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
Sign the Petition
Support a New York State Biomedical Institute for a Healthier, More Affordable Future
c.org
November 24, 2025 at 3:53 PM
📢 SIGN & SHARE THE PETITION! 📢
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
New York needs an Empire Biomedical Research Institute to create new statewide funding opportunities for scientists & physician-scientists so that patients and their families get the life-saving and life-changing new therapeutics they're hoping for ✏️ c.org/TDMy2H9JTW
Reposted by Jose Clemente
🚨⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️🚨
🎉 Registration is NOW OPEN! 🎉
We’re excited to welcome you to next year’s International Conference on Innate Lymphoid Cells, where leading experts, innovators, and researchers will come together to share insights, spark collaborations, and shape the future of ILCs and beyond.
#ILC6
(1/3)
We’re excited to welcome you to next year’s International Conference on Innate Lymphoid Cells, where leading experts, innovators, and researchers will come together to share insights, spark collaborations, and shape the future of ILCs and beyond.
#ILC6
(1/3)
November 22, 2025 at 9:44 PM
🚨⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️⬇️🚨
Reposted by Jose Clemente
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
PhyloWeaver – Interactive phylogenetic tree editor
Edit and visualize phylogenetic trees directly in your browser. PhyloWeaver lets you interactively rearrange tree topologies and export high-quality figures for publications and presentations.
yawak.jp
November 18, 2025 at 1:59 AM
I’ve released a tool to sketch and edit phylogenetic trees!
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
yawak.jp/PhyloWeaver/
Load a Newick file and intuitively add/remove/resize branches.
Useful for quick conceptual trees, extracting subtrees, or turning ideas into Newick.
Reposted by Jose Clemente
Proud to share that three Sinai Genetics and Genomics faculty have been named Clarivate Highly Cited Researchers 2025:
• José Clemente, PhD
• Guo-Cheng Yuan, PhD
• Bin Zhang, PhD
Their work spans #microbiome science, systems #genomics, single-cell biology, and AI-enabled disease modeling.
• José Clemente, PhD
• Guo-Cheng Yuan, PhD
• Bin Zhang, PhD
Their work spans #microbiome science, systems #genomics, single-cell biology, and AI-enabled disease modeling.
November 17, 2025 at 5:10 PM
Proud to share that three Sinai Genetics and Genomics faculty have been named Clarivate Highly Cited Researchers 2025:
• José Clemente, PhD
• Guo-Cheng Yuan, PhD
• Bin Zhang, PhD
Their work spans #microbiome science, systems #genomics, single-cell biology, and AI-enabled disease modeling.
• José Clemente, PhD
• Guo-Cheng Yuan, PhD
• Bin Zhang, PhD
Their work spans #microbiome science, systems #genomics, single-cell biology, and AI-enabled disease modeling.
Reposted by Jose Clemente
My lab is recruiting a post-doc ! please share ! emploi.cnrs.fr/Offres/CDD/U...
November 14, 2025 at 2:27 PM
My lab is recruiting a post-doc ! please share ! emploi.cnrs.fr/Offres/CDD/U...
Reposted by Jose Clemente
Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4
November 13, 2025 at 11:12 AM
Excellent work from @aroneys.bsky.social here. Free to read version at rdcu.be/ePJp4
Reposted by Jose Clemente
🟠 SCIENCE |
Don't forget it‼️
6th IBiS-Winter International Symposium of External Young Investigators 2025! #IBiSWISE
🗓️10-11/12 ONLINE for PhD students & postdocs researching abroad, especially if consider joining Spanish research system.
⏳Deadline for abstracts 14/11!
@unisevilla.bsky.social
Don't forget it‼️
6th IBiS-Winter International Symposium of External Young Investigators 2025! #IBiSWISE
🗓️10-11/12 ONLINE for PhD students & postdocs researching abroad, especially if consider joining Spanish research system.
⏳Deadline for abstracts 14/11!
@unisevilla.bsky.social
October 29, 2025 at 11:36 AM
🟠 SCIENCE |
Don't forget it‼️
6th IBiS-Winter International Symposium of External Young Investigators 2025! #IBiSWISE
🗓️10-11/12 ONLINE for PhD students & postdocs researching abroad, especially if consider joining Spanish research system.
⏳Deadline for abstracts 14/11!
@unisevilla.bsky.social
Don't forget it‼️
6th IBiS-Winter International Symposium of External Young Investigators 2025! #IBiSWISE
🗓️10-11/12 ONLINE for PhD students & postdocs researching abroad, especially if consider joining Spanish research system.
⏳Deadline for abstracts 14/11!
@unisevilla.bsky.social
Reposted by Jose Clemente
Hi #GIsky and #GIresearch friends, who has had success culturing mouse small intestinal enteroid monolayers? We could use some wisdom!
a man wearing glasses says i very much need your help
ALT: a man wearing glasses says i very much need your help
media.tenor.com
October 24, 2025 at 6:25 PM
Hi #GIsky and #GIresearch friends, who has had success culturing mouse small intestinal enteroid monolayers? We could use some wisdom!
