iiinova — where your digital self keeps evolving

Reposted by Sean Bresnahan

Kristian G. Andersen @kgandersen.bsky.social · 20/09/2026

"White House Moves to Take Control of N.I.H. Grants" [everybody up in arms, as they should be, but for those who have been paying close attention, this has pretty much already happened - the realization just hasn't sunk in yet] www.nytimes.com/2026/09/20/s...

nytimes.com

White House Moves to Take Control of N.I.H. Grants (Gift Article)

Federal officials are drafting an executive order that would place grants under review by an outside panel, the latest effort to redirect billions of dollars in research spending.

1015271

Sean Bresnahan @seantbres.bsky.social · 11/09/2026

Little peak at "Epigenetics & development" - can't wait to share the full video... I"m still learning so, hoping to get the first full video out w/in a month. Also! I'm in search of collaborators for this project (concepts! assets! music! etc!) - reach out if interested! youtube.com/shorts/rzh-9...

youtube.com

What does "epigenetics" actually mean?

YouTube video by epialleles

051

Sean Bresnahan @seantbres.bsky.social · 10/09/2026

Generating some data for a grant required returning to a side project... scAmbi, my R package for correcting single-cell RNA-seq transcript abundance estimates for overdispersion from mapping ambiguity, is now at v0.3.2. Looks like tissue-specific references help 5' 10X. github.com/sbresnahan/s...

github.com

GitHub - sbresnahan/scAmbi: Correct read-to-transcript mapping ambiguity in scRNA-seq

Correct read-to-transcript mapping ambiguity in scRNA-seq - sbresnahan/scAmbi

120

Sean Bresnahan @seantbres.bsky.social · 09/09/2026

Working on a series of videos, “Epigenetics in development and evolution,” exploring evolution of gene regulation, mechanisms, developmental and health impacts, omics-wide observational and experimental study designs, causal inference, and a focus on the placental epigenome.

051

Sean Bresnahan @seantbres.bsky.social · 06/09/2026

🧬🫄🧪 I’ve been inspired by @3blue1brown.com for a long time, but always wished someone was making educational content in that style on epigenetics, evolution, and human development. I’ve started “Epialleles” to do just that! Made with @manim.community youtu.be/UhOSPa2sDfw?...

youtu.be

Hello world!

YouTube video by epialleles

1132

Sean Bresnahan @seantbres.bsky.social · 31/08/2026

Our new preprint introduces ✨ICONIC✨: an R package making causal inference accessible for observational omics. It unifies genetic instruments (Mendelian randomization) and negative controls (proximal inference) for mediation analysis under unmeasured confounding. www.medrxiv.org/content/10.6...

medrxiv.org

ICONIC: An R Package for Integrating Instrumental Variable- and Negative-Control-Informed Causal Discovery and Diagnostics in Multiomic Studies

Unmeasured confounding threatens causal inference and replicability in observational multi-omic studies across variable environments. Genetic instrumental variables (Mendelian randomization) and negat...

1115

Reposted by Sean Bresnahan

Jeffrey Brainard @jeffreybrainard.bsky.social · 20/05/2026

U.S. researchers who coauthor research papers with scientists affiliated with foreign institutions are drawing fresh scrutiny from NIH, NASA. #scientificpublishing @science.org www.science.org/content/arti...

science.org

U.S. researchers face new restrictions on publishing with foreign collaborators

NIH, NASA grantees are confused and concerned amid agencies’ piecemeal communication

23623

Sean Bresnahan @seantbres.bsky.social · 07/05/2026

I ❤️ @cshlmeetings.bsky.social @cshlnews.bsky.social! Beautiful place. One of those places that surrounds you with the feelings of wonder/purpose/etc that made you fall in love with science. And there’s a bar!

Man with beard and tattoos smiles and points to his scientific poster in an auditorium with walls lined with photographs of notable scientists, including the late great Barbara McClintock.

0101

Sean Bresnahan @seantbres.bsky.social · 06/05/2026

Shout-out to @taylorhead.bsky.social who is presenting prescient work for TWAS studies at #bog26 today! Using long-read RNA-seq to inform isoform-level priors, this work enables Bayesian fine-mapping of causal isoforms by integrating tissue-specific annotation and structural similarity. Poster 108!

