supriya khedkar
@khedkarsupriya.bsky.social
Principal Investigator at BioQuant, University of Heidelberg
https://www.bioquant.org/groups/khedkar
Interested in Mobile Genetic Elements | Antibiotic resistance | (meta)genomics | evolution
Previously @borklab @embl @ncbsbangalore
https://www.bioquant.org/groups/khedkar
Interested in Mobile Genetic Elements | Antibiotic resistance | (meta)genomics | evolution
Previously @borklab @embl @ncbsbangalore
Reposted by supriya khedkar
From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓
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academic.oup.com/nar/advance-...
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academic.oup.com/nar/advance-...
eggNOG v7: phylogeny-based orthology predictions and functional annotations
Abstract. The eggNOG (evolutionary genealogy of genes: Non-supervised Orthologous Groups) database is a phylogenomic resource for orthology inference, evol
academic.oup.com
December 9, 2025 at 1:39 PM
From @jhcepas.bsky.social and colleagues in the @narjournal.bsky.social #NARDatabaseIssue | eggNOG v7: phylogeny-based orthology predictions and functional annotations | #Bioinformatics #ProteinCentric #Database #OpenScience 🧬 🖥️🧪🇨🇭🇪🇸🇩🇪🔓
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academic.oup.com/nar/advance-...
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academic.oup.com/nar/advance-...
Reposted by supriya khedkar
pluralistic.net/2025/12/05/p... Cory Doctorow on AI:
"And if the AI misses a tumor, this will be the human radiologist's fault, because they are the 'human in the loop.' It's their signature on the diagnosis." This [...] a specific kind of reverse-centaur: [...] an "accountability sink."
"And if the AI misses a tumor, this will be the human radiologist's fault, because they are the 'human in the loop.' It's their signature on the diagnosis." This [...] a specific kind of reverse-centaur: [...] an "accountability sink."
Pluralistic: The Reverse-Centaur’s Guide to Criticizing AI (05 Dec 2025) – Pluralistic: Daily links from Cory Doctorow
pluralistic.net
December 8, 2025 at 7:20 AM
pluralistic.net/2025/12/05/p... Cory Doctorow on AI:
"And if the AI misses a tumor, this will be the human radiologist's fault, because they are the 'human in the loop.' It's their signature on the diagnosis." This [...] a specific kind of reverse-centaur: [...] an "accountability sink."
"And if the AI misses a tumor, this will be the human radiologist's fault, because they are the 'human in the loop.' It's their signature on the diagnosis." This [...] a specific kind of reverse-centaur: [...] an "accountability sink."
Reposted by supriya khedkar
Tech elites are starting their own for-profit cities. What could wrong? www.ft.com/content/b127...
Tech elites are starting their own for-profit cities
They want to escape from regulation and ‘failing’ democracy — but are they more opportunistic than libertarian?
www.ft.com
December 8, 2025 at 8:53 AM
Tech elites are starting their own for-profit cities. What could wrong? www.ft.com/content/b127...
Reposted by supriya khedkar
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Creation of new junior research groups at the Institut Pasteur - Call for applications 2026 - Research
The Institut Pasteur is launching an international call to recruit new junior research group leaders leveraging cutting-edge transdisciplinary approaches to exploring infectious diseases, host-microbe...
research.pasteur.fr
December 8, 2025 at 8:53 AM
🔬 Call to create junior research groups at the Institut Pasteur
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Focus: Infectious diseases, host-microbe interactions, vaccines
Special interest: AI methodologies
📅 Deadline: Feb 9, 2026
👥 2-12 years post-PhD
Apply now 📝 research.pasteur.fr/en/call/crea...
#JobOpportunity #Research
Reposted by supriya khedkar
Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)
Antibiotic Resistance Microbiology Dataset Mass General Brigham (ARMD-MGB) v1.0.0
ARMD-MGB contains detailed microbiology and clinical metadata for >225,000 patients and >970,000 cultures collected over 10 years
physionet.org
December 5, 2025 at 7:39 AM
Today I am very proud to announce the release of the Antibiotic Resistance Microbiology Dataset - Mass General Brigham (ARMD-MGB; physionet.org/content/armd...) , as part of an NIH-funded collaboration led by Jonathan Chen at Stanford. (1/6)
Reposted by supriya khedkar
Viruses are found in almost every ecosystem across the planet.