Reposted by Jose Clemente
Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social
rdcu.be/eMmcT
@quadraminstitute.bsky.social
rdcu.be/eMmcT
Systematic metaproteomics mapping reveals functional and ecological landscapes of Ex vivo human gut microbiota responses to therapeutic drugs
Nature Communications - Here, the authors systematically map metaproteomic responses of ex vivo human gut microbiota to common therapeutics, identifying several drug classes inducing strong...
rdcu.be
October 24, 2025 at 4:20 PM
Interested in #drugs, #microbiome and #antibiotic resistance, then check out our paper on the effects of over 300 drugs on the gut microbiome. Exciting results as well on the role of antibiotic resistance defining how microbiomes respond to drugs.
@quadraminstitute.bsky.social
rdcu.be/eMmcT
@quadraminstitute.bsky.social
rdcu.be/eMmcT
Reposted by Jose Clemente
NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!
www.nature.com/articles/s41...
🧵⬇️
1/8
www.nature.com/articles/s41...
🧵⬇️
1/8
Predicting functions of uncharacterized gene products from microbial communities - Nature Biotechnology
FUGAsseM predicts protein function in microbiomes using coexpression patterns from metatranscriptomes and diverse community-wide data.
www.nature.com
October 23, 2025 at 6:53 PM
NEW publication from our lab: One of the first methodologies (FUGAsseM) for gene function prediction from microbial community multi-omics data!
www.nature.com/articles/s41...
🧵⬇️
1/8
www.nature.com/articles/s41...
🧵⬇️
1/8
Reposted by Jose Clemente
1/5 Today we are introducing the Key-Cutting Machine (KCM) for protein and peptide design. Like cutting a key to fit a lock, KCM sculpts sequences to match a target backbone—on a single GPU. No retraining. No clusters. 🧬🔑
October 23, 2025 at 7:50 AM
1/5 Today we are introducing the Key-Cutting Machine (KCM) for protein and peptide design. Like cutting a key to fit a lock, KCM sculpts sequences to match a target backbone—on a single GPU. No retraining. No clusters. 🧬🔑
Reposted by Jose Clemente
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Long-read metagenomics for strain tracking after faecal microbiota transplant
Nature Microbiology - A long-read metagenomics method empowers faecal microbiota transplantation studies by precisely tracking bacteria from donors to recipients, distinguishing co-existing strains...
rdcu.be
October 22, 2025 at 3:39 PM
Excited to share our LongTrack study out in
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
@natmicrobiol.nature.com today!
Fecal microbiota transplant (FMT), donor 💩 => patients' gut, is an effective treatment for recurrent C. difficile infection & is being evaluated for Inflammatory Bowel Diseases (IBD) & other conditions 1/
📄 rdcu.be/eL8mR
Reposted by Jose Clemente
🟠SCIENCE |
6th IBiS-Winter International Symposium of External Young Investigators 2025 is coming! #IBiSWISE
10th-11th December ONLINE, for PhD students & postdocs researching abroad, especially if consider joining Spanish research system
Deadline: 14th November
@unisevilla.bsky.social
6th IBiS-Winter International Symposium of External Young Investigators 2025 is coming! #IBiSWISE
10th-11th December ONLINE, for PhD students & postdocs researching abroad, especially if consider joining Spanish research system
Deadline: 14th November
@unisevilla.bsky.social
October 10, 2025 at 12:28 PM
🟠SCIENCE |
6th IBiS-Winter International Symposium of External Young Investigators 2025 is coming! #IBiSWISE
10th-11th December ONLINE, for PhD students & postdocs researching abroad, especially if consider joining Spanish research system
Deadline: 14th November
@unisevilla.bsky.social
6th IBiS-Winter International Symposium of External Young Investigators 2025 is coming! #IBiSWISE
10th-11th December ONLINE, for PhD students & postdocs researching abroad, especially if consider joining Spanish research system
Deadline: 14th November
@unisevilla.bsky.social
We recently got two papers published on the relation between microbiome and arthritis, in collaboration with the groups of Jose Scher (NYU), Frances Williams (King's College) and Monica Guma (UCSD). In both papers with Kevin Bu, postdoc extraordinaire in my lab, as first co-author!
October 16, 2025 at 3:42 PM
We recently got two papers published on the relation between microbiome and arthritis, in collaboration with the groups of Jose Scher (NYU), Frances Williams (King's College) and Monica Guma (UCSD). In both papers with Kevin Bu, postdoc extraordinaire in my lab, as first co-author!
Reposted by Jose Clemente
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
October 13, 2025 at 7:48 AM
Excited to share our preprint led by Carlos Voogdt et al
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
We developed new genetic tools & genome-wide libraries for species of the Bacteroidales order; constructed saturated barcoded transposon libraries in key representatives of three genera.
www.biorxiv.org/content/10.1...
Reposted by Jose Clemente
New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium)
academic.oup.com/ismej/advanc...
academic.oup.com/ismej/advanc...
Validate User
academic.oup.com
October 10, 2025 at 3:56 PM
New paper out demonstrating how we can use strain-level analyses of soil metagenomes to investigate the biogeographical patterns exhibited by a dominant group of soil bacteria (Bradyrhizobium)
academic.oup.com/ismej/advanc...
academic.oup.com/ismej/advanc...
