Ragothaman Yennamalli
@structbioinfo.bsky.social
Sr. Asst Prof SASTRA Univ | Computational Biologist | YIM2024 organizer | Editor: CSBJ, BMC Bioinfo | Spl issue Ed: Biophys J | He/Him.
I would love to be a student in this course!
Great things still happen all around us. Each your UNC Biology's Bob Goldstein and Art's Beth Grabowski co-teach ARTS/BIOL 409, that brings together artists and scientists to explore an intersection of two disciplines. It culminated this year with a remarkable show Friday 1/n
January 12, 2026 at 3:27 AM
I would love to be a student in this course!
@vikasnavaratna.bsky.social This is right up your alley! farzanashaju.github.io/how-does-ind...
Haven't read it fully, yet! Sounds interesting...
Haven't read it fully, yet! Sounds interesting...
How Does India Cook Biryani?
A large-scale dataset and VLM-based pipeline for analyzing procedural differences across 12 regional Indian biryani variants using 120 cooking videos.
farzanashaju.github.io
January 9, 2026 at 4:04 PM
@vikasnavaratna.bsky.social This is right up your alley! farzanashaju.github.io/how-does-ind...
Haven't read it fully, yet! Sounds interesting...
Haven't read it fully, yet! Sounds interesting...
Way to start the year with a huge humblebrag!
🎉🎉🎉 I have been selected as the Indian Ambassador for @biophysicalsoc.bsky.social seventh cohort (2026-2028)!!! Eagerly looking forward to working with other ambassadors to promote biophysics and bioinfo in India. 🥳 🙌
biophysics.cld.bz/Biophysical-...
🎉🎉🎉 I have been selected as the Indian Ambassador for @biophysicalsoc.bsky.social seventh cohort (2026-2028)!!! Eagerly looking forward to working with other ambassadors to promote biophysics and bioinfo in India. 🥳 🙌
biophysics.cld.bz/Biophysical-...
January 8, 2026 at 7:00 AM
Way to start the year with a huge humblebrag!
🎉🎉🎉 I have been selected as the Indian Ambassador for @biophysicalsoc.bsky.social seventh cohort (2026-2028)!!! Eagerly looking forward to working with other ambassadors to promote biophysics and bioinfo in India. 🥳 🙌
biophysics.cld.bz/Biophysical-...
🎉🎉🎉 I have been selected as the Indian Ambassador for @biophysicalsoc.bsky.social seventh cohort (2026-2028)!!! Eagerly looking forward to working with other ambassadors to promote biophysics and bioinfo in India. 🥳 🙌
biophysics.cld.bz/Biophysical-...
Reposted by Ragothaman Yennamalli
📣 Still 11 days to submit proposals for workshops and tutorials for #ECCB2026! Don't miss the opportunity to be an active part of one of Europe's leading conference in #Bioinformatics and #ComputationalBiology.
Deadline: 16 January 2026
🔗 eccb2026.org/call-tutoria...
Deadline: 16 January 2026
🔗 eccb2026.org/call-tutoria...
January 5, 2026 at 10:33 AM
📣 Still 11 days to submit proposals for workshops and tutorials for #ECCB2026! Don't miss the opportunity to be an active part of one of Europe's leading conference in #Bioinformatics and #ComputationalBiology.
Deadline: 16 January 2026
🔗 eccb2026.org/call-tutoria...
Deadline: 16 January 2026
🔗 eccb2026.org/call-tutoria...
Reposted by Ragothaman Yennamalli
Excited to share our book chapter on method development advances in integrative structural modeling in Springer Handbooks now online! @shreyasarvindekar.bsky.social @kartikmajila.bsky.social doi.org/10.1007/978-...
Recent Methods from Statistical Inference for Integrative Structural Modeling
Integrative modeling of macromolecular assemblies allows for structural characterization of large assemblies that are recalcitrant to direct experimental observation. A Bayesian inference approach fac...
doi.org
January 2, 2026 at 1:52 AM
Excited to share our book chapter on method development advances in integrative structural modeling in Springer Handbooks now online! @shreyasarvindekar.bsky.social @kartikmajila.bsky.social doi.org/10.1007/978-...
