Ben Kellman
@bkell1123.bsky.social
Bioinformatics PhD @ UCSD | Research Fellow @ Ragon Institute at MGH, MIT, and Harvard | Founder
glycan metabolism, gene expression, NGS, pathology (he/him)
Boston MA, San Diego CA, Rochester NY, NYC NY
glycan metabolism, gene expression, NGS, pathology (he/him)
Boston MA, San Diego CA, Rochester NY, NYC NY
Pinned
Ben Kellman
@bkell1123.bsky.social
· Nov 16
Reposting for continuity... 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.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
What is the most appropriate platform for roasting a #bioinformatics colleague?
You simply put them on BLAST
You simply put them on BLAST
May 6, 2025 at 8:59 PM
What is the most appropriate platform for roasting a #bioinformatics colleague?
You simply put them on BLAST
You simply put them on BLAST
Important work! Generally we either think about specialized glycan binding proteins (lectins) or we don't think about glycans.
Canner et al help us see the massive world proteins, 35-40%, that also bind glycans!
Thanks Sam for bringing glycan-protein interactions into focus!
Canner et al help us see the massive world proteins, 35-40%, that also bind glycans!
Thanks Sam for bringing glycan-protein interactions into focus!
I’m happy to announce my latest paper has been released as a preprint on BioRxiv: Predictions from Deep Learning Propose Substantial Protein-Carbohydrate Interplay. This paper was only able to happen thanks to both @jeffreyjgray.bsky.social and Dr. Ronald L Schnaar
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
April 12, 2025 at 1:36 PM
Important work! Generally we either think about specialized glycan binding proteins (lectins) or we don't think about glycans.
Canner et al help us see the massive world proteins, 35-40%, that also bind glycans!
Thanks Sam for bringing glycan-protein interactions into focus!
Canner et al help us see the massive world proteins, 35-40%, that also bind glycans!
Thanks Sam for bringing glycan-protein interactions into focus!
Reposted by Ben Kellman
#Medsky update: I've added label support to the following feeds:
Family Medicine: bsky.app/profile/meds...
Cardiology: bsky.app/profile/meds...
Int Medicine: bsky.app/profile/meds...
Nephrology: bsky.app/profile/meds...
Gastro: bsky.app/profile/meds...
Rheum: bsky.app/profile/meds...
Family Medicine: bsky.app/profile/meds...
Cardiology: bsky.app/profile/meds...
Int Medicine: bsky.app/profile/meds...
Nephrology: bsky.app/profile/meds...
Gastro: bsky.app/profile/meds...
Rheum: bsky.app/profile/meds...
November 18, 2024 at 1:54 AM
#Medsky update: I've added label support to the following feeds:
Family Medicine: bsky.app/profile/meds...
Cardiology: bsky.app/profile/meds...
Int Medicine: bsky.app/profile/meds...
Nephrology: bsky.app/profile/meds...
Gastro: bsky.app/profile/meds...
Rheum: bsky.app/profile/meds...
Family Medicine: bsky.app/profile/meds...
Cardiology: bsky.app/profile/meds...
Int Medicine: bsky.app/profile/meds...
Nephrology: bsky.app/profile/meds...
Gastro: bsky.app/profile/meds...
Rheum: bsky.app/profile/meds...
Reposted by Ben Kellman
Boltz-1: Open source (MIT license) protein + PPI + PLI structure prediction method performs on par with AlphaFold3 by Gabriel Corso, Barzilay et al. & Genesis Therapeutics
Blog-post jclinic.mit.edu/boltz-1/
Technical report: t.co/px0spnTA0S
Model and code: github.com/jwohlwend/boltz
Blog-post jclinic.mit.edu/boltz-1/
Technical report: t.co/px0spnTA0S
Model and code: github.com/jwohlwend/boltz
Introducing Boltz-1: Democratizing Biomolecular Interaction Modeling – MIT Jameel Clinic
jclinic.mit.edu
November 18, 2024 at 1:37 AM
Boltz-1: Open source (MIT license) protein + PPI + PLI structure prediction method performs on par with AlphaFold3 by Gabriel Corso, Barzilay et al. & Genesis Therapeutics
Blog-post jclinic.mit.edu/boltz-1/
Technical report: t.co/px0spnTA0S
Model and code: github.com/jwohlwend/boltz
Blog-post jclinic.mit.edu/boltz-1/
Technical report: t.co/px0spnTA0S
Model and code: github.com/jwohlwend/boltz
Important numbers to know for the difficult years ahead.
