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!
They smell like heaven!!!
January 11, 2026 at 1:11 PM
They smell like heaven!!!
Also @vikasnavaratna.bsky.social there is this: cvit.iiit.ac.in/research/pro...
What is there in an Indian Thali?
The Centre for Visual Information Technology (CVIT) is a research centre at the International Institute of Information Technology, Hyderabad.
cvit.iiit.ac.in
January 9, 2026 at 11:34 PM
Also @vikasnavaratna.bsky.social there is this: cvit.iiit.ac.in/research/pro...
LOL!!! I will read the paper now more throughly.
January 9, 2026 at 11:26 PM
LOL!!! I will read the paper now more throughly.
@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...
Thanks and congratulations to you as well for selected as an BPS Ambassdor, Canada! And being in the same cohort!!! π₯³π
January 9, 2026 at 2:42 PM
Thanks and congratulations to you as well for selected as an BPS Ambassdor, Canada! And being in the same cohort!!! π₯³π
It is perhaps not hungry enough!π
January 9, 2026 at 2:41 PM
It is perhaps not hungry enough!π
I don't see your posts these days. Some algorithm. Missed seeing all these food pics for a long time.
January 9, 2026 at 8:11 AM
I don't see your posts these days. Some algorithm. Missed seeing all these food pics for a long time.
Many congratulations Vikas!
January 9, 2026 at 8:11 AM
Many congratulations Vikas!
Thanks @madamescientist.bsky.social for the kind words! Much appreciated!
January 9, 2026 at 8:08 AM
Thanks @madamescientist.bsky.social for the kind words! Much appreciated!
Way to start the year with a huge humblebrag!
πππ 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. π₯³ π
biophysics.cld.bz/Biophysical-...
πππ 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. π₯³ π
biophysics.cld.bz/Biophysical-...
January 8, 2026 at 7:00 AM
Way to start the year with a huge humblebrag!
πππ 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. π₯³ π
biophysics.cld.bz/Biophysical-...
πππ 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. π₯³ π
biophysics.cld.bz/Biophysical-...
Reposted by Ragothaman Yennamalli
π£ 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
π eccb2026.org/call-tutoria...
Deadline: 16 January 2026
π eccb2026.org/call-tutoria...
January 5, 2026 at 10:33 AM
π£ 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
π eccb2026.org/call-tutoria...
Deadline: 16 January 2026
π eccb2026.org/call-tutoria...
Congratulations!
January 2, 2026 at 4:16 AM
Congratulations!
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 π¨!
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 π¨!
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
So cool! Will be using these two tools in my classes this semester.
December 29, 2025 at 1:49 PM
So cool! Will be using these two tools in my classes this semester.
I think the BWT link is different?
December 29, 2025 at 7:14 AM
I think the BWT link is different?
These two tools are superb!!!! We used to do the coding for global and local alignments as class assignments. But, the interactive version makes it so cool!
December 29, 2025 at 7:13 AM
These two tools are superb!!!! We used to do the coding for global and local alignments as class assignments. But, the interactive version makes it so cool!
Why this matters π€
This work shows how structural systems biology can:
βοΈ Improve phenotype prediction
βοΈ Enable rational strain design
βοΈ Bridge molecular mechanism β metabolic engineering
π Code & data: github.com/raghuyennama...
7/7
This work shows how structural systems biology can:
βοΈ Improve phenotype prediction
βοΈ Enable rational strain design
βοΈ Bridge molecular mechanism β metabolic engineering
π Code & data: github.com/raghuyennama...
7/7
GitHub - raghuyennamalli/levan_ssbio
Contribute to raghuyennamalli/levan_ssbio development by creating an account on GitHub.
github.com
December 29, 2025 at 4:43 AM
Why this matters π€
This work shows how structural systems biology can:
βοΈ Improve phenotype prediction
βοΈ Enable rational strain design
βοΈ Bridge molecular mechanism β metabolic engineering
π Code & data: github.com/raghuyennama...
7/7
This work shows how structural systems biology can:
βοΈ Improve phenotype prediction
βοΈ Enable rational strain design
βοΈ Bridge molecular mechanism β metabolic engineering
π Code & data: github.com/raghuyennama...
