Dawn Chen
@dawnchenx.bsky.social
PhD student at Broad Institute. Plasmid Engineer!
Pinned
Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation
Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular conte...
www.biorxiv.org
Announcing our new preprint! We built SPICE, a framework that combines large-scale experiments and generative AI to design RNA sequences that control cell type-specific gene expression using alternative splicing – a powerful, underexplored modality.
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Announcing our new preprint! We built SPICE, a framework that combines large-scale experiments and generative AI to design RNA sequences that control cell type-specific gene expression using alternative splicing – a powerful, underexplored modality.
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Generative Design of Cell Type-Specific RNA Splicing Elements for Programmable Gene Regulation
Programmable control of gene expression in specific cell types is essential for both basic discovery and therapeutic intervention, yet current strategies lack scalability across diverse cellular conte...
www.biorxiv.org
November 6, 2025 at 6:59 PM
Announcing our new preprint! We built SPICE, a framework that combines large-scale experiments and generative AI to design RNA sequences that control cell type-specific gene expression using alternative splicing – a powerful, underexplored modality.
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Preprint: www.biorxiv.org/content/10.1...
(1/10)
Thank you to the award committee, my PI Fei Chen and my lab, all my mentors, collaborators, family and friends for your support!
We’re thrilled to congratulate to Jeremy Hollis in the @melodygcampbell.bsky.social and @harmitmalik.bsky.social Labs on being named a 2025 Weintraub Awardee! Jeremy is carrying on the late Hal Weintraub's legacy of curiosity and discovery through his research on cell surface receptors.
A huge congratulations to the recipients of the 2025 Weintraub Award! These ten exceptional graduate students exemplify the bold, creative, and pioneering spirit embodied by Dr. Hal Weintraub. www.fredhutch.org/en/news/rele...
March 4, 2025 at 6:37 PM
Thank you to the award committee, my PI Fei Chen and my lab, all my mentors, collaborators, family and friends for your support!
Reposted by Dawn Chen
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
December 17, 2024 at 12:56 AM
1/ In two back-to-back papers, we present our de novo TRACeR platform for targeting MHC-I and MHC-II antigens
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
TRACeR for MHC-I: go.nature.com/4gcLzn5
TRACeR for MHC-II: go.nature.com/4gj5OQk
Reposted by Dawn Chen
So at the beginning of my postdoc I struggled to amplify Chlamy genes (easily 75%+ GC) and did pretty much the same comparison and found the same results
DMSO= helps but kills pol processivity
Betaine= Lots of spurious products
1,2-propandiol= processivity retained and usually specific product
DMSO= helps but kills pol processivity
Betaine= Lots of spurious products
1,2-propandiol= processivity retained and usually specific product
RESULTS
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n
Gel order:
Upstream homology arm, downstream homology arm, full length locus with target gene in middle, a not so great detection primer set. Ladders are NEB 1KB Plus. Arms 1kbp. Full locus 2880bp. All amplified in same conditions.
10/n
December 12, 2024 at 7:00 AM
So at the beginning of my postdoc I struggled to amplify Chlamy genes (easily 75%+ GC) and did pretty much the same comparison and found the same results
DMSO= helps but kills pol processivity
Betaine= Lots of spurious products
1,2-propandiol= processivity retained and usually specific product
DMSO= helps but kills pol processivity
Betaine= Lots of spurious products
1,2-propandiol= processivity retained and usually specific product
Reposted by Dawn Chen
I took biochem in 2001, and for nearly 20 years read amino acid sequences daily… and I never knew Dayhoff named them or even the logic behind things like Q until last Friday (h/t Mike Janech). Also, this is another big Dayhoff moment for me. She was incredible!
#proteomics #bioinformatics
#proteomics #bioinformatics
Dr. Margaret Oakley Dayhoff
biology.arizona.edu
November 24, 2024 at 12:39 PM
I took biochem in 2001, and for nearly 20 years read amino acid sequences daily… and I never knew Dayhoff named them or even the logic behind things like Q until last Friday (h/t Mike Janech). Also, this is another big Dayhoff moment for me. She was incredible!
#proteomics #bioinformatics
#proteomics #bioinformatics
Reposted by Dawn Chen
Did you know there’s a site to search for starter packs of people to follow? Built by @mubashariqbal.com
blueskydirectory.com/starter-pack...
blueskydirectory.com/starter-pack...
Bluesky Starter Packs - Bluesky Directory
Browse a list of Bluesky Starter Packs. Discover and connect with your community on Bluesky
blueskydirectory.com
November 23, 2024 at 9:43 PM
Did you know there’s a site to search for starter packs of people to follow? Built by @mubashariqbal.com
blueskydirectory.com/starter-pack...
blueskydirectory.com/starter-pack...
Reposted by Dawn Chen
Congratulations to the team for this work! An innovative way to use #CRISPR 🧬 ! This study uses CRISPR-gRNA to barcode small extracellular vesicles, enabling subpopulation-specific analysis of their biogenesis and release. A groundbreaking tool for studying sEV heterogeneity!
#MolecularBiology
#MolecularBiology
Barcoding of small extracellular vesicles with CRISPR-gRNA enables comprehensive, subpopulation-specific analysis of their biogenesis and release regulators - Nature Communications
The release processes of small extracellular vesicles (sEVs) remain poorly understood despite their importance. Here, Kunitake et al. present a screening platform called CIBER screening that enables e...
www.nature.com
November 20, 2024 at 9:43 PM
Congratulations to the team for this work! An innovative way to use #CRISPR 🧬 ! This study uses CRISPR-gRNA to barcode small extracellular vesicles, enabling subpopulation-specific analysis of their biogenesis and release. A groundbreaking tool for studying sEV heterogeneity!
#MolecularBiology
#MolecularBiology
Reposted by Dawn Chen
Here’s my spreadsheet of starter packs (>80!) related to broadly ‘mechanistic biology’ plus some intriguing extras
Complete with collective nouns
I’ve been tracking these but now can’t keep up
Hope it’s helpful
2/2
docs.google.com/spreadsheets...
Complete with collective nouns
I’ve been tracking these but now can’t keep up
Hope it’s helpful
2/2
docs.google.com/spreadsheets...
@mjafreeman.bsky.social's BlueSky starter packs for 'mechanistic' biologists
docs.google.com
November 19, 2024 at 9:58 PM
Here’s my spreadsheet of starter packs (>80!) related to broadly ‘mechanistic biology’ plus some intriguing extras
Complete with collective nouns
I’ve been tracking these but now can’t keep up
Hope it’s helpful
2/2
docs.google.com/spreadsheets...
Complete with collective nouns
I’ve been tracking these but now can’t keep up
Hope it’s helpful
2/2
docs.google.com/spreadsheets...