Kaia Mattioli
@kaiamattioli.bsky.social
K99/R00 postdoc, 24/7 feminist @ Harvard/BWH. generally fascinated by genomes. big fan of reality tv, good writing, crosswords, and cats. obsessed with my e-bike. she/her
Pinned
Kaia Mattioli
@kaiamattioli.bsky.social
· Mar 26
our work on the molecular differences between transcription factor isoforms is out now in Molecular Cell!
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
key point: 2/3rds of TF isos differ in properties like DNA binding & transcriptional activity
many are "negative regulators" & misexpressed in cancer
www.sciencedirect.com/science/arti...
unbelievably poignant and devastating. if we're not putting as many possible resources towards treating cancer as we can, what are we even doing here?
“When you are dying, at least in my limited experience, you start remembering everything.” Tatiana Schlossberg, the daughter of Caroline Kennedy, writes about receiving a terminal diagnosis. https://newyorkermag.visitlink.me/4SkkDI
A Battle with My Blood
When I was diagnosed with leukemia, my first thought was that this couldn’t be happening to me, to my family.
newyorkermag.visitlink.me
November 23, 2025 at 3:11 AM
unbelievably poignant and devastating. if we're not putting as many possible resources towards treating cancer as we can, what are we even doing here?
Reposted by Kaia Mattioli
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs
Low-affinity transcription factor (TF) motifs are an important element of the cis-regulatory code, yet they are notoriously difficult to map and mechanistically incompletely understood, limiting our a...
www.biorxiv.org
November 19, 2025 at 8:57 PM
We are pleased to announce a new preprint by @mlweilert.bsky.social: “Widespread low-affinity motifs enhance chromatin accessibility and regulatory potential in mESCs” (www.biorxiv.org/content/10.1...). See summary and longer recap below:
(TLDR; low-affinity motifs matter as pioneers!)
(TLDR; low-affinity motifs matter as pioneers!)
in other news, sorry to report that Rosalía's LUX has become my entire personality
November 15, 2025 at 1:08 PM
in other news, sorry to report that Rosalía's LUX has become my entire personality
first daycare-induced respiratory virus of the season... while i'm on deadline..... before thanksgiving even..... the world is cruel
November 13, 2025 at 5:32 PM
first daycare-induced respiratory virus of the season... while i'm on deadline..... before thanksgiving even..... the world is cruel
i remember this great talk from Biology of Genomes - the sparkle phenotype!
I am so excited to share new work on a TE insertion that regulates iridescence in swordtails, led by fantastic grad student @nadiahaghani.bsky.social and with help from many coauthors! In a time that has been so difficult to navigate, this & other projects have kept my spirits up: shorturl.at/NE65A
Insertion of an invading retrovirus regulates a novel color trait in swordtail fish
For over a century, evolutionary biologists have been motivated to understand the mechanisms through which organisms adapt to their environments. Coloration and pigmentation are remarkably variable wi...
shorturl.at
November 12, 2025 at 8:52 PM
i remember this great talk from Biology of Genomes - the sparkle phenotype!
there's a lot to worry about these days but my toddler just started calling all of his meals "yummies" and my heart overflows every time. so.
November 9, 2025 at 10:37 PM
there's a lot to worry about these days but my toddler just started calling all of his meals "yummies" and my heart overflows every time. so.
word on the street says this year the (fewer) assistant prof posts are averaging 800 applicants...
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
November 6, 2025 at 9:24 PM
word on the street says this year the (fewer) assistant prof posts are averaging 800 applicants...
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
pray for us friendly neighborhood senior postdocs: doing it all despite the bleak reality that the academic system as we know it is going to have to shrink, and we'll bear (a lot of) the brunt.
"...we’ve become so used to scarcity and slow progress that anyone building differently is primarily treated as a threat, instead of a fellow human hoping for something better."
(esp true in biology imo; we all have reason to look for cures, we should assume some good faith!)
(esp true in biology imo; we all have reason to look for cures, we should assume some good faith!)
We’ve been heads down @ArcadiaScience for a bit but the @arenabioworks news this week caused me to dump thoughts. hard things are hard; don’t be such a fucking hater. Reflections on parallels w our own institutional experiment here seemay.substack.com/p/big-experi...
Big experiments are only big if they can fail
Some reflections on Arena Bioworks' unexpected wind down as a fellow institutional experimentalist
seemay.substack.com
November 6, 2025 at 5:45 PM
"...we’ve become so used to scarcity and slow progress that anyone building differently is primarily treated as a threat, instead of a fellow human hoping for something better."
(esp true in biology imo; we all have reason to look for cures, we should assume some good faith!)