050

Reposted by Sean Bresnahan

Taylor Head, PhD @taylorhead.bsky.social · 06/05/2026

Shout-out to @seantbres.bsky.social who will be presenting some really interesting work at #bog26 this evening! Using long-read, isoform-resolved placental transcriptomics, this work shows how PFAS exposure impacts placental transcriptional networks and imprinting (poster #70)

072

Sean Bresnahan @seantbres.bsky.social · 03/04/2026

🎉 It's published! Our placental long-read transcriptome is now in @natcomms.nature.com! Thank you to @arjunbhattac.bsky.social, @jonhuang.bsky.social, and @mikelove.bsky.social for collaborating on this first project of my postdoc @mdanderson.bsky.social. A recap 🧬🫄🧵 www.nature.com/articles/s41...

Fig 1: Study design and transcript discovery pipeline showing Nanopore cDNA libraries from villous placenta (n=72 term births, 36 controls and 36 GDM-affected); comparison of annotated features between GENCODE v45 and lr-assembly showing 63.5% reduction in isoforms and 73.1% reduction in genes; transcript distribution by structural category (FSM, ISM, NIC, NNC, and other classes) for all and high-confidence isoforms; transcriptional breadth across 15 GTEx tissues and cell lines; isoforms detected at increasing expression thresholds with placenta shown as thick black line; and transcriptional complexity as mean isoforms per gene (±1 SD) with placenta maximum of 108..

2198

Reposted by Sean Bresnahan

Arjun Bhattacharya @arjunbhattac.bsky.social · 26/03/2026

Another preprint from our group @mdanderson.bsky.social led by talented postdoc @seantbres.bsky.social! Joint with @jonhuang.bsky.social, exploring the intersection of environmental toxins, maternal/fetal health, and placental txomics. Tweet thread below!

074

Sean Bresnahan @seantbres.bsky.social · 26/03/2026

🧬Another new preprint with @jonhuang.bsky.social @uhmanoa.bsky.social & @arjunbhattac.bsky.social @mdanderson.bsky.social ! We used variation in how PFAS cross the placenta to dissect the transcriptional architecture of effects on birthweight & gestational age🧵 www.biorxiv.org/content/10.6...

Transplacental transfer efficiency reveals dose-dependent network architectures linking PFAS exposure to birth outcomes. Per- and polyfluoroalkyl substances (PFAS) exhibit varied transplacental transfer efficiencies (TPTE), quantified as the ratio of fetal cord blood to maternal blood concentrations. PFOS shows low TPTE with limited fetal exposure, while PFBS demonstrates high TPTE with substantial transfer to the fetus. PFAS concentrations were measured in maternal blood and fetal cord blood alongside placental transcriptomics, gestational age at delivery, and birth weight. Placental transcripts mediating PFAS effects on birth weight were characterized by four network properties: mediator count (number of significant mediating transcripts), co-expression strength (|kME|, representing correlation with module eigengene and shown as network connectivity), network centrality (hub positioning within the network), and compartmentalization (spatial clustering of maternal versus fetal mediators). Birth weight exhibited coordinated TPTE-dependent responses across these network metrics, with high-TPTE compounds engaging more numerous, strongly co-expressed mediators occupying central network positions with distinct maternal-fetal compartmentalization. In contrast, gestational age showed minimal coordinated network reorganization in response to TPTE variation, indicating distinct molecular architectures underlying PFAS effects on these different outcomes.

182

Reposted by Sean Bresnahan

Kevin Bird @stairwaytokevin.bsky.social · 24/03/2026

A lot of very good food for thought here of where population and quantitative/statistical genetics have room for improvement in thinking about, performing, and communicating their research

13417

Reposted by Sean Bresnahan

Taylor Head, PhD @taylorhead.bsky.social · 24/03/2026

New preprint on the genetic regulation of isoform expression and breast cancer risk! TL;DR: tissue-specific, long-read transcript annotations shape eQTL mapping, TWAS, and isoforms we prioritize at GWAS loci. @arjunbhattac.bsky.social www.biorxiv.org/content/10.6...

