Aidan Quinn
@aidoq.bsky.social
Systems Biologist studying Cancer Epigenomics (biochemistry + genomics) in the Kadoch Lab @ Harvard DFCI Broad • Postdoctoral Fellow • KC1TXH • opinions are my own • Boston + NYC
Fine-tuning GPT-4o mini on amino acid sequence with biological significance text + structural features mapping enables *function-directed* protein design!
Folks @ Retro achieved 50x improvement on iPSC generation using engineered versions of OSKM over wild-type!
🧪🧬💻👾
openai.com/index/accele...
Folks @ Retro achieved 50x improvement on iPSC generation using engineered versions of OSKM over wild-type!
🧪🧬💻👾
openai.com/index/accele...
Accelerating life sciences research
OpenAI and Retro Biosciences achieve 50x increase in expressing stem cell reprogramming markers.
openai.com
September 26, 2025 at 7:27 PM
Fine-tuning GPT-4o mini on amino acid sequence with biological significance text + structural features mapping enables *function-directed* protein design!
Folks @ Retro achieved 50x improvement on iPSC generation using engineered versions of OSKM over wild-type!
🧪🧬💻👾
openai.com/index/accele...
Folks @ Retro achieved 50x improvement on iPSC generation using engineered versions of OSKM over wild-type!
🧪🧬💻👾
openai.com/index/accele...
Big step forward in phenotype-directed drug discovery:
By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping.
Super cool!!
www.nature.com/articles/s41...
#AI #drugdiscovery #cancer
By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping.
Super cool!!
www.nature.com/articles/s41...
#AI #drugdiscovery #cancer
September 9, 2025 at 3:52 PM
Big step forward in phenotype-directed drug discovery:
By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping.
Super cool!!
www.nature.com/articles/s41...
#AI #drugdiscovery #cancer
By learning the latent representation of phenotype space, they speed up and directly learn the phenotype transition --> perturbagen mapping.
Super cool!!
www.nature.com/articles/s41...
#AI #drugdiscovery #cancer
Reposted by Aidan Quinn
New collaborative paper between JPArmache and Bowman (@bowmanlab-jhu.bsky.social) labs show how the yeast CHD1 chromatin remodeler depends on activator elements to distort nucleosomal DNA. This explains how the NegC inhibitor blocks activity. www.nature.com/articles/s41...
A competitive regulatory mechanism of the Chd1 remodeler is integral to distorting nucleosomal DNA - Nature Structural & Molecular Biology
Nodelman, Folkwein et al. define a regulatory region in Chd1 containing adjacent inhibitor and activator elements that compete for binding to the remodeler ATPase. The competition between these elemen...
www.nature.com
May 30, 2025 at 2:35 PM
New collaborative paper between JPArmache and Bowman (@bowmanlab-jhu.bsky.social) labs show how the yeast CHD1 chromatin remodeler depends on activator elements to distort nucleosomal DNA. This explains how the NegC inhibitor blocks activity. www.nature.com/articles/s41...
Beautiful foggy morning run on Martha’s Vineyard… a little time away from the lab goes a long way to help keep me focused back in the lab!
May 30, 2025 at 5:31 PM
Beautiful foggy morning run on Martha’s Vineyard… a little time away from the lab goes a long way to help keep me focused back in the lab!
Nice to see my colleague and friend Sangwoo’s PhD work out and about! Bravo, Dr Park!! 🎉
Native nucleosomes intrinsically encode genome organization principles www.nature.com/articles/s41...
▶️Condensed purified native mononucleosomes with polyamines
▶️Nucleosomes from A compartments have low condensability and those from B compartments have high condensability
▶️Condensed purified native mononucleosomes with polyamines
▶️Nucleosomes from A compartments have low condensability and those from B compartments have high condensability
May 11, 2025 at 7:12 PM
Nice to see my colleague and friend Sangwoo’s PhD work out and about! Bravo, Dr Park!! 🎉
Great round up of cGAS-STING mediated dsDNA sensing with Zhijian Chen - lots to think about!
#HarvardImmunology 🧪
#HarvardImmunology 🧪
May 7, 2025 at 12:46 PM
Great round up of cGAS-STING mediated dsDNA sensing with Zhijian Chen - lots to think about!