7/7
Beyond sequences: fold-level insight
Using Foldseek, we clustered ~4,200 AlphaFold structures:
β’ 563 fold clusters
β’ Levan enzymes grouped into 4 structural clusters
β’ Enabled functional hints for 7 uncharacterized proteins 6/7
Using Foldseek, we clustered ~4,200 AlphaFold structures:
β’ 563 fold clusters
β’ Levan enzymes grouped into 4 structural clusters
β’ Enabled functional hints for 7 uncharacterized proteins 6/7
December 29, 2025 at 4:43 AM
Beyond sequences: fold-level insight
Using Foldseek, we clustered ~4,200 AlphaFold structures:
β’ 563 fold clusters
β’ Levan enzymes grouped into 4 structural clusters
β’ Enabled functional hints for 7 uncharacterized proteins 6/7
Using Foldseek, we clustered ~4,200 AlphaFold structures:
β’ 563 fold clusters
β’ Levan enzymes grouped into 4 structural clusters
β’ Enabled functional hints for 7 uncharacterized proteins 6/7
Regulation matters βοΈ
We built a Boolean gene regulatory network (BooleSim) for levan biosynthesis.
β‘οΈ Identified stable core genes (e.g., sacB, sacY, levB)
β‘οΈ Captured oscillatory regulators (abrB, gmuR, gmuE) across conditions. 5/7
We built a Boolean gene regulatory network (BooleSim) for levan biosynthesis.
β‘οΈ Identified stable core genes (e.g., sacB, sacY, levB)
β‘οΈ Captured oscillatory regulators (abrB, gmuR, gmuE) across conditions. 5/7
December 29, 2025 at 4:43 AM
Regulation matters βοΈ
We built a Boolean gene regulatory network (BooleSim) for levan biosynthesis.
β‘οΈ Identified stable core genes (e.g., sacB, sacY, levB)
β‘οΈ Captured oscillatory regulators (abrB, gmuR, gmuE) across conditions. 5/7
We built a Boolean gene regulatory network (BooleSim) for levan biosynthesis.
β‘οΈ Identified stable core genes (e.g., sacB, sacY, levB)
β‘οΈ Captured oscillatory regulators (abrB, gmuR, gmuE) across conditions. 5/7
Why structure matters (example: SacB)
Levansucrase has many structures, many mutants, many catalytic states.
By embedding these into the pathway, we connect polymer length, mechanism, and metabolic context β not just fluxes. 4/7
Levansucrase has many structures, many mutants, many catalytic states.
By embedding these into the pathway, we connect polymer length, mechanism, and metabolic context β not just fluxes. 4/7
December 29, 2025 at 4:43 AM
Why structure matters (example: SacB)
Levansucrase has many structures, many mutants, many catalytic states.
By embedding these into the pathway, we connect polymer length, mechanism, and metabolic context β not just fluxes. 4/7
Levansucrase has many structures, many mutants, many catalytic states.
By embedding these into the pathway, we connect polymer length, mechanism, and metabolic context β not just fluxes. 4/7
What we built π§
A structure-annotated GEM where:
β’ 508 PDB structures
β’ 168 proteins
β’ 331 reactions (~27% of the model) are explicitly linked. This is NOT a cosmetic improvement. The model has AF2 structures as well. 3/7
A structure-annotated GEM where:
β’ 508 PDB structures
β’ 168 proteins
β’ 331 reactions (~27% of the model) are explicitly linked. This is NOT a cosmetic improvement. The model has AF2 structures as well. 3/7
December 29, 2025 at 4:43 AM
What we built π§
A structure-annotated GEM where:
β’ 508 PDB structures
β’ 168 proteins
β’ 331 reactions (~27% of the model) are explicitly linked. This is NOT a cosmetic improvement. The model has AF2 structures as well. 3/7
A structure-annotated GEM where:
β’ 508 PDB structures
β’ 168 proteins
β’ 331 reactions (~27% of the model) are explicitly linked. This is NOT a cosmetic improvement. The model has AF2 structures as well. 3/7