Fairlie Reese
@fairlie.bsky.social
Postdoc in the Transcriptomics and Functional Genomics Lab at the Barcelona Supercomputing Center studying the impact of human variation on the transcriptome. California -> Catalunya
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...
👉 Read the preprint: www.biorxiv.org/content/10.1...
July 18, 2025 at 12:06 PM
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...
👉 Read the preprint: www.biorxiv.org/content/10.1...
Reposted by Fairlie Reese
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
https://go.nature.com/4kOmXDy
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.
go.nature.com
June 16, 2025 at 11:24 PM
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
https://go.nature.com/4kOmXDy
Reposted by Fairlie Reese
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 🤷♂️🙃
"Sources said the administration is specifically considering a full termination of federal grant funding for the University of California and California State University systems."
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Pure vandalism.
This could never happen in a country with functioning checks and balances.
Trump preparing large-scale cancellation of federal funding for California, sources say | CNN Politics
The Trump administration is preparing to cancel a large swath of federal funding to California, an effort which could begin as soon as Friday, according to multiple sources.
www.cnn.com
June 6, 2025 at 11:56 PM
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 🤷♂️🙃
Reposted by Fairlie Reese
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! 🧬
May 28, 2025 at 2:03 PM
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! 🧬
Reposted by Fairlie Reese
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
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
May 27, 2025 at 1:06 PM
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
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
Reposted by Fairlie Reese
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...
doi.org/10.1101/2025...
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...
www.biorxiv.org
May 5, 2025 at 3:44 PM
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...
doi.org/10.1101/2025...
Reposted by Fairlie Reese
📢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🧵
We found that aging in the female reproductive system unfolds in unexpected, organ-specific ways. 🔗 www.biorxiv.org/content/10.1...
1/8🧵
May 23, 2025 at 12:19 PM
📢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🧵
We found that aging in the female reproductive system unfolds in unexpected, organ-specific ways. 🔗 www.biorxiv.org/content/10.1...
1/8🧵
Reposted by Fairlie Reese
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:
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:
Assembling unmapped reads reveals hidden variation in South Asian genomes https://www.biorxiv.org/content/10.1101/2025.05.14.653340v1
May 15, 2025 at 2:19 PM
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:
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:
Reposted by Fairlie Reese
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...
🧬 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...
May 14, 2025 at 7:46 AM
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...
🧬 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...
Reposted by Fairlie Reese
📢 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...
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...
May 12, 2025 at 1:15 PM
📢 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...
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...
Reposted by Fairlie Reese
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!!
May 11, 2025 at 12:05 AM
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!!
Reposted by Fairlie Reese
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...
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...
April 9, 2025 at 10:41 AM
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...
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...
Reposted by Fairlie Reese
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...
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...
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...
www.medrxiv.org
April 2, 2025 at 7:45 AM
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...
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! 😁
Do you work in 💫human genetics💫?
Have you ever worried about what’s inside your gene annotation GTF⁉️
WELL, YOU SHOULD! 😱
Especially when studying a genetically diverse 🌍 cohort!
🔴We discover that gene annotations are European-biased 👉 impacting downstream analyses!
Don't miss this thread🧵⬇️
1/13
Have you ever worried about what’s inside your gene annotation GTF⁉️
WELL, YOU SHOULD! 😱
Especially when studying a genetically diverse 🌍 cohort!
🔴We discover that gene annotations are European-biased 👉 impacting downstream analyses!
Don't miss this thread🧵⬇️
1/13
Long-read transcriptomics of a diverse human cohort reveals widespread ancestry bias in gene annotation
Accurate gene annotations are fundamental for interpreting genetic variation, cellular function, and disease mechanisms. However, current human gene annotations are largely derived from transcriptomic...
www.biorxiv.org
March 21, 2025 at 4:52 PM
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! 😁
Reposted by Fairlie Reese
📢 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? 👇🧵
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
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.
www.nature.com
March 17, 2025 at 9:27 AM
📢 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? 👇🧵
👉 www.nature.com/articles/s41...
We mapped & characterized genetic risk factors for 42 female reproductive health diagnoses. What we found & why it matters? 👇🧵
Reposted by Fairlie Reese
Still processing what this means. www.statnews.com/2025/03/17/t...
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.
www.statnews.com
March 18, 2025 at 11:21 AM
Still processing what this means. www.statnews.com/2025/03/17/t...
Reposted by Fairlie Reese
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
March 17, 2025 at 7:34 PM
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
Reposted by Fairlie Reese
As a field, I believe we must move towards COMIC SANS logo plots immediately.
nbviewer.org/github/saket...
nbviewer.org/github/saket...
March 14, 2025 at 7:28 PM
As a field, I believe we must move towards COMIC SANS logo plots immediately.
nbviewer.org/github/saket...
nbviewer.org/github/saket...
Reposted by Fairlie Reese
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
March 4, 2025 at 6:56 AM
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
Reposted by Fairlie Reese
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...
www.nytimes.com/2025/03/01/u...
March 1, 2025 at 6:07 PM
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...
www.nytimes.com/2025/03/01/u...
Reposted by Fairlie Reese
Just saw this. NIH is capping indirects at 15%. This will crush so many institutions. grants.nih.gov/grants/guide...
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
grants.nih.gov
February 8, 2025 at 12:19 AM
Just saw this. NIH is capping indirects at 15%. This will crush so many institutions. grants.nih.gov/grants/guide...
Reposted by Fairlie Reese
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.
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.
February 8, 2025 at 3:04 AM
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.
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.
Reposted by Fairlie Reese
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...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
NOT-OD-25-068: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates
NIH Funding Opportunities and Notices in the NIH Guide for Grants and Contracts: Supplemental Guidance to the 2024 NIH Grants Policy Statement: Indirect Cost Rates NOT-OD-25-068. OD
grants.nih.gov
February 8, 2025 at 12:18 AM
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...
I want to provide some context on what that means and why it matters.
grants.nih.gov/grants/guide...
Reposted by Fairlie Reese
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
@melelab.bsky.social @bsc-cns.bsky.social
February 5, 2025 at 7:32 AM
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
@melelab.bsky.social @bsc-cns.bsky.social
Reposted by Fairlie Reese
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
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
January 8, 2025 at 8:35 PM
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
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