#HarvardImmunology 🧪
#HarvardImmunology 🧪
Really nice seminar by Liling Wan here @DFCI! "Chromatin Regulation in Cancer: Molecular Insights and Therapeutic Opportunities"
Many of the DFCI Seminars in Oncology are recorded and open to the public, enjoy!
seminarsinoncology.dana-farber.org/2025.html
🧪
Many of the DFCI Seminars in Oncology are recorded and open to the public, enjoy!
seminarsinoncology.dana-farber.org/2025.html
🧪
March 27, 2025 at 3:29 PM
Really nice seminar by Liling Wan here @DFCI! "Chromatin Regulation in Cancer: Molecular Insights and Therapeutic Opportunities"
Many of the DFCI Seminars in Oncology are recorded and open to the public, enjoy!
seminarsinoncology.dana-farber.org/2025.html
🧪
Many of the DFCI Seminars in Oncology are recorded and open to the public, enjoy!
seminarsinoncology.dana-farber.org/2025.html
🧪
⚠️ Dangerous article alert ⚠️
This article makes huge, speculative leaps about treatment for a disease based only on correlative findings.
Science communication matters 🧪
This article makes huge, speculative leaps about treatment for a disease based only on correlative findings.
Science communication matters 🧪
“The researchers found the changes in gut bacteria communities were associated with a decrease in riboflavin and biotin in people with Parkinson's disease.” #dna #isogg #epigenetics #parkinsons #gutbiome
www.sciencealert.com/parkinsons-g...
www.sciencealert.com/parkinsons-g...
Parkinson's Gut Bacteria Link Suggests an Unexpected, Simple Treatment
Researchers have suspected for some time that the link between our gut and brain plays a role in the development of Parkinson's disease.
www.sciencealert.com
March 25, 2025 at 3:56 PM
⚠️ Dangerous article alert ⚠️
This article makes huge, speculative leaps about treatment for a disease based only on correlative findings.
Science communication matters 🧪
This article makes huge, speculative leaps about treatment for a disease based only on correlative findings.
Science communication matters 🧪
Actuarial studies aren’t going to convince anyone who wants to defund the #NIH but in terms of ROI that seems like a pretty solid multiple, not to mention the benefits to life and health! 🧪
NIH funding delivers exponential economic returns — Harvard Gazette
Report finds all 50 states reap gains in patient health, job creation, research resources, business development.
news.harvard.edu
March 17, 2025 at 2:28 PM
Actuarial studies aren’t going to convince anyone who wants to defund the #NIH but in terms of ROI that seems like a pretty solid multiple, not to mention the benefits to life and health! 🧪
Interested in joining an exciting new translational gyn/onc research group?! Check out my colleague Jess St. Laurent’s group at MGB and Harvard Medical School!
I cannot recommend Dr St Laurent as a mentor highly enough, she is brilliant, passionate, kind & dedicated! 🧪
www.stlaurentlab.org/join
I cannot recommend Dr St Laurent as a mentor highly enough, she is brilliant, passionate, kind & dedicated! 🧪
www.stlaurentlab.org/join
St. Laurent Lab - Join
We're hiring! Reach out if you know folks looking for postdoc or research associate positions
The St. Laurent Lab at the Brigham and Women’s Hospital and Dana Farber Brigham Cancer Center in Boston i...
www.stlaurentlab.org
March 13, 2025 at 12:59 PM
Interested in joining an exciting new translational gyn/onc research group?! Check out my colleague Jess St. Laurent’s group at MGB and Harvard Medical School!
I cannot recommend Dr St Laurent as a mentor highly enough, she is brilliant, passionate, kind & dedicated! 🧪
www.stlaurentlab.org/join
I cannot recommend Dr St Laurent as a mentor highly enough, she is brilliant, passionate, kind & dedicated! 🧪
www.stlaurentlab.org/join
Reposted by Aidan Quinn
Genome-coverage single-cell histone modifications for embryo lineage tracing www.nature.com/articles/s4...
March 5, 2025 at 3:15 PM
Genome-coverage single-cell histone modifications for embryo lineage tracing www.nature.com/articles/s4...
Reposted by Aidan Quinn
In the most recent episode of the Epigenetics Podcast, we talked with Geeta Narlikar from UCSF about her work on chromatin remodeling, Heterochromatin Protein 1, and the molecular mechanisms that influence the genome. #podcast #epigenetics
Listen here: buff.ly/4ibPPUD
Listen here: buff.ly/4ibPPUD
March 3, 2025 at 9:00 AM
In the most recent episode of the Epigenetics Podcast, we talked with Geeta Narlikar from UCSF about her work on chromatin remodeling, Heterochromatin Protein 1, and the molecular mechanisms that influence the genome. #podcast #epigenetics
Listen here: buff.ly/4ibPPUD
Listen here: buff.ly/4ibPPUD
It turns out I am a stage of lymphocyte differentiation, apparently a CLP gives rise to a fully differentiated @aido!