This year on Bluesky I wrote 121 posts and 159 replies. I received 303 likes, whereas 27 was from my most popular post, and apparently I love saying "not" and 🚨!
www.madebyolof.com/bluesky-wrap...
www.madebyolof.com/bluesky-wrap...
structbioinfo.bsky.social's Bluesky Wrapped 2025
Check out structbioinfo.bsky.social's year on Bluesky!
www.madebyolof.com
December 31, 2025 at 6:53 AM
This year on Bluesky I wrote 121 posts and 159 replies. I received 303 likes, whereas 27 was from my most popular post, and apparently I love saying "not" and 🚨!
www.madebyolof.com/bluesky-wrap...
www.madebyolof.com/bluesky-wrap...
Finally, the special issue is out! Read the editorial here:
www.cell.com/biophysj/ful...
@florencetama.bsky.social @frettinglab.bsky.social @biophysicalsoc.bsky.social @biophysj.bsky.social
www.cell.com/biophysj/ful...
@florencetama.bsky.social @frettinglab.bsky.social @biophysicalsoc.bsky.social @biophysj.bsky.social
December 31, 2025 at 5:20 AM
Finally, the special issue is out! Read the editorial here:
www.cell.com/biophysj/ful...
@florencetama.bsky.social @frettinglab.bsky.social @biophysicalsoc.bsky.social @biophysj.bsky.social
www.cell.com/biophysj/ful...
@florencetama.bsky.social @frettinglab.bsky.social @biophysicalsoc.bsky.social @biophysj.bsky.social
End-of-year preprint drop from Yennamalli Lab 🎯
Genome-scale metabolic models tell us what flows.
Protein structures tell us how. We asked: what happens if you combine each other? 👉 Structural systems biology. Funding: Sastra Univ & ANRF-India 1/7
Genome-scale metabolic models tell us what flows.
Protein structures tell us how. We asked: what happens if you combine each other? 👉 Structural systems biology. Funding: Sastra Univ & ANRF-India 1/7
Structural and Boolean Network Modeling of the Levan Biosynthetic Pathway in Bacillus subtilis. https://www.biorxiv.org/content/10.64898/2025.12.25.696451v1
December 29, 2025 at 4:43 AM
End-of-year preprint drop from Yennamalli Lab 🎯
Genome-scale metabolic models tell us what flows.
Protein structures tell us how. We asked: what happens if you combine each other? 👉 Structural systems biology. Funding: Sastra Univ & ANRF-India 1/7
Genome-scale metabolic models tell us what flows.
Protein structures tell us how. We asked: what happens if you combine each other? 👉 Structural systems biology. Funding: Sastra Univ & ANRF-India 1/7
Reposted by Ragothaman Yennamalli
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
December 16, 2025 at 10:32 PM
Organelles harbour pH gradients https://www.biorxiv.org/content/10.64898/2025.12.12.694065v1
This changes everything about what I was taught about pH in organelles like lysosomes. This also changes the way pH dependent fusion mechanisms were understood for some viral proteins.
Which means:
local proton production or consumption can generate persistent pH microdomains, tens to hundreds of nanometers wide. 15/n
local proton production or consumption can generate persistent pH microdomains, tens to hundreds of nanometers wide. 15/n
December 17, 2025 at 6:16 AM
This changes everything about what I was taught about pH in organelles like lysosomes. This also changes the way pH dependent fusion mechanisms were understood for some viral proteins.
Reposted by Ragothaman Yennamalli
Please repost:
Undergraduates (globally) can receive free membership in the professional scientific society for plant pathogens, the American Phytopathological Society (APS).
This society provides excellent professional development.
www.apsnet.org/members/comm...
Undergraduates (globally) can receive free membership in the professional scientific society for plant pathogens, the American Phytopathological Society (APS).
This society provides excellent professional development.
www.apsnet.org/members/comm...
Borlaug’s Army: an undergraduate membership initiative of the American Phytopathology
Borlaug’s Army: an undergraduate membership initiative of APS....Welcome to Borlaug’s Army —a recruitment, engagement, and outreach initiative of the American Phytopathological Society. Free membersh...
www.apsnet.org
December 11, 2025 at 3:25 PM
Please repost:
Undergraduates (globally) can receive free membership in the professional scientific society for plant pathogens, the American Phytopathological Society (APS).
