Ben Kellman bkell1123.bsky.social (@bkell1123) - Twitter Profili

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Ben Kellman bkell1123.bsky.social@bkell1123·16 May

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. biorxiv.org/content/10.110… #Glycotime

Ben Kellman bkell1123.bsky.social tweet media

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Ben Kellman bkell1123.bsky.social@bkell1123·18 Kas

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. 🦋🦋🦋🦋🦋

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Ben Kellman bkell1123.bsky.social@bkell1123·17 Kas

@chorye Thanks! I'll give it a shot

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Emma J Chory@chorye·16 Kas

@bkell1123 It's exceptionally easy. As soon as you open it up there are dozens of science starter packs to follow everyone who has moved over. Follow them & they'll follow back!

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Emma J Chory@chorye·15 Kas

Actual pre-prints/science: $0 Multiple Nobel laureates: $0 1000 sci-followers day3: $0 No porn-bots: Priceless

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Ben Kellman bkell1123.bsky.social@bkell1123·2 Kas

@Nathan_E_Lewis @universityofga Congrats! So excited about this!

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Nathan Lewis@Nathan_E_Lewis·2 Kas

It's official! Super excited to join great colleagues at the @universityofga Center for Molecular Medicine and Complex Carbohydrate Research Center

Georgia Research Alliance@ga_res_alliance

Top story in the just-out October GRA Notes: The @universityofga's recruitment of a renowned systems biologist from California as the newest GRA Eminent Scholar. Get to know Nathan Lewis, whose work propels drug discovery and development. mailchi.mp/gra/oct24

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Ben Kellman bkell1123.bsky.social@bkell1123·7 Eyl

@lpachter Well sed

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Lior Pachter@lpachter·6 Eyl

s/1970s/2020s/g

c0nc0rdance@c0nc0rdance

Some people think scientists are very smart, but counter-point: mouth pipetting was standard practice until the 1970's.

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Ben Kellman bkell1123.bsky.social@bkell1123·9 Ağu

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: biorxiv.org/content/10.110…

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Ben Kellman bkell1123.bsky.social@bkell1123·17 Haz

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

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Vidhi✨🧠🌱🦠️@vidseh·17 Haz

Our #Glycoshield in action for such a useful project🤩🫶 #glycotime #dioscuri

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. biorxiv.org/content/10.110… #Glycotime

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Ben Kellman bkell1123.bsky.social@bkell1123·17 Haz

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

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Vidhi✨🧠🌱🦠️@vidseh·29 Şub

If you work with #proteins, you for sure clearly (or secretively 🤫) work with #glycans too! And that’s where #glycoshield will come handy! Why? Find out in our fresh paper in @CellCellPress 🔥🔥🔥 #glycotime @MCB_UJ @MPIbp

Matt Sikora@BioPhysMatt

Worried about your supercomputer electricity bill⚡️ We got your back! Model your glycans in minutes with #GlycoSHIELD! Amazing collab w/ @cyril_hanus & Shang-Te Danny Hsu, now in @CellCellPress tinyurl.com/bdhuzbnu @MCB_UJ @MPIbp @maxplanckpress @Inserm @AcadSinica #glycotime

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Ben Kellman bkell1123.bsky.social@bkell1123·28 May

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

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Daniel Bojar@daniel_bojar·28 May

Probably won't reach the right people here but I have seen *so* many papers using our original 2020 glycan-taxonomy 13k dataset for building stuff; for the love of god, *please* use the 37k dataset from glycowork 😵‍💫It's not only bigger but also much cleaner

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Ben Kellman bkell1123.bsky.social@bkell1123·22 May

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

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Elisabeth Bik@MicrobiomDigest·21 May

I have arrived at the place to give my talk. Door is locked. Contact person is not answering phone. Please send help 😁 ⁦@RutgersU⁩

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Ben Kellman bkell1123.bsky.social@bkell1123·18 May

@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.

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Ben Kellman bkell1123.bsky.social@bkell1123·16 May

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. biorxiv.org/content/10.110… #Glycotime

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Ben Kellman bkell1123.bsky.social@bkell1123·17 May

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

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Ben Kellman bkell1123.bsky.social@bkell1123·17 May

@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).

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Ben Kellman bkell1123.bsky.social@bkell1123·17 May

@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).

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Ben Kellman bkell1123.bsky.social@bkell1123·17 May

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.

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Ben Kellman bkell1123.bsky.social@bkell1123·17 May

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

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Ben Kellman bkell1123.bsky.social@bkell1123·16 May

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. biorxiv.org/content/10.110… #Glycotime

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