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Aidan Quinn

@aidoq.bsky.social

270 followers 310 following 66 posts

Systems Biologist studying Cancer Epigenomics (biochemistry + genomics) in the Kadoch Lab @ Harvard DFCI Broad • Postdoctoral Fellow • KC1TXH • opinions are my own • Boston + NYC

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Aidan Quinn @aidoq.bsky.social · 16d

The cool thing about this transformer model based approach (over diffusion, eg) is that they were able to abstract away the issues diffusion models face with intrinsically disordered regions, engineering IDRs without knowing structure. Very elegant & results-focused solution

🧪🧬🔬💻👾

Aidan Quinn @aidoq.bsky.social · 16d

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...

Accelerating life sciences research

OpenAI and Retro Biosciences achieve 50x increase in expressing stem cell reprogramming markers.

Aidan Quinn @aidoq.bsky.social · Sep 9

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

Reposted by Aidan Quinn

Jean-Paul Armache @valendraica.bsky.social · May 30

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...

Aidan Quinn @aidoq.bsky.social · May 30

Congrats, JP! It's a really intriguing model for regulation over early ATP-dependent remodeling events! I wonder if there are PTMs that regulate transition or even more distal events like TF binding that could promote it... Very nice story!

Aidan Quinn @aidoq.bsky.social · May 30

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!

Aidan Quinn @aidoq.bsky.social · May 11

Nice to see my colleague and friend Sangwoo’s PhD work out and about! Bravo, Dr Park!! 🎉

Teif lab @teiflab.bsky.social · May 10

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

Aidan Quinn @aidoq.bsky.social · May 7

3b/ This underscores the double-edged sword of #aging intervention: cGAS-activation of senescence helps prevent oncogenic transformation, but too much cellular senescence means runaway inflammation. Maybe we should treat the underlying genomic instability and distal inflammation separately?

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Aidan Quinn @aidoq.bsky.social · May 7

3a/ Chen highlighted the age-related increase in cGAMP and mused about the use of cGAS inhibitors in inflammation associated with #aging. But should we really be thinking about inhibiting the proximal sensor of age-related genomic instability?

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Aidan Quinn @aidoq.bsky.social · May 7

2/ Nuclear cGAS seems to be very strongly associated with nucleosomal DNA - does it have a role on #chromatin or is it just sequestration?

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Aidan Quinn @aidoq.bsky.social · May 7

1/ Why does haploinsufficency of cGAS nearly completely rescue Trex1-loss? Chen mentioned that monoalellic loss of STING is also sufficient, so can’t just be cGAMP levels, right?

Source: Gao et al, PNAS 2105 doi.org/10.1073/pnas...

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Kaplan-Meyer curves demonstrating cGas haploinsufficency nearly fully rescues Trex1 complete loss. Source: Gao et al, PNAS 2105 https://doi.org/10.1073/pnas.1516465112

Aidan Quinn @aidoq.bsky.social · May 7

Great round up of cGAS-STING mediated dsDNA sensing with Zhijian Chen - lots to think about!

#HarvardImmunology 🧪

Zhijian J. Chen presenting an introduction slide of the cGAS-STING pathway in an auditorium at Harvard Medical School

Aidan Quinn @aidoq.bsky.social · Apr 3

Hahahaha, I was looking for the same!They use AlphaFold for structure prediction of their hit, I think that’s it… such silly clickbait for an actually quote interesting paper that has almost nothing to do with AI

Aidan Quinn @aidoq.bsky.social · Mar 27

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

🧪

Aidan Quinn @aidoq.bsky.social · Mar 25

This is a report of correlational findings in an observational study. If you make many measurements (as they did) you will find some correlate. Nothing about this is 'critical'. It might constitute preliminary data in support of doing an actual experiment to validate any possible role, likely none

Aidan Quinn @aidoq.bsky.social · Mar 25

⚠️ Dangerous article alert ⚠️

This article makes huge, speculative leaps about treatment for a disease based only on correlative findings.

Science communication matters 🧪

International Society of Genetic Genealogy @isogg.bsky.social · Mar 25

“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...

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

Aidan Quinn @aidoq.bsky.social · Mar 17

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

Aidan Quinn @aidoq.bsky.social · Mar 13

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

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

Reposted by Aidan Quinn

Ming Tommy Tang @tommytang.bsky.social · Mar 5

Genome-coverage single-cell histone modifications for embryo lineage tracing www.nature.com/articles/s4...

Reposted by Aidan Quinn

Epigenetics Podcast @epigeneticspod.bsky.social · Mar 3

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

Aidan Quinn @aidoq.bsky.social · Feb 26

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

Scientists sitting around a table looking at a presentation of B-cell differentiation

Aidan Quinn @aidoq.bsky.social · Feb 25

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 🧬🧪

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

Aidan Quinn @aidoq.bsky.social · Feb 24

www.sciencedirect.com/science/arti... and its open! Enjoy!! 🧪

Nucleosomal asymmetry shapes histone mark binding and promotes poising at bivalent domains

Promoters of developmental genes in embryonic stem cells (ESCs) are marked by histone H3 lysine 4 trimethylation (H3K4me3) and H3K27me3 in an asymmetr…

www.sciencedirect.com

Aidan Quinn @aidoq.bsky.social · Feb 24

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)!
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Graphical abstract of the paper which highlights The asymmetric state of bivalent nucleosomes regulates reader recruitment. Bivalency recruits H3K27me3 but not H3K4me3 readers, promoting a poised state. Bivalency also promotes recruitment of specific factors such as the acetylase KAT6B. KAT6B is required for proper activation of bivalent genes during differentiation

Aidan Quinn @aidoq.bsky.social · Feb 16

Dickson was enormously optimistic and always sought to better the world around him. More than a microbiologist, he was an epidemiologist, environmentalist and a humanitarian working on some of the biggest challenges facing the world. Even writing a super interesting book about vertical farming:

Vertical Farms: From Vision to Reality

Dr. Dickson Despommier believes vertical farming—the growing of crops indoors in multi-story urban buildings—can help feed the growing global population and undo the environmental damage caused by con...

news.climate.columbia.edu