Also worth asking if the "next dollar" will yield similar returns. How much more would we need to invest in research to see less than a 250% return?
Also worth asking if the "next dollar" will yield similar returns. How much more would we need to invest in research to see less than a 250% return?
Research funded by NIH generated $2.46 in economic activity for every $1 of funding in 2023 [a total of $92.9 billion]
www.fiercebiotech.com/research/rep...
www.fiercebiotech.com/research/rep...
Report: Every dollar of NIH research funding doubles in economic returns
Research funded by the National Institutes of Health (NIH) generated $2.46 in economic activity for every $1 of funding in 2023, a total of $92.9 billion, according to an
www.fiercebiotech.com
November 18, 2024 at 12:42 AM
Important numbers to know for the difficult years ahead.
Also worth asking if the "next dollar" will yield similar returns. How much more would we need to invest in research to see less than a 250% return?
Also worth asking if the "next dollar" will yield similar returns. How much more would we need to invest in research to see less than a 250% return?
My starter packs
(1) handy list of all (blueskydirectory.com/starter-packs), ...
(1) handy list of all (blueskydirectory.com/starter-packs), ...
Starter Packs - Bluesky Directory
A curated collection of all things relating to the Blue Sky social media platform.
blueskydirectory.com
November 17, 2024 at 5:32 PM
My starter packs
(1) handy list of all (blueskydirectory.com/starter-packs), ...
(1) handy list of all (blueskydirectory.com/starter-packs), ...
Reposted by Ben Kellman
New bit of work from CCG, with our newest cellular framework - GlycoCarrier
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Mammalian cell-based production of glycans, glycopeptides and glycomodules - Nature Communications
Access to defined human glycans is crucial for biomedical research. Here, authors report Glycocarriers, a mammalian cell-based method for the sustainable and scalable production of O-, N-glycans, and ...
www.nature.com
November 12, 2024 at 4:39 PM
New bit of work from CCG, with our newest cellular framework - GlycoCarrier
www.nature.com/articles/s41...
www.nature.com/articles/s41...
Reposted by Ben Kellman
A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses www.science.org/doi/full/10....
A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses
Profiling of ERV-reactive B-1 cells in mice reveals natural antibodies against terminal N-acetylglucosamine on multiple viral envelope proteins.
www.science.org
November 12, 2024 at 5:33 PM
A B cell screen against endogenous retroviruses identifies glycan-reactive IgM that recognizes a broad array of enveloped viruses www.science.org/doi/full/10....
Reposted by Ben Kellman
Download our database of 313 different postdoctoral fellowships.
For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship).
Download our database here: research.jhu.edu/rdt/funding-...
For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship).
Download our database here: research.jhu.edu/rdt/funding-...
November 16, 2024 at 7:05 PM
Download our database of 313 different postdoctoral fellowships.
For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship).
Download our database here: research.jhu.edu/rdt/funding-...
For each entry, we provide link to funder, description, amount, deadline, and eligibility criteria (e.g. citizenship).
Download our database here: research.jhu.edu/rdt/funding-...
Partner and I got an icecream maker. Tldr, we think we can make some weird icecream with a bit of help from glycans!
Will share if it's good or weird.
Will share if it's good or weird.
November 17, 2024 at 3:09 AM
Partner and I got an icecream maker. Tldr, we think we can make some weird icecream with a bit of help from glycans!
Will share if it's good or weird.
Will share if it's good or weird.
Reposting for continuity... 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.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...
November 16, 2024 at 11:23 PM
Reposting for continuity... 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.
www.biorxiv.org/content/10.1...
www.biorxiv.org/content/10.1...