Fairlie Reese

Happy to see the ENCODE4 long-read RNA tracks now up on UCSC! Thank you to Jeltje, Mark, and any others at UCSC for working to make this happen 🤩

👉 Read the preprint: www.biorxiv.org/content/10.1...

Judge rules against NIH grant cuts — and calls them discriminatory The decision means that the US biomedical agency has to restore funding to hundreds of research projects, but the government will likely appeal.

A US judge has ordered hundreds of terminated research projects at the US National Institutes of Health to be reinstated, calling the processes that led to their cancellation “bereft of reasoning”.

https://go.nature.com/4kOmXDy

The University of California and California State University systems are two of the pinnacles of American academia. This, plus all the other attacks on scientific funding, make it clear Trump wants to just concede all of the scientific and medical excellence of the USA to the rest of the world 🤷‍♂️🙃

Just got back from Milan after attending #ESHG2025. I had a great time presenting our poster and seeing so much interest in our preprint on calling rDNA variants: shorturl.at/p1D0C. Huge thanks to everyone who stopped by, asked questions, and shared insights. Let’s keep the conversation going! 🧬

ESHG2025# Early Career awards:
For outstanding science presented at the conference

- Allison Newman, Exeter, UK
- Hristiana Lyubenova, Berlin, Germany
- Robin J. Hofmeister, Lausanne, Switzerland
- Pau Clavell-Revelles, Barcelona, Spain

The impact of sex, age, and genetic ancestry on DNA methylation across tissues Background: Understanding the consequences of individual DNA methylation variation is crucial for the study of human biology and disease. However, the collective impact of demographic traits on DNA me...

Excited to share our new preprint: The impact of sex, age, and genetic ancestry on DNA methylation across tissues. Briefly, we explored how sex, age, and genetic ancestry shape DNA methylation across tissues and individuals. Want to know a bit more? Follow this “bluetorial”!
doi.org/10.1101/2025...

📢Menopause affects half the population — yet it's been one of the most overlooked areas in aging research.
We found that aging in the female reproductive system unfolds in unexpected, organ-specific ways. 🔗 www.biorxiv.org/content/10.1...
1/8🧵

Our pre-print on investigating variation in South Asian genomes is now out!

Thank you to @mikeschatz.bsky.social, @rajivmccoy.bsky.social and @aabiddanda.bsky.social for all their work on this.

🧵 A thread on the key results and takeaways from our work:

Congratulations! Super cool to talk to you about this project at BoG!

Our lab had dual presence at #BoG25 @cshlmeetings.bsky.social!
🧬 Silvia González-López spoke on chromatin dynamics & transcriptional regulation.
🌍 @fairlie.bsky.social presented ancestry-aware gene annotations — a @guigolab.bsky.social × @melelab.bsky.social collab:
www.biorxiv.org/content/10.1...

📢 HPRC Release 2 is here!

Now with phased genomes from 200+ individuals, a 5x increase from Release 1.

Explore sequencing data, assemblies, annotations & alignments in our interactive data explorer ⬇️:

humanpangenome.org/hprc-data-re...

This was such a cool idea!

had an awesome time at my first Biology of Genomes; what a privilege to be able to share my work with such a kind, smart, and welcoming group of folks. cannot wait to come back!!

A #bloodtest for early detection of #Alzheimer's disease

A study involving more than 1,700 people from five hospitals in Barcelona, Sweden and Italy has validated the usefulness of a biomarker in blood to detect Alzheimer's disease in the clinical setting

www.researchmar.net/news/716/a-b...

Beyond the Gene in Genetics: How Isoform-Resolved Analysis Empowers the Study of Both Common and Rare Genetic Variation Genetics is rapidly deepening our understanding of human health and disease by investigating common and rare genetic variants and their influence on gene expression1,2. Alternative splicing is a molec...

The Genetics research community has a problem. Most recent articles do not consider #splicing/isoforms.

Here, we analyze how important this opportunity gap is - and spoiler warning - we find it is essential for both analysis of common and rare variants

More info👇

www.medrxiv.org/content/10.1...

I’m so excited to share the work I’ve been part of from the first year of my postdoc at the @melelab.bsky.social. We analyze a long-read RNA-seq dataset derived from genetically-diverse samples. To see what we found please read the thread below! 😁

Atlas of genetic and phenotypic associations across 42 female reproductive health diagnoses - Nature Medicine This study provides a cross-trait atlas of genetic and phenotypic associations across 42 female reproductive health diagnoses.

📢 Excited to share our study in @natmedicine.bsky.social
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵

Eric Green is out as head of National Human Genome Research Institute The longtime director of the National Human Genome Research Institute is stepping down, as the larger NIH braces for more changes.

Still processing what this means. www.statnews.com/2025/03/17/t...

Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation https://www.biorxiv.org/content/10.1101/2025.03.14.643250v1

🥰🥰🥰

As a field, I believe we must move towards COMIC SANS logo plots immediately.

nbviewer.org/github/saket...

Thrilled to see our Perspective on long-read transcriptomics Published in Advance in @genomeresearch.bsky.social, with #AdamFrankish and @carolinamonzo.bsky.social. We discuss the opportunities and challenges of LRS to uncover Transcript Divergence and for Genome Annotation. tinyurl.com/bdeteu4j

Francis Collins, the NIH Director for 12 years, led the Human Genome Project and other NIH efforts for 32 years, resigned today. Key words from his resignation letter
www.nytimes.com/2025/03/01/u...

🦅🦅🦅

Just saw this. NIH is capping indirects at 15%. This will crush so many institutions. grants.nih.gov/grants/guide...

What's happening is precisely outlined in Project 2025. Read it to understand what's coming next. None of this is a surprise.

Also, I know this is extremely unnerving if u weren't expecting this. But let's not panic. Let's organize & give this the best fking fight of our lives.

1. Today the NIH director issued a new directive slashing overhead rates to 15%.

I want to provide some context on what that means and why it matters.

grants.nih.gov/grants/guide...

Last week, I presented my work on sex differences in immune aging at the Women's Health conference, @eventswcs.bsky.social. Great discussions and inspiring science highlighting the need for more research with a gender and sex perspective! #WomensHealth2025
@melelab.bsky.social @bsc-cns.bsky.social

Schematic overview of the ENCODE 4 project's framework for identifying and classifying candidate cis-regulatory elements (cCREs). The process begins by defining regulatory anchors, such as DNase hypersensitive sites (rDHSs) and transcription factor (TF) clusters, which are filtered and classified using histone marks and other features. Elements are classified into functional categories, including promoters, proximal and distal enhancers, and CTCF-bound sites. The resulting registry includes millions of cCREs for human (GRCh38) and mouse (mm10), depicted alongside their classifications. Additional annotations, such as transcription activity, chromatin structure, genetic variation, and sequence motifs, are integrated for functional characterization. Image modified from https://www.biorxiv.org/content/10.1101/2024.12.26.629296v1.full

Now available as preprint:

The ENCODE 4 expanded registry of regulatory elements
- 2.35M 🧍 human cCREs
- 927k 🐭 mouse cCREs

www.biorxiv.org/content/10.1...

Led by @moorejille.bsky.social, this preprint summarizes data and analyses generated by hundreds of contributors across ENCODE 4

Excited to present my latest results from my PhD project about long-read transcriptomics at Jornades de Bioinformàtica i Genòmica by @scb.iec.cat
Stay tuned as in the following months @fairlie.bsky.social and I will be unveiling an exciting discovery from a human population-diverse perspective!