This society provides excellent professional development.
www.apsnet.org/members/comm...
Undergraduates (globally) can receive free membership in the professional scientific society for plant pathogens, the American Phytopathological Society (APS).
This society provides excellent professional development.
www.apsnet.org/members/comm...
Reposted by Ragothaman Yennamalli
Every full professor:
December 1, 2025 at 8:48 AM
Every full professor:
Wonderful read with my morning coffee. It was an absolute delight to read a fine piece of writing. It reaffirms the practice that scientific writing is not in linear time scale. It is in the presentation, where details are lost, and this leads to utter confusion in reproducibility. History Matters!!
Every biologist knows the story of Fleming's chance discovery of penicillin. But is it true?
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
Here, with @asimovpress.bsky.social, I write about inconsistencies in the canonical story, and explore a few alternative theories about what really happened in that St. Mary's lab in the summer of 1928.
The Penicillin Myth
Competing theories seek to explain inconsistencies surrounding Alexander Fleming’s famed discovery.
press.asimov.com
November 25, 2025 at 12:30 AM
Wonderful read with my morning coffee. It was an absolute delight to read a fine piece of writing. It reaffirms the practice that scientific writing is not in linear time scale. It is in the presentation, where details are lost, and this leads to utter confusion in reproducibility. History Matters!!
Reposted by Ragothaman Yennamalli
Editors have a really hard job, and the good ones can make something unreadable readable, and the great ones can make something unreadable into something good. But they're basically invisible, until someone tries to write without one.
November 17, 2025 at 3:35 PM
Editors have a really hard job, and the good ones can make something unreadable readable, and the great ones can make something unreadable into something good. But they're basically invisible, until someone tries to write without one.
Reposted by Ragothaman Yennamalli
Tout va bien, c'est humoristique
31 illegible black metal band logos
It’s one of the strange quirks of the extreme metal scene: band names have to be written in an ornate, impossible-to-decipher font. Here are few of our favourites. Check the caption on each one to fin...
www.nme.com
November 10, 2025 at 5:22 PM
Tout va bien, c'est humoristique
Reposted by Ragothaman Yennamalli
Nicolas-Sébastien Adam - Prometheus Bound 1762 - Marble (Louvre)
November 7, 2025 at 2:45 PM
Nicolas-Sébastien Adam - Prometheus Bound 1762 - Marble (Louvre)
Send us your proposals!
📣 The call for tutorials & workshops at #ECCB2026 is now open! Share your tools, methods or expertise with the community.
🗓️ Deadline: 5 January 2026
👉 Submit: tinyurl.com/tw-eccb26
💡 ECCB will take place on 31 Aug–4 Sept in Geneva, gathering 1,000+ scientists from academia, industry, & healthcare.
🗓️ Deadline: 5 January 2026
👉 Submit: tinyurl.com/tw-eccb26
💡 ECCB will take place on 31 Aug–4 Sept in Geneva, gathering 1,000+ scientists from academia, industry, & healthcare.
November 5, 2025 at 8:19 AM
Send us your proposals!
Reposted by Ragothaman Yennamalli
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
November 3, 2025 at 12:26 PM
Our new preprint is out 🥳🥳🥳
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Henipaviruses, like Nipah and Hendra, package their genomes inside helical shells built by thousands of nucleoproteins. These nucleocapsids are essential to protect the viral RNA, but how do they ever let the polymerase in to read the sequence?
👇
Happy to share that our collaborative paper got featured as the cover page of the latest issue of JBC!
November 3, 2025 at 11:53 AM
Happy to share that our collaborative paper got featured as the cover page of the latest issue of JBC!
Reposted by Ragothaman Yennamalli
Who did this?!
November 1, 2025 at 8:38 PM
Who did this?!