1113

Sean Bresnahan @seantbres.bsky.social · 24/03/2026

🧬New preprint from @arjunbhattac.bsky.social’s group at @mdanderson.bsky.social, led by @taylorhead.bsky.social ! Transcript annotation is not just a technical detail, it fundamentally shapes what regulatory mechanisms you find when studying cancer risk. 🧵 www.biorxiv.org/content/10.6...

Panel A: “In this project, we developed three de novo transcriptome assemblies in healthy breast tissue, fibroblasts, and breast tumor tissue derived from publicly available LR RNA-seq data. Next, we used these tissue-specific LR assemblies, the GENCODEv45 reference transcriptome, and combined annotations each to re-quantify short-read RNA-seq samples in healthy breast tissue, fibroblasts, and breast cancer tumor tissue. We performed isoform- and gene-level eQTL mapping and fine-mapping, as well as colocalization and TWAS analyses with overall breast cancer GWAS risk loci and subtype-specific breast cancer loci.”
Panel B: “In this example, the GENCODE transcript reference annotation contains four structurally similar isoforms for a gene. Only two are relevant to the tissue of interest and only one is causal for a trait, leading to misattribution of reads to irrelevant isoforms in GENCODE. This can propagate downstream and manifest as inaccurate isoform expression quantification, spurious eQTL mapping, and false positives and negatives in colocalization with GWAS loci.”
Abbreviations: LR, long-read; eQTL, expression quantitative trait loci; TWAS, transcriptome-wide association study; isoQTL, isoform-level eQTL; GWAS, genome-wide association study.

2156

Reposted by Sean Bresnahan

Chris Murphy @chrismurphyct.bsky.social · 14/03/2026

It’s crystal clear now that Trump has lost control of this war. He badly misjudged Iran’s ability to retaliate. The region is on fire. 1/ I’m going to explain to you in this🧵what I’ve learned - in part from closed door briefings - about the four biggest current crises.

333109944507

Reposted by Sean Bresnahan

Maryam Jamshidi @msjamshidi.bsky.social · 08/03/2026

The horror Israel/US has unleashed on Iran is going to unfold over time, over generations x.com/arianajasmin...

3271147

Reposted by Sean Bresnahan

Gregg Gonsalves @gregggonsalves.bsky.social · 28/02/2026

This piece by Elizabeth Ginexi is a must read. Trump, Vought, RFK and Bhattacharya are destroying the NIH simply ignoring the law and the US Congress. It’s illegal and immoral. The NIH Restructuring Congress Rejected Is Happening Anyway open.substack.com/pub/elizabet...

open.substack.com

The NIH Restructuring Congress Rejected Is Happening Anyway

(I used Gemini Nano Banana 2 to create this fictional image.)

211662

Reposted by Sean Bresnahan

ProPublica @propublica.org · 09/02/2026

1/ ProPublica collected handwritten letters in mid-January from children held at the Dilley Immigration Processing Center, the same facility where 5-year-old Liam Conejo Ramos was taken. Hundreds of kids are still detained. We’ll let the children’s words speak for themselves. 🧵

203115217373

Reposted by Sean Bresnahan

Mark Histed @markhisted.org · 07/02/2026

This. Science and democracy are linked. We can’t put science advocacy in a bubble and do it alone— the fascism, division, and attack on experts and trust are *the reason* science is under attack. Plus the inside advocacy alone does not work! Just look at what happened with MYF this year.

210134

Reposted by Sean Bresnahan

Colette Delawalla, PhD @cdelawalla.bsky.social · 30/01/2026

If you have the privilege of living in a democracy, it is your civic duty to protect democracy when it’s in peril. If you have the privilege of being a scientist, you have the civic duty of protecting science. So yeah, scientists in America: ITS TIME TO BE YELLIN.

19315

Sean Bresnahan @seantbres.bsky.social · 28/01/2026

Tulsa stands with you, Minneapolis. More than 100 people showed up to a vigil Tuesday evening at LaFortune Park in Tulsa, OK to remember people murdered by federal officers of the Trump regime. Photos by Mike Simmons, Tulsa World.