(esp true in biology imo; we all have reason to look for cures, we should assume some good faith!)
having a child has radicalized me in many ways but one of the strongest is that I now know standard time is good, actually. waking up at 6am in the pitch black is NOT IT! much easier to deal with darkness at 4pm than in the early morning, and early mornings are non-negotiable 🥴
November 5, 2025 at 12:19 PM
having a child has radicalized me in many ways but one of the strongest is that I now know standard time is good, actually. waking up at 6am in the pitch black is NOT IT! much easier to deal with darkness at 4pm than in the early morning, and early mornings are non-negotiable 🥴
neurodegenerative diseases hate to see these guys coming. beyond proud of my better half @pierceogden.bsky.social & the super team at Manifold Bio 🚀
Roche has signed a $55 million upfront deal with Manifold Bio, paying to the Boston startup to hunt for better ways of getting drugs into the brain.
endpoints.news/roche-manifo...
endpoints.news/roche-manifo...
Roche pays $55M upfront to Manifold Bio in new research deal for better brain shuttles
Roche partners with Manifold Bio in $55M upfront deal for brain-penetrating drug development, with potential $2B in milestones. Companies to advance blood-brain barrier crossing proteins.
endpoints.news
November 3, 2025 at 6:16 PM
neurodegenerative diseases hate to see these guys coming. beyond proud of my better half @pierceogden.bsky.social & the super team at Manifold Bio 🚀
Reposted by Kaia Mattioli
It’s been a pleasure to organize the Rules of Protein-DNA Recognition meeting in Cancun. Spectacular talks and an amazing and supportive scientific community!
October 17, 2025 at 12:14 PM
It’s been a pleasure to organize the Rules of Protein-DNA Recognition meeting in Cancun. Spectacular talks and an amazing and supportive scientific community!
Reposted by Kaia Mattioli
Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation https://www.biorxiv.org/content/10.1101/2025.10.12.681955v1
October 14, 2025 at 3:04 AM
Massively parallel assay of human splice variants reveals cis-regulatory drivers of disease-associated and cell type-specific splicing regulation https://www.biorxiv.org/content/10.1101/2025.10.12.681955v1
absolutely delighted to be attending the Rules of Protein-DNA Recognition Meeting in Cancún this week; wonderful talks, wonderful people, & the first conference of my postdoc that hasn't been in New England or the Mid-Atlantic 🌞☺️
October 16, 2025 at 7:28 PM
absolutely delighted to be attending the Rules of Protein-DNA Recognition Meeting in Cancún this week; wonderful talks, wonderful people, & the first conference of my postdoc that hasn't been in New England or the Mid-Atlantic 🌞☺️
I have reached the stage of application writing where I think I have never accomplished a single thing and I have no good ideas or any useful technical skills. Progress 💖
October 10, 2025 at 12:58 AM
I have reached the stage of application writing where I think I have never accomplished a single thing and I have no good ideas or any useful technical skills. Progress 💖
ever since i was a little girl i have wanted to spend all day changing the length of my research proposals to be in compliance with different arbitrary page number requirements
October 2, 2025 at 8:43 PM
ever since i was a little girl i have wanted to spend all day changing the length of my research proposals to be in compliance with different arbitrary page number requirements
tepid take: a lotttttt of job postings for bio-AI researchers, not enough job postings for generating-the-extremely-necessary-data-for-bio-AI researchers
October 2, 2025 at 2:16 PM
tepid take: a lotttttt of job postings for bio-AI researchers, not enough job postings for generating-the-extremely-necessary-data-for-bio-AI researchers
Reposted by Kaia Mattioli
Really cool, conceptually simple approach here: cross-referencing grant proposal scores with literature citations and explicit acknowledgments in drug patents to identify patents linked to projects that wouldn't have been funded given a smaller budget
This may be the most important paper ever published about NIH funded research.
www.science.org/doi/10.1126/...
www.science.org/doi/10.1126/...
What if NIH had been 40% smaller?
Replaying history with less NIH funding shows widespread impacts on drug-linked research
www.science.org
September 25, 2025 at 9:32 PM
Really cool, conceptually simple approach here: cross-referencing grant proposal scores with literature citations and explicit acknowledgments in drug patents to identify patents linked to projects that wouldn't have been funded given a smaller budget
Reposted by Kaia Mattioli
More about @drwendieberg.bsky.social and self-advocacy leading to early cancer detection in her dense breast tissue.
More than 10 years ago now..
www.auntminnie.com/clinical-new...
She channeled the lessons from this experience to launch densebreast-info.org
Follow her to keep up with this field
More than 10 years ago now..
www.auntminnie.com/clinical-new...