File under: Things I learn in lab meetings
File under: Things I learn in lab meetings
February 26, 2025 at 8:53 PM
It turns out I am a stage of lymphocyte differentiation, apparently a CLP gives rise to a fully differentiated @aido!
File under: Things I learn in lab meetings
File under: Things I learn in lab meetings
Is anyone aware of an exhaustive list of all human histone PTMs identified?
Something like CST’s, except (1) continuously updated and (2) describing the actual modification (e.g. ‘symmetric dimethylation’, instead of ‘methylation’)…
#epigenetics #biochemisty 🧬🧪
Something like CST’s, except (1) continuously updated and (2) describing the actual modification (e.g. ‘symmetric dimethylation’, instead of ‘methylation’)…
#epigenetics #biochemisty 🧬🧪
Histone Modification Table | Cell Signaling Technology
The Histone Modification Table provides a referenced list of many known histone modifications, associated modifying enzymes, and proposed functions.
www.cellsignal.com
February 25, 2025 at 4:27 PM
Is anyone aware of an exhaustive list of all human histone PTMs identified?
Something like CST’s, except (1) continuously updated and (2) describing the actual modification (e.g. ‘symmetric dimethylation’, instead of ‘methylation’)…
#epigenetics #biochemisty 🧬🧪
Something like CST’s, except (1) continuously updated and (2) describing the actual modification (e.g. ‘symmetric dimethylation’, instead of ‘methylation’)…
#epigenetics #biochemisty 🧬🧪
Super paper out of the Voigt group, that answers some longstanding questions about bivalent #histone marks!
They show asymmetric bivalency recruits repressive readers (but not H3K4me3 readers) and have emergent properties that neither of the two alone do (e.g. recruitment of KAT6B complex)!
🧪
They show asymmetric bivalency recruits repressive readers (but not H3K4me3 readers) and have emergent properties that neither of the two alone do (e.g. recruitment of KAT6B complex)!
🧪
February 24, 2025 at 11:22 PM
Super paper out of the Voigt group, that answers some longstanding questions about bivalent #histone marks!
They show asymmetric bivalency recruits repressive readers (but not H3K4me3 readers) and have emergent properties that neither of the two alone do (e.g. recruitment of KAT6B complex)!
🧪
They show asymmetric bivalency recruits repressive readers (but not H3K4me3 readers) and have emergent properties that neither of the two alone do (e.g. recruitment of KAT6B complex)!
🧪
The world lost a truly brilliant scientist & professor Dickson epitomized the joyful curiosity, collaboration and broadly engaging nature that is the whole point of academic science He inspired me to join Columbia PhD program and no doubt inspired countless more around the world on TWiV & TWiP 🧬🦠 🧪
With great sadness remembering this giant in the field of parasitology. He was such an interesting man of many talents, and a great character. He was one of my favorite contributors to This Week In Virology podcast. He is greatly missed. parasiteswithoutborders.com/dickson-desp...
Dickson Despommier, PhD | Parasites without Borders
Dickson Despommier, PhD Dickson Despommier, PhD Date of Birth: June 5, 1940 | Place of Birth: New Orleans, Louisiana CURRENT POSITIONEmeritus Professor with ...
parasiteswithoutborders.com
February 16, 2025 at 3:29 AM
The world lost a truly brilliant scientist & professor Dickson epitomized the joyful curiosity, collaboration and broadly engaging nature that is the whole point of academic science He inspired me to join Columbia PhD program and no doubt inspired countless more around the world on TWiV & TWiP 🧬🦠 🧪
Super nice cancer #biomarker study! Low cost, and fairly sensitive, making strides toward a screening test for early-stage pancreatic #cancer. Doesn’t appear to be *quite* specific enough for use in broad populations but looks promising!
Early detection in pancreatic cancer will be game-changer 🧪
Early detection in pancreatic cancer will be game-changer 🧪
Early detection of pancreatic cancer by a high-throughput protease-activated nanosensor assay
A high-throughput, noninvasive, rapid protease-activated nanosensor identifies patients with pancreatic cancer in a small volume of blood.
www.science.org
February 13, 2025 at 7:24 PM
Super nice cancer #biomarker study! Low cost, and fairly sensitive, making strides toward a screening test for early-stage pancreatic #cancer. Doesn’t appear to be *quite* specific enough for use in broad populations but looks promising!