Vigil participants stand with signs and flags. Photos by Mike Simmons, Tulsa World.

Man in orange beanie and brown jacket lights Taper candles planted into a snow bank.

Vigil participants kneel beside the makeshift vigil.

A closeup of the vigil: candles planted into the snowbank, with flowers and notes strung about.

051

Reposted by Sean Bresnahan

Dumb Megan @dmbmeg.bsky.social · 25/01/2026

This administration is cooked. Literally no one is scared of them.

470149284306

Sean Bresnahan @seantbres.bsky.social · 25/01/2026

As we prepare for the coming weeks and think about how we will choose to face this moment, remember that in his last few minutes alive, Alex Pretti was rendering aid.

151

Reposted by Sean Bresnahan

Stand Up for Science! @standupforscience.net · 24/01/2026

This is Alex Pretti. This morning he was murdered by ICE. Six ICE agents held him down and shot him at point blank range. Alex was a nurse and researcher at the VA. Our thoughts are with his loved ones and we stand united in action calling for the abolishment of ICE. #ScientistsAgainstICE

Alex Pretti, wearing a green sweater with his VA badge on.

271635762

Sean Bresnahan @seantbres.bsky.social · 23/01/2026

We should be doing this in every state.

031

Reposted by Sean Bresnahan

David Ho @davidho.bsky.social · 20/01/2026

This is the most astonishing graph of what the Trump regime has done to US science. They have destroyed the federal science workforce across the board. The negative impacts on Americans will be felt for generations, and the US might never be the same again. www.nature.com/immersive/d4...

This line graph illustrates the percentage change in agency staff levels from the previous year for nine major U.S. federal scientific and health organizations between the fiscal years 2016 and 2025. The agencies tracked include the CDC, Department of Energy, EPA, FDA, NASA, NIH, NIST, NOAA, and NSF. For the majority of the timeline between 2016 and 2023, the agencies show relatively stable fluctuations, generally staying within a range of +5% to -5% change per year. However, there is a dramatic and uniform plummet starting in the 2024–25 period. Every agency depicted shows a sharp downward trajectory, with staffing losses ranging from approximately -15% to over -25%. The Environmental Protection Agency (EPA) shows the most significant decline, dropping to roughly -26%, while the National Institute of Standards and Technology (NIST) shows the least severe but still substantial drop at approximately -15%.

91147838504

Sean Bresnahan @seantbres.bsky.social · 19/01/2026

“heroism is neither being perfect, nor doing something spectacular. In fact, it’s just the opposite: it’s regular, flawed human beings choosing to put others before themselves, even at great cost, even if no one will ever know, even as they realize the walls might be closing in around them.”

000

Sean Bresnahan @seantbres.bsky.social · 19/01/2026

“Somewhere I read of the freedom of speech. Somewhere I read of the freedom of the press. Somewhere I read that the greatness of America is the right to protest for rights.”

0124

Reposted by Sean Bresnahan

Nicole Bedera @nbedera.bsky.social · 16/01/2026

I’m seeing posts from people (outside of MN) about how US citizens should carry their passports. And let me say that *inside* MN, we are calmly responding to requests with: “No, I don’t have to show you any documentation.” Because that’s how you protect everyone, regardless of immigration status.

577334918599

Reposted by Sean Bresnahan

Jonathan Pritchard @jkpritch.bsky.social · 01/10/2023

I'm delighted to release the first half of my new textbook in human genetics: web.stanford.edu/group/pritch... "An Owner's Guide to the Human Genome: an introduction to human population genetics, variation and disease"

web.stanford.edu

An Owner's Guide to the Human Genome

8296175

Reposted by Sean Bresnahan

Kathleen E. Kennedy @themedievaldrk.bsky.social · 10/01/2026

To be clear, they're play-fighting and also: this video improved my day measurably and I wish I'd've watched it earlier. If you haven't, fix that now.