She channeled the lessons from this experience to launch densebreast-info.org
Follow her to keep up with this field
A radiologist confronts her own breast cancer
University of Pittsburgh radiologist Dr. Wendie Berg, PhD, was diagnosed with breast cancer in June 2014, after discovering that she has dense breast tissue and undergoing a breast MRI. In this articl...
www.auntminnie.com
September 24, 2025 at 7:15 PM
More about @drwendieberg.bsky.social and self-advocacy leading to early cancer detection in her dense breast tissue.
More than 10 years ago now..
www.auntminnie.com/clinical-new...
She channeled the lessons from this experience to launch densebreast-info.org
Follow her to keep up with this field
More than 10 years ago now..
www.auntminnie.com/clinical-new...
She channeled the lessons from this experience to launch densebreast-info.org
Follow her to keep up with this field
Reposted by Kaia Mattioli
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
September 18, 2025 at 4:14 PM
Excited for a major milestone in our efforts to map enhancers and interpret variants in the human genome:
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
The E2G Portal! e2g.stanford.edu
This collates our predictions of enhancer-gene regulatory interactions across >1,600 cell types and tissues.
Uses cases 👇
1/
Reposted by Kaia Mattioli
New video! Discover how transcription factors find their way through tightly packed DNA. 🧪🧬💻👩🔬
www.youtube.com/watch?v=gOta...
Luca Mariani & Martha Bulyk introduce PIONEAR-seq, revealing how DNA flexibility shapes gene regulation.
Recently published in @natsmb.nature.com
www.youtube.com/watch?v=gOta...
Luca Mariani & Martha Bulyk introduce PIONEAR-seq, revealing how DNA flexibility shapes gene regulation.
Recently published in @natsmb.nature.com
DNA Bendability Regulates Transcription Factor Binding to Nucleosomes (PIONEAR-seq)
YouTube video by GenomeTDCC
www.youtube.com
September 18, 2025 at 2:21 PM
New video! Discover how transcription factors find their way through tightly packed DNA. 🧪🧬💻👩🔬
www.youtube.com/watch?v=gOta...
Luca Mariani & Martha Bulyk introduce PIONEAR-seq, revealing how DNA flexibility shapes gene regulation.
Recently published in @natsmb.nature.com
www.youtube.com/watch?v=gOta...
Luca Mariani & Martha Bulyk introduce PIONEAR-seq, revealing how DNA flexibility shapes gene regulation.
Recently published in @natsmb.nature.com
are there any gene regulation/genomics paper/preprint-aggregating accounts on here I should be following?
September 17, 2025 at 11:48 PM
are there any gene regulation/genomics paper/preprint-aggregating accounts on here I should be following?
editorial manager: your manuscript status is none of your business, actually
September 16, 2025 at 2:28 PM
editorial manager: your manuscript status is none of your business, actually
what postdocs actually want:
- to not have their grants canceled
- reasonable chances at getting an academic position
- job security
- a thriving private sector so the entire research system can flourish <3
higher ed institutions in 2025:
- best i can do is an origami night
- to not have their grants canceled
- reasonable chances at getting an academic position
- job security
- a thriving private sector so the entire research system can flourish <3
higher ed institutions in 2025:
- best i can do is an origami night
September 15, 2025 at 3:14 PM
what postdocs actually want:
- to not have their grants canceled
- reasonable chances at getting an academic position
- job security
- a thriving private sector so the entire research system can flourish <3
higher ed institutions in 2025:
- best i can do is an origami night
- to not have their grants canceled
- reasonable chances at getting an academic position
- job security
- a thriving private sector so the entire research system can flourish <3
higher ed institutions in 2025:
- best i can do is an origami night
Earlier this year, I learned I have a pathogenic variant in BRCA2, which gives me a very high lifetime risk of breast cancer (55-69%), as well as an increased risk of ovarian cancer (12-29%) and pancreatic cancer (5-10%).
🧵1/ …
🧵1/ …
September 10, 2025 at 3:36 PM
Earlier this year, I learned I have a pathogenic variant in BRCA2, which gives me a very high lifetime risk of breast cancer (55-69%), as well as an increased risk of ovarian cancer (12-29%) and pancreatic cancer (5-10%).
🧵1/ …
🧵1/ …
Reposted by Kaia Mattioli
Don't miss hearing from Shubham Khetan and Martha Bulyk in this publication highlight video where they discuss their work developing PADIT-seq. 🧪
youtu.be/45hdZ6R9fX4
youtu.be/45hdZ6R9fX4
PADIT-seq: Protein affinity to DNA by in vitro transcription and RNA sequencing
YouTube video by GenomeTDCC
youtu.be
September 3, 2025 at 8:09 PM
Don't miss hearing from Shubham Khetan and Martha Bulyk in this publication highlight video where they discuss their work developing PADIT-seq. 🧪
youtu.be/45hdZ6R9fX4
youtu.be/45hdZ6R9fX4