Early detection in pancreatic cancer will be game-changer 🧪
Early detection in pancreatic cancer will be game-changer 🧪
These moves feel targeted at the big, elite research institutes - and no doubt it hurts - but often labs at the big research schools have private funding to buffer #NIH losses. Make no mistake, this will hurt *all research* but especially smaller, local universities and new labs
NIH announces new funding policy that rattles medical researchers
The National Institutes of Health has dramatically changed its grant-making terms by limiting how much it will disburse for costs such as equipment and administration.
www.npr.org
February 9, 2025 at 6:34 PM
These moves feel targeted at the big, elite research institutes - and no doubt it hurts - but often labs at the big research schools have private funding to buffer #NIH losses. Make no mistake, this will hurt *all research* but especially smaller, local universities and new labs
The Boston sunset view from my bench never gets old!
🧪
🧪
February 1, 2025 at 10:05 PM
The Boston sunset view from my bench never gets old!
🧪
🧪
Finally had a chance to read this one from Rabadan group @columbiamed.bsky.social
It’s amazing the information stored in accessibility profiles! The generalized expression model they learned can accurately predict TF activity & interactions and infer cis regulatory elements
#epigenetics 🧪 🧬
It’s amazing the information stored in accessibility profiles! The generalized expression model they learned can accurately predict TF activity & interactions and infer cis regulatory elements
#epigenetics 🧪 🧬
A foundation model of transcription across human cell types - Nature
A foundation model learns transcriptional regulatory syntax from chromatin accessibility and sequence data across a range of cell types to predict gene expression and transcription factor interactions...
www.nature.com
February 1, 2025 at 9:13 PM
Finally had a chance to read this one from Rabadan group @columbiamed.bsky.social
It’s amazing the information stored in accessibility profiles! The generalized expression model they learned can accurately predict TF activity & interactions and infer cis regulatory elements
#epigenetics 🧪 🧬
It’s amazing the information stored in accessibility profiles! The generalized expression model they learned can accurately predict TF activity & interactions and infer cis regulatory elements
#epigenetics 🧪 🧬
Reposted by Aidan Quinn
Hey science 🧪 bluesky! Anyone have suggestions for benchtop bioprocess controllers / bioreactors for mammalian cell culture?
I’m looking at the Eppendorf SciVario Twin (maybe 320?) or the Thermo G3Lab system. Any other systems I should consider?
Thanks!
🧬 🧫 🦠
I’m looking at the Eppendorf SciVario Twin (maybe 320?) or the Thermo G3Lab system. Any other systems I should consider?
Thanks!
🧬 🧫 🦠
January 30, 2025 at 12:37 AM
Hey science 🧪 bluesky! Anyone have suggestions for benchtop bioprocess controllers / bioreactors for mammalian cell culture?
I’m looking at the Eppendorf SciVario Twin (maybe 320?) or the Thermo G3Lab system. Any other systems I should consider?
Thanks!
🧬 🧫 🦠
I’m looking at the Eppendorf SciVario Twin (maybe 320?) or the Thermo G3Lab system. Any other systems I should consider?
Thanks!
🧬 🧫 🦠
Awesome recap, so many exciting developments!!
Weekly recap, Jan 2025 part 1: Directed evolution by a protein language model, AI learning to run transcript assemblers, a review/introduction to pangenomics, Alphafold2 refinement for protein design, metagenomic binning, new Python & #RStats pkgs... doi.org/10.59350/2zj... 🧬🖥️🧪
Weekly Recap (Jan 2025, part 1)
Directed evolution by a protein language model, AI learning to run transcript assemblers, a review/introduction to pangenomics, Alphafold2 refinement for proteindesign, metagenomic binning...
doi.org
January 4, 2025 at 9:03 AM
Awesome recap, so many exciting developments!!
Reposted by Aidan Quinn
🔬Decoding Silencing: How Heterochromatin Transcribes to Silence Itself!
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
January 3, 2025 at 3:46 PM
🔬Decoding Silencing: How Heterochromatin Transcribes to Silence Itself!
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
🧬 Discover how a pioneer transcription factor-like complex infiltrates repressive heterochromatin, producing transcripts with hidden introns that kickstart RNAi-mediated heterochromatin formation www.nature.com/articles/s41...
Reposted by Aidan Quinn
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
December 20, 2024 at 3:46 PM
We often speak about chromatin as being accessible or inaccessible, but what does it mean? We wrote a short review on this, 🔬 focused:
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.
sciencedirect.com/science/arti...
A big thank you to Tom Fillot for his efforts on this and to
@hansen_lab
@marcelonollmann
for their help as editors.