Reposted by Ragothaman Yennamalli
maslow's hierarchy of cells
1. physiological needs: oxygen, nutrients
2. safety: a tissue culture dish to adhere to
3. love and belonging: contact with surrounding cells
1. physiological needs: oxygen, nutrients
2. safety: a tissue culture dish to adhere to
3. love and belonging: contact with surrounding cells
November 2, 2025 at 12:20 AM
maslow's hierarchy of cells
1. physiological needs: oxygen, nutrients
2. safety: a tissue culture dish to adhere to
3. love and belonging: contact with surrounding cells
1. physiological needs: oxygen, nutrients
2. safety: a tissue culture dish to adhere to
3. love and belonging: contact with surrounding cells
Reposted by Ragothaman Yennamalli
Success. Nearly 259 Foldscope deployed in hands of unsuspecting candy crazy kids. Halloween is always more colorful with the microscopes - specially in a few weeks they could look at the micro-fauna of the teeth with so much sugar consumption.
November 1, 2025 at 10:10 AM
Success. Nearly 259 Foldscope deployed in hands of unsuspecting candy crazy kids. Halloween is always more colorful with the microscopes - specially in a few weeks they could look at the micro-fauna of the teeth with so much sugar consumption.
Reposted by Ragothaman Yennamalli
I have started making a homemade electrolyte drink with sodium salt, potassium salt, powdered ginger, lemon juice, mint leaves, and carbonated water and I love it (and I feel noticeably better with 1/day).
Just ordered freeze dried lemon and mint leaves to make a dry mix 💪🏻
Just ordered freeze dried lemon and mint leaves to make a dry mix 💪🏻
October 30, 2025 at 3:59 AM
I have started making a homemade electrolyte drink with sodium salt, potassium salt, powdered ginger, lemon juice, mint leaves, and carbonated water and I love it (and I feel noticeably better with 1/day).
Just ordered freeze dried lemon and mint leaves to make a dry mix 💪🏻
Just ordered freeze dried lemon and mint leaves to make a dry mix 💪🏻
Reposted by Ragothaman Yennamalli
Just because this came up a few times recently
If you need to compare two or more ensembles (like RMSD for structures) we developed algorithms and code (ENCORE) to do just that
Similarity Measures for Protein Ensembles
journals.plos.org/plosone/arti...
ENCORE
journals.plos.org/ploscompbiol...
If you need to compare two or more ensembles (like RMSD for structures) we developed algorithms and code (ENCORE) to do just that
Similarity Measures for Protein Ensembles
journals.plos.org/plosone/arti...
ENCORE
journals.plos.org/ploscompbiol...
October 27, 2025 at 8:00 AM
Just because this came up a few times recently
If you need to compare two or more ensembles (like RMSD for structures) we developed algorithms and code (ENCORE) to do just that
Similarity Measures for Protein Ensembles
journals.plos.org/plosone/arti...
ENCORE
journals.plos.org/ploscompbiol...
If you need to compare two or more ensembles (like RMSD for structures) we developed algorithms and code (ENCORE) to do just that
Similarity Measures for Protein Ensembles
journals.plos.org/plosone/arti...
ENCORE
journals.plos.org/ploscompbiol...
A Sunday morning Data Wrangling Exercise...
Gaurav Sharma and I discussed what this new Sh-Index means. Post-preprint and now featured in Nature Index, there has been vocal criticism and rightly so. We discussed again and I have been using it not actually intended. Also.. 🧵 1/8
Gaurav Sharma and I discussed what this new Sh-Index means. Post-preprint and now featured in Nature Index, there has been vocal criticism and rightly so. We discussed again and I have been using it not actually intended. Also.. 🧵 1/8
I know the modified H index (or the Sh index) is getting a lot of grief in social media discussions but it allows a simple calculation: what’s the difference between your h index and your Sh index? If that difference is small or zero, what does that tell us about what kind of collaborator you are?
October 27, 2025 at 7:25 AM
A Sunday morning Data Wrangling Exercise...
Gaurav Sharma and I discussed what this new Sh-Index means. Post-preprint and now featured in Nature Index, there has been vocal criticism and rightly so. We discussed again and I have been using it not actually intended. Also.. 🧵 1/8
Gaurav Sharma and I discussed what this new Sh-Index means. Post-preprint and now featured in Nature Index, there has been vocal criticism and rightly so. We discussed again and I have been using it not actually intended. Also.. 🧵 1/8