Reposted by Jose Clemente
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
AIR 2026: Genomic and Systems Approaches to Respiratory Infection, Microbiomes and Immunity — 20260211
Course exploring how genomics, microbiome profiling, and systems biology reshape our understanding of respiratory infections and immune dynamics.
coursesandconferences.wellcomeconnectingscience.org
October 8, 2025 at 2:48 PM
New respiratory 🫁 infection and microbiomes conference in Hinxton with stellar line up of speakers.
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
🚨 Submit your abstracts now! 🚨
Please RT
coursesandconferences.wellcomeconnectingscience.org/event/air-20...
Reposted by Jose Clemente
Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org
July 10, 2025 at 7:29 PM
Many of you gave me so much encouragement when I posted here earlier about my 10 year long passion project to make a microbial map of the ocean. Pinch me because I can't believe I get to update you that today that research was published in the journal SCIENCE! @science.org
Reposted by Jose Clemente
Dear #microbiology and #immunology community- I took a break from social media after I deleted my Twitter account, but am back here. Please help me rebuild my community by following me and amplifying this message- I will follow you back. Thank you and I look forward to our many interactions!
October 5, 2025 at 4:10 PM
Dear #microbiology and #immunology community- I took a break from social media after I deleted my Twitter account, but am back here. Please help me rebuild my community by following me and amplifying this message- I will follow you back. Thank you and I look forward to our many interactions!
Reposted by Jose Clemente
📚🩺Nuestro académico y virólogo Luis Enjuanes ha colaborado en este libro "La expedición Balmis. Primer modelo de lucha global contra las pandemias" 🦠
[...] Hoy podemos afirmar que el modelo de lucha contra la covid-19 tiene su germen en esta epopeya médica pionera @cnb-csic.bsky.social #geoplaneta
[...] Hoy podemos afirmar que el modelo de lucha contra la covid-19 tiene su germen en esta epopeya médica pionera @cnb-csic.bsky.social #geoplaneta
October 6, 2025 at 3:05 PM
📚🩺Nuestro académico y virólogo Luis Enjuanes ha colaborado en este libro "La expedición Balmis. Primer modelo de lucha global contra las pandemias" 🦠
[...] Hoy podemos afirmar que el modelo de lucha contra la covid-19 tiene su germen en esta epopeya médica pionera @cnb-csic.bsky.social #geoplaneta
[...] Hoy podemos afirmar que el modelo de lucha contra la covid-19 tiene su germen en esta epopeya médica pionera @cnb-csic.bsky.social #geoplaneta
Reposted by Jose Clemente
Reposted by Jose Clemente
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Faculty Professor Associate - Full-Time | Vaughn Cooper
We are recruiting Faculty microbiologists in three (3) different, complementary, and collaborative areas at the University of Pittsburgh associated with the School of Medicine.
1) Fundamental researc...
www.linkedin.com
September 23, 2025 at 10:31 PM
🚨 Microbiologists! We are recruiting Assistant / Associate Professors in 3 collaborative areas of our U. Pittsburgh School of Medicine.
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
1) MMG (my dept): fundamental research in med micro
2) Peds ID / I4Kids institute
3) Center for Vaccine Research
🔗 to all 3 w/info: www.linkedin.com/posts/vaughn...
Reposted by Jose Clemente
If you made it this far, thanks for reading. I hope you enjoyed it.
I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.
I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.
September 23, 2025 at 11:24 AM
If you made it this far, thanks for reading. I hope you enjoyed it.
I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.
I am currently looking for my next research adventure. If you have insights on the microbiome/microbial genomics job market in Europe (academia & industry), or want to chat about this work, please reach out.
Reposted by Jose Clemente
Re-upping this: For those of you having new students in the lab, I have curated a YouTube playlist on molecular biology: www.youtube.com/playlist?lis...
I usually have my students watch it before I show them how to do it in the lab.
I usually have my students watch it before I show them how to do it in the lab.
Molecular_Bio - YouTube
www.youtube.com
September 21, 2025 at 8:42 PM
Re-upping this: For those of you having new students in the lab, I have curated a YouTube playlist on molecular biology: www.youtube.com/playlist?lis...
I usually have my students watch it before I show them how to do it in the lab.
I usually have my students watch it before I show them how to do it in the lab.
Reposted by Jose Clemente
Tenure-track Assistant Professor in Computational Ecology and/or Evolution @columbiauniversity.bsky.social.
Deadline to apply September 30.
Reach out if you have questions.
apply.interfolio.com/172496
Deadline to apply September 30.
Reach out if you have questions.
apply.interfolio.com/172496
Apply - Interfolio
{{$ctrl.$state.data.pageTitle}} - Apply - Interfolio
apply.interfolio.com
September 20, 2025 at 3:20 PM
Tenure-track Assistant Professor in Computational Ecology and/or Evolution @columbiauniversity.bsky.social.
Deadline to apply September 30.
Reach out if you have questions.
apply.interfolio.com/172496
Deadline to apply September 30.
Reach out if you have questions.
apply.interfolio.com/172496