Ben Kellman bkell1123.bsky.social

Bioinformatics PhD @ UCSD | Research Fellow @ Ragon Institute at MGH, MIT, and Harvard | glycan metabolism, gene expression, NGS, pathology (he/him)

[Ben Kellman bkell1123.bsky.social @bkell1123]

1/5 Today, I’m sharing 7yrs of work. I believe we discovered a comprehensive mapping from protein structure to glycan structure, a genetic encoding for specific glycans, and a new paradigm in extracellular biology.
https://t.co/eba5yTub5x
#Glycotime

[Ben Kellman bkell1123.bsky.social @bkell1123]

@prash_singh I agree that glycans are the missing piece but how do you get to the data volume necessary form learning?

[Ben Kellman bkell1123.bsky.social @bkell1123]

Seems like its finally happening. See you on the new platform. My handle and name are the same.

And honestly, its much more fun and much less icky there.
🦋🦋🦋🦋🦋

[Ben Kellman bkell1123.bsky.social @bkell1123]

@chorye Thanks! I'll give it a shot

[Ben Kellman bkell1123.bsky.social @bkell1123]

@Nathan_E_Lewis @universityofga Congrats! So excited about this!

[Ben Kellman bkell1123.bsky.social @bkell1123]

@lpachter Well sed

[Ben Kellman bkell1123.bsky.social @bkell1123]

It takes two brilliant scientists like @hhefzi and @Nathan_E_Lewis to add fresh insight to a 100-year old phenomenon (subversion of the Warburg effect) AND turn that insight into a perfectly named tool (CHOZeLa) to transform biologics manufacturing.

Check out the preprint!

[Hooman Hefzi @hhefzi]

After ~8 years, happy to share work done w/@Nathan_E_Lewis showing you can eliminate the Warburg effect in mammalian cells-w/out impacting growth rate!-by simultaneous knock out of pyruvate dehydrogenase kinases and lactate dehydrogenases.

Thread below:

https://t.co/MDUI7CVOF4

[Ben Kellman bkell1123.bsky.social @bkell1123]

@vidseh thanks for making and sharing such a useful approach!

[Ben Kellman bkell1123.bsky.social @bkell1123]

@vidseh @CellCellPress @MCB_UJ @MPIbp Love this "If you work with #proteins, you for sure clearly (or secretively 🤫) work with #glycans too!"

[Ben Kellman bkell1123.bsky.social @bkell1123]

@daniel_bojar Is there a liftover from the 2020 reference to current?

[Ben Kellman bkell1123.bsky.social @bkell1123]

@MicrobiomDigest @RutgersU Were you expecting a-door-ation?

[Ben Kellman bkell1123.bsky.social @bkell1123]

@chrashwood @GlycomicsExpasy @GlyCosmos @gly_gen The training/test paradigm is more appropriate for predictive modeling which is what we did in manuscript #2. Manuscript #1 is more descriptive analysis which is why we focus more on in-depth validations with specific molecules.

[Ben Kellman bkell1123.bsky.social @bkell1123]

So why does it matter that glycans are genetically encoded?

Glycans can be >50% of protein’s weight, cover >50% of protein surface, and vital in immunology, metastasis, and autoimmune pathogenesis. Yet, many biologists ignored them because they are hard to measure and control

[Ben Kellman bkell1123.bsky.social @bkell1123]

1/5 Today, I’m sharing 7yrs of work. I believe we discovered a comprehensive mapping from protein structure to glycan structure, a genetic encoding for specific glycans, and a new paradigm in extracellular biology.
https://t.co/eba5yTub5x
#Glycotime

[Ben Kellman bkell1123.bsky.social @bkell1123]

@glycocode Thanks for sharing Lara! Looking forward to hearing your thoughts!

[Ben Kellman bkell1123.bsky.social @bkell1123]

@hirenj @chrashwood @GlycomicsExpasy @GlyCosmos @gly_gen Noting the skew in the input data, we also used hierarchical regressions to adjust for representation across proteins (methods section 4, IMR-GEE).

[Ben Kellman bkell1123.bsky.social @bkell1123]

@hirenj @chrashwood @GlycomicsExpasy @GlyCosmos @gly_gen Hi Hiren, in the corresponding text (results section 1) we describe the input data set (FigS1), dimensionality reduction approach (FigS2), and methods for feature engineering (Methods section 1).

[Ben Kellman bkell1123.bsky.social @bkell1123]

Thanks to Meghan Altman, Isaac Shamie, @LCasalino88, @chem_christian, and @RommieAmaro for helping us explore the implications of GlycoTemplating in Influenza back when we could barely predict anything.

[Ben Kellman bkell1123.bsky.social @bkell1123]

1/5 Today, I’m sharing 7yrs of work. I believe we discovered a comprehensive mapping from protein structure to glycan structure, a genetic encoding for specific glycans, and a new paradigm in extracellular biology.
https://t.co/eba5yTub5x
#Glycotime

[Ben Kellman bkell1123.bsky.social @bkell1123]

Thanks to Philip Bartels, Thi Nguyen, and again Daniel Sandoval for chasing pathogenic variants with us.