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
December 3, 2025 at 3:57 PM
Viruses are found in almost every ecosystem across the planet.
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Now, researchers have released VIRE – a comprehensive viral genome database covering diverse ecosystems to advance understanding of viral evolution and ecosystem functions.
Learn more: www.embl.org/news/science...
Reposted by supriya khedkar
Applications are open for @dev-journal.bsky.social 2026 Pathway to Independence (PI) programme, supporting postdocs applying for group leader positions:
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
Development's Pathway to Independence Programme
Our grants support and encourage the sharing of knowledge throughout the community by facilitating international collaboration, event attendance and the organisation of scientific meetings, conference...
www.biologists.com
December 3, 2025 at 6:56 AM
Applications are open for @dev-journal.bsky.social 2026 Pathway to Independence (PI) programme, supporting postdocs applying for group leader positions:
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
Mentoring
Profile raising
Leadership training
Network building
Spread the word...
www.biologists.com/grants/devel...
Reposted by supriya khedkar
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
December 2, 2025 at 5:52 PM
We're excited to release metaTraits.embl.de! 🦠 Interactively explore 140+ 𝗺𝗶𝗰𝗿𝗼𝗯𝗶𝗮𝗹 𝗽𝗵𝗲𝗻𝗼𝘁𝘆𝗽𝗶𝗰 𝘁𝗿𝗮𝗶𝘁𝘀, harmonized & integrated from culture-derived collections 🔬 & genome-based predictions 🧬 for >2M MAGs & genomes.
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Publication at NAR: doi.org/10.1093/nar/... @narjournal.bsky.social #microsky 🧵 1/8
Reposted by supriya khedkar
Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
EIPOD-LinC Fellowship Programme – Postdoctoral Programme
www.embl.org
December 1, 2025 at 11:00 AM
Join EMBL's Interdisciplinary Postdoc Programme!
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
3 years funding, self-designed interdisciplinary project co-led between EMBL PI and PI in one of EMBL's actual, prospect or associate member states.
In particular: AI&Theory, use mathem. models, physics principles and AI
www.embl.org/about/info/p...
Reposted by supriya khedkar
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
metaTraits: a large-scale integration of microbial phenotypic trait information
Abstract. Microbes differ greatly in their organismal structure, physiology, and environmental adaptation, yet information about these phenotypic traits is
academic.oup.com
November 30, 2025 at 4:47 AM
metaTraits: a large-scale integration of microbial phenotypic trait information
academic.oup.com/nar/advance-...
academic.oup.com/nar/advance-...
Reposted by supriya khedkar
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
VIRE: a metagenome-derived, planetary-scale virome resource with environmental context
Abstract. Viruses are the most abundant biological entities on Earth, yet their global diversity remains largely unexplored. Here, we present VIRE, a compr
academic.oup.com
December 1, 2025 at 4:41 AM
Happy to announce VIRE, a planetary-scale database of >1.7M viral genomes reconstructed from 100k+ metagenomes across diverse environments! In collaboration with @fullam.bsky.social, @tsbschm.bsky.social, and @borklab.bsky.social.
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
academic.oup.com/nar/advance-article/doi/10.1093/nar/gkaf1225/8356007
Reposted by supriya khedkar
Excited to share our latest research in @natmicrobiol.nature.com . We uncover hundreds of inhibitory interactions between common chemical pollutants and human gut bacteria. A thread🧵 (1/10) #microbiomesky #microsky @kiranrpatil.bsky.social lab @mrc-tu.bsky.social www.nature.com/articles/s41...