8435104

Sean Bresnahan @seantbres.bsky.social · 08/01/2026

can i let them both be? this fickle faith and this college science that heckles from the back of the classroom now i can’t believe— that the bible and qur’an and bhagavad gita are sliding long hairs behind my ear like mom used to & exhaling from their mouths “make room for wonder”

010

Sean Bresnahan @seantbres.bsky.social · 06/01/2026

Having a 🍺 with Mr PEG tomorrow who wants to join

031

Sean Bresnahan @seantbres.bsky.social · 01/01/2026

In 2025, I learned a lot about chronic illness as my spouse and I navigated the US healthcare system to get diagnoses and options for managing symptoms. 1/

100

Sean Bresnahan @seantbres.bsky.social · 31/12/2025

Happy new year! Sharing a 🧬🚨REVISED PREPRINT🚨 with major updates to our placental long-read transcriptome paper! Thanks to thorough reviewer feedback, we've strengthened the manuscript with new analyses & clarifications. Key figures in this thread 🧵 www.biorxiv.org/content/10.1...

biorxiv.org

Long-read transcriptome assembly reveals vast transcriptional complexity in the placenta associated with metabolic and endocrine function

The placenta is critical for fetal development and mediates the effects of pregnancy complications on offspring metabolic health, yet it is often poorly characterized in genomic studies. Existing tran...

154

Sean Bresnahan @seantbres.bsky.social · 27/12/2025

Looking into industry bioinformatics / comp bio / data science careers. If you have any leads, message me! CV is in bio. Currently a postdoc data scientist at @mdanderson.bsky.social, have published work in both wet + dry lab multi-omics of non-model organisms & humans. 🧪🧬🖥️

398

Reposted by Sean Bresnahan

Harmit Singh Malik @harmitmalik.bsky.social · 13/12/2025

@pravrutharaman.bsky.social got super intrigued about EZHIP/CATACOMB, previously identified as a histone H3K27M mimic of PRC2. You can read about her efforts here: www.biorxiv.org/content/10.6... We hope these analyses will help spur more analyses in this very cool gene! 1/

biorxiv.org

Dynamic evolution of EZHIP, an inhibitor of the Polycomb Repressive Complex 2 in mammals

The Polycomb Repressive Complex 2 (PRC2) is an ancient, conserved chromatin-interacting complex that controls gene expression, facilitating differentiation and cellular identity during development. It...

38437

Reposted by Sean Bresnahan

Kaia Mattioli @kaiamattioli.bsky.social · 11/12/2025

delighted to share our review, out today in @cp-trendsgenetics.bsky.social! check it out if you're curious about how recent advances in technology & biology have contributed to our understanding of how alternative isoforms diversify the proteome.

175

Reposted by Sean Bresnahan

Jeremy Berg @jeremymberg.bsky.social · 10/12/2025

Another day, another day dragging NIH into areas where it doesn't belong and demeaning himself and the agency...

23811

Reposted by Sean Bresnahan

Kevin Bird @stairwaytokevin.bsky.social · 28/11/2025

I'm increasingly interested in race science as a form of cultivated, weaponized statistical illiteracy. Take this figure, one of the most common propaganda plots, plotting national IQ data against education polygenic scores. "The correlation is so high! Clearly IQ differences are genetic!" Oops!

910720

Reposted by Sean Bresnahan

Polina Tikanova @polinatikanova.bsky.social · 24/11/2025

Happy to share that my PhD project is finally published!🪱✨ Selfish genes are found across the tree of life. They can disrupt inheritance patterns and at the same time act as units for molecular innovation. Here we tried to answer one big question: how do selfish genes emerge in the first place?

37636

Reposted by Sean Bresnahan

Harmit Singh Malik @harmitmalik.bsky.social · 25/11/2025

I am procrastinating on writing by reading this interview of one of the true pioneers in evolutionary biology (and one of the nicest people I have ever met in my life) Why we should be thinking of Welwitschia. What is Welwitschia you might ask (I did!)? Read on. www.edge.org/conversation...

edge.org

GENOMIC IMPRINTING | Edge.org

2328

Reposted by Sean Bresnahan

crystal @cim.bsky.social · 21/11/2025

The Zohran press conference is your regular reminder that the entire administration folds like tissue paper at the slightest hint of confidence and conviction, and thus the fact that national democrats are playing a game of capitulation and weakness is exactly why they're all getting away with it

41251339