Industrial and agricultural chemicals exhibit antimicrobial activity against human gut bacteria in vitro - Nature Microbiology
Screening of 1,076 compounds reveals 168 chemical pollutants with inhibitory effects on gut bacteria and genetic screens indicate commonality between pollutant and antibiotic resistance.
www.nature.com
November 26, 2025 at 10:30 AM
Excited to share our latest research in @natmicrobiol.nature.com . We uncover hundreds of inhibitory interactions between common chemical pollutants and human gut bacteria. A thread🧵 (1/10) #microbiomesky #microsky @kiranrpatil.bsky.social lab @mrc-tu.bsky.social www.nature.com/articles/s41...
Reposted by supriya khedkar
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
November 20, 2025 at 10:12 PM
What is the best strategy to win any contest?
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Eliminate your opponents of course.
Recently, my friend @fernpizza.bsky.social showed how plasmids compete intracellularly (check out his paper published in Science today!). With @baym.lol, we now know they can fight.
www.biorxiv.org/content/10.1...
Reposted by supriya khedkar
We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Hidden but discoverable diversity in the global microbiome
Cataloguing Earth's biodiversity remains one of the most formidable challenges in biology, and the greatest diversity is expected to reside among the smallest organisms: microbes. Yet the ongoing cens...
www.biorxiv.org
November 18, 2025 at 8:53 PM
We've updated our recent @biorxivpreprint.bsky.social on 'Hidden but discoverable diversity in the global microbiome', led by @vishnuprasoodanan.bsky.social & @omaistrenko.bsky.social
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
Reposted by supriya khedkar
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
November 10, 2025 at 1:26 PM
🌍Open call: Junior Group Leader positions!
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Join a world-class biomedical research institute at the heart of the Vienna BioCenter, where curiosity drives discovery.
Lead your own lab, pursue bold ideas, and shape the future of science at the IMP: www.imp.ac.at/career/open-...
Reposted by supriya khedkar
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
November 10, 2025 at 9:32 AM
Opportunity!
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Anybody knows of young marine ecologists (within 7 years from earned PhD) that would like to come to Gothenburg, Sweden, for a nationally funded Assistant Professorship? It is highly competitive but well funded. (1) of (3)
Reposted by supriya khedkar
Are you setting up your own life science lab and feel that you could use some input on leadership skills? Maybe this workshop is for you:
Starting your own lab is exciting—but challenging.
Join our GBM Young Investigator leadership workshop in Regensburg, April 13–16th, 2026.
Professional coaching, peer networking & practical tips for new PIs.
Apply by Nov 30, 2025.
👉https://yi-workshop.gbm-online.de/yi-workshop-2.html
Join our GBM Young Investigator leadership workshop in Regensburg, April 13–16th, 2026.
Professional coaching, peer networking & practical tips for new PIs.
Apply by Nov 30, 2025.
👉https://yi-workshop.gbm-online.de/yi-workshop-2.html
November 6, 2025 at 10:53 AM
Are you setting up your own life science lab and feel that you could use some input on leadership skills? Maybe this workshop is for you:
Reposted by supriya khedkar
Between @python.org and @carpentries.carpentries.org, the open-source ecosystem is rejecting the administration's inquisition against DEI. If you can support them with a donation please do. I just did!
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
TLDR; The PSF has made the decision to put our community and our shared diversity, equity, and inclusion values ahead of seeking $1.5M in new revenue. Please read and share. pyfound.blogspot.com/2025/10/NSF-...
🧵
🧵
The official home of the Python Programming Language
www.python.org
October 27, 2025 at 5:47 PM
Between @python.org and @carpentries.carpentries.org, the open-source ecosystem is rejecting the administration's inquisition against DEI. If you can support them with a donation please do. I just did!
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Does anyone know about others who have declined NIH or NSF grant funding over over these terms?
Reposted by supriya khedkar
If you’re applying to your dream lab for an internship/PhD/postdoc, always send a second email 1-2 weeks after the first one if you don’t hear back.
I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support
I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support
October 4, 2025 at 5:47 AM
If you’re applying to your dream lab for an internship/PhD/postdoc, always send a second email 1-2 weeks after the first one if you don’t hear back.
I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support
I promise we will be grateful rather than annoyed. My email inbox is a disaster and I’m quite junior - and very few of us have secretarial support
Reposted by supriya khedkar
Deadline extension for #EMBLDataCarpentry! 📣 Apply by 10 November to save your spot in either Heidelberg or Barcelona: s.embl.org/dtc26-01-bl
This course teaches life science researchers essential skills in data management, R programming, genomics analysis, and more.
This course teaches life science researchers essential skills in data management, R programming, genomics analysis, and more.
October 28, 2025 at 9:25 AM
Deadline extension for #EMBLDataCarpentry! 📣 Apply by 10 November to save your spot in either Heidelberg or Barcelona: s.embl.org/dtc26-01-bl
This course teaches life science researchers essential skills in data management, R programming, genomics analysis, and more.
This course teaches life science researchers essential skills in data management, R programming, genomics analysis, and more.
Reposted by supriya khedkar
#ResearchCareers: Just finishing your #PhD and wondering if the DFG’s Walter Benjamin Programme is a #funding option for your next step in academia? Come and find out in our digital info talk on 14 October. No registration, the meeting link will be published here:
➡️ www.dfg.de/en/research-...
➡️ www.dfg.de/en/research-...
October 2, 2025 at 10:23 AM
#ResearchCareers: Just finishing your #PhD and wondering if the DFG’s Walter Benjamin Programme is a #funding option for your next step in academia? Come and find out in our digital info talk on 14 October. No registration, the meeting link will be published here:
➡️ www.dfg.de/en/research-...
➡️ www.dfg.de/en/research-...
Reposted by supriya khedkar
Still need to use 2025 funding? Places still available in @embo.org Lab #Leadership for #Postdocs courses in 🇩🇪. Take time to focus on your interpersonal skills + discover tools to support your development. Sign up now 28-30 Oct, 11-13 Nov & 2-4 Dec 2025: www.embolableadership.org/course/embol...
October 1, 2025 at 1:57 PM
Still need to use 2025 funding? Places still available in @embo.org Lab #Leadership for #Postdocs courses in 🇩🇪. Take time to focus on your interpersonal skills + discover tools to support your development. Sign up now 28-30 Oct, 11-13 Nov & 2-4 Dec 2025: www.embolableadership.org/course/embol...
Reposted by supriya khedkar
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
September 25, 2025 at 9:29 PM
Delighted to see our paper studying the evolution of plasmids over the last 100 years, now out! Years of work by Adrian Cazares, also Nick Thomson @sangerinstitute.bsky.social - this version much improved over the preprint. Final version should be open access, apols.
Thread 1/n
Thread 1/n
Reposted by supriya khedkar
🏆 Fighting the Gender Award Gap: Microbiologist Prof Dr Lisa Maier from @unituebingen.bsky.social received the main award of the German Association for #Microbiology and Hygiene at the #DGHM meeting in Jena. Congratulations to @lisamaierlab.bsky.social we are proud of you! 💜
📸 Gabriele Pradel
📸 Gabriele Pradel
September 23, 2025 at 8:39 AM
🏆 Fighting the Gender Award Gap: Microbiologist Prof Dr Lisa Maier from @unituebingen.bsky.social received the main award of the German Association for #Microbiology and Hygiene at the #DGHM meeting in Jena. Congratulations to @lisamaierlab.bsky.social we are proud of you! 💜
📸 Gabriele Pradel
📸 Gabriele Pradel
Reposted by supriya khedkar
Pleased to announce that our #preprint on the evolutionary history of gene functions is now online at #bioRxiv! We overlayed functional annotations on the evolutionary history of ~4.5M genes from 508 species across the tree of life and found some very cool stuff!
tinyurl.com/FuncEvol
🧵 1/10
tinyurl.com/FuncEvol
🧵 1/10
September 23, 2025 at 9:53 AM
Pleased to announce that our #preprint on the evolutionary history of gene functions is now online at #bioRxiv! We overlayed functional annotations on the evolutionary history of ~4.5M genes from 508 species across the tree of life and found some very cool stuff!
tinyurl.com/FuncEvol
🧵 1/10
tinyurl.com/FuncEvol
🧵 1/10